While there has been great progress in understanding the genomic architecture of autism, only a moderate number of the hundreds of genes and genomic regions thought to be involved in ASD have been identified. Next-generation sequencing (NGS) has proven its utility to rapidly identify variants underlying ASD, and this approach is being carried out in ca. 6,000 independent ASD samples through multiple studies. There is an urgent need to develop a framework to integrate and expand these current studies, and to jointly analyze emerging data to maximize the identification of valid ASD loci, because validated risk variants present opportunities for genetic counseling, understanding pathogenesis, and drug development. The Autism Sequencing Consortium (ASC) represents a coordinated effort by more than 20 independent groups to rapidly identify and validate ASD risk genes, which represent lead targets for neurobiological analyses and drug discovery. The long-term goal of the ASC is to make use of genetics to identify therapeutic targets in ASD, while contributing to translating such research findings to clinical practice. The overall objective of tis proposal is to rapidly identify ASD genes representing lead targets for high impact neurobiological studies and drug discovery. Our central hypothesis - formulated based on data with SNV, indels, and CNV, as well as review of medical genetic conditions in ASD and targeted sequencing in ASD - is that multiple independent rare variants account for a very significant proportion of risk to ASD. Our rationale for this proposal is that the identification of genetic variants conferring high-risk risk to ASD and associated neurodevelopmental disorders can form the bases of studies to understand pathogenesis as well as the bases for novel therapies. Moreover, such variants have direct implications for patients and their families in terms of etiological diagnosis, genetic counseling and patient care. These objectives will be accomplished with the following Specific Aims: 1) Maintain the infrastructure to support the ASC objectives;2) Deploy pipelines for data cleaning and harmonization and variant calling;3) Implement novel statistical methods for identifying ASD-associated genes;and, 4) Carry out whole-exome sequencing of 3,000 ASD subjects and parents. This contribution is significant because it represents the first step in research to understand pathogenesis of ASD and to the development of pharmacological strategies for treatment of core symptoms of ASD and etiologically related neurodevelopmental disorders. The research proposed in this application is innovative, in our opinion, because it involves an entirely new model of sharing data before publication, uses state-of-the-art methods for calling diverse types of variants in NGS data, incorporates novel methods for updating variant calling and sharing data, and includes highly innovative statistical methods to identify risk loci. This is a new and substantively different approach to gene discovery in ASD that departs significantly from the status quo and provides the means to achieve these important goals.

Public Health Relevance

The proposed research is relevant to public health because a better understanding of risk in autism will lead to improved methods for prevention and treatment. It is also relevant to the NIH mission and to the IACC recommendations around identifying genetic risk in at least 50% of people with ASD, including an exploration of de novo variation.

Agency
National Institute of Health (NIH)
Institute
National Institute of Mental Health (NIMH)
Type
Research Project--Cooperative Agreements (U01)
Project #
5U01MH100239-02
Application #
8729398
Study Section
Special Emphasis Panel (ZRG1-PSE-P (60))
Program Officer
Koester, Susan E
Project Start
2013-09-01
Project End
2016-07-31
Budget Start
2014-08-01
Budget End
2015-07-31
Support Year
2
Fiscal Year
2014
Total Cost
$674,849
Indirect Cost
$229,034
Name
University of California San Francisco
Department
Psychiatry
Type
Schools of Medicine
DUNS #
094878337
City
San Francisco
State
CA
Country
United States
Zip Code
94143
Willsey, A Jeremy; State, Matthew W (2015) Autism spectrum disorders: from genes to neurobiology. Curr Opin Neurobiol 30:92-9
Krystal, John H; State, Matthew W (2014) Psychiatric disorders: diagnosis to therapy. Cell 157:201-14
Dong, Shan; Walker, Michael F; Carriero, Nicholas J et al. (2014) De novo insertions and deletions of predominantly paternal origin are associated with autism spectrum disorder. Cell Rep 9:16-23
De Rubeis, Silvia; He, Xin; Goldberg, Arthur P et al. (2014) Synaptic, transcriptional and chromatin genes disrupted in autism. Nature 515:209-15