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Many SFARI resources, including genetic and phenotypic data, can still be requested by researchers at this time. Researchers may be particularly interested in taking advantage of these online data sets now, when many labs are shuttered and experiments put on hold due to the COVID-19 pandemic. Biospecimens and postmortem brain tissue can also be requested and shipped in some cases. Furthermore, researchers can continue to submit applications to recruit individuals with autism and their families for new research studies.
Summary of resources
The following SFARI resources can be requested at this time (see Table 1 for more details):
The types of phenotypic data that are available include clinician assessments, data from self-reported (and/or caregiver-reported) behavioral surveys and medical histories. Not all data types are available for each cohort.
Genomic data are available for the following cohorts:
- SSC
- Simons Searchlight
- SPARK
The types of genomic data that are available include whole-exome sequencing (WES), whole-genome sequencing (WGS), single nucleotide polymorphisms (SNPs) and molecular inversion probe sequencing (MIPS) data. Not all data types are available for each cohort.
Biospecimens are available for the following cohorts:
- SSC
- Simons Searchlight
Biospecimens include cell lines (fibroblasts, lymphoblastoids and induced pluripotent stem cells [iPSCs]), DNA samples (sourced from saliva, whole blood and lymphoblastoids) and plasma. Not all biospecimens are available for each cohort.
Researchers can submit an application for any of these biospecimens. SFARI is able to fulfill requests for all biospecimens at this time as long as someone is available in the lab to receive them.
Associated costs for obtaining and shipping biospecimens can be found here.
Recruitment of individuals with autism and their families into investigator-initiated studies is available from the following cohorts:
- SSC (a subset of the cohort is available via the SSC Registry)
- SPARK
- AIC (via the AIC subcommunity in SPARK)
While individuals may not be able to participate in in-clinic studies at the present time, SFARI is still reviewing applications for new studies that wish to recruit subjects from these cohorts. Since the application process can take some time, we encourage researchers who are interested in recruiting participants from SFARI cohorts to submit an application in the interim (see below for further information on how to apply). Recruitment can then begin once any pandemic-related restrictions have been lifted.
We also note that there are some studies that do not require in-person visits (such as those that use online surveys/apps to collect data). These studies may be able to begin work on building the project and initiating recruitment as soon as the application is approved by SFARI.
Postmortem brain tissue is available from Autism BrainNet. Applications continue to be reviewed, but tissue will be shipped only after verification that the laboratories are able to carry out the work.
“SFARI has made a significant investment in developing these resources,” says SFARI Deputy Scientific Director John Spiro. “It is our hope that researchers can continue to take advantage of SFARI data at a time when other studies and experiments may be on pause.”
Adds Stephan Sanders (SFARI Investigator and associate professor at University of California, San Francisco), “This has been a challenging time with lockdowns preventing or delaying the generation of new data from our lab and those we collaborate with. Fortunately, the SFARI data sets remain an incredible and accessible resource for testing new hypotheses about autism genetics and genotype-phenotype correlations. These resources have been especially valuable while trainees and programmers are working remotely, and the scale of the data are so large that they continue to yield important findings.”
Who can use data and biospecimens from SFARI cohorts?
Data and biospecimens are available for use by all approved researchers, regardless of SFARI funding.
SSC, Simons Searchlight and AIC data and biospecimens must be used for projects related to advancing the field of autism and related neurodevelopmental disorder research. SPARK data do not have this limitation and can be used for any research project that advances biomedical science.
Applications will be reviewed to ensure the use of data and biospecimens is in compliance with the Institutional Review Board (IRB-)approved consent language.
Once approved, researchers must agree to not share access or distribute the data sets or biospecimens to any other researchers without prior SFARI approval.
How can researchers access data and biospecimens from SFARI cohorts?
Researchers can log in to SFARI Base and apply to use the data and biospecimens from SFARI cohorts. The application will be reviewed by SFARI staff, and once approved, researchers will be provided with information on how to download the data or will be contacted to discuss the shipment of samples.
Instructions on how to access SFARI Base and request access to resources are detailed here.
How can researchers recruit participants for their studies?
Researchers can submit an application via SFARI Base to recruit participants into investigator-initiated research studies.
Applications are reviewed by a standing committee on a quarterly basis. Researchers will receive further information about how to contact participants once their application is approved.
The SPARK Recruitment Process Document provides answers to many frequently asked questions about the research matching program.
How can researchers request postmortem tissue?
Any researcher who is interested in studying autism and related neurodevelopmental disorders is eligible to apply to use postmortem brain tissue via the tissue request form that can be found at AutismBrainNet.org.
All applicants must submit a short research proposal and demonstrate that they have adequate funding to carry out the proposed project. Applications are reviewed by a standing committee that meets at least four times a year.
Are any online tools available to help researchers explore SFARI data sets?
The Genotypes and Phenotypes in Families tool is an online platform that enables users to visualize and analyze genetic and phenotypic data from the SSC, Simons Searchlight and SPARK. It was developed by SFARI Investigator Ivan Iossifov in collaboration with SFARI.
SFARI Gene is an online database that helps researchers keep track of genetic links to autism. The site currently lists over 900 genes and 17 recurrent copy number variants (CNVs) associated with autism risk, with annotations and links to published papers. Each of the genes is given a score that reflects the strength of the evidence implicating it in autism susceptibility. Access to CNV calls for the SSC is available in the database. Annotations and links to published papers for over 1,000 mouse models of relevance to autism are also included on the site. The database was developed by MindSpec Inc. and is actively maintained in collaboration with SFARI.
SFARI also participates in the Beacon Project, hosted by the Global Alliance for Genomics and Health (GA4GH). A beacon answers questions of the form, “Do you have information about the following mutation?” and responds with either yes or no. SSC data are available in aggregate through the Beacon Network.
Additional information
Questions about data, biospecimens and the recruitment of participants from SFARI cohorts should be emailed to collections@sfari.org.
Questions about applying for postmortem tissue from Autism BrainNet should be emailed to requests@autismbrainnet.org.
