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SUMMARY:Whole-Genome Analysis for Autism Risk Variants Request for Applica
 tions
DTSTART:20150814T165900
DTEND:20150814T170000
DTSTAMP:20260603T085739Z
UID:9b4cfecaf7f3ab8cbebf0e2b29f2eaffff61b12bf0cc06f86b30294d
CATEGORIES:Call for proposal
DESCRIPTION:Simons Foundation Autism Research Initiative\nGrants awarded t
 hrough this request for applications (RFA) are intended to advance our und
 erstanding of the genetic basis of autism\, and in particular\, to begin t
 o assess genetic variants conferring risk in non-coding regions and in cod
 ing regions of the genome that may be less accessible to whole-exome seque
 ncing (WES).\nThe Simons Simplex Collection (SSC) is a rigorously characte
 rized collection optimized to support the discovery of genetic events that
  increase risk of developing autism. The collection consists of approximat
 ely 2\,600 simplex families\, all of which have one child with autism\, un
 affected parents\, and in over 80 percent of families at least one unaffec
 ted sibling. Analyses based on WES data from the SSC have already identifi
 ed at least 30 risk genes for autism and have nominated several hundred ot
 her genes as strong candidates1\,2.\nWhole-genome sequencing (WGS) of the 
 SSC is expected to increase the detection of rare variants of clinical imp
 ortance. In addition to identifying variants in non-coding regions of the 
 genome\, WGS analyses are anticipated to identify novel copy number varian
 ts (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.\nTo this end\, SFARI has partnered with the New York Genome Ce
 nter (NYGC) to sequence whole-genomes from the whole blood DNA of 500 SSC 
 quartet families (2\,000 genomes at 30X sequence coverage).\nSFARI plans t
 o make the alignment and variant call data available to all eligible resea
 rchers (i.e.\, not contingent on funding through this RFA) without delay f
 ollowing standard quality control and data processing steps by the NYGC. T
 he 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 b
 y January 2016. There will be a publication embargo on whole-genome analys
 es that prevents submission of manuscripts for publication until SFARI has
  announced that data generation for the full cohort is finished and has pa
 ssed quality controls and that a first level due diligence on confirmation
  of calls is complete.\nSFARI will work with successful applicants to make
  the WGS data (estimated to be about 400 TB) available to their academic o
 r cloud-based computing resources. SFARI understands that validation of pr
 ioritized hits is a key part of this project and will coordinate some of t
 his confirmation of de novo calls with awardees and the NYGC.\nThe current
  RFA seeks applications from investigators who plan to develop innovative 
 and efficient ways to analyze WGS data from the 500 SSC families.Eligibilt
 y\nAll applicants and key collaborators must hold a Ph.D.\, M.D. or equiva
 lent degree and have a faculty position or the equivalent at a college\, u
 niversity\, medical school or other research facility. Applications may be
  submitted by domestic and foreign nonprofit organizations\; public and pr
 ivate institutions\, such as colleges\, universities\, hospitals\, laborat
 ories and units of state and local government\; and eligible agencies of t
 he federal government. Applications may also be submitted by for-profit co
 mpanies\, in which case the funds provided for the grant are to be used on
 ly for charitable purposes toward research related to autism spectrum diso
 rders. There are no citizenship or national residence requirements.\nIf th
 e proposal includes investigators at more than one site\, all investigator
 s should have demonstrated prior success in similar collaborations.Deadlin
 e for full proposal submission is 14 August 2015.
LOCATION:
STATUS:CONFIRMED
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