Whole-Genome Analysis for Autism Risk Variants Request for Applications
Event details
| Date | 14.08.2015 |
| Hour | 16:59 › 17:00 |
| Speaker | Simons Foundation Autism Research Initiative |
| Category | Call for proposal |
Grants awarded through this request for applications (RFA) are intended to advance our understanding of the genetic basis of autism, and in particular, to begin to assess genetic variants conferring risk in non-coding regions and in coding regions of the genome that may be less accessible to whole-exome sequencing (WES).
The Simons Simplex Collection (SSC) is a rigorously characterized collection optimized to support the discovery of genetic events that increase risk of developing autism. The collection consists of approximately 2,600 simplex families, all of which have one child with autism, unaffected parents, and in over 80 percent of families at least one unaffected sibling. Analyses based on WES data from the SSC have already identified at least 30 risk genes for autism and have nominated several hundred other genes as strong candidates1,2.
Whole-genome sequencing (WGS) of the SSC is expected to increase the detection of rare variants of clinical importance. In addition to identifying variants in non-coding regions of the genome, WGS analyses are anticipated to identify novel copy number variants (CNVs) and single nucleotide variants (SNVs) in protein-coding regions that have not previously been detected with WES. Preliminary WGS analyses of a separate group of 40 families (160 genomes) from the SSC compared WGS results with WES data from the same 40 families and support the value of WGS in identifying additional variants of potential clinical significance for autism.
To this end, SFARI has partnered with the New York Genome Center (NYGC) to sequence whole-genomes from the whole blood DNA of 500 SSC quartet families (2,000 genomes at 30X sequence coverage).
SFARI plans to make the alignment and variant call data available to all eligible researchers (i.e., not contingent on funding through this RFA) without delay following standard quality control and data processing steps by the NYGC. The first batch of data will likely be available starting in October 2015, and it is anticipated that 90 percent of the WGS data will be available by January 2016. There will be a publication embargo on whole-genome analyses that prevents submission of manuscripts for publication until SFARI has announced that data generation for the full cohort is finished and has passed quality controls and that a first level due diligence on confirmation of calls is complete.
SFARI will work with successful applicants to make the WGS data (estimated to be about 400 TB) available to their academic or cloud-based computing resources. SFARI understands that validation of prioritized hits is a key part of this project and will coordinate some of this confirmation of de novo calls with awardees and the NYGC.
The current RFA seeks applications from investigators who plan to develop innovative and efficient ways to analyze WGS data from the 500 SSC families.
Eligibilty
All applicants and key collaborators must hold a Ph.D., M.D. or equivalent degree and have a faculty position or the equivalent at a college, university, medical school or other research facility. Applications may be submitted by domestic and foreign nonprofit organizations; public and private institutions, such as colleges, universities, hospitals, laboratories and units of state and local government; and eligible agencies of the federal government. Applications may also be submitted by for-profit companies, in which case the funds provided for the grant are to be used only for charitable purposes toward research related to autism spectrum disorders. There are no citizenship or national residence requirements.
If the proposal includes investigators at more than one site, all investigators should have demonstrated prior success in similar collaborations.
Deadline for full proposal submission is 14 August 2015.
The Simons Simplex Collection (SSC) is a rigorously characterized collection optimized to support the discovery of genetic events that increase risk of developing autism. The collection consists of approximately 2,600 simplex families, all of which have one child with autism, unaffected parents, and in over 80 percent of families at least one unaffected sibling. Analyses based on WES data from the SSC have already identified at least 30 risk genes for autism and have nominated several hundred other genes as strong candidates1,2.
Whole-genome sequencing (WGS) of the SSC is expected to increase the detection of rare variants of clinical importance. In addition to identifying variants in non-coding regions of the genome, WGS analyses are anticipated to identify novel copy number variants (CNVs) and single nucleotide variants (SNVs) in protein-coding regions that have not previously been detected with WES. Preliminary WGS analyses of a separate group of 40 families (160 genomes) from the SSC compared WGS results with WES data from the same 40 families and support the value of WGS in identifying additional variants of potential clinical significance for autism.
To this end, SFARI has partnered with the New York Genome Center (NYGC) to sequence whole-genomes from the whole blood DNA of 500 SSC quartet families (2,000 genomes at 30X sequence coverage).
SFARI plans to make the alignment and variant call data available to all eligible researchers (i.e., not contingent on funding through this RFA) without delay following standard quality control and data processing steps by the NYGC. The first batch of data will likely be available starting in October 2015, and it is anticipated that 90 percent of the WGS data will be available by January 2016. There will be a publication embargo on whole-genome analyses that prevents submission of manuscripts for publication until SFARI has announced that data generation for the full cohort is finished and has passed quality controls and that a first level due diligence on confirmation of calls is complete.
SFARI will work with successful applicants to make the WGS data (estimated to be about 400 TB) available to their academic or cloud-based computing resources. SFARI understands that validation of prioritized hits is a key part of this project and will coordinate some of this confirmation of de novo calls with awardees and the NYGC.
The current RFA seeks applications from investigators who plan to develop innovative and efficient ways to analyze WGS data from the 500 SSC families.
Eligibilty
All applicants and key collaborators must hold a Ph.D., M.D. or equivalent degree and have a faculty position or the equivalent at a college, university, medical school or other research facility. Applications may be submitted by domestic and foreign nonprofit organizations; public and private institutions, such as colleges, universities, hospitals, laboratories and units of state and local government; and eligible agencies of the federal government. Applications may also be submitted by for-profit companies, in which case the funds provided for the grant are to be used only for charitable purposes toward research related to autism spectrum disorders. There are no citizenship or national residence requirements.
If the proposal includes investigators at more than one site, all investigators should have demonstrated prior success in similar collaborations.
Deadline for full proposal submission is 14 August 2015.
Practical information
- General public
- Free