New HPV Diagnostic Assay
Presented by
Dr Ivan Brukner
Dr Damian Labuda
Hôpital Sainte-Justine
COMMERCIALIZATION AND TRANSFER
ASSISTANCE PROGRAM
Ministère du Développement Économique,
de l’Innovation et de l’Exportation
Le 26 septembre 2008
Table des matières
CONTENTS OF THE GRANT APPLICATION ........................................................................................ 1
1.
GRANT APPLICATION FORM ................................................................................................ 1
2.
PROJECT SUMMARY MAXIMUM THREE PAGES (in French) ................................................ 1
3.
PRINCIPAL RESEARCHER: PRESENTATION AND CONTACT INFORMATION ......................... 2
4.
DESCRIPTION OF THE TECHNOLOGY ................................................................................... 3
5.
6.
4.1.
Background - HPV as etiological agent of cervical cancer. .......................................... 3
4.2.
Technology developed and scientific basis ................................................................. 4
4.3.
Current development status of the technology – functional prototype ..................... 6
4.4.
Scientific value ............................................................................................................. 8
INTELLECTUAL PROPERTY .................................................................................................... 8
5.1.
Invention disclosure .................................................................................................... 8
5.2.
Previous disclosure and/or anterior art .................................................................... 10
5.3.
Freedom to operate analysis (FTO) ........................................................................... 13
5.4.
Revenue sharing ........................................................................................................ 15
TECHNOLOGY DEVELOPMENT PLAN ................................................................................. 16
6.1.
Identification of current stage of technology development. .................................... 16
6.2.
Remaining Steps and Time to Market ....................................................................... 18
6.3.
Technical and technological challenges to be met and anticipated progress........... 19
6.4.
Objectives sought ...................................................................................................... 23
6.5.
Type of activities to be carried out ............................................................................ 24
6.6.
Work plan and timetable ........................................................................................... 30
6.7.
Deliverables and result indicators ............................................................................. 31
6.8.
Decision-making milestones (go/no go) for measurable and clearly identified results
32
6.9. Proposal for granting the subsidy according to the decision-making milestones
reached .................................................................................................................................. 32
7.
RESEARCH TEAM ............................................................................................................... 32
8.
ESTABLISHMENT’S PROJECT MANAGER (In French) ......................................................... 33
9.
PARTNER ORGANIZATION ................................................................................................. 34
9.1. Role, experience and qualifications of the partner organization in conjunction with
the project ............................................................................................................................. 34
9.2.
Description of the partner organization's project selection process ........................ 35
9.3.
Professional who will support the valorization process ............................................ 36
10.
POTENTIAL MARKET ...................................................................................................... 36
10.1.
Target market ........................................................................................................ 37
10.2.
Business opportunity: Cervical cancer prevention program and HPV screening. . 37
10.3.
Technological competition and benchmarking ..................................................... 38
11.
COMMERCIALIZATION STRATEGY ................................................................................. 42
11.1.
Commercialization of the assay in Canada – Warnex partnership........................ 43
11.2.
Commercialization of the assay in Africa – Continental Diagnostic partnership .. 43
11.3.
Other partnership and future development ......................................................... 45
12.
PRO FORMA BUDGET (in French) .................................................................................. 45
12.1.
Coûts du projet de maturation technologique ...................................................... 45
12.2.
Montage financier ................................................................................................. 47
12.3.
Documents démontrant la nature des engagements des partenaires financiers . 47
12.4.
Démonstration que les autres sources de financement possibles ont été prises
en considération .................................................................................................................... 48
13.
OUTSIDE OPINIONS ....................................................................................................... 49
13.1.
Evaluator 1 ............................................................................................................. 49
13.2.
Evaluator 2 ............................................................................................................. 64
Letters of support ...................................................................................................................... 71
Annex 1. Extended patent searches and comments .................................................................... 73
Annex 2. Analysis of documents cited in the PCT research report ............................................... 80
Annex 3. Curriculum vitae – Research team ................................................................................. 83
Annex 3.1. Ivan Brukner’s CV ................................................................................................ 84
Annex 3.2. Damian Labuda’s CV ............................................................................................ 92
Annex 3.3. Maja Krajinovic’s CV .......................................................................................... 113
Annex 4. ....................................................................................................................................... 121
CONTENTS OF THE GRANT APPLICATION
1. GRANT APPLICATION FORM
Please see attached form.
2. PROJECT SUMMARY MAXIMUM THREE PAGES (in French)
Le projet proposé par le CHU Sainte-Justine consiste à développer d’un point de vue
commercial leur nouvelle méthode de sélection de sondes spécifiques, nommée
« hybridation itérative » dans le cadre d’un essai fonctionnel pour le diagnostic du virus
du papillome humain (VPH) pouvant être utilisé au sein d’un laboratoire de diagnostic
clinique au Québec et en Afrique du Sud. Cette technique permet le typage efficace de
génomes montrant de hauts niveaux de similitudes de séquences. À l’heure actuelle, dans
le cas du dépistage et du typage du virus du papillome humain (VPH), il n’existe aucun
système de sondes offrant une solution de diagnostic dont l’éventail soit complet et
satisfaisant. Pour parvenir à améliorer la conception des sondes d'hybridation, les
chercheurs se sont attaqués au problème de leurs spécificités et leur pouvoir
discriminatoire.
Leur méthode peut être étendue pour générer un système diagnostic qui repose sur
l'hybridation d’acides nucléiques de courtes séquences étroitement liées. Au lieu d'ajuster
les conditions d'hybridation à la sonde, un ensemble de sondes est sélectionné de manière
à fonctionner dans les conditions d'hybridation. Cette méthode permettant d'obtenir une
détection spécifique offre une plus grande efficacité et un plus large éventail
d'applications. Un ensemble de 39 sondes spécifiques pour chacun des types de VPH
ciblés a été testé. Les résultats obtenus à partir d’échantillons cliniques positifs pour le
VPH, y compris les six types les plus fréquents (6, 11, 16, 18, 31 et 33), montrent que ces
sondes permettent la discrimination de tous les sous-types. Ainsi, les résultats démontrent
que cette stratégie permet de détecter des changements de 3-7 nucléotides entre les
différents amplicons / types, en conditions d'hybridation à température ambiante et dans
un tampon PCR adapté.
La preuve de concept préclinique ayant été réussie, la prochaine étape réside dans la
validation à l’aide d’échantillons cliniques. Une fois cette preuve de principe obtenue, la
technologie pourra alors être adaptée dans un outil de détection et de typage plus général.
Le but du projet est donc de développer et de valider la technique de « l’hybridation
itérative » dans le cadre d’un test diagnostic en :
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1. Effectuant une validation de l’essai prototype sur des échantillons
cliniques;
2. Élaborant un format de l’essai dont le design facilitera la
commercialisation. L’objectif étant d’en arriver à un essai de typage du
VPH qui soit simple, efficace et peu coûteux;
3. S’assurant le respect des exigences réglementaires afin de permettre une
commercialisation rapide de l’essai;
4. Optimisant le format commercial de l’essai pour une plus grande sensibilité
et une plus grande spécificité;
5. Validant la performance de l’essai commercial final à l’aide d’échantillons
cliniques.
Plusieurs raisons justifient que nous entreprenions ce projet, dont les avantages très
concurrentiels de la méthode qui sont:
1er) Capacité d'adaptation et haut pouvoir discriminatoire: Bien que plusieurs trousses de
diagnostic pour la détection et / ou de typage soient actuellement disponibles sur le
marché ou décrits dans la littérature, la grande variété de techniques disponibles pour la
détection et la sous-typage des ~ 40 types de virus du papillome humain (VPH) au niveau
des muqueuses démontre le fait qu'aucune autre d’entre elles n’offrent une solution
complète à ce problème.
2e) Faibles coûts et facilité d'emploi: Il existe deux obstacles importants et inter liés
ralentissant le typage universel dans la population en générale, soit la complexité
technique de l'essai et le prix par dosage. Cette technique, lorsqu’intégrée à un outil
diagnostic, ne nécessite ni instruments coûteux, ni personnel hautement qualifié. En
outre, cette méthode offre la possibilité d'unifier les tests de diagnostic pour les différents
agents pathogènes dans les mêmes conditions de réaction qui, à terme, conduira à des
tests de diagnostic qui soient plus simples, rapides et moins coûteux.
3. PRINCIPAL RESEARCHER: PRESENTATION AND CONTACT
INFORMATION
Damian Labuda, Ph.D., D.Sc.
Professor, Pediatrics Department, Montreal University
Sainte-Justine Hospital Research Center, room B-607 b
3175 Cote Sainte-Catherine
Montreal, PQ
Canada H3T 1C5
Telephone: (514) 345-4931 ext.3586 [sec. 3282] fax: (514) 345-4731
damian.labuda@umontreal.ca
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Damian Labuda studied biology and biochemistry at Adam Mickiewicz University in
Poznan, Poland, where he also obtained his Ph.D. and D.Sc. He received additional
training in Szeged, Hungary, in Saclay, France, and in Göttingen, Germany (post-doctoral
fellow of Max-Planck Institute). His early works concerned structure-function
relationship in transfer RNA, origin of the genetic code, biochemistry and physicochemistry of nucleic acids. Since 1982, he continued his research on RNA structure and
interactions, in Cedergren’s lab in the Department of Biochemistry, University of
Montreal. In 1984 he joined the Research Center of the Sainte-Justine Hospital and the
Department of Pediatrics, University of Montreal, developing DNA based diagnostics
program as well as research in molecular, medical, population and evolutionary genetics.
Presently, he carries studies in human population genetics on the origins and the
evolutionary history of human populations, the founder effects and the genetic history of
French-Canadians. His laboratory is also involved in genetic epidemiology studies
aiming genetic bases of complex diseases, the underlying genetic models, the
identification of cancer susceptibility variants as well as genetic variants influencing the
disease outcome
4. DESCRIPTION OF THE TECHNOLOGY
4.1.
Background - HPV as etiological agent of cervical cancer.
HPVs are genetically diverse; those infecting genital epithelium represent types with low
and high oncogenic potential. Low-risk HPVs, such as types 6, 11, 34, 40 44 and others,
cause benign genital warts, whereas high risk HPVs (16, 18, 31, 33, 35, 39, 45, 51, 52,
56, 58, 59, 68) lead to cervical cancer. The most frequent 16 and 18 account for about
70% of infections seen in cervical carcinoma (Bosch et al., 2002; Franco et al., 2001);
HPV 16 alone being found in nearly 50% of high grade lesions. There exists a substantial
degree of DNA sequence identity among types as well as between malignant and benign
HPV strains. The difference between particular HPV types in their sequence segments
that are relevant to the HPV molecular testing can be as small as few nucleotides (Villa et
al., 2000; zur Hausen, 2000).
Cervical cancer is presently the second most common cancer affecting women
worldwide, and the most frequent malignancy among women in developing countries
(Ferenczy & Franco, 2002). It was estimated that 493,000 new cases of invasive cervical
cancer were diagnosed worldwide in 2002, representing nearly 10 % of all cancers in
women (Ferenczy & Franco, 2002). Indeed, the HPV-attributable proportion of the
cervical cancer is estimated at more than 95%. The relative risk associating HPV
infection to cervical neoplasia is very high and increases to several hundred in the case of
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the persistent infection with types 16 and 18 (Bosch et al., 2002; Clavel et al., 2001;
Franco et al., 2001). Once molecular pathogenesis of cervical cancer was recognized, it
became clear that an accurate type-specific testing of HPV is absolutely required for the
disease prevention and management, as recurrent detection of high-risk HPV types is a
strong predictor of high grade cervical intraepithelial neoplasia (CIN) and invasive cancer
lesions. (Brummer et al., 2006; Schlecht et al., 2001; Trottier & Franco, 2005)
Importantly, in the era of HPV vaccination, planning cervical cancer screening will
inevitably have to change, emphasizing need for HPV type-specific assays. (Franco et al.,
2006). Several diagnostic kits are commercially available and numerous diagnostic
systems have been described. However, of significant importance is the recent study by
the World Health Organization (WHO) which carried detection of 24 samples of seven
most frequent HPV types, using commercial individual typing kits, such as PGMY line
blot (Roche), SPF10-LiPa (Innogenetics), Deg GP5+/6+ reverse line blot and DNA chip
(Biomed Lab Seoul, Korea). The measurements were performed in 29 independent
laboratories and 12 different countries. The overall detection rate of HPV16 was 62% and
that of HPV18 was 73.9%; approximately, half of the laboratories failed to identify HPV
type 6. In 2008, WHO issued recommendation guidelines for the use of “reconstructed”
clinical samples and therefore make a common cross-reference among different
diagnostics tests and different platforms on the identically “reconstituted” samples.
4.2.
Technology developed and scientific basis
Four years ago we proposed a novel and generally applicable approach consisting of the
development of nucleic acid probes by selection in vitro. This differs from commonly
used approaches based on the rational design of probes. Addressing the common problem
of DNA diagnostics to distinguish between closely related population variants, similar
strains or subtypes, we developed a novel technology that would allow generation of
probes discriminating DNA targets that differ only by few sequence positions. Specific
probes are selected from a random oligonucleotides mixture by a process of iterative
hybridization. Repetitive rounds of forward and subtractive hybridization lead to specific
pools of probes with high discriminatory power from which individual probes can be
cloned.
In the summer 2004, we obtained the funding from CIHR to develop this technology and
show its applicability using a model system of HPV infection. The first task was to
develop proposed technology. For that, we used a specific segment of the viral L1 gene
of six HPV types differing by one to seven sequence positions. Starting from the initial
pool of probes we obtained pooled probes, and subsequently, target-specific cloned
probes. Both pooled and cloned probes were shown to discriminate well between six
HPV types. (Brukner et al, NAR, Brukner et al, Nature protocols, 2007). Once the
technology was developed, we extended the experiments to 39 HPV types. For the
selection we used the HPV genome region corresponding to the PCR amplified HPV
segment usually used in the clinical diagnostics (GP5+/6+ region of the viral L1 gene).
We have obtained a set of 39 probes specific for each of the targeted HPV type and
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efficiently discriminating against the remaining 38 types in a single experiment under the
ambient temperature of hybridization (Brukner et al., J. Clinical Virology, 2007).
In summer 2007 we obtained proof of principal grant from CIHR to simplify our assay
and render it generally applicable in the research and diagnostic setting. We tested the
probes in the reverse format (as opposed to previously used direct format) in which the
array of the HPV specific probes is immobilized on solid support. This format is more
suitable for diagnostic use and allows simultaneous detection of distinct HPV variants in
the clinical sample. Miniaturization of the assay was achieved by single compartment
hybridization (as opposed to previously used 96-well format). For this, the attachment of
probes was performed via streptavidin-biotin connection using SAM membranes
(Promega, WI). For all testing we used full-length GP5+/6+ target oligonucleotides (and
double strand amplicons derived from these oligonucleotides, mimicking thus PCR from
clinical samples) labeled with [32P] for initial optimization (Fig 1).
1
1
HPV 6
HPV 16
HPV 11
HPV 18
4
5
11
HPV 31
HPV39
8
12
HPV 33
HPV 51
9
18
HPV 35
HPV 68
Figure 1. Example of HPV typing probes in reverse format. Hybridization signal between 39 selected HPV
type-specific probes (each 100 pmols), y spotted on SAM membrane (7 cm x 3 cm) and particular intended
targets (HPV 6, HPV 11, HPV 16 and HPV 18 on upper panel and HPV 31, HPV 33, HPV 35, HPV 39
HPV 51 and HPV 68, on lower panel) each presented in the concentration of 3 pmols per 5 mL of
hybridization solution. (P32 autoradiography). Hybridizaton is performed at ambient temperatue (26+/4oC) using buffers compatable with colorimetric detection. No false positives (cross-hybriization) with
remaining 38 HPV types was seen.
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As a result of these successful developments, we subsequently focused our assay on four
most relevant HPV types (6, 11, 16 and 18). These types are the most common
worldwide and the most relevant from the point of view of recently introduced national
vaccination programs (duration and liability of vaccination strategy can be monitored). At
the same time, we can guarantee that probes that we obtained during selection will not
produce significant cross-talk with other relevant HPV types as shown in Fig. 2.
25
20
15
6
10
11
16
18
5
6
6
11
13
16
18
26
30
31
33
34
35
39
40
42
43
44
45
51
52
53
54
55
56
58
59
61
62
64
66
67
68
69
70
72
73
76
MM4
MM7
MM8
0
Figure 2 – Hybridization signal (y-axis) between selected 6-FAM labeled type-specific probes (HPV 6, 11, 16
and 18, using 20 pmol of each) and 39 HPV GP56 targets, where HPV types-specific numbering nomenclature is
ranked in the growing order on x-axis. Each target (20 pmol) is bound to one well (using 96-well steptavidincoated Pierce plate) and hybridization is performed in 100L volume (see Brukner et al, 2007, J. Clinical
Virology, for more details).
4.3.
Current development status of the technology – functional prototype
Processes/algorithm for the generation of spectrum of specific nucleic acid (NA) probes
able to discriminate against plurality of similar targets is not yet known. When sequences
that are to be distinguished are similar, the difference in their binding energy is small,
restricting the window of adjustable experimental conditions, which would allow
discrimination between all potentially reacting species. Finding such conditions is usually
problematic in multiplex applications, when many probes and/or many targets are
considered simultaneously. Moreover, if probes with such a requirement have to perform
under robust conditions, the design process is especially prone to failure. Here the term
“specificity” is used as an ability to discriminate NA target in the context of similar NA
targets (differentiating up to 87% sequence identity), while assay is considered “robust”
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if stability of the assay performance within a wide range of performing conditions is
preserved.
Following urgent need for developing more robust and more accurate HPV typing assay,
we applied this approach to obtain new generation of probes. These probes are selected to
discriminate among 39 clinically relevant HPV types, based upon the previously
characterized GP5+/6+ L1 segment of the HPV. In a series of hybridization steps, starting
from a mixture of random oligonucleotides, we iteratively enriched mixture in
oligonucleotides that selectively recognize each specific HPV type out of the 39 HPV
targets. (Brukner et al, NAR, J Clin Virol, Nature protocols, 2007). A detailed analysis of
data showed clearly that, given the number of variables, the rational design of probes
would not be as efficient and straightforward as selection performed in vitro. Analysis of
sequences of obtained probes showed that specificity of binding between probes and
targets is achieved through a fine balance between non consecutive stretches of basepairs, segments of mismatches and often accommodation of secondary structures. These
combinations allow maximizing the difference in binding energy between probe-specific
target and probe-unspecific target complexes.
In the next phase, we optimized a reverse format of probes (Fig 3). The performance of
the assay was examined using clinical samples containing HPV 16 and HPV 6.
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Figure 3. HPV typing of pre-characterized clinical samples containing HPV6 and HPV16 to the array of 39
immobilized type specific clonded probes (CP). (A) the arrangements of CP probes; (B) hybridization with
HPV6; (C) hybridization with HPV16. Arrows indicate the orientation of the probes array. (see Brukner et
al, J Clinical Virol. 2007, for more details)
We confirmed specificity of our probes and stability of our novel assay at the wide range
of temperatures, starting from 20°C to 28°C and in the different spectrum of nondenaturing buffers (classical hybridization buffers, as well as simple, PCR-like and
colorimetric-compatible buffers).
Such assay performance is prerequisite for the future point-of-care medical device,
contrary to the present genotyping assays, whose setting performance is not only
challenging for similar NA targets, but also based on sophisticated technological
platforms.
4.4.
Scientific value
The main advantage of our method resides in its enhanced power of identification and
discrimination between multiple short nucleic acid sequences that differ by a few
mutations, as it is the case with different HPV types, in a multiplex hybridization assay.
In other words, instead of adjusting hybridization conditions to the whole set of probe:
target pairs that we want to include in the diagnostic device, by using iterative
hybridization we adjust the probes to the conditions we have chosen.
Example of direct expected outcome using our HPV typing assay in clinical follow-up is
to estimate HPV vaccine performance and its protective time in industrial countries
where HPV vaccine program is available. It will also provide a cost-effective but accurate
and easy to use diagnostic tool, an essential requirement for deployment of HPV
screening program in developing countries.
Finally, the methodology of probe selection is applicable to many other medical
conditions where investigation or diagnosis or detection of resistant strains is based upon
a differentiation of highly similar nucleic acid sequences (HIV, hepatitis virus,
tuberulosis..).
5. INTELLECTUAL PROPERTY
5.1.
Invention disclosure
In January 2006, Dr. Brukner, Dr. Labuda and Dr. Krajinovic filed an invention
disclosure at the research administration of Hôpital Sainte-Justine. The inventorship’s
contribution is presented in Table 1.
Inventors
Status
MDEIE – Commercialization and Transfer Assistance Program
Institution
%
inventorship
8
Îvan Brukner
Damian Labuda
Maja Krajinovic
Research associate
Professor
Associate professor
CHU Ste-Justine
45 %
CHU Ste-Justine
35 %
CHU Ste-Justine
20 %
Table 1. List of the inventors and their contribution to the invention
The invention describes a new method for generating sequences of hybridization probes,
suitable for multiplex target detection, even if the plurality of targets are very similar at
the sequence level. The method is based on the hybridization of nucleic acids. A
prototype for genotyping HPV virus was built and performance of 6 selected probes was
tested and compared with complementary probes. A set of 39 oligonucleotide probes for
HPV typing was generated and more recently a prototype assay was optimised for 4
probes (see section 6.1.). A provisional patent application entitled “NUCLEIC ACID
PROBES, METHODS FOR THEIR PREPARATION AND USES THEREOF” was filed
in the US in August 2006. We filed a complete PCT application in August 2007 and we
expect to enter the National Phase in different markets in February 2009 (see section
5.3.1.). M. Serge Shahinian from the firm Goudreau Gage Dubuc in Montreal is the
patent agent handling the file.
The data base “Derwent World Patents Index”, where specialist editors provide a
comprehensive summary of the patent contents with its advantages gives the following
description of the invention:
NOVELTY - Identifying an oligonucleotide for discriminating a first nucleic acid from a second
nucleic acid comprises: (a) hybridizing the first nucleic acid with oligonucleotides comprising a
random nucleotide sequence flanked by primer recognition sequences; (b) amplifying the bound
oligonucleotides to obtain amplified oligonucleotide duplexes; and (c) repeating hybridization in the
presence of a second nucleic acid, where an oligonucleotide comprising the random nucleotide
sequence can be used for discriminating the first nucleic acid from the second nucleic acid.
DESCRIPTION - Identifying an oligonucleotide for discriminating a first nucleic acid from a second
nucleic acid comprises:
1.hybridizing the first nucleic acid with a pool of oligonucleotides in a hybridization mixture, the
oligonucleotides comprising a random nucleotide sequence flanked by primer recognition sequences;
2.removing oligonucleotides which are not bound to the first nucleic acid from the hybridization
mixture; 3.dissociating bound oligonucleotides from the first nucleic acid; 4.amplifying the bound
oligonucleotides using primers capable of binding to the primer recognition sequences to obtain
amplified oligonucleotide duplexes comprising a first strand corresponding to the bound oligonuc
leotides and a second strand corresponding to the complement of the bou nd oligonucleotides;
5.treating the duplexes to remove or degrade the second strand to obtain single-stranded amplified
oligonucleotides; 6.repeating (a) to (e), where the pool of oligonucleotides of (a) is the amplified
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oligonucleotides obtained in (e) thus to obtain further ampli fied oligonucleotides; and 7.repeating (a)
to (e), where the hybridization in (a) is performed in th e further presence of the second nucleic acid;
where an oligonucleotide comprising the random nucleotide sequence of the further amplified oli
gonucleotides can be used for discriminating the first nucleic acid fro m the second nucleic acid.
INDEPENDENT CLAIMS are:
1.an oligonucleotide (a) identified by the method above, (b) capable of discriminating a first nucleic
acid from a second nucleic acid, where the oligonucleotide is not exactly complementary to the first
nucleic acid, and (c) comprising a nucleotide sequence selected from SEQ ID NO. 1- 43, 100-104, and
116; 2.a method for detecting the presence or absence of a first nucleic acid in a sample; 3.a kit for
detecting the presence of a first nucleic acid in a sample, the kit comprising the oligonucleotide; 4.a
collection of two or more oligonucleotides, where the oligonucleotides comprise a nucleotide
sequence selected from SEQ ID NO. 1-43, 100-104 , and 116; 5.an array comprising the
oligonucleotide or the collection of two or more oligonucleotides; and 6.a kit for identifying an
oligonucleotide for discriminating a first nucleic acid from a second nucleic acid, the kit comprising
the pool of oligonucleotides.
USE - The methods are useful for identifying an oligonucleotide for discriminating a first nucleic acid
from a second nucleic acid, and for detecting the presence or absence of a first nucleic acid in a
sample. The kit is for detecting the presence of the pathogen in the sample, for detection of the
pathogen in the subject, and for diagnosing a disease or condition associated with the pathogen in the
subject (all claimed). The methods can be used for discriminating between closely related or similar
nucleic acids, and for identifying or preparing an oligonucleotide for discriminating a desired or
intended target nucleic acid from other undesired or non-intended non-target nucleic ac ids. The
oligonucleotides, methods, and kits may be used in analytical, diagnostic (e.g. infection of an animal,
plant, or organism by a pathogen), detection, manufacturing/quality control, research, environmental
monitoring (e.g. pollution/contamination of air/water/reagents) intended for use in biological systems
(e.g. culture or animal systems/other materials), microbiology (detection studies of organisms difficult
to c ultivate), and forensic applications.
ADVANTAGE - The method has the capacity of identifying or preparing an oligonucleotide for
discriminating nucleic acids, which share sequence similarities, e.g. similar nucleic acid sequences
from different organisms (e.g. orthologous genes), variants (e.g. polymorphisms, different alleles) of a
given nucleic acid sequence, nucleic acid sequences derived from genes belonging to the same family
or nucleic acids derived from subtypes of a given organism (e. g. virus, bacteria, parasites).
5.2.
Previous disclosure and/or anterior art
In conjunction with Univalor, the organization that provides commercialization services
to the research centre of Hôpital Sainte-Justine (see section 9), we performed a review of
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the prior art. The search was carried out using Delphion patent databases, and literature
(PubMed) together with a web-based search.
5.2.1. Method of selection probes
The concept of selecting nucleic acid sequences that specifically bind particular targets
has been developed using an approach called SELEX (systematic evolution of ligands by
exponential amplification. However that patented method (see Gold, Table 2a) and other
related methods described in the literature (c.f. Kyung 2003) do not teach the use of
iterative selections for generation of nucleic acid ligands against nucleic acid targets for
the purpose of genotyping or identifying/detecting nucleic acids. Therefore, our iterative
hybridization method to select probes that can discriminate between closely related or
similar nucleic acids is entirely novel.
Patent
(filing date)
US5475096
June 10,
1991
Title
Nucleic
acid
ligands
376 family
members
Inventor
(Assignee)
Gold, et al.
(University
Research
Corporation)
Abstract
A new class of nucleic acid compounds, referred to as
nucleic acid ligands, have been shown to exist that have a
specific binding affinity for three dimensional molecular
targets. In a preferred embodiment the nucleic acid ligands
are identified by the method of the invention referred to as
the Systematic Evolution of Ligands by EXponential
enrichment (SELEX), wherein a candidate mixture of
nucleic acids are iteratively enriched in high affinity nucleic
acids and amplified for further partitioning.
Table 2a. Patent related to the method
5.2.2. HPV probes
Our search revealed, that prior art taught the use of nucleic acid probes to detect HPV
types. Several patents (see examples in table 2b and in Annex 1) and articles (Hwang et
al., 2003; Klaassen et al., 2004; Kleter et al., 1999; Schmitt et al., 2006; van den Brule et
al., 2002) describe typing systems based on PCR/classical hybridization but in all cases
they rely on complementary sequences to discover HPV types (hybridization rules based
on Watson-Crick base-pairing). Our probes do not rely on complementary sequences and
also none of our probes sequences are disclosed or claimed in these documents.
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Patent
(filing date)
Title
Inventor
(Assignee)
US6583278
November
14, 1996
11 family
members
Nucleic acid probes
complementary to human
papillomavirus nucleic
acid and related methods
and kits
Gordon, et al.
US6265154
October 25,
1996
8 family
members
Nucleic acid primers and
probes for detecting
oncogenic human
papillomaviruses
Kroeger, et al.
(Abbott
Laboratories)
US5364758
July 16,
1992
20 family
members
Primers and process for
detecting human
papillomavirus genotypes
by PCR
Meijer, et al.
(Stichting
researchfonds
pathologie)
US5712092
July 7, 1994
39 family
members
Papillomavirus probe and
process for in vitro
diagnosis of
papillomavirus infections
Orth, et al.
(Gen-Probe
Corporation)
(Institut Pasteur)
Abstract
The present invention describes oligonucleotides targeted to HPV
Type 16 and/or Type 18 nucleic acid sequences which are
particularly useful in aiding the detection of HPV Type 16 and or
18 by, for instance, acting as hybridization assay probes, helper
probes, and/or amplification primers.
Probe sequences that are useful for detecting oncogenic HPV
types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59 and 68 are
herein provided. These sequences can be used in hybridization
assays or amplification based assays designed to detect the
presence of these oncogenic HPV types in a test sample.
Additionally, the sequences can be provided as part of a kit.
The invention relates to primers and a method of detecting
human papilloma virus (HPV) genotypes by means of the
Polymerase Chain Reaction (PCR). The invention provides such
primers and such PCR conditions that in principle any genital
HPV genotype is detected. The invention enables a sensitive and
reliable preselection of samples to be examined, such as cervical
smears.
The invention relates to human papillomaviruses HPV,
particularly to HPV-DNAs isolated from papillomaviruses HPV-2d,
HPV-10b, HPV-14a, HPV-14b, HPV-15, HPV-17a, HPV-17b,
HPV-19, HPV-20, HPV-21, HPV-22, HPV-23, HPV-24, HPV-28,
HPV-29, HPV-31, HPV-32, HPV-IP2 and HPV-IP4. The invention
also relates to DNA capable of hybridizing with the HPV-DNAs or
fragments thereof, to kits containing distinct groups of probes
containing one or more of these HPV-DNAs or fragments thereof,
and to procedures for detecting and identifying HPV in tissue.
Table 2b. Patent related to our HPV assay
5.2.3. Research report on the PCT patent application
In November 2007, we received the international research report and the written opinion
of the international searching authority.
Seven documents, including four documents published by our inventors were found to
oppose our invention in terms of both novelty and inventive step (nothing was opposed to
the industrial applicability of the invention). We carefully analyzed these documents and
our conclusion, which was validated by our patent agent, is that none of these documents
teach, disclose or can be considered as anterior art of what we claim in our invention (see
Annex 2 for a summary of our analysis).
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In conclusion, based on our analysis of the prior art, we do not anticipate any problems
for the patentability of our invention and we are confident that we would be in an
excellent position to argue potential objections from patent Examiners at the regional and
national phases of protection, should there be any. This confidence was validated by the
patent agent handling the file. It might be important to mention that Univalor’s team has
experience in patent prosecution and with interpretation of PCT written search and
opinion reports.
5.3.
Freedom to operate analysis (FTO)
We do not see any FTO problems related to the commercial use of our new method for
generating sequences of hybridization probes concerning the SELEX patent (see section
5.2.1) The SELEX process is described in two issued US Patents, No. 5,270,163 (filed
Aug 1992), which claims the SELEX method itself, and No. 5,475,096 (see table 2a)
which claims the use of the method to identify nucleic acid ligand for target molecules
“other than a polynucleotide that binds to said nucleic acid ligand,” and “wherein said
nucleic acid ligand is not a nucleic acid having the known physiological function of being
bound by the target molecule.”
Our preliminary FTO search and analysis gives us no indication that the commercial
production, marketing and use of our new assay for HPV detection would infringe the
intellectual property rights of other patents. Our analysis included the US patents listed in
table 2c and in Annex 1. It appears that these inventions relate mainly to the HPV DNA
isolated from the appropriate strain, the probes containing these DNA sequences, and the
kits containing these probes. Because the intrinsic nature of our probes is not fully
complementary to any of the HPV DNA, our probes are not covered by the claims of
these patents. Our position was validated by our patent agent. Note that most of the HPV
types were covered by patents that are now expired or will expire in the near future.
Consequently, we do not anticipate a need to license any patent on either SELEX or any
specific sequence of HPV variants in order to commercialize our technology.
Patent number (priority date)
Comments
No. 6,391,539 (November 1984), No. 5,958,674
(November 1984), No. 5,876,723 (March 1986), No.
5,824,466 (May 1988), No. 5,656,423 (December 1990)
and No. 5,981,173 (February 1996)
Patents that are part of the broad HPV
patent portfolio developed at the Institut
Pasteur that were licensed to Roche in June
2002;
No. 4,849,334 (June 1987), No. 4,849,332 (May 1987), No.
4,849,331 (June 1987) and No. 4,908,306 (June 1987)
Patents were assigned to Life Technologies
(now Invitrogen)
No. 5,057,411 (April 1985) and No. 5,643,715 (October
1988)
Patents were assigned to Georgetown
University.
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Table 2c US patents related to HPV types
5.3.1. Acquired or planned protection
A provisional patent application entitled “NUCLEIC ACID PROBES, METHODS FOR
THEIR PREPARATION AND USES THEREOF” was filed in the US in August 2006.
That patent application claims a method for identifying and preparing probes for selective
detection of nucleic acids. This method is particularly useful in discriminating between
closely related nucleic acid sequences. Such a method may be used in a variety of
analytical and diagnostic research and related applications. Probes selected for 39
different HPV types are covered in the patent application. A complete PCT application
was filed in August 2007.





Priority Application Number (Number Kind Date): US 2006822153 P 20060811
PCT Application Number WO 2008017162
Patent Assignee: SAINTE-JUSTINE UHC
Inventors: BRUKNER I; KRAJINOVIC M; LABUDA D
PCT filing date: 20080214
We plan on entering the Regional and National phases in February or March 2009 as
described in the following table (Table 3).
1)
2)
3)
4)
Canada (February 2009)
USA (February 2009)
South Africa (February 2009)
ARIPO (March 2009). ARIPO is considered a regional phase covering the
following countries: Botswana, Gambia, Ghana, Kenya, Lesotho, Malawi,
Mozambique, Namibia, Sierra Leone, Sudan, Swaziland, Tanzania, Uganda,
Zambia, and Zimbabwe.
We will budget another patent filing in a territory that will be chosen between the
following: Europe, Angola (a relevant territory for our financial partner in this
application) and Brazil (the translation of the application into Portuguese for the Angola
application can be subsequently used for the Brazil application and will reduce the cost of
filing in this country by 50%).
The IP protection in Canada, South Africa and ARIPO is justified by the partnership with
the company Continental Diagnostic, based in South Africa (see section 14), and the
interest of Warnex, based in Laval, Québec to provide HPV diagnostic services through
Canada. It is also strategically important to get protection in US which is the largest
market for HPV testing presently. Europe and Brazil are also two relevant territories for
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IP protection since vaccines clinical trials were done in these territories. However the
final choice between Europe, Brazil and/or Angola will be decided in January 2009.
5.4.
Revenue sharing
The documents attesting to the assignments of titles, rights and revenue sharing between
the researchers, the CHU Sainte-Justine Research Centre (“CHU Ste-Justine”), its
commercialisation entity (i.e. Valorisation-HSJ, limited partnership) and/or the
Université de Montréal (“UdeM”), shall be concluded prior to the start of the project, the
whole according to the provisions of the intellectual property policies and related
agreements in force between these institutions.
As a precision, CHU Ste-Justine is an affiliated institution of UdeM and as such, CHU
Ste-Justine and UdeM jointly own, in equal parts (50%/50%), the undivided ownership
rights in any invention originally disclosed at CHU Ste-Justine by a researcher who holds
an academic qualification or a faculty title of UdeM. CHU Ste-Justine and UdeM also
jointly own, in equal shares (50%/50%), the institutional share of the benefits or revenues
which will be allotted to CHU Ste-Justine, as mutually agreed between these institutions.
The share of the proceeds of commercialization of the invention (the “Proceeds”) shall
therefore be divided and paid as follows:
(A) fifty percent (50%) of the Proceeds shall be allotted to the researchers, which
portion shall be divided between each of Îvan Brukner (22,5%), Damian Labuda
(17,5%) and Maja Krajinovic (10%); and
(B) fifty percent (50%) of the Proceeds shall be allotted to Valorisation-HSJ, limited
partnership (the valorisation entity of CHU Ste-Justine), which portion shall be
divided in equal shares (50%/50%) between Valorisation-HSJ, limited
partnership and UdeM.
Party
Share of Proceeds
Îvan Brukner
22,5%
Damian Labuda
17,5%
Maja Krajinovic
10%
Valorisation-HSJ, limited partnership (CHU Ste-Justine)
25%
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Party
Share of Proceeds
UdeM
25%
TOTAL:
100%
Table 3. Final sharing of the Proceeds between the parties
6. TECHNOLOGY DEVELOPMENT PLAN
The proposed development plan will allow optimizing and validating the efficacy of a
new HPV assay and will provide us with convincing arguments that it can fulfill all
principal requirements of clinical and market needs: multiplex detection, detection of
different HPV types in the same patient (super infection), low production cost and ease of
use.
6.1.
Identification of current stage of technology development.
The actual prototype kit is composed of 4 probes designed to detect 4 HPV vaccinerelevant types (6, 11, 16 and 18), including two positive controls: one reflecting presence
of any HPV in the sample and the other controlling for sample DNA integrity (see Figure
4). HPV targets are 150 nucleotides long GP5+6+ DNA segments, derived through
amplification or chemical synthesis.
6
11
100
100
16
18
100
100
UP
CD
0.5
10
Figure 4: Schematic presentation of 4 cm x 2cm Steptavidin-coated Membrane (SAM, Promega) with
biotinilated oligonucletide probes Optimal number of picomoles (right panel) spotted on the membrane
(left panel) for each HPV probe and controls (UP, universal HPV probe, CD, control DNA designed for the
control of the quality of DNA extraction
HPV 6, HPV 11, HPV 16 and HPV 18 are the most frequent virus types. In fact, HPV
types 16 and 18 account for 70% of HPV infections. Accurate and affordable HPV
genotyping for these strains will also be in high demand for the next few decades due to
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HPV vaccination studies. Recently, two experimental vaccines to prevent infection with
HPV 6, 11, 16 and 18 became available. HPV screening is needed here: i) to identify
individuals that are eligible for vaccination and ii) to monitor the efficiency of vaccines.
The Advisory Committee of Immunization Practices (ACIP, US) recommended the
continuation of HPV screening protocols until (i) other type-dependent vaccines are
developed and (ii) the protective time period of the vaccine is fully characterized. The
advantage of our assay is in the selection of probes in the context of 39 viruses.
Therefore, the probes are highly specific for these types and do not cross-hybridize with
other HPV amplicons (see Figure 2).
We also developed an HPV universal probe, which is designed to detect any HPV
infection (Fig. 5, probe UP). This “promiscuous probe” allows for the follow-up of HPV
positive cases (but HPV 16 and 18 negative ones), which is of particular interest to
researchers and to public health. Despite typing only 4 viruses, all cases of HPV-positive
cases could be clinically registered. Further type-specific analysis can be then performed
by complementary methods.
Recently, we also introduced a strategy that will allow monitoring of DNA quality and
quantity of a clinical sample. This strategy includes new PCR and a corresponding new
probe. The probe was designed to detect monomer repeat of 29 adenines (A29), present
in a single copy locus of human genome of well-described BAT26 amplicon (Fig. 5
probe CD).
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The performance of each type-specific probe and its corresponding intended targets is
presented in Figure 6A.
6.2.
Remaining Steps and Time to Market
Class II, III and IV medical devices need to have Canadian licenses in order to be sold in
Canada. After speaking with Sarah Chandler, Acting Head of the Regulatory and
Scientific Section at the Device Licensing Services Division of the Medical Devices
Bureau at Health Canada, we believe our HPV test is most likely a Class III product. We
plan to validate the classification status of our device before the end of 2008. This is the
first step toward getting a medical device license.
The regulatory process in South Africa starts with a letter to the authority mentioning the
intention to file clinical information for registration of a new test. The authority can call
for local clinical information and trials if deemed necessary. When the information has
been submitted, questions could follow on the proof of concept and clinical validation
methodology results. The whole process takes up to 3 years right now, but when the new
authority steps in it might be shortened to 18 months and if fast tracked, 9 months.
Our strategy is to partner with a company already established in the molecular diagnostic
market who will be responsible for the final stages of our product development, including
all aspects of clinical validation and regulatory affairs. We will have the opportunity to
work with the Quebec company Warnex (see letter of support) to define the regulatory
path for our HPV assay.
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6.3.
Technical and technological challenges to be met and anticipated progress
1)
Preservation of assay specificity and sensitivity under different assay
conditions
Our results indicate that we will be able to develop a new format of HPV typing kit that
will preserve clinical sensitivity (genome equivalent, GE, 1000 or more), but will have
unique specificity features preserved in a wider-than-usual range of assay conditions.
What remains is to prove that our type-specific probes will produce better assay stability
than any other probes on the market. It is well known from literature data that small
variations in HPV genotyping assay conditions can lead to the wrong interpretation of
hybridization intensity patterns when using known commercial kits. The most critical
issues are in the domain of specificity of hybridization among multiplicity of similar
targets, where even a 1oC deviation from the intended temperature, or small variations in
buffer conditions can be detrimental. In fact, recent data (Journal of Clinical Virology 42
(2008) 412–414) showed that even intra-laboratory repetitions with the same clinical
samples (but different DNAextractions) did not produce the same results using Roche
Linear Array assay (83% concordance). We believe that our HPV typing probes have
inherent (sequence-dependent) features which preserve stability under a wider range of
assay conditions. Considering that this issue presents a major barrier to the current
accuracy of hybridization-based assays, overcoming it by confirming our data in a
clinical setting would be important accomplishment. As an example of anticipated
progress, we recently perform hybridizations between HPV 6, 11, 16 and 18 single
stranded targets (GP5+ strand) at 4 different temperatures (20, 25, 30 and 35oC) and
recorded hybridization pattern, as presented on Figure 6B
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2)
Optimization of a prototype assay format and developing it into its final
product
We already have a functional prototype assay format which will be challenged with
reconstructed samples having 1,000 and 10,000 genome equivalents (GE) of different
types of HPV in the background of 1,000 GE of human DNA (see Figure 7).
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We do not foresee obstacles in detecting 1,000 genome equivalents of HPV in the
hybridization assay. In fact, our present developments indicate that a hybridization
assay is not an obstacle per se, since 1,000 GE of HPV 6, 11, 16 and 18 are
amplifiable by PCR (using oligonucleotide targets as substrates) in sufficient quantity
to guarantee detection of the hybridization signal. We will have to do HPV GP56
amplification in the context of human DNA, where we will have to satisfy “normal”
PCR yield requirements (1-10pmols) and at the same time be able to perform CD
PCR (i.e. produce amplicons which reflect DNA quality of sample).
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3)
PCR amplification from clinical samples
Protocols designed to collect, store and purify DNA from cervical swabs are welldescribed. And the expertise of Dr Gòrska-Flipot Izabella from the Hotel-Dieu
diagnostics laboratory, guarantees that this challenge will be addressed in a professional,
effective fashion given the long clinical experience and expertise she has in the domain of
molecular diagnostics.
4)
Technology transfer with the group from South Africa
The present assay format is functional at Saint-Justine Hospital and we have to be sure
that all parameters of protocol are well defined and universal, so the assay can be
reproduced, without technical help from the person who developed the protocol.
Therefore, we will establish a technological transfer procedure and a corresponding
manual, which will guarantee that the assay can be independently repeated with the same
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quality of assay performance as originally described. Here is the summary of current
optimal conditions for each procedural step: (the details of protocol 4a to 4d might as
well go to Appendix if you think it is a good idea)
4a) PCR The 50 l volume PCR was performed as originally suggested (van den
Brule, et al., 2002) with minor modifications including shortening elongation and
denaturation time to 20 seconds. Yield of PCR was monitoring by loading 10l reaction
mix over agarose gel and EtBr staining.
4b) Conversion of PCR product to single stranded (ss) DNA and labeling The
40L were digested for 15 minutes at 37C, with EXO1 (NEB), following enzyme
inactivation (20min, 85C), and lambda exonuclease (15 min, 37C, following 20 min,
85C). Sample was passed over S25 column for buffer exchange reaction compatibility
with downstream T4 Polynucleotide Kinase labeling step. The conversion of double
stranded to single stranded form of PCR product was monitored by disappearance of EtBr
stained bend before and after digestion.
4c) Membranes Streptavidine-coated Promega membranes (SAM, Biotin Capture
Membrane, Medison, WI) were used in the following manner. The 1 l of 100pmols/l
of type specific (CP) 5’ biotinilated oligonculeotide probes were manually sported
(HPV6, HPV11, HPV 16 and HPV 18) on the surface of 3cm x 2cm membrane (see
Figure 1 for spotting schematic). The HPV universal probes (UP) were spotted using 1 l
of 0.3 pmols/l of oligonucleotide. Spotted drops were dried at ambient temperature for
5 minutes, membrane was washed in ddH2O for 1-2 minutes and pre-hybridized in 2 mL
hybridization buffer SSPE (150 mM NaCl, 10 mM NaH2PO, 1.1 mMEDTA, pH 7.4),
0.75MNaCl, 70mMTris–HCl, pH 7.4) containing 1% SDS and 200 mg/ml heparin
(hybridization oven, Model 400, Robbins Scientific ) for 1-12h at 55oC. These
membranes were either stored at room temperature for couple of days, or immediately
used for hybridization assay.
4d) Hybridization Labeling of 2-20 pmols of PCR and/or oligonucleotide was
perfomed using 5 l of [32P] ATP (6000 Ci/ mmol) and 1 L of T4 Polynucleotide
Kinase to a specific activity of 105 to 106 cpm/pmol, following produce manual
recommendation (Invitorogen). Hybridization was carried out for 1-12 hours. The
membranes were then washed with 1x SSPE containing 0.1% SDS for 10 min at room
temperature and either exposed overnight at -80°C with intensifying screens, or exposed
in Cyclone Storage Phosphore Screen (Perkin Elmer) for 10-30 minutes and read by
Cyclones software (OptiQuant, version 4.00).
6.4.
Objectives sought
The overall goal of this project is to develop a functional HPV assay that will be
implemented in a clinical diagnostic laboratory in Quebec and in South Africa.
The specific objectives required to reach this goal are
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1. Clinical validation of the prototype assay
2. Design of the commercial format of the assay (simple and cost-effective HPV
typing assay)
3. Establish the regulatory pathway for the commercial use of the assay
4. Optimization of the commercial format of the assay for high sensitivity and
specificity
5. Validation of the performance of the commercial assay with clinical samples.
6.5.
Type of activities to be carried out
The point by point summary given below refers to major issues needed for assay
optimization as well as validation of sensitivity and specificity of assay with standardized
and clinical samples.
1. Preparation of the test: Spotting of 4 type-specific DNA probes (6, 11, 16, 18) on
SAM membranes (Promega); Inclusion of the positive control that is universal
control positive for any HPV type; Introduction of probe for the control of DNA
extraction (DNA integrity) from clinical sample collection. To this end,
independent PCR will be subsequently performed from reconstructed and clinical
samples (see below). This PCR is amplifying single copy human genome segment
known as BAT26 locus. Preliminary data demonstrating the performance of
recently designed universal HPV probe are shown in the figures 3 to 8. The
preliminary data using oligonucleotide mimicking BAT26 PCR product (without
primers) are given in Figures 5.
2. Verification of the amplification sensitivity of standardized (in vitro reconstructed)
samples. Range of genome equivalents (GE) of HPV (1000-10 000) will be tested.
Multiplex PCR that is simultaneously amplifying any HPV genome and BAT26
locus from human DNA will be developed.
3. Evaluate the performance of different variant of GP56 primers. This would be done
to see performance of different variant of GP56 primers in the context of different
number of HPV genome equivalents and particularly in the context of different
combinations of mixed infections (GE 1000, 10 000 and 100 000), spiked with
human DNA (1000 GE)) and co-amplification of other HPVs except those here
tested. Amplification products should enter into the yield range of 1-10pmols for all
39 types, where HPV16 amplicon (known to perform well) will be used as a
reference point (producing 100% “standard” yield).
4. Amplification of DNA from 40 clinical samples for which custom HPV typing is
already available. Samples from Department of Pathology of Centre Hospitalier de
l’Université de Montréal will be used. Cervical biopsies were evaluated by service
pathologists as cervical intraepithelial neoplasia of a different grade. Custom HPV
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detection was performed by PCR amplification with PGMY09/11 primers designed
to amplify a product from the L1 open reading frame of a wide spectrum of HPV
types. The HPV types were assigned by restriction fragment length polymorphism
based on comparison with known HPV sequences. Two restriction enzymes, RsaI
and Dde I, were used which gave characteristic restriction patterns for most HPV
types (Fig .9) (Gorska-Flipot et al. Ann Biochem Clin, 1996, 35, 66-70). To avoid
confusion, we will call this assay the CHUM HPV assay. We are aware of tha fact
that each primer set used in amplification has its own bais toward particular type of
viruses. Therefore, the GP5+6+ PCR will be done using PCR product from MY9/11
primer sets and original DNA. Although, this first strategy is known as nested PCR,
using this strategy we would be able to minimize the effect of primer bias in both
MY9/1 and GP56 primer systems.
5. Analysis of the same reconstructed and clinical samples with commercial Roche
HPV typing kit.
6. Comparative analysis with custom and commercial HPV typing. This analysis will
be done in collaboration with Dr Eduarod Franco (Professor of Epidemiology and
Oncology Director, Division of Cancer Epidemiology, McGill University), which
for many years leads the study in HPV epdemilology (see letter).
Cloning and sequencing of HPV PCR products will be performed in the case of
discordant results.
Activities which are currently performed to reach each objective are described in the
following sections.
6.5.1. Clinical validation of the prototype assay
As presented in section 6.1, the actual prototype kit is composed of 4 probes designed to
detect 4 HPV vaccine- relevant types (6, 11, 16 and 18) including two positive controls,
one reflecting presence of any HPV in the sample and second, controlling for sample
DNA integrity. HPV targets are 150 nucleotides long GP5+6+ DNA segments, derived
through amplification or chemically synthesized. We use of in vitro “reconstructed
clinical samples” of HPV 6, 11, 16 and 18 following suggestion of Word Health
organization for optimizing HPV tests. The variable input of GP5+/6+ HPV
oligonucleotides or HPV plasmids is spiked prior to PCR with a constant amount of
human DNA, originating from HPV negative cervical samples, to mimic molecular
complexity of biological samples. In particular, range of genome equivalents (GE) of
HPV (1000-10000) is added to human DNA. The concentration of human genomic DNA
in reconstructed samples is comparable to the amount of DNA that is generally found in
cervical scrape specimens (~106 human genomes/ml), (Quint et al., 2006). These
“sample-reconstruction” experiments are allowing simulation of single and double HPV
infection and controllable measure of analytical performance of our type-specific probes.
In the next step, clinical samples (n=40) with known HPV status, as confirmed by the
CHUM HPV assay (Fig. 9), will be used for estimating the performance of HPV assay.
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The results of HPV typing obtained with our probes and custom approach will be
compared with the results of Roche LA HPV Genotyping Test.
HPV - PCR-RLFP
16
31
6
11
?
Rsa
16
31
6
11
Figure 9. Schematic presentation of the CHUM HPV assay (a custom PCR-RFLP used for HPV typing)
6.5.2.
Design of the commercial format of the assay
There are multiple formats of multiplex hybridization kits on the market and custom
assays in research or clinical laboratories. Several options for commercial format exist for
our technology including solid support for DNA probe attachement and for hybridization
signal detection. As previously stated, our prototype assay cannot reach the market in its
current format, with its large SAM membrane, radioactive detection (P32), and high cost
of production.
As presented in Table 4, our rough estimation of the cost of production per kit is $26
which is highly expensive for such a kit. It should be noted that our kits have actually
been manufactured in the researcher’s laboratory and there is no economy of scale. The
membrane cost is clearly the main issue if we want to substantially reduce production
cost.
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Materials
Oligo probe 6*
Oligo probe 11*
Oligo probe 16*
Oligo probe 18*
Cost/ kit (CDN$)
0.04
0.04
0.04
0.04
comments
umol scale needs 100pmol per spot
umol scale needs 100pmol per spot
umol scale needs 100pmol per spot
umol scale needs 100pmol per spot
Two DNA control oligos to be
spotted
0.08
umol scale needs 100pmol per spot
Membrane SAM-Promega
25.00
$200 per membrane/8 HPV kits of
2cmX3cm
Blocker (needed to block
membrane)
0.08
reduce background signal; increase
ratio signal/background
Technician time to prepare
membrane ($50/hr) - cut
membrane, spot DNA, etc)
Package (plastic )
total=
* 67 mer single strands with biotin
0.50
0.50
26.32
100 membranes prepared per hour
plastic 15mL Falcon tubes
Table 4. Cost breakdown for the current production of our HPV prototype assay
Our data obtained so far shows that other membrane-based hybridization (Immunodyne
ABC membrane, Pall) could replace SAM membranes (Promega). Preliminary data
showing performance using modified streptavidin coated Immunodyne ABC membranes
are given in Fig. 10. This might be an excellent alternative for reducing the cost of the
final assay given the 100 fold lower price of Immunodyne ABC versus SAM membranes.
Immunodyne ABC membrane (Pall)
Example of HPV 18
6
11
16
18
UP
CD
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Figure 10. Example of possible reduction of final product prize (100x) using Immunodyne ABC-Pall
instead SAM-Promega, Immunodyne membrane can replace SAM (Promega) membranes used in the
experiments shown in previous slides reducing thus the most significant material cost by 100 times (20$ to
0.2$)
Development of an alternative system of visualization of probe–target hybridization is
also essential for the simplicity and commercialization of the assay. One of the
possibilities is a colorimetric assay with the use of 6-FAM labeled primers to produce
PCR and a corresponding anti-6FAM-antibody with downstream alkaline phosphatecoupled colorimetric detection.
Another important aspect will be to reduce the size of the assay. A 10X reduction of
hybridization volume and corresponding solid support surface (beads, or array) will
reduce PCR yield requirement to 50-100ng, typical for PCR volumes of 10uL. Detection
of hybridization will be adequately adjusted. For example, the Luminex platform would
require Cy3 fluorophore, while a slide micro-array format would allow use of DIG
(digoxigenin-modified nucleic acids), or 6-FAM and the corresponding horseradish
peroxidase-conjugated anti-fluorescein, or anti-DIG antibodies (Roche, Invitrogen and
number of other suppliers). It is worthwhile mentioning that gold-nanoparticles are the
simplest alternative for colorimetric detection of DNA (post-PCR) with robust chemistry
and existing expertise in Canada (Yingfu Li, Department of Chemistry and Department
of Biochemistry and Biomedical Sciences, School of Biomedical Engineering, McMaster
University).
In order to define the best format for the assay for commercialization, a deep analysis of
the available options will be done. We plan to outsource this activity to a consultant with
strong expertise in molecular diagnostics. This consultant has yet to be identified, but one
possible candidate is Dr Yvan Côté, VP at Warnex, who has not only industrial
experience but also who has expressed his interest in performing this analysis as a private
consultant (independently from Warnex). It is worthwhile to mention that Yvan Coté has
suggested that Warnex provides support to help in the design of the final format of the
assay (see letter of support).
Briefly, the analysis will have to take into account the scientific aspects (specificity &
sensitivity), the commercial aspects (cost, license from third parties, others), as well as
the regulatory requirement for the commercialization of the assay in Canada and South
Africa.
At least three meetings will be held with a consultant over the 8 week mandate.
Participating in the meeting will be the inventors, Anne-Marie Larose from Univalor, and
one representative from our potential commercial partners (Continental Diagnostic and
Warnex). Meetings will include:
1) An initial meet and greet of the inventors, Anne-Marie Larose from Univalor, one
representative from each of our potential commercial partners (Continental
Diagnostic and Warnex).
2) A follow-up meeting midway through the mandate.
MDEIE – Commercialization and Transfer Assistance Program
28
3) An oral presentation of the final report and recommendations (a written report will
also be produced).
Experimental testing of the new format design will be performed before the beginning of
the second phase of the project.
6.5.3.
Establish the regulatory pathway for the commercial use of the assay
The objective to get clinical validation of our HPV assay, in a commercial format, is to
conclude licensing agreement with commercial partners. It is clearly not the scope of this
project to get regulatory approvals in Canada or South Africa. However, we consider it is
important to establish what the regulatory requirements to reach the market are. These
aspects have to be taken in account for the final design of the assay and in the licensing
negotiation (will help both parties to better define license milestones). This task will be
driven by Anne-Marie Larose from Univalor.
6.5.4. Optimization of the commercial format of the assay for high sensitivity and
specificity
The outcome of phase 1 (first 20 weeks, i.e. five months) will define the choice of
technological platform. Sensitivity and specificity of the assay will be re-assessed on the
new assay format.
This optimization step will required the following:
1) Evaluation of the right amount of DNA probes to be spotted on the new support
2) Optimization of the hybridization conditions to reduce background
3) Optimization of the signal detection
4) Development of a new reproductive procedures to perform the analysis, from the
PCR product to the detection
5) Optimization of the control probes, including the HPV control probe
Since we anticipate a 10X reduction of hybridization volume and corresponding solid
support surface (beads or array) this will allow reduction of total PCR yield (50-100ng),
typical to the volume of 10uL. At this phase of the project, technique for visualization of
the hybridization signal will be adjusted to best serve the chosen platform. Comparison
with results obtained with the prototype assay will help the development and optimization
of the new format of the assay.
Optimization will be performed with the in vitro reconstructed sample, before testing
clinical samples (see section 6.5.5).
Some testing will also be conducted in at least one external laboratory, ideally by one of
our commercial partners, in order to validate the reproducibility of new protocols. These
MDEIE – Commercialization and Transfer Assistance Program
29
experiments are not covered by this proposal and will be performed at the company’s
expenses.
6.5.5. Validation of the performance of the commercial assay with clinical samples.
The performance (sensitivity and specificity) of the probes using the new platform will be
compared with the typing results obtained in the first phase of the project. More
precisely, the commercial format of the test will be used for HPV typing of the same 40
samples tested with our prototype assay, as described in section 6.5.1. Additional 100
clinical samples that are already charactrized by commercial tests like Roche or Hybrid
Capture will be tested in this phase. The samples will be obtained through collaboration
with Dr Francis Coutlée, Molecular Virology Laboraty at the Research Center of CHUM
(see letter) who were running and partipating in variety of projects addressing biology,
epidemilogy and diagnostics of HPV. The concordance analysis will follow.
6.6.
Work plan and timetable
The maturation project will require 12 months for its completion. As illustrated in table 5
the activities to meet the first objectives will start immediately while the activities for the
second and third objectives will be performed concomitantly at the end of phase 1, most
likely from week 10 to week 32. The activities for the last two objectives will be done
successively.
Dr Damian Labuda, Ms Sylvie Cossette and Ms Anne-Marie Larose, respectively the
principal investigator with the inventors, the project manager and the representative of
the partner organization, will meet on a regular basis, every 3 months to evaluate the
progress of the project and the achievement of the milestones. The same committee will
meet if necessary to evaluate any project of disclosure generated within the framework of
this project in order not to reveal information that could preclude the filling of patent
application.
Objectives/Activities
Phase 1 - 32
weeks
Phase 2 - 20
weeks
1 Clinical validation of the prototype assay
2 Design of the commercial format of the assay
Establish the regulatory pathway for the commercial use of the
3 assay
Go/No go decision
4 Optimization of the commercial format of the assay
MDEIE – Commercialization and Transfer Assistance Program
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5 Validation of the performance of the commercial assay
Table 5: Gantt Chart for work plan
6.7.
Deliverables and result indicators
At the end of phase 1 we should have reach the first 3 objectives:
1. Clinical validation of the prototype assay
2. Design of the commercial format of the assay (simple and cost-effective HPV
typing assay)
3. Establish the regulatory pathway for the commercial use of the assay
More specifically this means that we will get specificity and sensitivity data with clinical
samples with the prototype assay and obtain the following results:



Ability to detect HPV 6, 11, 16 and 18 alone (1-10 pmols) or in a combination, where
individual types are presented in final PCR product in the low picomolar ranges.
No cross-hybridization with non-specific probes, under 10 pmols of one HPV types
(from reconstructed samples) which represent a scenario where PCR yield is very
abundant (10 pmols in total is around 1000 ng of GP56 PCR).
Universal HPV probe will detect any HPV type present in PCR, while control DNA
(CD) probe would be indicator of clinical sample DNA quality.
The design of the final format of the commercial product will need to be defined as well
as the main regulatory requirement for the commercialization of the HPV kit. We will
also need to get recommendations for the final design of the project. At the end of the
second and last phases of the project we should have reach the 4th and 5th objectives:
4. Optimization of the commercial format of the assay for high sensitivity and
specificity
5. Validation of the performance of the commercial assay with clinical samples:
Anticipated results in terms of specificity and sensitivity should be at least as
good as what we get at the end of phase I with the prototype assay: specific
detection of the 4 types of HPV, no cross-hybridization and positive results with
the Universal HPV probes and de CD probe. Importantly, our comparative study
should demonstrate that the performance of our assay is as good or superior to the
Roche assay. The stability of both assays (reproducibility) using repeated typing
of critical samples with PCR yield approaching 2 extreme situations (very low
and very high yield) will be performed. We expect that this comparative test
produce more stabile typing results with our assay format, then with Roche assay.
MDEIE – Commercialization and Transfer Assistance Program
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Implementation of the new assay format in at least one clinical laboratory in Quebec, or
South Africa will be performed.
6.8.
Decision-making milestones (go/no go) for measurable and clearly
identified results
At the end of phase 1, the project will be pursued only if we get positive results on
clinical samples with the current prototype (SAM membrane and P32). Herein, clinical
sample will have to give yield of GP56 PCR product in the minimal range of 100-1000ng
(150nt long), which is in fact 1-10 pmols in total, the quantity typically detected in our
present developmental experiments. This is, according to our observation and literature
data, an average PCR yield of 50uL reaction volume of “classical” GP56 PCR after 40-45
cycles. We know that present solution for GP56 primers perform well for majority of
HPV types, using 39 artificial targets. If our hybridization assay does not work in this
range of concentrations we will consider that there is a significant failure in the process
which will justify first NO GO.
6.9.
Proposal for granting the subsidy according to the decision-making
milestones reached
Total disbursement
Phase 1 32 weeks
Phase 2 20 weeks
End of phase 2
114 000 $
70 000 $
16 000 $
25 000 $
15 000 $
89 000 $
55 000 $
Valorization-HSJ
MDEIE
16 000 $
Table 6. Proposed distribution of granting
7. RESEARCH TEAM
In 2004, Ivan Brukner (see CV in Annex 3) joined our team to develop the iterative
technology in its practical application focusing on the small sequence segments. His
knowledge in nucleic acid chemistry matched the expertise of other members of the team
in the physical chemistry of nucleic acids, in diagnostic application, in the development
of genotyping tools, in the genetic epidemiology and pharmacogenetics, and importantly
in the HPV DNA testing and in the epidemiology of HPV infections.
Damian Labuda (see CV in Annex 3) has considerable experience in physical chemistry
of nucleic acids, in genetic diagnostics, genetic epidemiology and in vitro selection. Ivan
Brukner is the principal inventor of the proposed technology; he will be responsible for
the technology implementation and daily follow-up of the experiments. Maja Krajinovic
(see CV in Annex 3) has experience with the HPV DNA analysis, as well as in genetic
epidemiology and pharmacogenetics; she will be involved in design of reconstructed
MDEIE – Commercialization and Transfer Assistance Program
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sample experiments, selection of clinical samples (with Izabella Gorska-Flipot) and
between tests concordance analysis. Izabella Gorska-Flipot (see CV in Annex 3), at the
Hospital Hotel-Dieu, has a longstanding experience in the molecular diagnostics and in
the HPV cervical infections in particular; she will be responsible for the analysis of
clinical samples using custom approach and commercial kit.
Our achievements are summarized in 4 published manuscripts Nucleic Acids Research,
2007; Journal of Clinical Virology, 2007; Nature Protocols, 2007 and Int. J Cancer.,
2008. In addition, intellectual property related to our technology is protected. The present
application is to finalize the prototype of the HPV diagnostic device and to validate its
use in the clinical setting.
8. ESTABLISHMENT’S PROJECT MANAGER (In French)
Gestionnaire de projet au Centre hospitalier universitaire Sainte-Justine
(CHU Sainte-Justine)
Le CHU Sainte-Justine est un des plus grands centres hospitaliers universitaires pédiatriques du
Canada. Il a pour mission d’améliorer la santé des enfants, des adolescents et des mères du
Québec. Afin d’arriver à assumer pleinement sa mission et surtout son rôle en tant que centre
universitaire d’enseignement et de recherche, le CHU Sainte-Justine compte sur l’excellence de la
recherche de ses chercheurs regroupés dans son Centre de recherche.
Au cours des dix dernières années, le Centre de recherche du CHU Sainte-Justine a connu une
croissance sans égal parmi les dix-neuf centres et instituts de recherche subventionnés par le
FRSQ. Depuis sa fondation en 1973, le Centre de recherche s'est transformé en un réseau d'axes
de recherche pluridisciplinaire allant de la recherche biomédicale à la recherche clinique en
passant par la recherche sur les soins et le système de santé, la santé des populations et
l'évaluation des technologies. Le leadership du CHU Sainte-Justine en recherche est aussi fondé
sur un partenariat actif et engagé dans des réseaux de recherche. Depuis 2003, 30 nouveaux
chercheurs ont été recrutés portant le nombre de chercheurs à temps complet à 90. La progression
du nombre d'étudiants qui est passé de 276 à 402 au cours des cinq dernières années témoignent
du pouvoir attractif du Centre, de la qualité de ses chercheurs et de sa mission de former du
personnel hautement qualifié au niveau académique de même que pour l'industrie biomédicale et
pharmaceutique. Les publications témoignent de notre productivité scientifique comme centre de
recherche. De 2004-2005 à 2007-2008, le nombre d'articles avec comité de pairs a augmenté
annuellement de façon constante passant de 364 à 385.
Parallèlement à cette productivité scientifique du Centre de recherche, le CHU Sainte-Justine aura
été le foyer d'une importante activité en valorisation de la recherche et des connaissances dans le
domaine de la santé. Au cours des cinq dernières années, plus d'une trentaine de chercheurs ont
soumis une soixantaine de déclarations d'inventions menant à trente-deux demandes de brevets,
aboutissant à une dizaine d'accords commerciaux, dont neuf licences et la création d'une
MDEIE – Commercialization and Transfer Assistance Program
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entreprise dérivée. Également, le Centre de recherche a assisté à une croissance continue des
contrats de recherche en partenariat avec l'industrie et autres centres d’enseignement, totalisant
plus de 100 nouveaux contrats en 2006 dont la valeur atteint plus de 22 millions de dollars,
témoignage tangible de la valorisation du savoir-faire et connaissance de la communauté des
chercheurs du CHU Sainte-Justine.
Le Centre de recherche, sous la direction du Dr Guy A. Rouleau depuis près de trois ans s’est
doté d’une structure administrative qui facilite le support à la recherche et la valorisation des
résultats. Sous la direction de Madame Sylvie Cossette CA, adjointe au directeur et comptant plus
de 15 ans d’expérience comme gestionnaire au Centre de recherche, deux professionnels
spécialisées en ententes de recherche et en valorisation sont à la disposition des chercheurs. De
plus, un chercheur clinicien est délégué par le Centre de recherche pour siéger sur le comité
d’évaluation des technologies de sa société de valorisation Univalor.
Madame Cossette sera la gestionnaire de projet de maturation technologique du CHU SainteJustine et sera responsable de s’assurer de son bon déroulement. Elle devra notamment :

S’assurer que l’équipe de chercheurs et le partenaire financier respectent leurs
engagements;

S’assurer que les objectifs poursuivis dans le projet soient en harmonie avec la stratégie
de commercialisation;

S’assurer avec les chercheurs que toute nouvelle propriété intellectuelle développée dans
le cadre du projet soit protégée adéquatement et avec diligence;

S’assurer que les ententes à intervenir entre les partenaires soient conformes aux
politiques institutionnelles.
9. PARTNER ORGANIZATION
9.1. Role, experience and qualifications of the partner organization in conjunction
with the project
Gestion Univalor, Limited partnership ("Univalor") is a limited partnership whose
mission is to commercialize discoveries made by researchers at the Université de
Montréal, École Polytechnique de Montréal, CHU Sainte-Justine-Mother and Child
University Hospital Center, HEC Montréal, Hôpital Maisonneuve-Rosemont, Hôpital du
Sacré-Coeur de Montréal, Institut de recherches cliniques de Montréal and the Institut
universitaire de gériatrie de Montréal. Univalor also provides commercialization services
to the limited partnerships of the Montréal Heart Institute.
Univalor strives to develop profitable and long term business relationships with
companies wishing to maintain or improve their competitive position in their industry by
having access to cutting edge technologies developed by internationally acclaimed
researchers.
MDEIE – Commercialization and Transfer Assistance Program
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Univalor's multidisciplinary team is made up of 12 professionals in business development
and commercialization with expertise in life sciences, engineering, intellectual property,
legal affairs, and finance.
Achievements
Between 2001 and 2008, about 520 discoveries from Université de Montréal and its
affiliated institutions have been evaluated by Univalor and more than 900 patents
applications have been filed. Univalor currently has approximately 265 patents and
patents pending in its portfolio, has signed over 33 license agreements and has been
involved in the creation of 23 spin-off companies over the years.
Since 2001, funding provided for commercial maturation from Valorisation-Recherche
Québec and the Ministère du Développement Économique, de l’Innovation et de
l’Exportation (“MDEIE”) have allowed many technologies to reach maturity and
demonstrate operational capabilities. More than 8.2 million dollars have been invested in
our most commercially promising technologies and 130 million dollars into our spin-off
companies.
9.2.
Description of the partner organization's project selection process
Over time, Univalor has developed its own methods and tools for evaluating technologies
emerging from research laboratories and for helping researchers who wish to
commercialize their inventions. Internal evaluation is conducted by the business
development manager and the project leader using a 5-point criteria: scientific and
technological quality, intellectual property, market size, business opportunity, and
relevancy for Univalor. Different databases such as Dialog Pro Competitive Intelligence,
Medtrack, and Delphion are used to accomplish this evaluation. Meetings with the
inventor(s) and a literature review are also very important steps in order to thoroughly
evaluate the technology on its scientific basis.
Results of the internal evaluations are discussed weekly during our evaluation committee,
which is comprised of all of Univalor’s professionals. This allows us to take full
advantage of our multidisciplinary team. Relevant questions regarding intellectual
property, technical issues, time-to-market, etc. often arise. The manager of business
development may either pursue the evaluation after this meeting or retain the services of
one or more experts. These experts, skilled in the specific technology, are asked to give
their opinion about the technology on both a scientific and commercial basis under a
confidential agreement. If the technology is recommended for commercialization, a
technology transfer strategy is then drawn up by the evaluation committee and rapidly
implemented.
When a technology shows a real commercial potential, Univalor’s business development
manager, along with the help of the researcher and the research administrator at the
MDEIE – Commercialization and Transfer Assistance Program
35
institution, looks for financial resources to perform proof of concept or validation when
the development status of the technology is not mature enough to start licensing
discussions with a company. Once a grant is procured and the maturation project is
started, the manager of business development carefully follows the progression of the
project. Results are communicated to potential partners if discussions have already been
initiated and interest in the technology has been shown. Business development activities
start (if they have not already started) once the maturation project begins and intensifies
once the proof of principal is accomplished.
9.3.
Professional who will support the valorization process
Anne-Marie Larose, Ph.D, MBA, Business Development Manager, is currently
responsible of this technology at Univalor. Ms. Larose has more than ten years of
experience in the life sciences industry. After having obtained her doctoral degree in
cellular and molecular biology, she joined a young biotech company at the pre-startup
stage. During the five years that followed, Ms. Larose was directly involved in the
different aspects of the company's corporate and technological development, notably in
the elaboration of business and commercial strategies, the protection of intellectual
property, the planning and management of R&D projects, and the management of the
quality control department. Afterwards, as commercial attaché for the British consulate in
Montréal, Ms. Larose was responsible for commercial exchanges with the Canadian
biopharmaceutical sector. More recently, Ms. Larose has contributed to the fulfillment of
various industrial and institutional development mandates in the Life Sciences sector as
main advisor in an advisory office. As of March 2004, Ms. Larose has been developing
business relations with corporations in the Life Sciences field who wish to commercialize
technologies with the greatest growth potential.
10. POTENTIAL MARKET
Why typing HPV in Canada now?
There are few distinct, but inter-related reasons why having “home”, provincial, or
national HPV typing assay, presents advantageous situation over not having it.
Commercial impact is for example one of the resons. In Canada, Roche is the only assay
approved by Health Canada with prize of 80-100$CA per screening (material cost), while
FDA approved HC2 assay is reaching value of 150-180$ per single patient (Qiagen,
2009, listing prices). Both assays are developed in US. In Europe, the situation is more
complex and diversified with more small companies trying to get part of the market. On
the contrary, to our knowledge, Canada does not have any force to address this challenge.
MDEIE – Commercialization and Transfer Assistance Program
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Another important factor is timing, as: 1) HPV vaccination era requires more rigorous
screening activity with new and specific HPV typing tests, as suggested by Canadian
and international authorities (see Franko et al, Vaccine 26S (2008) F46–F58). The urgent
need for new HPV screening guidelines and new biomarkers is also documented by Feng
et al. (JNCI Vol. 100, Issue 5, 2008). The current and future necessity and role of HPV
screening in the era of HPV vaccination is also well described by Smirh et al.,
Gynecologic Oncology 109 (2008) S31–S39). All these arguments are pointing out that
HPV screening has to be continued in the new form - if not inforsed by government,
because of the following reasons:
1) Vaccine is not clinically tested on already infected women,
2) The mother-child frequency of transition is not known,
3) The vaccine protective time is not yet defined and
4) 30% of cervical cancer will not be protected by the vaccine.
Target market
Sugestion:I would make few comments about local Montreal-Quebec-Canada market,
including private laboratories, clinics, hospitals and general public awareness for
diagnostics of STD.
The US molecular diagnostics field is the most dynamic segment of the in vitro
diagnostic (IVD) market, with an expected growth rate of approximately 17% through
2012. Infectious disease testing accounts for the bulk of this market, and HPV testing is
one of the fastest growing. As the second most prevalent molecular test, HPV testing has
been estimated in 2006 to have reached approximately 55 million tests that year alone,
representing an IVD market size of $500 million (Frost & Sullivan, 2006). Recently, the
company Third Wave Technologies has provided projections which suggest that the
global market for HPV testing could reach $250 million in 2008 with a market
penetration of only 28% but a growth rate in excess of 25%. This includes more than 10
million HPV tests being performed in the United States each year. Finally, the HPV
testing market in the EU is just emerging, as studies are underway to evaluate the use of
HPV tests as a primary screen for cervical cancer in women, replacing Pap testing.
10.1.
Business opportunity: Cervical cancer prevention program and HPV
screening.
Cervical cancer is the second largest cause of cancer deaths in women worldwide. The
estimated prevalence of HPV infection in women is 10.5%. Persistent infection with HPV
is a trigger for cervical cancer, and preventing this infection can avert this deadly disease.
The tests used in routine screening and clinical prevention of cervical cancer are so far
based mostly on a cytological examination known as the Papanicolaou (Pap) smear. In
2005, more than 60 million Pap smears were performed in the US, and it is estimated that
such screening programs and interventions have reduced the incidence of cervical cancer
MDEIE – Commercialization and Transfer Assistance Program
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by ~80% in the United States, but at a cost of more than $6 billion US a year (Wu et al.,
2006). Although the application of the conventional Pap test led to a dramatic reduction
in the incidence rate of cervical carcinoma in the last fifty years, this test has significant
limitations, including a sensitivity of only 50% to 60% in a routine screening setting
(Fahey et al., 1995; Nanda et al., 2000). Because of this, an improved cytological test has
been developed called the thin-layer liquid based cytology, or ThinPrep Pap test. This
new test is far from infallible, failing to detect from 15% to 35% of cervical
intraepithelial neoplasia (CIN) or cancer (Kulasingam et al., 2002). Recently published
results of ASCUS/LSIL Triage Study for Cervical Cancer (ALTS) underline the
importance of HPV DNA testing to improve specificity and reduce costs (ALTS, 2000;
Sherman et al., 2001; Solomon et al., 2002a; Solomon et al., 2001; Solomon et al.,
2002b; and http://www.cancer.gov/prevention/alts/results.html). Likewise, accurate
and affordable HPV genotyping will be in high demand for the next few decades for
ongoing HPV vaccination studies. The US Food and Drug Administration (FDA)
approved the first preventive HPV vaccine on June 8, 2006 for the immunization of
women between 9–26 years of age (Merck's quadrivalent vaccine Gardasil, targeting
HPV 6, 11, 16 and 18 ). A second vaccine, Cervarix from GlaxoSmithKline (targeting
HPV 16 and 18), is already available in Australia and in Europe. So far, these vaccines
have shown to offer 100% protection against persistent homologous HPV infections
(Stanley et al, 2006). In the current experimental phase of vaccine trials, HPV screenings
are needed to: i) identify HPV status of individuals before vaccination and ii) monitor the
efficacy of vaccines. Furthermore, the Advisory Committee of Immunization Practices
(ACIP) recommends continuation of HPV screening protocols until other type-dependent
vaccines are developed and until the protective time period of the vaccines has been fully
characterized. In spite of the above recommendations and the introduction of a number of
commercial HPV genotyping kits (see table 1), a DNA test of satisfactory specificity and
sensitivity to detect HPV types is still unavailable.
10.2.
Technological competition and benchmarking
Available HPV DNA tests, sensitivity and specificity.
Key industry participants in the molecular infectious disease diagnostics market in North
America are Roche, Gen-Probe, QIAGEN (QIAGEN-Digene), bioMerieux, and Becton
Dickinson. QIAGEN-Digene is the sole provider of molecular HPV tests in the US. The
company offers two HPV tests which distinguish two groups of HPV subtypes (benign
and malignant) and offers no subtypes differentiation. The Roche HPV genotyping test
(LA) and the new Genomica CLART® HPV2 test, are the only commercially available
test kits for the detection of 35 or more variants of HPV. The Roche test was expected to
hit the US market in 2008, but is still unavailable to date (Frost & Sullivan, 2006).
MDEIE – Commercialization and Transfer Assistance Program
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A recent WHO international collaborative study (Quint et al., 2006) addressed the
question of standardization of HPV molecular typing and detection. The methodology
used in this study was performed by twenty-four participating laboratories included
QIAGEN-Digene Hybrid Capture II, and by a variety of PCR/hybridization typing
systems. The results demonstrate that the sensitivity of detection and the specificity of
typing varied considerably among participating laboratories working with the eight most
frequent high-risk types (16, 18, 31, 33, 35, 45, 52 and 58) and one low risk HPV 6. The
sensitivity and specificity of the detection of HPV 16 and HPV 18 was only 62% and
74% respectively. For the other seven types, the adequate assessment varied from 95%
(HPV 33 and 45) to 43% (HPV 31). Some false positive results were also reported.
Clearly, an alternative approach to HPV typing is needed. Existing HPV DNA analyses
rely either on hybridization techniques using type-specific HPV DNA probes, or are
based on direct identification of HPV DNA PCR-products (see table 7). Several
hybridization based tests and their prototypes have been developed that either require the
viral DNA to be pre-amplified by PCR (Innogenetics, Roche Diagnostics, Genomica,
Greiner Bio One) or do not require it (QIAGEN-Digene and Ventana). The main
difficulty of hybridization approaches that use “classical probes” in these tests, is
obtaining specific results when multiple similar targets have to be assayed simultaneously
(note that here we use the term “classical” to distinguish from probes obtained by our
method of iterative hybridization). Probes that fully match their targets (Roche,
Genomica, Greiner Bio One) compromise accurate detection of multiple targets because
they cross-hybridize ((Sandri et al, 2006) and our unpublished observations). Another
group of hybridization-based tests that does not require prior amplification of HPV DNA
include QIAGEN-Digene’s Hybrid Capture 2 (HC2) assay and Ventana’s Inform HPV.
QIAGEN-Digene’s FDA-approved assay is widely used in clinical studies due to its
relative simplicity and sensitivity. However, several recent reports pointed out two main
disadvantages with HC2, questioning its use as a screening tool. First, it lacks individual
HPV type identification. Second, there is a significant degree of cross-reactivity between
the oncogenic and non-oncogenic types that leads to false-positive results 10% to 20% of
the time (Cox et al., 2000; Gravitt et al., 1998; Poljak et al., 2002; Schneede et al., 2001;
Terry et al., 2001; Yamazaki et al., 2001). In brief, the Ventana Inform HPV in situ
hybridization assay seems to be more specific and sensitive than HC2, but its efficacy in
predicting cervical lesions (positive predictive value) is no more than 48% (Qureshi et
al., 2003). Several companies offer PCR-based kits (see table 3) like GenoID which
became a small participant in the European molecular diagnostics market (Frost &
Sullivan, 2006).
It should be noted that another option exists for the sequencing of HPV PCR products.
This is performed by Visible Genetics (Toronto) (Mahony et al., 2003) and is also an inhouse test at the Hôpital Hôtel-Dieu de Montréal and at the Hôpital Sainte-Justine de
Montréal. Although these sequencing tests are highly specific, they require trained
personnel, expensive technology, and most significantly, are rendered useless when
multiple variants of the virus are present in the same patient. Numerous other typing
systems have been described (Hwang et al., 2003; Klaassen et al., 2004; Kleter et al.,
1999; Schmitt et al., 2006; van den Brule et al., 2002, Schmitt et al., 2006) and they
await a detailed clinical evaluation.
MDEIE – Commercialization and Transfer Assistance Program
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Competitive advantages
The main advantage of our method resides in its enhanced power of identification and
discrimination of multiple short nucleic acid sequences that differ by a few mutations, as
with the different HPV types in a multiplex hybridization assay. Because we select the
most specific probes in predefined hybridization conditions we considerably reduce
cross-hybridization problems inherent to the conventional hybridization approach used by
Roche and Genomica (such as requiring a 52oC (+/-2) special hybridization buffer). Other
important benefits are described below:

Market need: The American Cancer Society (ACS) and the American Society of
Colposcopy and Cervical Pathology (ASCCP) have issued new guidelines which
incorporate DNA testing for high-risk HPV types, along with Pap tests, as a
primary screen for women aged 30 and over. The capacity of our probes to detect
and also to identify HPV types is clearly an asset if we consider that prevention
by vaccine will address only specific HPV types.

Multiplex detection: Finding universal experimental conditions for hybridization
becomes problematic in multiplex applications where many DNA targets are
considered simultaneously. Our method overcomes this problem. Instead of
adjusting the hybridization conditions to the probes, a set of probes is selected in
such a way as to function under the intended hybridization conditions.

Detection of different types in the same patient: According to GeneticLab, the
frequency of HPV patient superinfection is 28%, where 71% are infected with 2
subtypes, 21% with 3 subtypes, and 8% with 4 subtypes. Kits that can not
discriminate HPV types are unable to differentiate new and persistent infections
and have poor diagnostic potential in regard to superinfection.

Low production cost and ease of use: A kit based on our technology would
require neither expensive instrumentation nor skilled personnel to use. Production
of our diagnostic is not expected to be expensive, which would allow the licensor
to get a high profit margin. This is crucial for commercial success in the
diagnostic field.
Even though QIAGEN-Digene presently dominates the HPV DNA diagnostic market and
there will be strong competition between new kits—such as the ones from Roche and
Genomica—we strongly believe there is an opportunity for these innovative kits to enter
this large, underpenetrated, growing market. By fulfilling all the main requirements of the
clinical and market needs, our superior kit could quickly become the test of choice for
HPV detection.
MDEIE – Commercialization and Transfer Assistance Program
40
Company
Test Name
Technology
Total number
of subtypes
detected
QIAGEN
(Digene)
Hybrid
Capture 2
RNA-DNA
hybridization
2
Detection of
multiple
subtypes in
same patient
No
Ventana
Medical
Systems
Ventana
Inform
PCR+ In situ
hybridization
2
No
Genomica
CLART® HPV low density
2
microarray
35
Yes
Cross-reactivity of probes
US, Canada,
Europe,
Japan, Asia,
Australia
Europe
Greiner Bio
One
PapilloCheck® DNA-Chip
(microarray)
18 high-risk
and 6 low-risk
types of HPV
Yes
Cross-reactivity of probes
Europe
GenoID
Reveal HPV
19
not in one
assay
Semi-quantitative analysis; Very complex Europe
and requires RealTime PCR
Roche
Amplicor
PCR+
Molecular
beacons
PCR +
hybridization
13 high-risk
types
No
No individual identification of HPV type;
Detects only high risk cases.
Roche (LA)
Linear Array
PCR +
hybridization
37
Yes
Involves amplification of a portion of the Europe
L1 gene by PCR, coding for the major
capsid protein, and a subsequent
hybridization of the amplification
products with the HPV type-specific
probes; Unable to distinguish hr-HPV 52
from other high-risk genotypes (33, 35,
and 58) presenting 2.2% of all cervical
cancers; Less sensitive if a sample has a
single infection with some specific HPV
genotypes that are poorly amplified by
MDEIE – Commercialization and Transfer Assistance Program
Comments
Market
The HC2 test uses specific antibodies
and chemiluminescent signal
amplification to measure the presence of
RNA (DNA hybrids formed between a
specific RNA probe and the viral DNA).
Cross-reactivity of probes; No individual
identification of HPV type; Detects only
high risk HPV
Cytogenetic HPV testing; Allows choice
of sample types; No individual
identification of HPV type; Poor accuracy
US, Canada,
Brazil, Europe,
Asia, Australia
Europe
41
PGMY (HPV 33 and 52); Hybridization
probe for HPV 51 not sensitive enough;
Requires very controlled temperature of
hybridization 52+/-2°C; Presently the
most accurate typing kit on the market.
BioMerieux
Protect HPVProofer assay
(based on
NucliSens
Easy Q
platform of
bioMerieux)
Detection of
oncogenic
HPV gene
expression
5 high risk
types
n/d
Aims at the early detection of cervical
carcinogenesis. Technology licensed
from the company NorChip in January
2007.
Europe
Innogenetics
Inno-LiPA
HPV
Genotyping
CE
PCR +
hybridization
25
Yes, but have
problems with
sensitivity, due
to the bias
induced by
'universal'
primers
Europe
QIAGEN
(through
acquisition of
Shenzhen
P.G. Biotech
Co.)
Third Wave
Technologies
HPV detection PCR -based
kit
Involves amplification of a portion of the
L1 gene by PCR, coding for the major
capsid protein, and a subsequent
hybridization of the amplification
products with the HPV type-specific
probes; Problems detecting multiple
infections reported, related to typespecific sensitivity of amplification; Full
set of HPV types not included; Crosshybridization reported; Requires
controlled temperature of hybridization.
n/d
only 4 most
n/d
common types
(6, 11, 16 and
18)
HPV
n/d
screening test
(14 high-risk
types of HPV)
Third Wave HPV
n/d
Technologies genotyping
test (HPV—16
and 18)
14
No
2
Yes
n/d
GeneticLab
PapiPlexTM
Multiplex PCR
16
Yes
SensiGen
AttoSense ™
HPV Test
MassArray
assay (mass
spectrometry
coupled with
competitive
PCR)
15 high risk
types
n/d
Multiplex detection; Complex handling
and assay performance, (requires gel
manipulation); Only 16 types; not clear
how non-including types will perform
Ultrasensitive detection kit (1 to 3 copies
of HPV DNA in blood or tissue sample).
The test is still in development. Licensed
from University of Michigan in February
2007
China
n/d
FDA
application for
approval
expected in
2008-2009
Japan
Not on the
market
Table 7. HPV molecular diagnostic kits
11.
COMMERCIALIZATION STRATEGY
MDEIE – Commercialization and Transfer Assistance Program
42
Our short-term goal is to grant licenses of the HPV test to companies or clinical
laboratories. We are in a position to conclude many license agreements within specific
fields of use and/or specific territories, since the inventors have developed both, a method
for generating specific probes for multiplex diagnostic assay and a specific application of
this method which is the HPV assay (both protected by the current patent application).
So far we have got serious interest from Warnex, a company based in Québec and
Continental Diagnostic, a company based in South Africa. They both would like to get
exclusive rights for the HPV assay, in their respective territories. We have also got
interest from Dr Gorska at CHUM to implement the HPV assay in their clinical
laboratory. It is clear that the clinical validation of the commercial assay will be decisive
to consolidate the interest of these groups and to conclude licensing agreement.
11.1.
Commercialization of the assay in Canada – Warnex partnership
Warnex is a life sciences company devoted to protecting public health by providing
laboratory services to the pharmaceutical and healthcare sectors. With its three divisions
(analytical, bioanalytical and medical laboratory), Warnex provides, to clients in the
pharmaceutical and biotechnology industries, a variety of quality control services as well
as method development and validation. They also conduct bioavailability and
bioequivalence studies for clinical trials, and perform contract R&D. Finally, Warnex
provides specialized genetic and biochemical testing for the healthcare industry. This
division also has extensive expertise in genetic testing for human identification,
molecular diagnostics, and pharmacogenetics.
They focus on the development of innovative assays as well as the refinement of existing
diagnostic tests to produce assays with greater clinical value and relevance for reliable
and cost-effective patient assessment and management. Warnex Medical Laboratories is
an important source of specialized testing for hospitals, private laboratories, and medical
specialists. As a development-driven medical laboratory, they work extensively in
collaboration with medical discovery companies to adapt their research into viable
clinical tools for improved diagnosis and monitoring of disease states.
Warnex is clearly a relevant partner to bring the HPV assay on the Canadian market.
Also, as mentioned in their letter of support, Warnex has accepted to provide in kind
contribution for the design of the final format of the assay. Their expertise will also be
highly valuable for the regulatory aspect of assay development.
11.2.
Commercialization of the assay in Africa – Continental Diagnostic
partnership
MDEIE – Commercialization and Transfer Assistance Program
43
Continental Diagnostics is a Sales and Marketing outfit that would be taking the HPV to
the market once the clinical validity of the HPV assay will be established. Their business
plan is to boost their current income with the HPV test, which represents a large market
in South Africa: cervical cancer accounts for about 25 percent of cancer deaths among
black women, there is no formal PAP smear program and women seeking PAP smears in
the public health sector are only eligible for one every 10 years after the age of 30. Also
the new vaccines are out of reach for most of these women and 15 out of every 100 000
die of Cervical Cancer every year.
There are four partners in Continental Diagnostics as presented in Table 8. The company
outsources research (validation studies and experience programs) to scientists at the
University of Natal who work under Professor Indres Moodley. Prof. Moodley has
satellite sites in most African countries through his work with the SA government
Department of Science and Technology, where he can conduct validity assays for the
HPV test.
The company’s customers include pharmacies, private doctors (including specialists and
physicians), government and private hospitals, private and government laboratories. Also,
the company has a distinct advantage over their competitors in this area as they are a
100% black-owned company and therefore qualify for 60% in the Black Economic
Empowerment (BEE) point system that the government uses to award tenders to those
who are wholly or partly black-owned. They can also infer points to groups who source
their products from us and therefore have a good standing with private companies
(laboratories and hospitals) that source from us.
Co-funding for the MDEIE project will come from the Industrial Development
Corporation in SA, whose brief from the government is to partner African entrepreneurs
who create sustainable businesses and jobs in South Africa.
Continental Diagnostics
Members
Masikana Millan
Mdleleni.PhD,MBA,LLB
Mbulelo Godffery Tabata.
Med.Tech
Samuel Ndaxola
Nkalashe.Med.Tech,MAP
Indres Moodley.PhD
Expertise
Biochemistry Research and
Development
Responsibility
Business Evaluation and Legal
Counsel
Sales Management
Sales Director
New Business Development and
Marketing
Product Research
Product Management
Pharmaceutical Research
Table 8. Continental Diagnostics
MDEIE – Commercialization and Transfer Assistance Program
44
11.3.
Other partnership and future development
Business development activities carried by Anne-Marie Larose at Univalor already bring
business relations with two relevant potential industrial partners, as described in the
previous section. Ms Larose will continue seeking for companies that would be interested
to commercialize the HPV kit in their own territory and/or to develop a new diagnostic
kit using this innovative method of generating highly specific probes for multiplex assay.
Worthwhile to mention, the proposed project focuses on the clinical validation of an HPV
assay for the most frequent HPV types. This will be the first generation of our HPV
assay. If we get success in developing a specific and sensitive assay and conclude
agreement with at least one company for the commercialization of the assay, we will
certainly pursue the development of a second generation of the HPV assay, to diagnose
all types of HPV, since we already have probes for 39 types.
12.
PRO FORMA BUDGET (in French)
12.1.
Coûts du projet de maturation technologique
Le budget global requis pour accomplir le projet de recherche et les activités de
protection de la propriété intellectuelle est de 200 000$. Les tableaux suivants présentent
les budgets requis.
Phase 1
R&D (salaries and material ) and indirect
expenses
Institution
research associate
HSJ
research assistant
CHUM
laboratory expenses
HSJ
laboratory expenses
CHUM
consultant for product design
External
(Outsource)
32 weeks
Phase 2
Total
20 weeks
52
semaines
45 000 $
30 000 $
75 000 $
4 500 $
8 000 $
12 500 $
16 000 $
21 000 $
37 000 $
6 000 $
6 500 $
12 500 $
15 000 $
0$
15 000 $
Sous-total (RDI)
86 500 $
65 500 $
152 000 $
Indirect expenses (on the 30% from external
contribution)
7 500 $
4 500 $
12 000 $
MDEIE – Commercialization and Transfer Assistance Program
45
Total
94 000 $
70 000 $
164 000 $
Table 9 - Estimé budgétaire pour la réalisation du projet de R-D - 12 mois
La réalisation du projet nécessitera le travail de 2 personnes sous la supervision du
Dr Damian Labuda du CHU Ste-Justine et la collaboration du Dr Isabelle Gorska du
CHUM (voir section 7). Il est à noter que ces salaires incluent les bénéfices marginaux.
Territory
Phase 1
Phase 2
32
semaines
20
semaines
Total
End of the
project
52
semaines
Canada
3 000 $
3 000 $
US
6 500 $
6 500 $
South Africa
5 500 $
5 500 $
ARIPO
6 000 $
6 000 $
15 000 $
15 000 $
(16 000 $)
(16 000 $)
Other territory (Europe, Brazil and/or
Angola)
Contribution of Univalor for patent cost
Reimbursement of Univalor for patent cost
Total
20 000 $
0$
16 000 $
16 000 $
16 000 $
36 000 $
Table 10 - Estimé budgétaire pour la protection de la propriété intellectuelle
Un budget de 36 000$ est requis pour poursuivre le maintient de la propriété intellectuelle
dans les différents territoires. Pour ne pas réduire le budget de recherche dans la
première phase du projet de recherche, Univalor va supporter des dépenses de brevet de
16 000$, qui lui seront toutefois rembourser à la fin du projet lorsque nous recevrons la
dernière contribution du MDEIE dans le cas ou le projet franchise la phase 2 du projet.
MDEIE – Commercialization and Transfer Assistance Program
46
12.2.
Montage financier
Le montant total requis dans ce projet de maturation technologique est de 200 000 $. Une
partie de cette somme, c'est-à-dire 164 000$ servira à accorder un contrat de recherche au
Dr Damian Labuda du CHU Ste-Justine. Un sous-contrat pour effectuer des travaux dans
le laboratoire du Dr Gorska au CHUM est prévu. Le restant du budget servira à défrayer
les frais du consultant ainsi que les coûts de protection de la propriété intellectuelle.
Source de financement
Valorisation-HSJ, société en commandite
Montant ($)
40 000
PMT du MDEIE
160 000
Total
200 000
Table 11 - Montage financier pour financer le projet de maturation technologique
12.3.
Documents démontrant la nature des engagements des partenaires
financiers
La contribution externe au financement du MDEIE, pour un montant de quarante mille
dollars (40 000 $), proviendra de Valorisation-HSJ, société en commandite. Cette
contribution est conditionnelle aux éléments suivants :
1) l’approbation du financement du projet de recherche annexé à la présente
lettre par le MDEIE;
2) la présentation du projet à la satisfaction des membres du Conseil
d’administration d’Univalor inc.;
3) la signature d’une option pour négocier des droits exclusifs d’exploitation de
la technologie utilisée pour la réalisation du Projet avec notre partenaire
Continental Diagnostics.
4) la réception par Valorisation-HSJ de la contribution financière de quarante
mille dollars (40 000 $) de notre partenaire Continental Diagnostics;
La contribution de Valorisation-HSJ sera décaissée en versements, selon l’avancement du
projet, au prorata des ratios de financement requis par le MDEIE et conformément à une
entente à intervenir entre le CHU Ste-Justine et Gestion Univalor, sec, au moment de
MDEIE – Commercialization and Transfer Assistance Program
47
l’acceptation du Projet par le MDEIE. La propriété intellectuelle développée dans le
cadre du Projet sera propriété du CHU Ste-Justine, le tout tel que décrit dans les
politiques de propriété intellectuelle de l’établissement. Elle sera ensuite cédée à
Valorisation-HSJ.
Une copie de la lettre signée par Valorisation HSJ, commandité du CHU Ste-Justine,
société en commandite est présenté à l’Annexe 4.
12.4.
Démonstration que les autres sources de financement possibles ont été
prises en considération
Le projet soumis dans cette demande ne fait l’objet d’aucune autre source de financement
ni d’aucune autre demande de financement. Le financement du projet par le programme
de maturation technologique est essentiel pour la réalisation du projet de recherche.
MDEIE – Commercialization and Transfer Assistance Program
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13.
13.1.
OUTSIDE OPINIONS
Evaluator 1
13.1.1. Independent scientific opinion
MDEIE – Commercialization and Transfer Assistance Program
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13.1.2.Summary CVs of the persons filing opinions and statement of independence
regarding the project
MDEIE – Commercialization and Transfer Assistance Program
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13.1.3. Answers to the questions raised in the outside opinions
During the different stages of the project, we will work with the external evaluator and certainly
going to take into consideration the recommendations and advises that will come up.
MDEIE – Commercialization and Transfer Assistance Program
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13.2. Evaluator 2
13.2.1. Independent preliminary technical and commercial
evaluation
MDEIE – Commercialization and Transfer Assistance Program
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13.2.2. Summary CV’s of the persons filing opinions and statement
of independence regarding
Anne-Marie Larose, Ph.D. MBA.
Manager, Business development, Life Sciences
Gestion Univalor, société en commandite
(514) 340-3243, poste 4239
anne-marie.larose@univalor.ca
www.univalor.ca
Civic address : 5160 Decarie Blvd. suite 770 Montréal (Québec) H3X 2H9
Postal address : P.O. Box 6079, Station Centre-ville Montréal (Québec) H3C 3A7
Professional Experience
2004-2008
2003-2004
2002
2001-2002
1996–2001
1986-1988
Gestion Univalor, société en commandite
Manager, Business development, Life Sciences
Innovitech
Senior consultant, Life Sciences
Solidarity Fund QFL
Senior Investment Advisor, Life Sciences
British Consulate General, Montreal
Commercial Officer, Biotechnology & Life Science sectors
Geneka Biotechnology Inc.
Chief Research Scientist, DNA microarray , 1999-2001
Supervisor of Quality Control Department, 1997-2001
Research Scientist, Development and production, 1996-1999
Cancer Research Center, Hôtel-Dieu de Québec
Research Assistant, Cellular and Molecular biology.
Formation
2003
1996
1990
1985
1985
MBA in Bio-Industry management
Université du Québec à Montréal, Quebec
Ph.D. in Cellular and Molecular Biology
Medicine Faculty, Université Laval, Quebec
M.Sc. in Cellular and Molecular Biology
Medicine Faculty, Université Laval, Quebec
Certificate in Genetic Engineering
Sciences and Engineering Faculty, Université Laval, Quebec
B.Sc. in Biochemistry
Sciences and Engineering Faculty, Université Laval, Quebec
Other training

Effective regulatory strategies and integrated drug development. BioQuébec,
Biotechnology Research Institute & Cato Research, November 2005.
MDEIE – Commercialization and Transfer Assistance Program
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


Le processus réglementaire des dispositifs médicaux et ses non-dits. Association de
l’industrie des technologies de la santé & PARI-CNRC. April 2005.
Microarray Methods & Analysis Workshop. IB3- George Mason University, Manassas
VA. October 1999.
Workshop : Bioinformatics – Integrating informatic tools for expression analysis and
drug discovery. Chips to Hits ’99,. Berkeley, CA. November 1999.
MDEIE – Commercialization and Transfer Assistance Program
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Letters of support
MDEIE – Commercialization and Transfer Assistance Program
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Annex 1. Extended patent searches and comments
Pub. No.:WO/2007/017699
International Application No.: PCT/GB2006/050231
Publication Date: 15.02.2007
International Filing Date: 04.08.2006
IPC:C12Q 1/70 (2006.01)
Applicants: GENOMICA S.A.U. [ES/ES]; Alcarria 7, Coslada, E-28820 Madrid (ES) (All
Except US).
Analytical information does not exist. Genomica (CLART® HPV 2) uses 450bp
amplicon which is known to be more difficult to amplify (same region as Roche). This
will cause resistance from the part of clinical experts due to the fact that the latest
generation of DNA based HPV kits uses smaller PCR product (SPF, GP56…) in order to
escape (false) negative results due to the quality of DNA extraction.
Specificity of detection is going to be a big issue, no single published validation of probes,
but nice technological platform, totally compatible with our probes. The specificity
(clinical accuracy of HPV typing) is not defined by the technological platform but by
the choice of probes.
Here is a segment of the probe selection strategy from their patent:
Specific probes for HPV type identification were designed as follows. Sequences for all
reference HPVs deposited in GenBank, including known variants, for the amplified Ll
region were aligned using a conventional nucleic acid alignment program, such as
BioEdit (4,8.6. version; Hall. Nucl Acids Symp Ser. 1999, 41:95-98) and most variable
sequences regions among different HPV types were located. Potential sequences of
oligonucleotides to be used as specific probes were selected from these variable
sequences regions, preferably having following features: length of 20 to 40 bases,
preferably an approximate length of 30 bases; preferably with no secondary structures
or strings of consecutive same nucleotide longer than 4; preferably with a G+C ratio of
50% and a Tm as much similar among all selected probes as possible; and preferably
with the mismatched nucleotides among the different HPV types sequences as much in
the centre of the oligonucleotide sequence as possible.
Each potential probe sequence selected as aforementioned was compared against all
known HPV sequences in the amplified Ll region using the BLAST program form the
NCBI webpage (Altschul et al. Nucleic Acid Res. 1997, 25: 3389-3402). Finally, probes
having at least three nucleotide mismatches when compared with all known HPV types
(except when compared to the HPV type that the oligonucleotide probe is specific for)
were chosen, with a preference for probes with greater than three mismatches.
=============================================================
Hybridization was suggested to be done at 55° C. Results showing specificity were not
reported in the patent. Overall: Considering mode of probe selection, short time for
validation (compared to 20 years for Roche) and unreported validation results, these
probes are either the same or more likely worse than Roche’s set of probes.
US20070037137A1
Method and kit for quantitative and qualitative determination of human papillomavirus
QUANTOVIR AB 2007-02-15 2003-10-01 C12Q
MDEIE – Commercialization and Transfer Assistance Program
73
Production of HPV L1 and HPV L2 using recombinant DNA cloning, expression and
potential use in downstream production of Ab suitable for vaccination and/or
diagnostics
US20060024686A1
Detection of human papillomaviruses
2006-02-02 2005-01-28 C12Q
Three sequences are derived from the highly conserved viral E1 genes. Use of the
sequences SEQ ID Nos. 1, 2 and 3, for example as hybridization probes (DNA markers)
or in the context of a DNA amplification method, is therefore particularly suitable for
detecting any HPV infection. This invention claimed another set of conserved universal
primers.
US6902899
A method for detection of human papillomaviruses 2005-06-07 2002-08-22 G01N
Eberhard-Karls-Universitat Tubingen Universitatsklinikum
Same as US20060024686A1
US20040214331A1
Papillomavirus vaccine 2004-10-28 2003-12-11 G01N
The University of Queensland and CSL Limited
Same as US20070037137A1
EP1471147A2
Method of making a recombinant molecule for the expression of HPV-16 L1 protein
THE UNIVERSITY OF QUEENSLAND
2004-10-27 1992-07-20 C12N
A method is described for making a recombinant molecule, for the expression of HPV-16
L1 protein
WO04031416A1
METHOD AND KIT FOR QUANTITATIVE AND QUALITATIVE DETERMINATION OF
HUMAN PAPILLOMAVIRUS
QUANTOVIR AB 2004-04-15 2003-10-01 C12N
Inventors are claiming a kit for detection and quantification of human papillomavirus,
comprising a) seven amplification primers and three probes for HPV 16,31, 18,45; and
optionally b) eight amplification primers and three probes for HPV 33, 35, 39, 52, and
58. This is a PCR-based assay, not designed to perform multiplex testing and not
covering the spectrum of HPV types.
US20030129585A1
Detection of human papillomaviruses
IFTNER THOMAS 2003-07-10 2002-08-22 G01N
Same as US20060024686A1
WO9513377A1
EPISOMAL EXPRESSION VECTOR FOR HUMAN GENE THERAPY
Not relevant
EP0302758B1
Viral expression inhibitors
Not relevant
MDEIE – Commercialization and Transfer Assistance Program
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WO9302184A1
PAPILLOMA VIRUS VACCINE
THE UNIVERSITY OF QUEENSLAND 1993-02-04 1992-07-20 G01N
Not relevant
WO9108312A1
DETECTION OF HPV TRANSCRIPTS
GENE-TRAK SYSTEMS 1991-06-13 1990-12-03 C12N
Detection of E6 gene, the E7 gene and spliced transcripts of the E6 or E7 gene, or both,
under conditions appropriate for hybridization of complementary nucleotide sequences to
occur. No early stage power of detection.
EP0402132A3
METHOD FOR THE DETECTION OF HUMAN PAPILLOMA-VIRUS
TAKARA SHUZO CO. LTD. 1991-05-08 1990-06-07 C12Q
Detection of human papilloma-virus HPV 16, HPV 18 and HPV 33. PCR-based.
WO9602563A1
EPSTEIN-BARR VIRUS NUCLEAR ANTIGEN 1 PROTEIN AND ITS EXPRESSION AND
RECOVERY
CORNELL RESEARCH FOUNDATION, INC.
1996-02-01 1995-07-13 C07K
Not relevant
EP0655091A1
HUMAN PAPILLOMAVIRUS DETECTION ASSAY
BAXTER DIAGNOSTICS INC.
1995-05-31 1994-05-06 C12Q
Amplification of specific gene E6/E7 messenger RNA from a biological specimen and
hybridization to a biotinylated capture reagent. Limited predictive value in early stage
cancer.
WO9426934A3
HUMAN PAPILLOMAVIRUS DETECTION ASSAY
Same as EP0655091A1
CA2139623AA
HUMAN PAPILLOMAVIRUS DETECTION ASSAY
Same as EP0655091A1
WO9220702A1
PEPTIDE NUCLEIC ACIDS
BUCHARDT
1992-11-26 1992-05-22
Not relevant
WO02103050A2
VIRUS DETECTION METHOD, PRIMERS THEREFOR AND SCREENING KIT
UNIVERSITY OF WALES COLLEGE OF MEDICINE
2002-12-27 2002-06-13 G01N
Real-time PCR – scorpion probes
MDEIE – Commercialization and Transfer Assistance Program
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WO0168915A1
GENOTYPING KIT FOR DIAGNOSIS OF HUMAN PAPILLOMAVIRUS INFECTION
BIOMEDLAB CORPORATION 2001-09-20 2000-10-26 G01N
Korean chip for HPV detection, full match design of probes, PCR amplification and
hybridization with chip over slide. Not impressive performance, but straightforward.
WO9110675A1
PRIMERS AND PROCESS FOR DETECTING HUMAN PAPILLOMAVIRUS
GENOTYPES BY PCR
STICHTING RESEARCHFONDS PATHOLOGIE 1991-07-25 1991-01-18 C07H
GP5/6 primers protected and few other sets of universal primers in the same region of L1
gene.
US7294488
Amplification-hybridisation method for detecting and typing human papillomavirus
Genoid KFT 2007-11-13 2003-03-10 C12P
Hungarian variant of real-time multiplex PCR assay.
CA2183758C
HUMAN PAPILLOMA VIRUS DETECTION IN A NUCLEIC ACID AMPLIFICATION
PROCESS USING GENERAL PRIMERS
STICHTING RESFONDS PATHOLOGIE 2007-09-25 1995-02-20 C07H
Same as WO9110675A1
US20070207456A1
Multiplexed assay and probes for identification of HPV types
The Board of Trustees of the Leland Stanford Junior University
2007-09-06 2007-02-13 C12Q
A 20-plex hybridization with primer extension. The array contains probes for HPV
genotypes 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 66, 69, 6, 11, 34, 40, 42, 43, and 44.
The probes are preferably between 30 and 60 nucleotides, but may be as small as 20
nucleotides and up to several hundred nucleotides in length. Preferably, each probe
comprises a sequence at least 90% identical and is approximately (within 10 percent) the
same length. A large mixture of primers may be used simultaneously because the primers
are designed to be similar in sequence so as to prevent dimerization and amplification
artifacts. As described above, the method may comprise the step of contacting the probes
with a positive control hybridizing to each probe. The method can simultaneously detect
all known HPV genotypes, i.e. genotypes 1 through 89, by binding unique probes under
stringent conditions to E1 gene target sequences. REAL 35-40 MULTIPLEXING not
documented!
KR5017703A
PRIMERS
AND
METHOD
FOR
DETECTING
HIGH
RISK
HUMAN
PAPILLOMAVIRUS(HPV) BY PCR
USING TWO KINDS OF PRIMERS CONSISTING OF GENERAL PRIMER AND
SYNTHESIZED PRIMER
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Limited multiplexing with 3 different primer sets. PCR based method using complement
probes for typing.
KR5014494A
PCR GENERAL PRIMERS AND METHOD FOR DETECTING DIVERSE TYPES OF
HUMAN PAPILLOMAVIRUS(HPV) BY PCR AT ONE TIME TO DIAGNOSE HPV AT
EARLY STAGE
PCR-based detection, not prone to multiplex. Uses 8 different primer sets for different
types.
US20040248085A1
General primers and process for detecting diverse genotypes of human papillomavirus by
PCR
LEE SANG-WHA 2004-12-09 2003-11-24 C12Q
Set of general primers for amplifying and detecting Human Papillomavirus genotypes is
claimed. DNA sequence homology studies were performed with the derived DNA
sequences using Clustal W computer program (DNSSTAR, MegAlign.TM. 5,
DNASTAR Inc.) for pairwise alignment, multiple sequence alignment and phylogenetic
tree to screen representative base sequences of groups. PCR general primers based on the
screened base sequences were designed using another computer program (primer premier
6, PREMIER Biosoft International Co.). The primers were set as a nucleotide sequence of
about 27 +/- 3 bps or about 31+/- .2 bps and their amplification products at about
200.about.500 bps. 30 PCR general primer pairs were designed.
WO04050917A1
GENERAL PRIMERS AND PROCESS FORDETECTING DIVERSE GENOTYPES OF
HUMAN PAPILLOMAVIRUS BY PCR
Same as US20040248085A1
US6583278
Nucleic acid probes complementary to human papilloma virus nucleic acid
Gen-Probe Incorporated
2003-06-24 1996-11-14 C12Q
Typing HPV 16 and/or HPV 18 using hybridization assay probes, helper probes, and/or
amplification primers.
US6509149
HPV-specific oligonucleotides
Hybridon, Inc. 2003-01-21 1995-06-06 C12N
Synthetic oligonucleotides complementary to a nucleic acid spanning the translational
start site of human papillomavirus gene E1, and including at least 15 nucleotides.
US6503704
Method, reagent and kit for genotyping human papilloma virus
Visible Genetics Inc. 2003-01-07 2001-06-25 C12Q
Amplifycation and sequencing a portion of the L1 open reading frame of human
papillomavirus genome with the claimed amplification primers.
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EP0746627B1 HUMAN PAPILLOMA VIRUS DETECTION
IN A NUCLEIC ACID AMPLIFICATION
PROCESS USING GENERAL PRIMERS
And US6352825 Human Papilloma Virus detection in a
nucleic acid amplification process
using general primers
same as WO9110675A1
US6265154
Nucleic acid primers and probes for detecting oncogenic human papillomaviruses
Abbott Laboratories 2001-07-24 1996-10-25 C12N
Probe sequences that are useful for detecting oncogenic HPV types 16, 18, 31, 33, 35, 39,
45, 51, 52, 56, 58, 59 and 68 are herein provided. These sequences can be used in
hybridization assays or amplification based assays designed to detect the presence of
these oncogenic HPV types in a test sample. Additionally, the sequences can be provided
as part of a kit.
US6218104
Method of detection of carcinogenic human papillomavirus
Biosearch International Pty 2001-04-17 1997-12-30 C12N
High risk carcinogenic human types 16, 18 and 33 are distinguished from low risk
human papillomavirus types 6 and 11 in a sample of human cervical tissue. A selected
characteristic portion of the E6 region of the virus defined by specific oligonucleotide
primers is amplified using a polymerase chain reaction. The presence or absence of the
characteristic portion of the E6 region is detected by gel electrophoresis or using a
labeled oligonucleotide probe.
US6045993
Method, reagent and kit for genotyping of human papillomavirus
Visible Genetics Inc. 2000-04-04 1998-05-30 C12Q
The sequence of human papillomavirus present in a sample is determined by amplifying a
portion of the L1 using sequence ARRGGAWACT GATCWARDTC
US5783412
Method of detection of carcinogenic human papillomavirus
Biosearch International Pty. Ltd. 1998-07-21 1989-08-25 C12N
PCR amplification of types 16 and 18
US5705627
Detection of human papillomavirus by the polymerase chain reaction using specific L1,
and E6 probes
1998-01-06 1995-05-26 C12Q
The primers used in this method are consensus primers that can be used to amplify a
particular region of the genome of any HPV. The presence of HPV in a sample is
indicated by the formation of amplified DNA. The HPV nucleic acid is detected by
consensus probes that may be short oligonucleotide probes or long generic probes. The
HPV is typed by the use of type-specific DNA probes specific for the amplified region of
DNA.
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CA2074069AA, WO9110675A1, US5364758 and CA2183758AA 1995
STICHTING RES FONDS PATHOLOGIE
GP5+/6+ primers protected and few other sets of universal primers in the same region of
L1 gene.
Small if any variation of 1991 patent.
EP1287165B1
Method for detection and localization of genes in situ using branched-DNA hybridisation
BAYER CORPORATION 2007-06-13 2001-06-01 C12Q
WO06117076A1
USE OF INDOLIN-PHENYLSULFONAMIDE DERIVATIVES
BAYER HEALTHCAREAG 2006-11-09 2006-04-19 A61P
Not relevant
==============================================================
Neither Institute de Pasteur nor Roche patents are relevant for our method of probe
selections
==============================================================
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Annex 2. Analysis of documents cited in the PCT research report
Sections taken from documents D1-D7 related to our patent 2007-2008 are written in
italics and we have underlined the critical parts of any claims or arguments to emphasize
the differences with our PCT application.
D1 WO 00/43538 (Université de Montréal); 27 July 2000
D2 (Biotechniques, 2002, Brukner et al).
(1) In the body of the text and in the claims of D1, there is a requirement for selection
of probes (OL) under stringent conditions, in order to minimize mismatches. In
our present PCR/CA2007/001398 it is exactly the opposite—in order to get better
discriminatory probes (recognizing only intended targets), selection is done under
non-stringent conditions to maximize mismatches.
D1: WHAT IS CLAIMED IS 1. A process for generating an oligonucleotide library which
originates from a chosen biological material, comprising: a) generating random
oligonucleotides, wherein said oligonucleotides are of a uniform length comprising a
central segment of randomly varied bases and segments of a defined sequence flanking
the central segment on each side; b) hybridizing said random oligonucleotide mixture of
a) with a nucleic acid template of biological origin under hybridization conditions which
enable the formation of duplexes, while minimizing or abrogating mismatches; c)
separating said duplexes from non-duplexed material; and d) amplifying said hybridized
oligonucleotides…
(2) The same procedure of selection is presented in D2 (Biotechniques, 2002,
Brukner et al). However, during the writing of MS it was realized and discussed
(by citing literature) that existence of mismatches was not detrimental to the
generation of diagnostics probes (OL). Still, the procedure was following
stringent conditions of selection. The crucial effect of selection under nondenaturing (non-stringent conditions) was not realized in D1 and D2.
(3) Negative selection-subtraction was completely changed in our PST application,
compared with documents D1 and D2, and accommodated to make simultaneous
positive and negative selections in the second segment of selection cycles. Both
D1 and D2 are describing separate (both physically and in terms of timing)
positive and negative selection (subtraction). Simultaneous selection (positive,
forward and negative-subtractive) is an essential feature not because it is faster,
but because it will guarantee affinity distribution of selected probes, which will be
higher for intended targets, but lower for unintended targets. Only affinities
falling in this range will have differential binding performance.
D3 US 2005/0175989 Claims in this patent include particular HPV hybridization probes.
However, claim 15 (cited here for illustration) is, “A probe which hybridizes to nucleic
acid from an HPV subtype, said probe being selected from the group consisting of: SEQ
ID NO: 1-SEQ ID NO: 12 and sequences fully complementary thereto.” Our PCT
application is describing hybridization probes that do not rely only on exact and/or full
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complement of targets. In fact, this is the essential feature of our probes. Further, our
method does not even need knowledge of nucleic acid target sequences, just the presence
of targets and non-targets. However, for the purpose of proving the concept and for the
purpose of facilitating and controlling the selection (generation of probes) we used
publicly available sequence information and chemically synthesized all relevant targets.
D4 WO 99/14377 Present consensus of the majority of the scientific community is that
the generation of a spectrum of specific probe sequences that will discriminate plurality
of similar targets is not known in the art, which is well described in D7 (our Nucleic
Acids Research, 2007 paper) and recent literature related to the hybridization theory.
However, D4 offers an example of type-specific probe sequences that do not cover a full
spectrum of HPV types and that do not have discrimination power over a full set of HPV
types.
Description:
“Type-specific probe sequences are well known in the art, and any such suitable
sequences can be used in the present invention. In the case of HPV, for example, suitable
type-specific probes are disclosed in W09914377. The invention is not restricted to the
nature or origin of the type-specific probes that are used in hybridization step in the
present invention.”
“Claims 1: A process for identification of type-specific polynucleotide sequences in a
sample, the process comprising the steps of: (i) contacting polynucleotides from the
sample, or derived from the sample, with a plurality of type-specific probes in the context
of a solid support, and detection of any type-specific hybridization; and (ii) contacting
polynucleotides in the sample, or derived from the sample, with type-specific primers for
those types capable of being detected by the hybridization step in step 1, but not so
detected, in a type-specific amplification reaction.”
D5 US 2005/0244851 (Affymetrix, INC).
This document describes the use of oligonucelotide probes for the purpose of expression
analysis and splicing analysis. However, this document is underestimating the issue of
probe specificity, especially differential detection of similar targets. The accumulation of
expression-relevant data suggests that the basic premise of nucleic acid hybridizations are
not well incorporated into the probe design criterion, leading to the inability to uniquely
interpret hybridization signals of multiplex probes with complex nucleic acid samples,
like total RNA or something similar. We don’t find any overlap with any segment of our
PCT amplification.
Claims (underlined by us)
10. A nucleic acid array comprising a plurality of at least 100,000 probe sets wherein
each probe set comprises: a plurality of different perfect match probes, wherein the
probes of each probe set are complementary to a single probe selection region, and
wherein each probe selection region is a single exon or a subsequence of an exon.
D6 is the sequence of HPV 16 late major capsid protein AF084952, Wang et al, 1998.
This document is not relevant since the process of generation/selection of probes:
(1) does not require any a priori knowledge of sequence data;
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(2) Our SEQ ID NO: 116 probe is not 100% identical to HPV 16, but contain extra
nucleotides both on the 5’ and 3’ sites from the central core of 14 nucleotides fullmatch containing segments. If an examiner is arguing that the short segment of 14
nucleotide long motif was known in advance, then any single nucleotide, or
dinucleotide, or trinucleotide…from any probe is 100% complementary with any
target. This raises questions of minimal probe length and of minimal length of a
target sequence motif good enough to keep specificity among similar
targets…questions that are not theoretically and practically resolved. Any of our
probes have short segments of complementarities. To our knowledge, there is no
software, algorithm, or known procedure that can pick-up or select very short
segments of fully-complementary sequences and can generate the probes that
keep differential discrimination among all spectrum of similar targets (HPV type).
D7 is our 2007 NAR paper. It is fully relevant to our PCT application, but it does not list
all HPV-relevant typing probes due to the fact that the choice of target segment was not
optimal (not variable enough). Importantly, this paper was published after we filed the
provisional patent application (priority date), so it can not affect novelty.
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Annex 3. Curriculum vitae – Research team
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Annex 3.1. Ivan Brukner’s CV
Curriculum Vitae
Name
Ivan Brukner
Office Address
Hospital Ste-Justine, B479, 3175 Cote-Ste-Catherine, Montreal, Qc, H3T 1C5 & Jewish
General Hospital, 3755 Côte-Sainte-Catherine Road, Montréal, Québec, Canada, H3T
1E2
Telephone 514 3454931 ext. 3376
Fax 514 3454731
Date of Birth
13-11-1960
Social Insurance No.
279602379
Citizenship
Canadian and Serbian
Home Address
3754 av. Kent, Montreal, H3S1N3, QC, Canada
Spouse's Name
Maja Krajinovic
Children
Danko Brukner
Place of Birth
Novi Sad, Serbia
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EDUCATION:
Undergraduate
Jovan Jovanovic Zmaj High School-Gymnasium, Novi Sad, Serbia, www.jjzmaj.edu.yu
Graduate
B.Sci Molecular Biology and Physiology, Faculty of Biology, University of Belgrade,
1985 http://www.bg.ac.yu/
(University courses and marks enclosed as a separate file)
M.Sci: Sequence-dependent structural variations of DNA revealed by DNase I, Molecular
Biology, Faculty of Biology, University of Belgrade, Yugoslavia, 1990. Supervisor, Prof
Dr Ana Savic
PhD: Structural polymorphisms of DNA, Molecular Biology, University of Belgrade,
Yugoslavia, 1993. Supervisor Prof. Ana Savic
Research training
Graduate training
International Center for Genetic Engineering and Biotechnology (ICGEB/UNIDO),
Trieste, Italy;
Practical
Course:
Computer
Methods
in
Molecular
biology,
1990,
http://www.icgeb.trieste.it/home.html
Biochemistry and Biophysics Department, University of Trieste, Italy;
Project: Triple helix formation and DNA methylation (09/91–01/92), supervisors Drs
Giorgio Manzini and Luigi Xodo, www.units.it/
EMBO fellowship, European Molecular Biology Organization Heidelberg, Germany;
Project: Biological Structures and Biocomputing Division, DNA-DNase I interactions
(01/92-07/1992), supervised by Dr Dietrich Suck, http://www.embl-heidelberg.de/
Postgraduate training
ICGEB/UNIDO postdoctoral fellow: International Center for Genetic Engineering and
Biotechnology, Trieste, Italy, Protein Structure and Function (07/1992-02/1995).
Project: sequence-dependent structural variations of DNA, supervised by Dr Sandor
Pongor, http://www.icgeb.trieste.it/home.html
MRC post-doctoral fellow, Red Cross Society and Cancer Institute de Montreal (CIM),
Montreal (03/1995-1997)
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Project: DNA structural and functional elements: impact on recombination; topology of
DNA and transfection capacity of vector supervised by Dr Pierre Chartrand, Director of
CIM
APOINTMENTS and WORK EXPERIENCE
Teaching Assistant 1986-1991, University of Belgrade, Faculty of Biology, Department
of Molecular Biology and Biochemistry, http://www.bg.ac.yu/
Assistant Professor, 1991, University of Belgrade, Faculty of Biology, Department of
Molecular Biology and Biochemistry, http://www.bg.ac.yu/
Lady Davis Institute (07/1997-10/1998), McGill AIDS Center, Montreal, Research
Associate;
Projects: monitoring cell distribution of non-nucleoside inhibitors of HIV RT, antisense
effect of arabinonucleic acids, cloning and expression of HIV nucleocapside 7,
supervised by Drs Michael Parniak and Masad Damha
Biochemistry Department, University of Montreal (10/1998–06/1999), Research
Associate;
Project: Oligonucleotide Libraries, supervised by Prof Dr Robert Cedergren
Procrea Bioscience Inc, Montreal, Research and Development, (06/1999-05/2000),
Research Associate;
Project: Cloning and expression of GFP-fused reporter genes relevant for beta oxidation
of fatty acids, supervised by Dr Pierre Chartrand, www.procrea.com/
Signal Gene Inc, Montreal, Research and Development, Scientist, 05/2000-10/2001,
DNA arrays;
Projects: RNA-related techniques, in vitro transcription, in vitro translation, NASBA
isothermal amplification, cloning and expression of GFP-fused reporter assay for genes
involved in apoptotic pathway, Director of Research and Development Dr Larry Malek
Genizon Inc., Montreal, Research and Development, (2001-2003) Senior Scientist,
Projects: Ligation Based Genotyping, Long Range PCR, Whole Genome Amplification
procedures, construction of cloning system based on inactivation of suicidal gene (ccdt),
expressed under arabinose promoter (pBAD derivative), Director of Research and
Development: Dr Bruno Paquin
CHU Sainte-Justine, Research Center, Montreal Senior Research Associate, (2003-now),
Projects: Whole Genome Amplification over small genomes or degraded DNA; Selection
of robust diagnostic probes using in vitro evolution, supervised by Drs Damian Labuda
and Maja Krajinovic
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Clinical Laboratory of Jewish General Hospital – Microbiology and Immunology,
Montreal, (2007-now), Senior Research associate;
Project: Clostridium Difficile, sample processing and assay development, supervised by
Dr Andre Dascal, www.jgh.ca
SPECIAL HONORS, AWARDS, RECOGNITION
Contribution of the year 1995: Curved DNA without AA-TT dinucleotide step: effect of
ions, 1995, Biological Structure and Dynamics, NY, Albany.
EMBO Heidelberg, fellowship, (01/92- 07/1992)
ICGEB/UNIDO, Italy, post-doctoral fellowship, (07/1992-02/1995)
MRC-CIHR, Montreal, post-doctoral fellowship (1996-1998)
Invited Lectures, Talks, Presentations
1. DNA bending, bendability and curvature: Biological Structure and Dynamics,
Volumes One and Two
The Proceedings of the Ninth Conversation held at The University-SUNY Albany, NY,
June 20-24, 1995.
2. Generating aptamers from complex biological mixtures/fluids: Differential SELEX,
University of Sherbooke, Department of Biochemistry, Medical Faculty, 1998.
3. Using combinatorial oligonucleotide approach in medicine: applications in diagnostic
and therapy, St-Justine Hopital, Montreal, 1998.
4. New diagnostic-relevant oligonucleotide probes, Innogenetics, Gent, Belgium, 2003,
http://www.innogenetics.com/
OTHER CONTRIBUTIONS
Journals Reviews
Current Drugs (5), Analytical Biochemistry (32) and European Biochemistry (2)
Grant Reviews and Panel Member
Current Drugs International panel of evaluators for new drugs and patents under
development (08/1996–2001).
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External expert for EC project proposals (DNA arrays, molecular biology and
biotechnology, European Union Commission, (October, 2003-2007)).
Professional and Scientific Contributions
Confidential Disclosure Agreements (CDA) with Invitrogen (US) 1997,
AmershamBioscience (US) 2003, HySeq (US), 2000, Affymetrics (US), 2000, Digene
(US), 2003; Innogenetics (EU), 2003, GE Bioscience (2006); Complete Genomics,
(2008).
Patents:
1. Brukner, I., Belmaaza, A. and Noureddine, R: SELECTIVE TECHNIQUE FOR
RAPID IDENTIFICATION OF PROTEINS AND GENES AND USES THEREOF (US
6.331.777), PolyGene, Montreal, 1997.
2. Paquin, B, Brukner, I., Tremblay, G.: PROCESS FOR THE GENERATION OF
OLIGONUCLEOTIDE LIBRARIES (OLs) REPRESENTATIVE OF GENOMES OR
EXPRESSED mRNAs (cDNAs) AND USES THEREOF (EP 12810.62 US 12810.63
and CA 12810.61), University of Montreal,1999.
3. Brukner, I., Belouchi, A. and Paquin, B US patent pending: PRIMER DESIGN FOR
REMOVING BACKGROUND IN AMPLIFICATION BASED ON RANDOM
PRIMING, Gallielo Genomics Inc, 2003
4. Brukner, I , Krajinovic, M and Labuda, D. (2006) US patent pending:
AMPLIFICATION OF NUCLEIC ACID SEQUENCES, St Justine HospitalUNIVALOR # 60/750,049; Filed 12-14-2005.
5. Brukner, I , Krajinovic, M and Labuda, D. (2006-now) Provisional US patent
application # 60/882,153: NUCLEIC ACID PROBES, METHODS FOR THEIR
PREPARATION AND USES THEREOF; WO-2008017162; Filed 08-11-2006).
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Publications
Articles in peer reviewed journals.
Drmanac, R., Labat, I., Brukner, I. and Crkvenjakov, R (1989): Sequencing of megabase
plus DNA by hybridization: Theory of the Method, Genomics, 4, 114-128.
Brukner, I., Jurukovski, V. and Savic, A. (1990): Sequence-dependent structural
variations of DNA revealed by DNase I, Nucleic Acids Res. 18, 891-894.
Brukner, I., Jurukovski, V., Konstantinovic, M. and Savic, A. (1991): Curved DNA
without AA/TT dinucleotide step, Nucleic Acids Res. 19, 3549-3551.
Brukner, I., Dlakic, M., Savic, A., Susic, S., Pongor, S. and Suck, D. (1993): Evidence
for opposite groove-directed curvature of GGGCCC and AAAAA sequence elements,
Nucleic Acids Res. 21, 1025-1029.
Brukner, I., Susic, S., Dlakic, M., Savic, A. and Pongor S. (1994): Physiological
concentration of Mg2+ ions induces a strong macroscopic curvature in GGGCCCcontaining DNA, J.Mol. Biol. 236, 26-32.
Wolf, E., Brukner, I. and Suck, D. (1995): Mutation analysis of DNase I-DNA
interaction: design, expression and characterization of a DNaseI loop-insertion mutant
with altered sequence selectivity, Protein Engineering 8, 283-291.
Brukner, I., Sanchez, R., Suck, D. and Pongor, S. (1995): Sequence-dependent bending
propensity of DNA as revealed by DNaseI: parameters for trinucleotides, EMBO J., 14,
1812-1818.
Brukner, I., Sanchez, R., Suck, D. and Pongor, S. (1995): Trinucleotide Models for
DNA Bending Propensity: Comparison of Models Based on DNaseI Digestion and
Nucleosome Packing Data, J. Biomol. Stuct. Dyn., 13, 309-317.
Brukner, I., Belmaaza A. and Chartrand, P. (1997) Differential behavior of curved DNA
upon untwisting, Proc. Natl. Acad. Sci. USA, 94, 403-406.
Damha, M.J., Wilds, C. J., Noronha, A., Brukner, I., Borkow , G. and Parniak, M.A.
(1998) Hybrids of RNA and Arabinonucleic Acids (ANA and 2’F-ANA) are Substrates
of Ribonuclease H, JACS, 120, 12976-12977.
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Brukner, I. & Tremblay G. (2000) RNA targeting by antisense oligonucleotides strongly
depends on protein-oligonucleotide interaction: new in vitro assay, Biochemistry.
39(37):11463-6.
Brukner, I., Tremblay, G. & Paquin, B. (2002) The generation of amplifiable genomespecific oligonucleotide probes-libraries, BioTechniques, 33:874-882.
Brukner, I., Paquin, B., Belouchi, M., Labuda, D. and Krajinovic, M. (2005) Decrease of
self-priming by random oligonucleotides increase the performance of whole genome
amplification, Analytical Biochemistry, 339(2):345-7.
Brukner, I., Labuda, D. and Krajinovic, M. (2006) Phi29-based amplification of small
genomes. Analytical Biochemistry, 354(1):154-6.
Brukner, I., El-Ramahi1 R, Gorska-Flipot, I., Krajinovic, M. and Labuda, D (2007) An
in vitro selection scheme for oligonucleotide probes to discriminate between closely
related DNA sequences, Nucl Acids Res. 2007;35(9):e66.
Brukner, I., El-Ramahi; R., Jacob Sawicki; J., Gorska-Flipot, I., Krajinovic, M. and
Labuda, D.(2007) Hybridization assay for typing high risk Human Papillomaviruses
performed at ambient temperature, Journal of Clinical Virology, 39 (2):113-8.
Brukner I, Krajinovic M, Dascal A, Labuda D. (2007) A protocol for the in vitro
selection of specific oligonucleotide probes for high-resolution DNA typing. Nature
Protoc. ;2 (11):2807-14.
Gorska-Flipot I, Sawick J, Gaboury LA, Krajinovic M, Labuda D, Brukner I, Rouleau
D, Ghattas G, Franco EL, Coutlée F. Newly-isolated HPV97, related to HPV18 and 45 is
frequently detected in HIV-positive men from the Montreal area. Int J Cancer. 2008,
122(5):1195-7.
Krajinovic, M. and Brukner, I. (2008) Further insight into the markers of methotrexate
resistance in childhood acute lymphoblastic leukemia patients. Personilized Medicine; 5
(4), 2008, 325-329.
Technical reports and books
Gabrielian, A., Vlahovicek, K., Munteanu, M., Gromiha, M, Brukner, I., Sanchez, R.
and Pongor, S. (1998) Prediction of bendability and curvature in genomic DNA in
Biomolecular Structures & Dynamics, Adenine Press
Brukner, I. C-1027 (2000) Taiho Pharmaceutical Co Ltd. Current Opinion in Oncologic,
Endocrine & Metabolic Investigational Drugs 2 (3), 344-352.
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Brukner, I. (2001) OvaRex AltaRex, IDdrugs, 4 (4), 457-462.
Brukner, I. (2001) INGN-201. Introgen Therapeutics. Curr Opin Investig Drugs, 2
(12):1776-85.
Reviews
Brukner, I. and Pongor, S. (1995): A trinucleotide Model for Sequence-Dependent DNA
Bending Propensity, Biological Structure and Dynamics, 2, 289-294.
Abstracts and conference presentations
Sawicki J, Gaboury LA, Krajinovic M, Labuda D, Brukner I, Coutlée F, Gorska I (2006)
Cloning strategy of a new type of Human Papilloma Virus from a clinical sample with
mixed HPV infection. 23 International Papillomavirus Conference and Workshop, Prague
Developing genome resources for Clostridium difficile V Forgetta, MT Oughton, I
Brukner, A Villeneuve, G Levesque, C Nagy, J Dias, V Magrini, M Hickenbotham, K
Haub, C Markovic, J Nelson, E Mardis, A Dascal, K Dewar; poster presentation at
Genome Canada annual conference, Quebec City, October 2007
Al-Shakfa F, Brukner I, St-Onge G, Moghrabi A, Krajinovic M (2008)
Pharmacogenetics of DHFR in childhood ALL. 1st Annual Canadian Human Genetics
Conference, 9-12 avril, St-Sauveur, Canada.
Al-Shakfa F, Brukner I, St-Onge G, Moghrabi A, Krajinovic M (2008)
Pharmacogenetics of DHRF in childhood ALL. Les Journées Génétiques RMGA, May
14-16, Québec, Canada
Al-Shakfa F, Brukner I, St-Onge G, Moghrabi A, Krajinovic M (2008)
Pharmacogenetics of DHFR in childhood ALL. IXth World Conference on Clinical
Pharmacology and Therapeutics - CPT2008 July 27 - August 1, Québec City, Canada.
MT Oughton, V Forgetta, I Brukner, A Villeneuve, G Levesque, C Nagy, J Dias, V
Magrini, M Hickenbotham, K Haub, C Markovic, J Nelson, E Mardis, A Dascal, K
Dewar; (2008) Comparative genomics analysis of Clostridium difficile: improving
methods for detection, epidemiology, therapeutics and understanding pathogenicity
poster presentation at AMMI Canada/CACMID annual conference
Brukner I, Krajinovic M, Labuda D (2008) Robust performance of in vitro generated
hybridizations probes: suitable for different nucleic-acid based diagnostic-detection
platforms. XX International Congress of Genetics, July 12-17, Berlin, Germany.
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Annex 3.2. Damian Labuda’s CV
CURRICULUM VITAE
DAMIAN LABUDA
Professor
Department of Pediatrics
University of Montreal
CHU Sainte-Justine
3175, chemin de la Côte-Sainte-Catherine
Montreal, Quebec H3T 1C5
Tel. (514) 345-4931 ext. 3586
E-mail: damian.labuda@umontreal.ca
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STUDIES AND DEGREES
1967-1971
M.Sc. Biology/Biochemistry (Supervisor: Jacek Augustyniak)
Adam Mickiewicz University (UAM), Poznan.
Thesis: Studies of iodination and tritiation of the ACTH
molecule.
1976
Ph.D., Biochemistry (Supervisor: Jacek Augustyniak) (UAM)
Thesis: Studies of phenylalanine-specific tRNA from barley.
1982
D.Sc. ("Habilitacja") (UAM)
"Code RNA: RNA. Mechanism of codon recognition by tRNA".
(UAM editions, 1983, biology series, vol. 22).
PRE AND POST-DOCTORAL TRAININGS
1971
Service of Biochemistry, Centre d'Énergie Nucléaire,
Saclay, France
1972-1973
Institute of Plant Physiology,
Hungarian Academy of Sciences, Szeged, Hungary
1978-1982 (3 full years)
Max-Planck Institute of Biophysical Chemistry,
Göttingen, Germany
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POSITIONS
1972-1976
1976-1981
Research Assistant
Adjunct
Department of Biochemistry,
Institute of Biology, UAM,
Poznan.
1982-1984
Research Associate
Department of Biochemistry,
Université de Montréal.
1984-1988
Research Assistant
Professor
Department of Pediatrics,
Université de Montréal.
1988-1990
Research Associate Professor
Department of Pediatrics,
Université de Montréal.
1990-1994
Associate Professor
Department of Pediatrics,
Université de Montréal.
1994-Present
Professor
Department of Pediatrics,
Université de Montréal.
AFFILIATIONS
Molecular Biology Program/University of Montreal
Chercheur titulaire de l’IREP (Institut Interuniversitaire de Recherche sur des Populations until
2001)
Comité de direction du RMGA (Réseau de Médecine Génétique Appliquée of FRSQ)
Scientific Advisor (Molecular Biology Diagnostic Laboratory at Hôpital Sainte-Justine)
FELLOWSHIPS
1971
Commissariat d'Énergie Atomique, France.
1972/1973
Hungarian Academy of Sciences, Hungary.
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1978/1982
(3 full years)
Max-Planck Gesellschaft, Germany.
1986-1992
Fonds de la recherche en santé du Québec, (FRSQ).
Scholarship - Sénior I/II
1992
Prize of Excellence - Conseil des Clubs de Service.
Published Refereed Papers (2003-present)
1.
Xu L, Pan-Hammarstrom Q, Forsti A, Hemminki K, Hammarstrom L, Labuda D,
Gustafsson JA and Dahlman-Wright K (2003) Human estrogen receptor Beta 548
is not a common variant in three distinct populations. Endocrinology 144:35413546.
2.
Bortolini M-C, Salzano FM, Thomas MG, Stuart S, Nasanen SPK, Bau CHD,
Hutz MH, Layrisse Z, Petzl-Erler ML, Tsuneto LT, Hill K, Hurtado AM, Castrode-Guerra D, Torres MM, Groot H, Michalski R, Nymadawa P, Bedoya G,
Bradman N, Labuda D and Ruiz-Linares A (2003) Y-chromosome evidence for
differing ancient demographic histories in the americas. Am J Hum Genet.
73:524-539.
3.
Zietkiewicz E, Yotova V, Gehl D, Wambach T, Arrieta I, Batzer M, Cole DEC,
Hechtman P, Kaplan F, Modiano D, Moisan J-P, Michalski R and Labuda D
(2003) Haplotypes in the dystrophin DNA segment point to a mosaic origin of
modern humans’ diversity. Am J Hum Genet. 73:994-1015.
4.
Mathonnet G, Krajinovic M, Labuda D and Sinnett D (2003) Role of DNA
mismatch-repair genetic polymorphisms in the risk of childhood acute
lymphoblastic leukemia. Br J Haematol. 123:45-48.
5.
Fleury I, Beaulieu P, Primeau M, Labuda D, Sinnett D and Krajinovic M (2003)
Characterization of BCL-1 polymorphism in the glucocorticoid receptor gene.
Clin Chem. 49:1528-1531.
6.
Mathonnet G, Labuda D (corresponding athor) Meloche C, Wambach T,
Krajinovic M and Sinnett D (2003) Variable continental distribution of
polymorphisms in the coding regions of DNA-repair genes. J Hum Genet. 48:
659-64.
7.
Brockstedt U, Uzarowska A, Montpetit A, Pfau W and Labuda D (2004) In vitro
evolution of RNA aptamers recognizing carcinogenic aromatic amines. Biochem
Biophys Res Commun. 313: 1004-8
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8.
Krajinovic M, Lamothe S, Labuda D, Lemieux-Blanchard E, Théorêt Y and
Sinnett D (2004) Role of MTHFR genetic polymorphisms in the susceptibility to
childhood acute lymphoblastic leukemia. Blood. 103:252-7
9.
Xiao F-X, Yotova V, Zietkiewicz E, Lovell A, Gehl D, Bourgeois S, Moreau C,
Spanaki C, Plaitakis A, Moisan J-P and Labuda D (2004) Human Xchromosomal lineages in Europe reveal Middle Eastern and Asiatic contacts. Eur
J Hum Genet. 12: 301-11
10.
Pastinen T, Sladek R, Gurd S, Ge B, Lepage P, Sammak A, Laverge K,
Villeneuve A, Gudin T, Forgetta V, Beck A, Zotti C, Bourgoin S, Verner A,
Harmsen E, Labuda D, Morgan K, Dewar K, Vohl M-C, Naumova AK, Sinnett
D and Hudson TJ (2004) A survey of genetic and epigenetic variation affecting
human gene expression. Physiol Genomics 16: 184-93
Published Refereed Papers (2003-present) (continued)
11.
Le Jossec M, Wambach T, Labuda D (corresponding author), Sinnett D and
Levy E (2004) Genetic diversity patterns in the SR-BI/II locus can be explained
by a recent selective sweep. Mol Biol Evol. 21: 760-9.
12.
Bourgeois S and Labuda D (2004) Dynamic allele-specific oligonucleotide
hybridization on solid support. Anal Biochem 324:309-311.
13.
El-Mabrouk N and Labuda D (2004) Haplotypes histories as pathways of
recombinations. Bioinformatics 20:1836-41.
14.
Lovell AD, Yotova V, Xian F-X, Batzer MA and Labuda D (2004)
Polymorphisms within a polymorphism: SNPs in and around a polymorphic Alu
insertion in intron 44 of the human dystrophin gene, detected by SSCP and
dHPLC. J Hum Genet 49:269-72.
15.
Brukner I, Paquin B, Belouchi M, Labuda D and Krajinovic M (2005) Decrease
of self-priming by modified random oligonucleotides incresase the performance
of whole genome amplification. Anal Biochem. 339:345-347.
16.
Duquette A, Roddier K, McNabb-Baltar J, Gosselin I, St-Denis A, Dicaire MJ,
Loisel L, Labuda D, Marchand L, Mathieu J, Bouchard JP and Brais B (2005)
Mutations in senataxin responsible for Quebec cluster of ataxia with neuropathy.
Ann Neurol. 57: 408-414.
17.
Laberge AM, Jomphe M, Houde L, Vézina H, Tremblay M, Desjardins B,
Labuda D, St-Hilaire M, Macmillan C, Shoubridge EA and Brais B (2005) A
“Fille du Roy” introduced the T14484C Leber hereditary optic neuropathy
mutation in French Canadians. Am J Hum Genet. 77:313-317.
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18.
Lovell A, Moreau C, Yotova V, Xiao F, Bourgeois S, Gehl D, Bertranpetit J,
Schurr E and Labuda D (2005) Ethiopia: between Sub-Saharan Africa and
western Eurasia. Ann Hum Genet. 69:275-287.
19.
Yotova V, Labuda D (corresponding author), Zietkiewicz E, Gehl D, Lovell A,
Lefebvre J-F, Bourgeois S, Lemieux-Blanchard É, Labuda M, Vézina H, Houde
L, Tremblay M, Toupance B, Heyer E, J.Hudson T, Laberge C (2005) Anatomy
of a founder effect: myotonic dystrophy in Northeastern Quebec. Hum Genet.
117: 177-187.
20.
Bélanger H, Beaulieu P, Moreau C, Labuda D, Hudson TJ and Sinnett D (2005)
Functional promoter SNPs in cell cycle checkpoint genes. Hum Mol Genet.
14:2641-2648.
21.
Sinnett D, Labuda D and Krajinovic M (2005) MTHFR genetic polymorphisms
and susceptibility to childhood acute lymphoblastic leukemia. Blood 106:25902591.
Published Refereed Papers (2003-present) (continued)
22.
Bedoya G, Montoya P, Garcia J, Soto I, Bourgeois S, Carvajal L, Labuda D,
Alvarez V, Ospina J, Hedrick PW and Ruiz-Linares A (2006) Admixture
dynamics in Hispanics: a shift in the nuclear genetic ancestry of a South
American population isolate. Proc Natl Acad Sci USA 103:7234-7239.
23.
Brukner I, Labuda D and Krajinovic M (2006) Phi29-based amplification of
small genomes. Anal Biochem. 354:154-156.
24.
Sinnett D, Beaulieu P, Bélanger H, Lefebvre JF, Langlois S, Théberge MC,
Drouin S, Zotti C, Hudson TJ and Labuda D (2006) Detection and
characterization of DNA variants in the promoter regions of hundreds of human
disease candidate genes. Genomics 87:704-710.
25.
Durocher F, Labrie Y, Soucy P, Sinilnikova O, Labuda D, Bessette P, Chiquette
J, Laframboise R, Lepine J, Lesperance B, Pichette R, Plante M, Tavtigian SV
and Simard J (2006) Mutation analysis and characterization of ATR sequence
variants in breast cancer cases from high risk French Canadian breast/ovarian
cancer families. BMC Cancer 6:230-251.
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26.
Healy J, Bélanger H, Beaulieu P, Larivière M, Labuda D and Sinnett D (2007)
Promoter SNPs in G1/S checkpoint regulators and their impact on the
susceptibility to childhood leukemia. Blood 109:683-92.
27.
Fuselli S, Gilman RH, Chanock SJ, Bonatto SL, De StefanoG, Evans CA,
Labuda D, Luiselli D, Salzano FM, Soto G, Vallejo G, Sajantila A, Pettener D
and Tarazona-Santos E (2007) Analysis of nucleotide diversity of NAT2 coding
region reveals homogeneityacross native American populations and high intrapopulations diversity. Pharmacogenomics J. 7: 144-152.
28.
Labuda D, Labbé C, Langlois S, Lefebvre J-F, Freytag V, Moreau C, Sawicki J,
Beaulieu P, Pastinen T, Hudson TJ and Sinnett D (2007) Patterns of variation in
DNA segments upstream of transcription start sites. Hum Mutat. 28: 441-450.
29.
Brukner I, El-Ramahi R, Gorska-Flipot I, Krajinovic M and Labuda D (2007a)
Generation of oligonucleotide probes to discriminate between closely related
DNA sequences. Nucleic Acids Res. 35: e66.
30.
Brukner I, Krajinovic M, Dascal A and Labuda D (2007) A protocol for the in
vitro selection of specific oligonucleotide probes for high-resolution DNA typing.
Nat Protoc. 11:2807-14.
31.
Brukner I, El-Ramahi R, Sawicki J, Gorska-Flipot I, Krajinovic M and Labuda D
(2007b) Hybridization probes for 39 different types of Human Papillomaviruses. J
Clin Virol. 39: 113-118.
Published Refereed Papers (2003-present) (continued)
32.
Pshezhetsky AV, Fedjaev M, Ashmarina L, Mazur A, Budman L, Sinnett D,
Labuda D, Beaulieu JF, Ménard D, Nifant’ev I and Levy E (2007) Subcellular
proteomics of cell differentiation: quantitative analysis of the plasma membrane
proteome of Caco-2 cells. Proteomics. July:7 (13): 2201-2215.
33.
Witsch-Baumgartner M, Braun I, Gruber M, Andria G, Bertranpetit J, Bieth E,
Clusellas N, Estivill X, Gasparini G, Giros M, Krajewska-Walasek M, Menzel J,
Miettinen T, Ogorelkova M, Rossi M, Schinzel A, Schmidt K, Schõnitzer D,
Seemanova E, Sperling K, Syrrou M, Talmud Philippa J, Wollnik B, Krawczak
M, Labuda D, Utermann G (2007) Age and origin of major Smith-Lemli-Opitz
syndrome (SLOS) mutations in European populations. J Med Gen. 45(4): 200-9.
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34.
Moreau C, Vézina H and Labuda D (2007) Effets fondateurs et variabilité génétique au
Québec. Médecine Sciences 11 :1008-13.
35.
Yotova V, Lefebvre JF, Kohany O, Jurka J, Michalski R, Modiano D, Utermann G,
Williams SM and Labuda D (2007) Tracing genetic history of modern humans using Xchromosomes lineages. Hum Genet. 122(5): 431-43.
36.
Wang S, Lewis CM, Jakobsson M, Ramachandran S, Ray N, Bedoya G, Rojas W,
Parrra MV, Molina JA, Gallo C, Mazzotti G, Poletti G, Hill K, Hurtado AM,
Labuda D, Klitz W, Barrantes R, Bortolini MC, Salzano FM, Petzl-Erler ML,
Tsuneto LT, Llop E, Rothhamner F, Excoffier L, Feldman MW, Rosenberg NA
and Ruiz-Linares A (2007) Genetic variation and population structure in Native
Americans. Plos Genetics. 3(11): e185.
37.
Dulucq S, St-Onge G, Gagné V, Ansari M, Sinnett D, Labuda D, Moghrabi A
and Krajinovic M (2007) DNA variants in dihydrofolate reductase gene and
outcome in childhood ALL. Blood. 111(7):3692-700.
38.
Gorska-Flipot I, Sawicki J, Gaboury LA, Krajinovic M, Labuda D, Brukner I,
Rouleau D, Ghattas G, Franco EL, Coutlée F (2008) Newly isolated HPV97,
related to HPV18 and 45 is frequently detected in HIV-positive men from the
Montreal area. Int J Cancer. 122(5) :1195-7.
39.
Lefebvre JF and Labuda D (2008) Fraction of Informative Recombinations: a
Heuristic Approach to Analyse Recombination Densities. Genetics. 178(4):206979.
40.
Gokcumen O, Dulik MC, Pai AA, Zhadanov SI, Rubinstein S, Osipova LP,
Andreenkov OV, Tabikhanova LE, Gubina MA, Labuda D and Schurr TG
(2008)Genetic variation in the enigmatic Altaian Kazakhs of South-Central
Russia: insights into Turkic population history. Am J Phys Anthropol.
136(3):278-93.
41.
Sirois F, Gbeha E, Sanni A, Labuda D et Mbikay M (2008) Ethnic Differences in
the Frequency of the Cardioprotective C679X PCSK9 Mutation in a West African
Population. Genet Test 12(3):377-80.
Published Refereed Papers (2003-present) (continued)
42.
Cruciani F, Trombetta B, Labuda D, Modiano D, Torroni A, Costa R and
Scozzari R (2008) Genetic diversity patterns at the human clock gene period 2
(PER2) are suggestive of population-specific positive selection. Eur J Hum Genet
(epub ahead of print – 25 June)
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Accepted or in press refereed papers (2003-present)
43.
Moreau C, Vézina H, Yotova V, Hamon R, de Knijff P, Sinnett D and Labuda D
(2008) Genetic Heterogeneity in Regional Populations of Quebec - Parental
Lineages in the Gaspe Peninsula. Am J Phys Anthropol (in revision)
Submitted refereed papers
44.
Bourgeois S, Yotova V, Bourtoumieu S, Moreau C, Michalski R, Moisan JP, Hill
K, Hurtado AM, Ruiz-Linares A and Labuda D (2008) X-chromosome lineages
reveal strong founder effect in the colonization of the Americas. (submitted – Am
J Phys Anthropol)
45.
Healy J, Dionne J, Bélanger H, Larivière M, Moreau C, Labuda D and Sinnett D
(2008) Functional variation of the promoter region of TGFβ1 and its impact on
childhood leukemia. (submitted)
46.
N’Diaye N, Pastinen T, Paterson A, Larivière M, Labuda D, Hudson TJ and
Sinnett D (2008) A Naurally Occuring Regulatory Haplotype Enhances BTN3A2
Expression. (submitted)
Published Contributions to a Collective Work/Book Chapters/Reviews (2003-present)
1.
Krajinovic M, Labuda D and Sinnett D (2003) Pharmacogenetics of childhood acute
lymphoblastic leukemia. Curr Pharmacogenetics 1:87-100.
2.
Simard J, Dumont M, Labuda D, Sinnett D, Meloche C, El-Alfy M, Berger L, Lees E,
Labrie F and Tavtigian SV (2003) Prostate cancer susceptibility genes: lessons learned
and challenges posed. Endocr Relat Cancer 10:225-259.
3.
Cardinal G, Deschênes M, Knoppers BM, Hudson T, Labuda D, Bouchard G, Racine É,
Fecteau C, Truong S and Laberge C (2003) Statement of principles on the ethical conduct
of human genetic research involving populations. RMGA http://rmga.qc.ca/index.html.
4.
Labuda D, Krajinovic M and Bourgeois S (2004) Allele specific oligonucleotide
hybridization (ASO). Encyclopedia of Diagnostic Genomics and Proteomics – Marcel
Dekker. pp. 38-41.
5.
Sinnett D, Mathonnet G, Meloche G, Moghrabi A, Labuda D and Krajinovic M (2004)
Genetic determinants to childhood acute lymphoblastic leukemia. In: Pandalai SG (ed)
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Recent Research Developments in Haematology. Vol 1 India. Transworld Research
Network 1:135-154.
Published Contributions to a Collective Work/Book Chapters/Reviews (2003-present)
(continued)
6.
Sinnett, D, Meloche C, Labuda D, Mathonnet G, Moghrabi A, Sabbagh A, InfanteRivard C and Krajinovic M (2004) Genetic susceptibility to childhood acute
lymphoblastic leukemia. Nova Science Publishers, Inc. pp. 1-31.
7.
Sinnett D, Labuda D and Krajinovic M (2006) Challenges identifying genetic
determinants of pediatric cancers – the childhood leukemia experience. Fam Cancer
5:35-47.
8.
Sinnett D, N’Diaye N, Labuda D and Krajinovic M (2006) Genetic determinants of
childhood leukemia. Bulletin du cancer. Sept, 93:857-865.
9.
Brais B, Desjardins B, Labuda D, St-Hilaire M, Tremblay M and Vézina H (2007) The
Genetics of French Canadians. IN: Cavalli-Sforza LL, Feldman M (eds.) Henry Stewart
Talks; Biomedical and Life Sciences – Human Population Genetics (CD-ROM) Londres,
Angleterre: Henry Stewart Group of Companies <http://www.hstalks.com/index.htm>
Oral presentations/Seminars (2003-present)
1.
Labuda D (2003) Genetic information: What it can tell us about our ancestry? 61st
Annual Meeting of the Polish Institute of Arts and Sciences of America, McGill
University, June 7th, McGill University, Montreal, Qc. (invited speaker)
2.
Labuda D (2003) Malaises autour de gènes mutés ; conference on : Génomique et
pluralisme au Canada échanges pour approfondir le dialogue. Bioethics Across Borders,
Joint Meeting of the Canadian Bioethics Society and the American Society for Bioethics
and Humanities, October 22-26, Montréal, Qc (invited presentation)
3.
Labuda D, (2003) Variabilité d’ADN – leçons sur notre histoire, le présent et le futur.
Les biotechnologies 50 ans après la découverte de l’ADN, 28e Congrès annuel de
l’Association des biologistes du Québec, December 4-5 (invited conference)
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4.
Labuda D (2004) What genetics can tell us about our ancestry, our present and future.
MUHC Research Seminar, Montreal Children’s Hospital Centenial Seminar, March 1st,
Montreal, Qc. (invited conference)
5.
Labuda D, Yotova V, Piché C, Gehl D, Moreau C, Jurka J, Kohany O, Michalski R,
Moisan JP, Schurr E, Utermann G, Williams S (2004) X-linked marker tracing history of
human populations. HUGO: Human Genome Meeting, April 4, Berlin, Germany. (oral
presentation and poster)
6.
Labuda D, Langlois S, Gehl D, Beaulieu P, Lefebvre JF, Vasquez H, Moreau C, Labbé
C, Théberge MC, Bourgoin S, Zotti C, Pastinien T, Lepage P, Hudson T, Dewar K,
Sinnett D. (2004) Genetic variability in gene segments upstream of coding regions.
Human Genome Variation Society Scientific Meeting, April 4, Berlin, Germany (oral
presentation)
Oral presentations/Seminars (2003-present) (continued)
7.
Labuda D, (2004) X Chromosome Markers & Human Population History. Population
genetics symposium, Human Genetic Student Society, April 22, Montreal, Quebec.
(conference)
8.
Labuda D, Yotova V, Zietkiewicz E, Gehl D, Lovell A, Lefebvre JF, Bourgeois S,
Lemieux-Blanchard E, Labuda M, Vézina H, Houde L, Tremblay M, Toupance B, Heyer
E, Fortin J, Lepage P, Hudson TJ, Lescault A, Laberge C (2004) Founder effect in NorthEastern Quebec and the extent of the genetic signature associated with the myotonic
dystrophy mutation. « Qui fait quoi » ; 5e Journées Génétiques, RMGA, May 17,
Montreal, QC. (oral presentation)
9.
Labbé C, Labuda D (2004) Diversité des régions promotrices des gènes du métabolisme
du glutathion. XIXe Congrès Annuel de la recherche des étudiants gradués et postgradués, Centre de recherche de l’Hôpital Sainte-Justine, Université de Montreal. June
4, Montreal, QC. (oral presentation)
10.
Labuda D (2004) X-linked markers tracing history of human populations, LMS Durham
Symposiums on Mathematical Genetics, University of Durham, July 5, United Kingdom.
(invited presentation)
11.
Labuda D, Lefebvre J, Moreau C, Labbé C, Langlois S, Beaulieu P, Theberge MC,
Bélanger H, Sinnett D and the Genome Quebec Regulatory Genetics Consortium (2005)
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Contribution of gene conversions to the genetic diversity of DNA segments. European
Human Genetics Conference, May 7-10, Prague, Czech Republic. (oral presentation)
12.
Labuda D (2006) Natural selection in the promoter regions: genetic diversity upstream
of transcription start sites. Genes and Populations in Health and Disease, Portugaliae
Genetica, 9th edition, March 6-8, Porto, Portugal. (invited presentation)
13.
Labuda D (2006) Reading history of human populations from genetic diversity of
chromosome Xp21. Genes and Populations in Health and Disease, Portugaliae
Genetica, 9th edition, March 6-8, Porto, Portugal. (invited presentation)
14.
Labuda D, Yotova V, Lefebvre J-F, Kohany O, Jurka J, Michalski R, Modiano D,
Utermann G and Williams S (2007) Structure complexe de la population ancestrale
humaine - une histoire génétique retracée par les lignages du chromosome Xp21, GALF,
31 mai, 1-2 juin, Genève, Suisse. (oral presentation)
15.
Labuda D, Moreau C, Yotova V, Hamon R, de Knijff P, Sinnett D and Vézina H. (2008)
Genetic heterogeneity in regional populations of Quebec – parental lineages in the Gaspé
Peninsula. 7ème Journées génétique RMGA. May 14-16, 2008, Québec, Canada. (oral
presentation)
International Conference Abstracts/posters (2003-present)
1.
Drouin S, Beaulieu P, Labuda D and Sinnett D (2003) Comparative genomic approach
to human transcription factor binding site validation. Oncogenomics 2003, January 28February 2, Phoenix, AZ.
2.
El-Mabrouk N and Labuda D (2003) Haplotypes histories as networks of
recombinations. Recomb 2003, April 10-13, Berlin.
3.
Witsch-Baumgartner M, Labuda D and Utermann G (2003) Origins of the common
DHCR7 mutations: IVS8-1G>C and W151X causing the Smith-Lemli-Opitz syndrome.
European Human Genetics Conference 2003, European Society of Human Genetics, May
3-6, Birmingham, England.
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4.
Vézina H, Bélanger J, Heyer E, Houde L, Tremblay M, Sinnett D and Labuda D (2003)
Patrimoine génétique des Gaspésiens. 71e congrès de l’ACFAS « Savoirs partagés », May
19-23, Rimouski, Qc.
5.
Labuda D (2003) Genetic information: what it can tell us about our ancestry. 61st Annual
Meeting of the Polish Institute of Arts and Sciences of America, McGill University, June
6-7, Montreal.
6.
Bélanger H, ThébergeM-C, Langlois S, Bourgoin S, Beaulieu P, Gehl D, Labuda D and
Sinnett D (2003) High-throughput detection of polymorphisms in regulatory regions of
candidate genes related to common genetic diseases. AACR, 94th Annual Meeting, July
11-15, Washington D.C., USA.
7.
Meloche C, Drouin S, Labuda D and Sinnett D (2003) Detection of putative regulatory
SNPs in DNA repair genes. AACR, 94th Annual Meeting, July 11-15, Washington D.C.,
USA.
8.
Hudson TJ, Pastinen T, Sladek R, Gurd S, Sammak A, Ge B, Brandstrom H, Lepage P,
Lavergne K, Villeneuve A, Gaudin T, Zotti C, Bourgoin S, Verner A, Harmsen E, Vohl
M-C, Naumova AK, Labuda D and Sinnett D (2003) Linking haplotypes with gene
regulation. AACR Special Conference in Cancer Research, September 13-17, Key
Biscayne, Florida.
9.
Krajinovic M, Lamothe S, Labuda D, Lemieux-Blanchard, Théorêt Y and Sinnett D
(2003) Role of MTHFR genetic polymorphisms in the susceptibility to childhood acute
lymphoblastic leukemia. AACR Special Conference in Cancer Research, September 1317, Key Biscayne, Florida.
10.
Birkett NJ, Maziak DE, Ambrosone C, Darling G, Inculet R, Labuda D, MckeownEussen G, Sinha R, Sinnnett D, Young E, Ghadirian P and Duranceau A (2004) Dietary
heterocyclic amines and risk of adenocarcinoma of the esophagus. AACR, 95th Anuual
Meeting, March 27-31, Orlando, FL.
International Conference Abstracts/posters (2003-present) (continued)
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11.
Witsch-Baumgartner M, Rossi M, Giros M, Kelley I, Clayton P, Lechner S, Labuda D
(2004) A mosaic pattern of common recurrent and founder DHCR7 mutations causing the
Smith-Lemli-Opitz Syndrome in Europeans. European Human Genetics Conference,
June 12-15, Munich, Germany.
12.
Bélanger H, Beaulieu P, Larivière M, Moreau C, Langlois S, Labuda D, Sinnett D
(2004) Functional ploymorphisms in the regulatory region of genes implicated in G1/S
checkpoint. Oncogenetics: achievement and challenges, October 7-8, Montreal, Canada.
13.
Gahier-Rudolf A, Doreau A, Labuda D, Sinnett D, Moghrabi A, Krajinovic M (2004)
Glucocorticoïd receptor gene polymorphisms:frequencies and impact on ALL outcome.
Annual Meeting of the American Society of Human Genetics, October 26-30, Toronto,
Canada.
14.
Sanchez R, Vasquez H, Labuda D, Yotova V, Costea F, Levy E, Sinnett D (2004)
Haplotype diversity and genetic determinants of the therapetic response. Annual Meeting
of the American Society of Human Genetics, October 26-30, Toronto, Canada.
15.
Labbé C, Moreau C, Yotova V, Gehl D, Lefebvre J-F, Beaulieu P, Langlois S, Théberge
M-C, Bélanger H, Zotti C, Sinnett D, Labuda D (2004) Polymorphisms in genes of
glutathione metabolism: promoter regions. Annual Meeting of the American Society of
Human Genetics, October 26-30, Toronto, Canada.
16.
Beaulieu P, Théberge M-C, Bélanger H, Langlois S, Larivière M, Lefebvre J-F, Gehl D,
Labuda D, Sinnett D (2004) In-silico assesment of the impact of single nucleotide
polymorphismsin the regulatory regions of human genes. Annual Meeting of the
American Society of Human Genetics, October 26-30, Toronto, Canada.
17.
Théberge M-C, Bourgoin S, Beaulieu P, Langlois S, Bélanger H, Gehl D, Labuda D,
Sinnett, D (2004) High-throughput detection of regulatory polymorphisms in candidate
genes relevant to common diseases. Annual Meeting of the American Society of Human
Genetics, October 26-30, Toronto, Canada.
18.
Bélanger H, Beaulieu P, Larivière M, Moreau C, Langlois S, Labuda D, Sinnett D
(2004) Functional ploymorphisms in the regulatory region of genes implicated in G1/S
checkpoint. Annual Meeting of the American Society of Human Genetics, October 26-30,
Toronto, Canada.
19.
Labrie Y, Durocher F, Soucy P, Labuda D, Simard J (2004) Characterization of
sequence variants in high-risk non-BRCA1/2 French Canadian families. Annual Meeting
of the American Society of Human Genetics, October 26-30, Toronto, Canada.
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20.
Yotova V, Lovell A, Moreau C, Bourgeois S, Xiao F, Gehl D, Bertranpetit J, Schurr E,
Labuda D (2004) Ethiopia: between Sub-Saharan Africa and Western Eurasia. Annual
Meeting of the American Society of Human Genetics, October 26-30, Toronto, Canada.
International Conference Abstracts/posters (2003-present) (continued)
21.
Leger C, Simoneau M, Théberge M-C, Vasquez H, Lefebvre J-F, Levy E, Sinnett D,
Labuda D (2004) Genetic diversity in the coding regions of three members of the
glutathione peroxidase family. Annual Meeting of the American Society of Human
Genetics, October 26-30, Toronto, Canada.
22.
Bourgeois S, Yotova V, Lovell A, Xiao F, Pich C, Moreau C, Bourthoumieu S,
Zietkiewicz E, Michalski R, Ruiz-Linares A, Labuda D (2004) X-chromosome
polymorphisms and the genetic structure of Amerindian populations. Annual Meeting of
the American Society of Human Genetics, October 26-30, Toronto, Canada.
23.
Moreau C, Yotova V, Gehl D, Cauvier C, Sinnett D, De Knijff P, Vezina H, Labuda D
(2004) Genetic diversity among European settlers of the Gaspe Peninsula (Quebec).
Annual Meeting of the American Society of Human Genetics, October 26-30, Toronto,
Canada.
24.
Labuda D, Moreau C, Langlois S, Gehl D, Beaulieu P, Lefebvre J-F, Vasquez H, Labbe
C, Théberge M-C, Bélanger H, Zotti C, Sinnett D (2004) Population genetics of bona
fides regulatory regions. Annual Meeting of the American Society of Human Genetics,
October 26-30, Toronto, Canada.
25.
Labuda D (2005) Diversity in DNA segments upstream of the transcription start sites.
HUGO Mutation Detection 2005: VIII International Symposium on Mutations in the
Genome, May 31-June 4, Santorini, Greece.
26.
Labuda D and Lefebvre J-F (2006) Heuristic approach for analysis of the recombination
density along DNA sequence. HGM 2006, HUGO’s 11th Human Genome Meeting, May
31-June 3, Helsinki, Finland.
27.
Sawicki J, Gaboury LA, Krajinovic M, Labuda D, Brukner I, Coutlée F, Gorska I (2006)
Cloning strategy of a new type of Human Papilloma Virus from a clinical sample with
mixed HPV infection. 23 International Papillomavirus Conference and Workshop,
Prague.
MDEIE – Commercialization and Transfer Assistance Program
106
28.
Dionne J, Ouimet M, Gagné V, Larivière M, Labuda D and Sinnett D (2007) Functional
impact of regulatory polymorphisms (rSNP) in G1/S cell cycle checkpoint genes. AACR
Annual Meeting, April 14-18, Los Angeles, CA.
29.
Gerbault P, Moreau C, Vézina H and Labuda D (2007) Regionalization of the founder
effect in Quebec. HGM2007, May 21-24, Montreal, Qc.
30.
Dionne J, Ouimet M, Gagné V, Larivière M, Labuda D and Sinnett D (2007) Functional
impact of regulatory polymorphisms (rSNP) in G1/S cell cycle checkpoint genes.
HGM2007, May 21-24, Montreal, Qc.
31.
Gerbeault P, Moreau C, Vézina H and Labuda D (2007) Régionalisation de l'Effet
Fondateur au Québec. GALF 2007, 31 mai, 1-2 juin, Genève, Suisse.
International Conference Abstracts/posters (2003-present) (continued)
32.
Bherer C, Labuda D, Houde L, Tremblay M and Vézina H (2007) Contribution
génétique différentielle des immigrants fondateurs aux pools géniques régionaux du
Québec. GALF 2007, 31 mai, 1-2 juin, Genève, Suisse.
33.
Roy-Gagnon MH, Moreau C, Sinnett D, Laprise C, Vézina H and Labuda D (2008)
Regional Genetic Variation and Linkage Disequilibrium in Quebec. 3rd Annual Canadian
Genetic Epidemiology and Statistical Genetics Meeting, Institute of Genetics, April 29May 1, 2008, Toronto, ON.
34.
Hussin J, Nadeau P, Lefebvre JF and Labuda D. (2008) Haplotype Allelic Classes In
The Lactase Persistence Locus. The Biology of Genomes, Cold Spring Harbour. May 610, 2008, New York, USA.
35.
Nadeau P, Hussin J, Lefebvre JF and Labuda D. (2008) Testing Haplotype Allelic
Classes By Coalescence Simulations. The Biology of Genomes, Cold Spring Harbour.
May 6-10, 2008, New York, USA.
36.
Lefebvre JF and Labuda D. (2008) InfRec: A Heuristic Tool To Analyze Recombination
Rate At The Sequence Level. The Biology of Genomes, Cold Spring Harbour. May 6-10,
2008, New York, USA.
Local Conference Abstracts/posters (2003-present)
MDEIE – Commercialization and Transfer Assistance Program
107
1.
Bourgeois S, Zietkiewicz E, Yotova V, Michalski R, Ruiz-Linares A and Labuda D
(2003) Effets fondateurs et colonisation de l’Amérique. IXe journée scientifique des
programmes de biologie moléculaire, IRCM, April 25, Montreal.
2.
Bélanger H, Théberge M-C, Langlois S, Bourgoin S, Beaulieu P, Gehl D, Zotti C,
Labuda D and Sinnett D (2003) Détection de variants d’ADN dans les régions
régulatrices de gènes candidats pour des maladies complexes. XVIIIe congrès annuel de
la recherche des étudiants gradués et post-gradués de l’Hôpital Sainte-Justine, June 6,
Montreal. (1st prize, poster presentation, M.Sc. category)
3.
Sinnett D, Lamothe S, Labuda D, Lemieux-Blanchard E, Théorêt Y, Moghrabi A and
Krajinovic M (2004) Role of MTHFR genetic polymorphisms in the susceptibility to
childhood acute lymphoblastic leukemia. “Qui fait quoi” ; 5e Journées Génétiques,
RMGA, May 17, Montreal, QC.
4.
Krajinovic M, Primeau M, Chiasson S, Costea I, Bournissen FG, Moghrabi A, Robaey P,
Labuda D and Sinnett D (2004) Genetic polymorphisms in predicting disease outcome.
« Qui fait quoi ? » ; 5e Journées Génétiques, RMGA, May 17, Montreal, QC.
Local Conference Abstracts/posters (2003-present)
5.
Vézina H, Cauvier C, Moreau C, Yotova V, Bélanger J, Houde L, Sinnett D, Tremblay
M, Labuda D (2004) Étude généalogique et moléculaire du patrimoine génétique des
gaspésiens. « Qui fait quoi ? » ; 5e Journées Génétiques, RMGA, May 17, Montreal, QC.
6.
Labuda D (2006) Les Québécois – des chasseurs-cueilleurs? Qui fait quoi? 6èmes
journées génétiques, RMGA, May 1-2, Montreal, Qc.
7.
Gerbault P, Moreau C, Yotova V and Labuda D (2006) Régionalisation de l’effet
fondateur au Québec. XXIe Congrès annuel de la recherche des étudiants gradués et postgradués, Centre de recherche CHU Sainte-Justine, June 2, Montreal, Qc.
8.
Bourgeois S, Yotova V, Lovell A, Piché C and Labuda D (2006) Structure génétique des
populations amérindiennes. XXIe Congrès annuel de la recherche des étudiants gradués
et post-gradués, Centre de recherche CHU Sainte-Justine, June 2, Montreal, Qc.
MDEIE – Commercialization and Transfer Assistance Program
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9.
Bherer C, Labuda D, Houde L, Tremblay M and Vézina H (2007) Contribution
génétique différentielle des immigrants fondateurs aux pools géniques régionaux du
Québec. XXIIe Congrès annuel de la recherche des étudiants gradués et post-gradués,
Centre de recherche CHU Sainte-Justine, May 15-16, Montreal, QC.
10.
Gerbault P, Moreau C, Vézina H and Labuda D (2007) Régionalisation de l’effet
fondateur au Québec. XXIIe Congrès annuel de la recherche des étudiants gradués et
post-gradués, Centre de recherche CHU Sainte-Justine, May 15-16, Montreal, QC.
11.
Dionne J, Ouimet M, Gagné V, Larivière M, Labuda D and Sinnett D (2007)
Caractérisation fonctionnelle des variants génétiques de la région régulatrice des gènes du
point de contrôle G1/S. XXIIe Congrès annuel de la recherche des étudiants gradués et
post-gradués, Centre de recherche CHU Sainte-Justine, May 15-16, Montreal, QC.
12.
Roy-Gagnon MH, Moreau C, Sinnett D, Laprise C, Vézina H and Labuda D. (2008)
Génome québécois : variabilité régionale et déséquilibre de liaison. Qui fait quoi? 7ème
Journées génétiques RMGA. May 14-16, 2008, Québec, Canada.
13.
N’Diaye N, Pastinen T, Paterson A, Larivière M, Labuda D, Hudson TJ and Sinnett D.
(2008) A naturally occurring regulatory Haplotype enhances BTN2A2 expression. Qui
fait quoi? 7ème Journées génétiques RMGA. May 14-16, 2008, Québec, Canada.
14.
Gbeha E, Yotova V, Moreau C, Sanni A and Labuda D. Variabilité Génétique des
Populations Ouest-africaines. Qui fait quoi? 7ème Journées génétiques RMGA. May 1416, 2008, Québec, Canada.
15.
Bherer C, Vézina H and Labuda D. Conséquences des histoires démographiques
régionales du Québec sur le spectre de fréquences alléliques. Qui fait quoi? 7ème
Journées génétiques RMGA. May 14-16, 2008, Québec, Canada.
Local Conference Abstracts/posters (2003-present)
16.
Hussin J, Nadeau P, Lefebvre JF and Labuda D. Haplotype allelic classes in the lactase
persistence locus. Qui fait quoi? 7ème Journées génétiques RMGA. May 14-16, 2008,
Québec, Canada.
17.
Nadeau P, Hussin J, Lefebvre JF and Labuda D. Testing haplotype allelic classes by
coalescence simulations. Qui fait quoi? 7ème Journées génétiques RMGA. May 14-16,
2008, Québec, Canada.
MDEIE – Commercialization and Transfer Assistance Program
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18.
Healy J, Dionne J, Larivière M, Ouimet M, Beaulieu P, Labuda D and Sinnett D.
Regulatory genetics in cancer research – the childhood leukemia story. Qui fait quoi?
7ème Journées Génétiques RMGA. May 14-16 , 2008, Québec, Canada.
SOURCE OF FUNDING
ORGANISM
FRSQ
FRSQ
CIHR
FRSQ
NSERC
TITLE
INVESTIGATOR
Échantillon de référence pour
la recherche en épidémiologie
génétique et en génétique des
populations humaines au
Québec - RMGA
D. Labuda
Étude de la diversité de la
population québécoise
contemporaine - RMGA
D. Labuda
Montreal Spring School of
Population Genomics and
Genetic Epidemiology
D. Labuda
Montreal Spring School of
Population Genomics and
Genetic Epidemiology
D. Labuda
Genetic history of human
populations
D. Labuda
AMOUNT /
YEAR
41,127$
PERIOD
04/200803/2009
47,372$
04/200803/2009
7,000$
04/200805/2008
7,000$
04/200805/2008
24,625$
04/200803/2009
CIHR (Pop)
Optimization and validation of M.Krajinovic
Human Papillomavirus probes
D. Labuda
obtained through in vitro
molecular evolution
I. G-Flipot
150,000$
03/200704/2008
CIHR (NPE-80218)
Genetic models of complex
conditions and population
structure of Quebec.
D. Labuda et al.
99,980$
04/200603/2009
Génome Québec /
Génome Canada
The GRID project: gene
regulators in disease.
T. Hudson et al.
72,000$
01/200603/2009
FQRNT
Méthodes formelles pour
l’inférence de relations
d’évolution entre les
séquences génomiques.
MDEIE – Commercialization and Transfer Assistance Program
N. El-Mabrouk et al.
75,000$
110
04/200503/2008
FRSQ/RMGA
Études des populations
régionales du Québec.
CIHR (MOP-67150)
CIHR (NTA-71859)
44,000$
04/200403/2008
Variability in genomic
D. Labuda
sequences : patterns of genetic
events in the human
populations
152,000$
04/200403/2007
Developing diagnostic tools
through in vitro molecular
evolution
D. Labuda, M.
Krajinovic, I.
Gorska-Flipot
197,326 $
07/2004
VRQ (VRQ 2201-146)
Cellule épithéliale de
l’intestin : identification de
gènes de susceptibilité et de
nouvelles cibles
thérapeutiques.
E.Levy et al.
Génome Québec /
Génome Canada
Regulatory genetics – high
throughput screening of gene
targets related to common
genetic diseases.
T. Hudson et al.
ORGANISM
TITLE
G. Rouleau, H.
Vézina et al.
INVESTIGATOR
06/2006
~450,000 $
09/200203/2006
Total of
$11,600,000
04/200109/2005
AMOUNT /
YEAR
PERIOD
CIHR (MOP-12782)
Variability in genomic
D. Labuda
sequences : patterns of genetic
events in human population
13,434$
10/200303/2004
NSERC
Modèles génétiques et
l’histoire de la population du
Québec dans le contexte de
données moléculaires
D. Labuda
$21,000
04/2002
03/2004
D. Labuda and
$21,000
04/199904/2002
(170180-99)
Modèles génétiques et
l’histoire de la population du
Québec dans le contexte de
données moléculaires.
FRSQ/RMGA
Axe démogénétique
D. Labuda
$30,000
2001-2004
(170180-02)
NSERC
E. Heyer
H. Vézina
E. Heyer
(C. Laberge et al.)
FRSQ/RMGA
Identification of SNPs for a
D. Labuda
marker haplotype of myotonic
dystrophy in Quebec.
budget HSJ
$19,000
(C. Laberge et al.)
MDEIE – Commercialization and Transfer Assistance Program
111
2001-2004
CIHR (MOP-12782)
Variability in genomic
sequences: Patterns of genetic
events in the human
populations.
D. Labuda
$107,469
10/200009/2003
MRC
Variability in human genomic
sequences: Patterns of genetic
events in the human
populations.
D. Labuda
$97,027
10/199709/2000
(MOP-37951)
Environment and genetic
polymorphisms in childhood
acute lymphoblastic leukemia
C. Infante-Rivard, D.
Labuda, D. Sinnett,
M. Bernstein
Ecogenix Inc. (Research
Contract)
Genetic polymorphisms in
cancer susceptibility genes
D. Labuda and D.
Sinnett
CRC
Nutritional factors and geneenvironment interactions in
the etiology of
adenocarcinoma of
N. Birkett, et al.
$85,000
09/199908/2002
D. Sinnett and D.
Labuda
$50,000
1999-2001
(MT-12782)
MRC
$89,285
$91,071
$69,716
$500,000
04/200003/2003
2000-2002
The esophagus.
CGDN
(Center of Excellence)
Genetic susceptibility factors
in complex diseases and
therapeutic response.
MDEIE – Commercialization and Transfer Assistance Program
112
Annex 3.3. Maja Krajinovic’s CV
CURRICULUM VITAE
MAJA KRAJINOVIC
Associate Professor
Departments of Pediatrics & Pharmacology
University of Montreal
CHU Sainte-Justine
3175, chemin de la Côte-Sainte-Catherine
Montreal, Quebec H3T 1C5
Tel. (514) 345-4931 ext. 6259
E-mail: maja.krajinovic@umontreal.ca
Studies and Degrees
1988-1991
Ph.D.
Molecular Biology
1984-1986
M.Sc.
Medical Genetics
1982-1984
Medical
License
M.D.
General Medical
Training
1977-1982
Institute of Biology and Human Genetics
and Institute of Molecular Genetics and
Genetic Engineering, Medical Faculty,
University of Belgrade: Human papilloma
virus: frequency and role in the cervical
cancer
Institute of Biology and Human Genetics,
Medical Faculty, University of Belgrade
Prenatal diagnosis in the first trimester of
pregnancy
Medical Faculty, University of Belgrade
Medical Faculty, University of Belgrade
Academic Positions and Hospital Appointments
Associate Professor
2006-
Associate Professor
Assistant Professor
20062002-2006
Assistant Professor
Scientist
2000-2006
2000-
Assistant Professor
1993-1998
Research Associate
1998-2000
Dept. of Pharmacology, University of Montreal
(secondary affiliation)
Dept. of Pediatrics, University of Montreal
Dept. of Pharmacology, University of Montreal
(secondary affiliation)
Dept. of Pediatrics, University of Montreal
Division of Hematology-Oncology, Research
Center, St-Justine Hospital
Institute of Biology and Human Genetics, Medical
Faculty, University of Belgrade, Yugoslavia
Division of Hematology-Oncology, Research
Center, St-Justine Hospital
MDEIE – Commercialization and Transfer Assistance Program
113
Teaching Assistant
1984-1992
Institute of Biology and Human Genetics, Medical
Faculty, University of Belgrade
Research Training
1995-1998
Postdoctoral training
1992-1995
Postdoctoral training
1990, 1992
Visiting Scientist
1998
Visiting Scientist
Division of Hematology-Oncology, Research
Center, St-Justine Hospital
International Centre for Genetic Engineering and
Biotechnology (ICGEB)/UNIDO, Trieste, Italy
German Cancer Research Centre, Heidelberg,
Germany
Department of Pediatrics, Guy’s Hospital, London
Scholarships and Distinctions
2007-2011
2003-2007
2001-2003
2000-2001
Scholarship
Scholarship
Scholarship
Scholarship
1998-2000
1999
Fellowship
Scholar Award for Promising
Clinical or Translational Cancer
Research
Fellowship
Fellowship
Fellowship
Best Medical Student Awards
1995-1998
1994-1995
1993-1994
1978-1981
FRSQ, National
FRSQ, senior
FRSQ, junior II
Relève 2000, Faculté de Médecine,
University of Montreal
St-Justine Hospital Foundation
Glaxo Wellcome Oncology, AACR 1999
meeting
Charles-Bruneau Foundation
Telethon, Italy
Heart Foundation, Italy
University of Belgrade
Published Refereed Papers (2003-present)
30)
Fleury I, Beaulieu P, Primeau M, Labuda D, Sinnett D, Krajinovic M (2003)
Characterization of BCL-1 polymorphism in the glucocorticoid receptor gene.
Clin Chem. 49:1528-1531.
31)
Krajinovic M, Lamothe S, Labuda D, Lemieux-Blanchard E, Théorêt Y,
Moghrabi A and Sinnett D (2004) Role of MTHFR genetic polymorphisms in the
susceptibility to childhood acute lymphoblastic leukemia. Blood 103:252-257.
32)
Costea I, Moghrabi A, Krajinovic M (2003) The influence of cyclin D1
(CCND1) 870A>G polymorphism and CCND1-thymidylate synthase (TS) gene-
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gene interaction on the outcome of childhood acute lymphoblastic leukemia.
Pharmacogenetics 13:577-580.
33)
Mathonnet G, Krajinovic M, Labuda D, and Sinnett D (2003) Role of DNA
mismatch repair genetic polymorphisms in the risk of childhood acute
lymphoblastic leukemia. Br J Haematol. 123:45-48.
34)
Mathonnet G, Labuda D, Meloche C, Wambach T, Krajinovic M and Sinnett D
(2003) Variable continental distribution of polymorphisms in the coding regions
of DNA-repair genes. J Hum Genet. 48:659-664.
35)
Krajinovic M, Lemieux-Blanchard É, Chiasson S, Primeau M, Costea I and
Moghrabi A (2004) Role of polymorphisms in MTHFR and MTHFD1 genes in
the outcome of childhood acute lymphoblastic leukemia. Pharmacogenomics J.
4:66-72.
36)
Fleury I, Primeau M, Doreau A, Costea I, Moghrabi A, Sinnett D and Krajinovic
M (2004) Polymorphisms in genes relevant for corticosteroid response and the
outcome of childhood acute lymphoblastic leukemia. Am J Pharmacogenomics.
4(5):331-341.
37)
Brukner I, Paquin B, Belouchi M, Labuda D and Krajinovic M (2005) Decrease
of self-priming by modified random oligonucleotides incresase the performance
of whole genome amplification. Anal Biochem. 339(2):345-7.
38)
Krajinovic M, Robaey P, Chiasson S, Lemieux-Blanchard E, Rouillard M and
Moghrabi A (2005) The polymorphism in genes encoding the enzymes of
homocysteine pathway and IQ score following the treatment for childhood acute
lymphoblastic leukemia. Pharmacogenomics. 6 (3):293-302.
39)
Krajinovic M, Costea I, Primeau M, Lemieux-Blanchard É, Chiasson S,
Moghrabi A (2005). Combining several polymorphisms of thymidylate synthase
gene for pharmacogenetic analysis. Pharmacogenomics J. 5(6):374-380.
40)
Thirumaran RK, Gast A, Flohr T, Burwinkel B, Bartram C, Hemminki K, Kumar
R, Sinnett D, Labuda D and Krajinovic M (2005) MTHFR genetic
polymorphisms and susceptibility to childhood acute lymphoblastic leukemia.
Blood 106:2590-1.
41)
Krajinovic M (2005) Further insight into the role of NQO1 in childhood
leukemia. Haematologica 90(11):1445.
42)
Brukner I, Labuda D and Krajinovic M (2006) Phi-29-based amplification of
small genomes. Anal Biochem. 354 (1): 154-156.
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43)
Todorovic Z, Dzocic E, Novakovic I, Mickovic D, Stojanovic R, Nesik Z,
Krajinovic M, Prostrau M and Kostic V (2006) Homocysteine serum levels
MTHFR C677T genotypes in patients with Parkinson’s disease with and without
levodopa therapy. J Neurol Sci. 248 (1-2) :56-61
44)
Costea I, Moghrabi A, Laverdiere C, Graziani A and Krajinovic M (2006) Folate
cycle gene variants and chemotherapy toxicity in pediatric patients with ALL.
Hematologica. 91 (8): 1113-1116.
45)
Garcia-Bournissen F, Moghrabi A and Krajinovic M (2007) Therapeutic
responses in childhood acute lymphoblastic leukemia (ALL) and haplotypes of
gamma glutamyl hydrolase (GGH) gene. Leukemia Res. 31(7) :1023-1025.
46)
Brukner I, El-Ramahi R, Gorska-Flipot I, Krajinovic M and Labuda D (2007) An
in vitro selection scheme for oligonucleotide probes to discriminate between
closely related DNA sequences. Nucleic Acid Res. 35(9):e66.
47)
Brukner I, El-Ramahi R, Sawicki J, Gorska-Flipot I, Krajinovic M and Labuda D
(2007) Hybridization assay performed at ambient temperature fur typing high-rish
human papillomaviruses. J Clin Virology 39(2) :113-8
48)
Brukner I, Krajinovic M, Dascal A and Labuda D (2007) A protocol for the in
vitro selection of specific oligonucleotide probes for high-resolution DNA typing.
Nature Protocols 2: 2807-2814
49)
Gorska-Flipot I, Sawicki J Krajinovic M, Labuda D, Brukner I, Rouleau D,
Ghattas G,. Franco E and Coutlée F (2008). Newly isolated HPV97 related to
HPV 18 and 45 is highly prevalent in HIV positive males in Montreal. Int J
Cancer. 122:1195-7
50)
Dulucq S, St-Onge G, gagné V., Labuda D, Sinnett D, Moghrabi A, Krajinovic
M (2008) DNA variants in dihydrofolate reductase gene and outcome in
childhood ALL. Blood. 111:3692-3670 (the article presented in the journal issue
by editorial)
51)
Joly Y, Sillon G., Silverstein T, Krajinovic M, Avard D (2008)
Pharmacogenomics : Don’t forget children. Current Pharmacogenomics 6 :77-84.
52)
Dulucq S, Bouchet S , Turcq B, Lippert E, Etienne G, Reiffers J , Molimard M ,
Krajinovic M, Mahon F-X (2008) Multidrug Resistance Gene (MDR1)
polymorphisms are associated with major molecular responses to standard-dose
imatinib in chronic myeloid leukaemia. Blood 112:2024-20277
53).
Krajinovic M. Brukner I., Iqbal O, Bender R., Joshi VA, John T, Tsao M-S, GL
(2008) Further insight into the markers of methotrexate resistance in childhood
acute lymphoblastic leukemia patients. Personalized Medicine, 5:325-329.
MDEIE – Commercialization and Transfer Assistance Program
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53)
Krajinovic M (2008) MTHFD1 gene: role in disease susceptibility and
pharmacogenetics, Pharmacogenomics 9:829-832.
54)
Ollivier M-L, Dubois M-F, Krajinovic M, Cossette P, Carmant L (2008): Risk
factors for valproic acid resistance in childhood absence epilepsy. J. Epilepsy
(submitted)
55)
Ansari M, Lauzon-Joset J-F, Vachon M-F, Duval M, Théorèt Y, Champagne M,
Krajinovic M (2008) Influence of GST gene polymorphisms on busulfan
pharmacokinetics in children. Blood (submitted)
Published contributions to a collective work/book chapters/reviews (2003 – present)
4)
Sinnett D, Mathonnet G, Meloche C, Moghrabi A, Labuda D and Krajinovic M
(2003) Genetic determinants to childhood acute lymphoblastic leukemia. Recent
Res Devel Haematol. 1:135-154.
5)
Labuda D, Krajinovic M and Bourgeois S (2004) Allele specific oligonucleotide
hybridization (ASO). Encyclopedia of Diagnostic Genomics and Proteomics,
Marcel Dekker, New York; pp38-41.
6)
Krajinovic M and Moghrabi A (2004) Pharmacogenetics of methotrexate.
Pharmacogenomics 5:819-834.
7)
Sinnett, D, Meloche C, Labuda D, Mathonnet G, Moghrabi A, Sabbagh A,
Infante-Rivard C and Krajinovic M (2005) Genetic susceptibility to childhood
acute lymphoblastic leukemia. Progress in Leukemia Research, Nova Science
Publishers, Inc. New-York. pp. 1-31
8)
Sinnett D, Labuda D, and Krajinovic M (2005) Challenges identifying genetic
determinants of pediatric cancers – the childhood leukemia experience. Familial
Cancer 5:35-47.
9)
Sinnett D, N’Diaye N, Labuda D and Krajinovic M (2006) Genetic determinants
of childhood leukemia. Bulletin du cancer. 93:857-865.
10)
Ansari M and Krajinovic M (2007) Pharmacogenomic in cancer treatment:
Defining genetic bases for interindividual differences in responses to
chemotherapy. Curr Opin Pediatr. 19:15-22.
11)
Ansari M and Krajinovic M (2007) Pharmacogenetics of acute leukemia.
Pharmacogenomics. 8 :817-834.
MDEIE – Commercialization and Transfer Assistance Program
117
12)
Robaey P, Krajinovic M, Marcoux S and Moghrabi A (2008) : Pharmacogenetics
of sensitivity to chemotherapy. Ment. Retard. Dev Disabil. Res. Rev. submitted.
13)
Krajinovic M (2008): Pharmacogenetics of acute lymphoblastic leukemia in
Advani A: Adult Acute Lymphocytic Leukemia: Biology and Treatment. Humana
Press (submitted)
Invited presentations (2003 - present)
5)
6)
7)
8)
9)
10)
11)
12)
“Pharmacogenetics of ALL”, Hôpital Hôtel-Dieu, October 16, 2003.
"Pharmacogenetics of methotrexate", 9th World Congress on Advances in
Oncology and 7th International Symposium on Molecular Medicine, October 1416, 2004, Hersinissos, Crete, Greece.
«Pharmacogénétique de la leucémie lymphoblastic aigue», Centre de Recherche,
Hôpital Sainte-Justine, Ocotber 28, 2005.
« Pharmacogenetics of immunosuppressors », 1ere Journée de Pharmacologie
clinique, Ste-Justine Hospital, June 2006.
“Pharmacogénétique de la leucémie lymphoblastic aigue”, Service d’hématologie,
Hôpital Sainte-Justine, Montréal, April 2007.
« Pharmacogénétique et leucémie lymphoblastique aigue » 10eme Congres de
BioACM, Université du Québec à Montréal, May 2007.
« Pharmacogenetics: principles and application », World University Service
(WUS) Brain Gain Program, Belgrade, June 11-15, 2007.
“Pharmacogenetics of acute lymphoblastic leukemia”, The IX th
World
Conference on Clinical Pharmacology and Therapeutics, July 27–August 1, 2008,
Québec City, Canada.
MDEIE – Commercialization and Transfer Assistance Program
118
Grant Support Received
Organism
Fondation de l’Hôpital
Ste-Justine (Fonds
d’installation)
Centre de recherche,
Hôpital Ste-Justine
(thematic funds)
Centre de recherche,
Hôpital Ste-Justine
(thematic funds)
Leukemia Research Fund
of Canada (operating
grant)
Canadian Institutes of
Health Research
(operating grant)
Cancer Research Society,
Inc. (operating grant)
Title
Principal
Applicant
Maja Krajinovic
Amount/
year
$50, 000
2000-2002
Genetic determinants of MTX
associated neurotoxicity.
Krajinovic, M
$30,000
2001-2002
Mining the archives for genetic material.
DNA extraction and whole genome
amplification of hematologic smears
from leukemic patients.
Genes relevant for methotrexate
response and the risk of relapse in
childhood acute lymphoblastic
leukemia.
Genetic determinants of the MTX
response in childhood ALL.
Infante-R, C
Krajinovic ,M
Damian, L
Sinnett, D
Krajinovic, M
$52,000
2001-2002
$40,000
2001-2003
Krajinovic, M
$56,000
2002-2005
The role of functional polymorphisms in Krajinovic, M
genes relevant for the corticosteroid
response in the outcome of childhood
acute lymphoblastic leukemia.
Set up of a laboratory for
Krajinovic, M
pharmacogenetics development.
$50,000
2002-2004
$524,000
2002
Krajinovic, M
$50,000
2002-2004
Labuda, D
Krajinovic, M
$10,000
2004-2005
Krajinovic, M
$10,000
2004-2005
Labuda, D
Krajinovic, M
Gorska-Flipot, I
Krajinovic, M
$197,326
2004-2006
$57,184
2005-2006
Principal
Applicant
Krajinovic, M
Amount/
year
$10,000
2006-2006
Carmant, L
Krajinovic, M
Champagne, M
Duval, M
Krajinovic, M
$21,750
2006-2007
$32,000
2006-2007
Genetic modulation of therapeutic
response
Canada Foundation for
Innovation (infrastructure
grant)
Société de la recherche sur The role of functional polymorphisms in
le cancer inc.
genes relevant for the corticosteroid
response in the outcome of childhood
acute lymphoblastic leukemia
Centre de recherche
Développement d’une nouvelle
pédiatrique de l’Hôpital
génération de sondes du diagnostic
Ste-Justine
moléculaire obtenues par la sélection in
vitro
Centre de recherche
Whole genome amplification (WGA)
pédiatrique de l’Hôpital
des échantillons génomiques en péril
Ste-Justine
CIHR
Developing diagnostic tools through in
vitro molecular evolution
CIHR
Organism
Centre de Recherche,
CHU Ste-Justine
Savoy Fondation
PDL BioPharma, Inc.
Genetic determinants of the response to
anticancer drugs in childhood acute
lymphoblastic leukemia
Title
Technological improvement for nucleic
acid amplification from clinical samples
Pharmacogenomics of refractory
childhood absence epilepsy
Polymorphisms and Busulfan
Pharmacokinetic Study
MDEIE – Commercialization and Transfer Assistance Program
Period
Period
119
Charles Bruneau
Foundation
The Leukemia &
Lymphoma Society of
Canada
CIHR (POP)
Centre d’excellence en
Oncologie pédiatrique et
en soins palliatifs
Fondation Télémaques
Suisse
Fondation Charles
Bruneau
CIHR
Methotrexate pharmacogenetics
Childhood ALL pharmacogenetics:
defining genetic bases for interindividual differences in therapeutic
response
Optimization and validation of human
papilloma virus probes obtained through
in vitro molecular evolution
Volet pharmacogénétique du centre
d'excellence
Pharmacogénétique du Busulfan
Ansari, M
Théoret,Y
Krajinovic, M
$50,000
2006-2007
Krajinovic, M.
$50,000
2007-2008
Labuda, D,
Krajinovic, M
Gorska-Flipot, I
Krajinovic, M
$150,000
2007-2008
$74, 000
2007-2010
$43,000
2007-2008
$100,000
2008-2009
$121,353
2006-2009
Ansari, M
Krajinovic, M
Génétique, polymorphisme et cancer
Maja Krajinovic
Yves Théoret,
Jean-Christophe
Fournet
The potential to optimise asthma
Krajinovic, M
treatment based on individual genetic
Laberge, S
predisposition to respond to major drugs Bérubé, D
classes used in therapy of asthma
MDEIE – Commercialization and Transfer Assistance Program
120
Annex 4.
MDEIE – Commercialization and Transfer Assistance Program
121
MDEIE – Commercialization and Transfer Assistance Program
122