Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform

Abstract

The exploration of genotypic variants impacting phenotypes is a cornerstone in genetics research. The emergence of vast collections containing deeply genotyped and phenotyped families has made it possible to pursue the search for variants associated with complex diseases. However, managing these large-scale data sets requires specialized computational tools to organize and analyze the extensive data. Genotypes and Phenotypes in Families (GPF) is an open-source platform that manages genotypes and phenotypes derived from collections of families. GPF allows interactive exploration of genetic variants, enrichment analysis for de novo mutations, phenotype/genotype association tools, and secure data sharing. GPF is used to disseminate two family collection data sets, SSC and SPARK, for the study of autism, built by the Simons Foundation. The GPF instance at the Simons Foundation (GPF-SFARI) provides protected access to comprehensive genotypic and phenotypic data for SSC and SPARK. GPF-SFARI also provides public access to an extensive collection of de novo mutations from individuals with autism and related disorders and to gene-level statistics of the protected data sets characterizing the genes’ roles in autism. However, GPF is versatile and can manage genotypic data from other small or large family collections. Here, we highlight the primary features of GPF within the context of GPF-SFARI.