Clinical Next Generation Sequencing Technologies for the NIHR BioResource – Rare Diseases
The NIHR BioResource Sequencing and Informatics Committee
Background
The NIHR BioResource - Rare Diseases is an integral part of the NIHR BioResource and has been
awarded NIHR funding for the clinical application of next generation sequencing techniques (NGST).
The application of NGST will be mainly used for the following categories of activities:
(a) to reduce the delay in ascertaining a genetic diagnosis for inherited and acquired genetic
disorders (including rare cancers), where the genotype causing phenotype is known, by developing
NGST-based diagnostic tests covering NHS diagnostically-important genes; such projects can include
translational projects on e.g. a subset of diagnostic genes,
(b) to determine the genetic basis of Inherited Rare Diseases, including rare cancers for which the
causative locus has hitherto not been identified, but which have potential wider relevance for the
common diseases that are the focus of Biomedical Research Centres/Units (BRC/BRU)-funded
translational and experimental medicine research, and
(c) to characterise induced pluripotent stem cell (iPSC) clones, particularly those established from
patients with Rare Diseases for which novel causative genes have been discovered.
For the purpose of this document Rare Diseases are defined as conditions with an incidence of less
than 5 in 10,000 individuals of the UK population (http://www.raredisease.org.uk/about-rarediseases.htm).
Sequencing of exomes, genomes and other sequencing applications
The NGST capacity for Rare Diseases has been mapped to (i) Exome sequencing (Exome-seq), (ii)
whole genome sequencing to clinical standard (30x coverage), but access to other platforms can also
be requested, e.g. RNA-seq. The NIHR BioResource NGST funding cannot be used for basic cell
biology research, e.g. ChIP-seq, etc in the field of Rare Diseases. It is expected that with the ongoing
reduction in sequencing costs that Exome-seq will increasingly be replaced by sequencing of the
entire genome and this switch-over is expected to happen in part in 2014.
How to get access to centrally funded NGST capacity
Requests for access to centrally funded NIHR BioResource NGST capacity for the above three
categories of activities can be made by any group of BRC/BRU researchers who have agreed to work
across at least three BRCs/BRUs participating in the NIHR BioResource. The NIHR BioResource SIC
can offer advice to ensure the maximum research, clinical and BRC/BRU benefits. Sequencing of
samples funded by the NIHR BioResource can ONLY be performed through the CAmbridge
Translation GenOmics laboratory (CATGO, http://www.catgo.org.uk/). The application can be
submitted to the SIC by submitting the completed “NGST-project” form by email to
info@catgo.org.uk (the form can be downloaded from http://www.catgo.org.uk/).
Requests for access to NIHR BioResource funded NGST capacity will be reviewed by the SIC.
Proposals for NGST capacity should be ambitious, central to the experimental medicine strategy of
the BRCs/BRUs, and are expected to result in publications in high impact journals. Proposals can be
based on existing national, and under certain circumstances international collections of DNA
samples or on new collections still to be established or to be expanded via the NIHR BioResource Rare Diseases. If a proposed NGST project falls within the aims and objectives of the NIHR
BioResource - Rare Diseases (as endorsed by the NIHR BioResource Steering Committee) then the
enrolment office of the NIHR BioResource - Rare Diseases (BRODO) will provide support in
establishing new collections or expanding existing ones. DNA samples to be sequenced with NIHRBioResource funds should have been consented where possible to the NIHR BioResource Stage 1
consent for Rare Diseases, but exemption may be considered on a study-by-study basis.
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Criteria used to assess applications?
The following criteria will be used by the NIHR BioResource SIC when considering a Category (b) or
(c) application:
-
-
The study is ambitious, internationally competitive and aligned with the disease categories
of interest to the NIHR BioResource,
The disorder is rare and there is an already existing collection or there is credible proposal to
establish a collection,
The application is of a collaborative nature and enrolment will be across at least three
BRCs/BRU with a clear plan to reach out across the NIHR Translational Research
Collaboration for Rare Diseases and the wider NHS,
The postulated genetic architecture of the disorder(s) is amenable to discovery of causative
variants by Exome-seq or other NGS techniques,
That the requesting team is able to provide feedback of Pertinent Findings and offer
segregation analysis and pedigree counseling (Feedback of Pertinent Findings to the Clinical
Care Team is current policy, Incidental Findings will NOT be returned to the Clinical Care
Team).
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Existing collections will be assessed against the following criteria
o Has the collection been established across at least three BRCs/BRU or does it
concern a national collection,
o Are the DNA samples of adequate quality and quantity and curated to NHS or similar
(in case of samples from overseas) standards,
o Samples have been obtained with consent to sequence the genome seeking genetic
changes relevant to the submitted phenotype,
o The study team agrees that cases can be re-contacted to seek their consent for
enrolment into the NIHR BioResource - Rare Diseases,
o Information about clinical phenotype and laboratory parameters are available and
applicants agree to transfer this information in its entirety to the NIHR BioResource
Phenotype database for Rare Diseases,
o The requesting team agrees to provide clinical manpower to transform the
phenotypic information into the Human Phenome Ontology (HPO) database terms
where applicable. The clinical study team is expected to engage in HPO term
definition.
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New collections
o New collections have to be established via the NIHR BioResource - Rare Diseases
using the universal Participant Information Leaflet and Consent Form (a modified
form will be generated for patients with psychiatric disorders).
For inherited Rare Diseases the power to discover the causative locus underlying autosomal
recessive disorders is far greater than for autosomal dominant ones. Informative and large pedigrees
remain attractive but are not essential. The initial approach to gene discovery is by sequencing nonrelated index cases from different pedigrees. Additional power of discovery can be achieved by
Exome-seq two cases per pedigree but there is only minimal gain of power by sequencing more than
two affected cases per pedigree (for all inheritance patterns, although the two cases must be chosen
wisely). All samples of pedigrees can be enrolled into the NIHR BioResource and samples can be
selected for sequencing afterwards using tools developed on the BRIDGE project website. For
example if a “de-novo” germline mutation is assumed to be causative then sequencing the DNA
samples from propositus as well as the parents can be highly informative.
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Category (a) proposals
Category (a) applications will be assessed against an additional set of criteria. Ideally, but not
necessarily Category (a) applications are aligned with approved and successful Category (b) projects.
The main purpose of the Category (a) projects is to modernize the genetic-based diagnosis of a
group of related Rare Diseases. There are an estimated 7000 Rare Diseases of man and the genetic
basis of about half has been resolved. It is hoped that the sequence variants for the remaining 3500
diseases will be identified by 2020. For a large number of Rare Diseases there is a considerable
diagnostic delay because candidate gene-based diagnostic approaches are generally sequential and
cost of the Wellcome Trust Sanger Institute sequencing are prohibitively high preventing the routine
uptake by the wider NHS. For certain Category (a) projects the chosen NGST approach may have to
be complemented, for the time being, by a high-density SNP array to detect the gene-to-exon sized
causative structural variants that cannot be revealed yet by exome-seq (although new algorithms are
under development).
More affordable and rapid diagnosis can be achieved by the application of NGST together with SNP
arrays for a group of candidate genes (100-300) that are associated with a certain clinical category of
rare disorders (e.g. X-linked learning disability, retinitis pigmentosa, cardiac malformation and
cardiomyopathies, bleeding and platelet disorders, etc.). Per sample-tested costs can be controlled
by the pooling of DNA samples from different patients. Category (a) projects may only be successful
if developed in partnership with commercial companies (e.g. Agilent, Roche/Nimblegen) and
projects should lead to the transfer of validated tests into routine service delivery for the NHS.
The following criteria will be used for the assessment of Category (a) applications:
- Current knowledge about causative mutations/variants and number of candidate genes,
- Aggregated incidence of the group of Rare Diseases and expected diagnostic case load,
- Will DNA-based diagnosis inform/improve clinical management,
- Can the project be completed before the scientific assessment during the site visit for the
NIHR BRC funding 2012-2017 period,
- Will clinical manpower be provided to drive the project forward, e.g. in partnership with the
NIHR BioResource team for Rare Diseases,
- Is phenotype information available and do applicants agree to transfer the phenotype
information on the NIHR BioResource Phenotype database,
- The requesting team agrees to provide clinical manpower to transform the phenotypic
information into the Human Phenome Ontology database terms,
- Is the case sample collection large enough to have adequate power to determine sensitivity
and specificity of the NGST platform of choice,
- Is the clinical team able to make resources available to curate the candidate genes and
append published information about causative variants. This requires bioinformatics
manpower with a review/approval process and sign-off by the clinical-genetics team.
Overseas samples
Samples from overseas cases can be included but the aggregated number is not to exceed 30% of
the total number of samples to be sequenced. The SIC may grant permission for a higher percentage
on a case-by-case basis (depending on capacity availability and rarity of disorder). If the committee
agrees on providing additional capacity then marginal costs will be charged per additional sample to
the research team that brings in these samples.
Analysis of NGST results, data deposition and archiving
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For approved projects standard bioinformatical analysis (e.g. mapping of sequence reads to the
reference genome, variant calling, assigning consequences according to PolyPhen and SIFT, archiving
of sequence BAM files, etc.) will be provided at no costs by the Clinical Bioinformatics team of the
NIHR BioResource - Rare Diseases. Requesters need to indicate on the request form whether they
have bioinformatical/statistical genetics capacity within their Team of Applicants (names need to be
provided on the request form) or whether they would seek access to central analytical NIHR
BioResource - Rare Diseases capacity or propose to work with another bioinformatical/statistical
genetics team in BRCs/BRUs or elsewhere.
Exome-seq (whole genome) results will be deposited at the European Genome-to-phenome Archive
(EGA, https://www.ebi.ac.uk/ega/) at the European Bioinformatics Institute (EBI) and be linked to
diagnostic categories and HPO terms from the NIHR BioResource clinical phenotype database. The
sequence data from EGA can be released together with “clinical diagnosis and related HPO terms” to
genuine requesters under a “click-it” agreement. Oversight of data release will be by the NIHR
BioResource Steering committee and will be aligned with permissions granted in the informed
consent, after discussion with the involved clinicians where appropriate. The research team will
have access to the variant-called sequence data 12 month before the same data will be released into
EGA.
Clinical and laboratory data deposition in the NIHR BioResource
A sample that has been deposited into the NIHR BioResource and is earmarked for sequencing will
not be sequenced until the clinical and laboratory data have been deposited in the NIHR
BioResource study database for Rare Diseases. The clinical phenotype has to be coded against HPO
terms.
Approval process
The NIHR BioResource SIC meets on a two-monthly basis, or less depending on the number of
applications. Applications received before noon 12 days before the meeting will be distributed and
discussed. Meeting dates will be initially publicised via the normal communication channels of the
NIHR BioResource and at later date on the NIHR BioResource website (under construction). Teams
of Applicants or their representative (e.g. the Principal Investigator(s) responsible for the proposed
project) may be invited to the SIC meeting to review and discuss their application.
What happens if a project is approved?
If an application is approved then a coordinator of the BRODO will liaise with the lead investigator of
the requesting team. A project plan with timelines for SSI application, case enrolment, clinical and
laboratory phenotype data capture, biological sample delivery, sample QA, sequencing and analysis
will be agreed. An inability to meet agreed timelines for DNA sample delivery may mean that the
allocated capacity will be void, and the applicants may have to re-apply for capacity at a later date.
The new application may result in a different allocated capacity than on the original application.
Batch-wise production
The NGST pipeline is expected to be on capacity by July 2013 and will be highly automated
(maximum throughput by December 2013: 3 x 96 samples/week). For the purpose of data
consistency and down-stream analysis samples will be batched where possible. Ideally all samples
from a single study are processed as a single batch. If collections are still being expanded but a
credible number of samples are already available then it could be agreed to split the sequencing of
study samples over a number of batches.
Partnerships
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The interpretation of sequencing results will be greatly supported by the UK10K project
(http://www.uk10k.org/) that will be realized by 2013 by the Wellcome Trust Sanger Institute and
their clinical research partners and the UK100K project (announced in December 2012). Substantial
collaborative connections with the EBI and the Wellcome Trust Sanger Institute are already in place
and will be expanded over the 2012-2017 period to reap the benefits of the genomics revolution for
the NHS and beyond.
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NIHR BioResource Sequencing and Informatics Committee (SIC)
Members
- Cambridge BRC: Prof Willem H Ouwehand (chair)
- Cambridge BRC: Dr Lucy Raymond
- KCL-SLaM BRC: Dr Gerome Breen
- KCL-SLAM BRC: Dr Richard Simpson
- KCL BRC: Dr Michael Simpson
- Leicester Cardiovascular BRU: Prof Nilesh Samani
- IC BRC: Dr John Chambers
- Oxford BRC: Prof Mark McCarthy
- UCL BRC: Prof Nicholas Wood
- Wellcome Trust Sanger Institute: Dr Matthew Hurles
- Patient representative: to be appointed
Observers
- NIHR BioResource: Dr Nathalie Kingston (assistant director)
- NIHR BioResource Rare Diseases Office (BRODO): Sofie Ashford
- Cambridge Translational GenOmics laboratory (CATGO): Dr Ilenia Simeoni
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