High Throughput Sequencing and Rare Diseases
Call for Proposals - 2015, January
WHOLE GENOME SEQUENCING (WGS)
PRE-PROPOSAL APPLICATION FORM
Submission deadline for pre-proposals: February 18, 2015 (midnight)
This file must be sent:
by email to: ngs@fondation-maladiesrares.com
Instructions for sending documents:
-
The application must be written in English.
-
The present cover page must be removed.
-
Annexes should be included in the research project and not on separate documents.
-
The Word file must not exceed 2 Mo (compress any figures).
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Document title: 2015-1-Name of applicant-WGS-RD
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Do not send pdf documents, or scanned documents.
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1. IDENTIFICATION OF THE PROJECT
Project title (maximum 120 signs):
Disease:
Group of diseases:
Research area:
- main:
- secondary:
Rare diseases project:
Yes
No
Previous exome sequencing for the same disease?
Yes
No
Previous exome sequencing on the same samples?
Yes
No
Number of samples for the present WGS project:
Request (tick the appropriate boxes):
Monogenic disorder:
Yes
No
Genetic heterogeneity:
Yes
Likely
Multifactorial disorder:
Yes
No
No
Mode of inheritance of the disease
Ascertained
Anticipated

Autosomal dominant

Complete penetrance

Other:
Autosomal recessive
Yes
No
Unknown
X-linked dominant
Phenocopies
Yes
X-linked recessive
No
Cases

Have large genomic rearrangements been excluded (CGH arrays…)?
Yes
No

Have all known disease related-genes been tested?
Yes
No

Cases history:
o
Familial
-
Yes
Consanguineous
No
Non consanguineous
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-
Large
-
Number of patients in each family (nbx/Fx; nby/Fy; etc):
-
Available DNA for: - patients (nb):
- parents (Y/N):
-
Genome wide linkage analyses performed:
Yes
No
Yes
No
Small
families
Number of families:
 Conclusive linkage
Not feasible
 If yes, specify: - the region delineated (and size):
- the maximum lod score obtained:
o
Sporadic
Yes
No
-
Consanguineous
-
From a clinically homogeneous cohort
-
Number of patients:
-
Available DNA for: - patients (nb):
Non consanguineous
families
Yes
No
- parents (Y/N):
Principal investigator of the project (from a French team):
Name
First name
Position
Institution / department
Laboratory name
Identification of the laboratory (unit n°)
Name of the team (if relevant)
Name, first name of the lab. director
Name, first name / head of the team
Full postal address
Email address
Phone number
Fax
Team members involved in the project:
Name, first name
1
Title
Laboratory / Team
Role and contribution
PI
2
3
Number of persons involved in the project (person-months):
Partners/collaborations:
Name, first name
Title
Laboratory (complete
name, address)
Role and contribution
1
2
3
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Signature of the principal investigator
I, the undersigned, full name, agree to be the principal investigator of the submitted project, as it is described
in the present application.
Electronic signature* :
Date
* The electronic signature is a scan of the signature as a jpeg image.
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2. DESCRIPTION OF THE PROJECT
1. Scientific project (1 page maximum, arial 10, single space)
Context of the proposal, objectives, strategy, expected results and impacts, relevance of the project in
relation to the state of knowledge.
2. Preliminary results on this research program (1/2 page maximum, arial 10, single space)
3. Abstract (not exceeding 1000 characters without spaces)
4. Rationale (1/2 page maximum, arial 10, single space)
Clearly state and justify the choice of the whole genome sequencing strategy, the choice of patients
included in the study and expected impacts of the project.
*Note that in full proposal application, results of previous WES studies on the same disease and/or on the
selected patients must be fully detailled.*
5. Data analysis (1/2 page maximum, arial 10, single space)
Indicate how data analysis will be managed and specify bioinformatics resources available.
6. Main publications (5)
List of 5 main publications and/or patents of the last three years with particular attention to those related to
the project (from the principal investigator and associated teams).
Please specify any potential conflict of interest:
-
‘High throughput sequencing and rare diseases’- WGS pre-proposal application form
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3. BUDGET INFORMATION
ONGOING funded projects related to the current application (principal investigator and associated
teams) which include funding for NGS
Name (coordinator
or associated team)
Name of the call for
projects/
Funding body/funding
amount
Project title
Project period
* Add as many columns as needed
Projects with requested funding for NGS related to the current application UNDER EVALUATION
(principal investigator and associated teams)
Name (coordinator
or associated team)
Name of the call for
projects/
Source/funding amount
Project title
Project period
* Add as many columns as needed
Previous funding by GIS-Institut des maladies rares or by Fondation maladies rares of sequencing
projects since 2009
Name (coordinator
or associated team)
Project title
Call session
Funding amount (HT)
* Add as many columns as needed
*Please mention all the funded projects of the TEAM. A detailed report on the results and impacts for
each project will be provided at full proposal stage*
‘High throughput sequencing and rare diseases’- WGS pre-proposal application form
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Annex :
WGS Full proposal application form - Description of the project: indicative list of items to be detailed
In the full proposal, the following items should be described in details (indicative and non exhaustive list):
1. Objectives
2. Description of samples available for the study
 Description of clinical phenotype, pedigree, available linkage studies for patients analyzed in the
project
 Criteria used for samples inclusion in the project
3. Strategy
 Justification of the choice of the whole genome sequencing strategy considering all criteria:
pathology, modes of inheritance, cases, genetic heterogeneity, etc.
 Context - If whole-exome studies have already been performed on the same disease and/or on the
selected patients, detailed results of these studies must be provided: technical aspects:
sequencing platform, coverage/depth sequencing, complete process of data analysis, variants
interpretation and validation…)
4. Expertise of the laboratory in analysis, annotation and sequences interpretation to be
produced in this project and strategy for mutations validation
 Management for data sequencing analysis and bioinformatics resources associated
 Cohorts available for validating results
5. Description of the downstream research intended to be performed (including possible
collaboration)
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