In a milestone for the autism research community, the Simons Foundation Autism Research Initiative (SFARI) has finished recruiting families to participate in its Simons Simplex Collection (SSC), a major new resource for researchers investigating the causes of autism and those developing educational and clinical interventions for individuals on the autism spectrum.
The foundation has now shifted from recruitment of these families to supporting their continued participation in future research studies.
Five years in the making, the completed collection stores both genetic and phenotypic data ― and biospecimens ― from nearly 2,800 “simplex” families. Simplex families have only one child with autism and unaffected parents. The collection is by far the largest repository of data from simplex families and has succeeded well beyond its original goal of recruiting of 2,000 families.
“This is a deeply satisfying accomplishment that will benefit autism research for years to come,” says Gerald Fischbach, scientific director of the Simons Foundation.
As most cases of autism are sporadic, the simplex family study design was chosen to increase the likelihood of identifying genetic variants in individuals with autism spectrum disorders that are not present in their parents and siblings. Recent data suggest that in simplex families, children with autism carry a higher burden of genetic microdeletions and microduplications, collectively known as “copy number variants (CNVs)”. Identifying new CNVs and other genetic variants that increase risk of developing an autism spectrum disorder is a major goal of autism research.
Two papers describing the results of genome-wide scans of the first (approximately) 1,000 families in the collection are about to be published in the 9 June edition of Neuron. These papers report results obtained by two SFARI-funded teams, one led by Michael Wigler of Cold Spring Harbor Laboratory, the other led by Matthew State of Yale University. Both confirmed previously described CNVs associated with autism and uncovered new ones. In keeping with the recent trend toward early access to large genomic datasets, both teams have allowed the Simons Foundation to distribute the raw data from their scans ahead of publication.
The SSC is notable for the rigor and quality control that went into curating its data. Because the data were collected by thirteen different institutions across North America, careful attention was paid to training clinicians at the sites, exchanging videotapes of interviews to ensure consistency, and performing logical checks on the data to catch coding or data entry errors. The result is an unprecedentedly clean data set for a study of this size, involving so many institutions.
“We worked very hard to make the data going in as precise and meaningful as possible,” says Catherine Lord of the University of Michigan in Ann Arbor, principal investigator of the SSC project.
The collection’s data and biospecimens from all participants are available to any qualified, approved researcher via SFARI Base, a web-based database which allows users to select and study a particular cohort or variable of interest, or to request biospecimens. Researchers can use SFARI Base’s statistical tools to aggregate their requested data in a variety of ways, to help facilitate discoveries and uncover links between genetic, phenotypic and biological data. Already, over 70 projects have begun, using the SSC’s available resources. “The goal is to make this a resource for the entire scientific community to mine,” says Marta Benedetti, an associate director of research at the Simons Foundation.
The Simons Foundation and the participating sites are now working to maintain contact with families to help ensure future access for researchers who wish to perform further studies of the collection’s participants. Happily, many of the collection’s families already maintain a connection with the site where they participated. A collaboration with the Interactive Autism Network (IAN) has been established to support an online registry of the SSC’s families. Each participant has also been assigned a Global Unique Identifier (GUID), which allows researchers to enroll the participant in future studies without any risk of duplication or overlap.
The Simons Foundation is grateful to the families who generously provided their data and time for the collection, as well as to the clinical staff and the research teams at the 13 sites that collected the data. “It was an unusually cooperative project, as the principal investigators at the various sites got very little direct professional benefit from participating,” Lord says. “They did it to contribute to the scientific community at large.”
“The Simons Foundation greatly appreciates the leadership of Catherine Lord, and every clinician, project coordinator, and staff member at the various clinics,” Fischbach adds. “We also appreciate the intense effort of the staff at the Simons Foundation. It was a great team that I hope will take new forms as new projects arise.”
The foundation also thanks Prometheus Research, LLC, which developed the SFARI Base platform, and the Rutgers University Cell and DNA Repository, which processes, stores and distributes the biospecimens. The Simons Foundation is also extends deep appreciation to the thirteen sites who made this work possible: Baylor College of Medicine, University of California, Los Angeles (UCLA), Columbia University, Emory University, Harvard University/Children’s Hospital-Boston, University of Illinois, University of Michigan, McGill University, University of Missouri, Vanderbilt University, Washington University, University of Washington and Yale University.