Description

The Simons Foundation Autism Research Initiative (SFARI) recruited a large cohort of families with autistic children who provided DNA samples and phenotypes. 54,558 families, parents and their children were sequenced, a total of 142,357 individuals with whole-exome (WES) and 12,519 with whole-genome sequencing (WGS). The data contains 32,559 trios and 8,895 quads (one sibling without autism), and 824 twins.

The same frequencies shown here are also available publicly on the SFARI Genome Browser. See (SPARK et al, Neuron 2018) for details.

Phenotype-stratified counts

In addition to the overall allele count (AC), allele number (AN), and allele frequency (AF), each variant record carries counts split by autism status (the asd column of the SPARK individual registration file):

• AC_AUT, AN_AUT, AF_AUT — individuals coded as autistic (asd=TRUE).
• AC_NON_AUT, AN_NON_AUT, AF_NON_AUT — individuals coded as non-autistic (asd=FALSE); these are mostly parents and unaffected siblings of the probands.

A small minority of samples have a blank asd value and so contribute only to the overall AC/AN/AF, not to either group total.

Data Access

Due to license restrictions, the data for this track cannot be downloaded from the UCSC Genome Browser. The Table Browser, Data Integrator, and download server are not available for this track.

Allele frequencies can also be displayed on the SFARI Genome Browser. Full CRAMs and VCFs with genotypes are available from SFARI Base. They require a data access request, which is usually reviewed quickly. More information is available in the SPARK Welcome Packet.

Methods

The genome browser track project was approved by the Simons Foundation under request number 14584.1. The multi-sample project VCFs (pVCFs) for both the WES and WGS releases were downloaded from SFARI Base using Globus. No minimum allele frequency cutoff was applied.

Because the genotype-level pVCFs cannot be redistributed, they were reduced to anonymous, sites-only VCFs carrying only the overall allele count (AC), allele number (AN) and frequency (AF), plus the autism-status counts described above, with the bcftools fill-tags plugin (its -S option produces the ASD/non-ASD splits), then normalized. The variants are also annotated with predicted protein consequences using bcftools csq against Ensembl gene models; that annotation is displayed in the combined frequency tracks of this collection. The exact commands for both steps are in the makeDoc file linked below.

The sequencing and variant-calling methods are documented as follows by SFARI:

• WGS: This release consists of sequence and variant call data for 12,519 unique individuals, of which 12,517 (99.98%) have available genome-wide SNP genotype data. Sequencing and genotyping of all samples in this release was performed at New York Genome Center (NYGC). DNA from saliva samples were extracted and prepared with PCR-free methods and sequenced with paired-end sequencing of 150 bases on the Illumina NovaSeq 6000 system. Alignment of reads to the human reference genome version GRCh38, duplicate read marking, and Base Quality Score Recalibration (BQSR) were performed by New York Genome Center (NYGC). Whole-genome sequencing data were processed using a standardized, functionally equivalent CCDG pipeline with alignment to the GRCh38DH (1000 Genomes) reference using BWA-MEM v0.7.15 (deterministic settings, no -M, use of .alt contigs), Picard-equivalent duplicate marking (Picard ≥2.4.1 or equivalent), no indel realignment, and base quality score recalibration with GATK (dbSNP138, Mills and 1000G gold-standard indels, known indels). Final outputs were stored as lossless CRAM files with complete SAM-compliant read-group annotations and mandatory 4-bin base-quality compression (Q2—6, 10, 20, 30), and all implementations were validated for functional equivalence across centers before use. Variant Calling was performed using DeepVariant. See CCDG pipeline details.
• WES: This release contains sequence data for 142,357 individuals and genotyping data for 141,368 individuals. DNA was sequenced from saliva for all samples and all participants consented to having their genetic data shared by Regeneron. Exomes for all samples were sequenced with short-read, paired-end sequencing of 150 bases on Illumina NovaSeq 6000 machines using S2/S4 flow cells. Sequencing and genotyping was performed across nine batches (WES1 through WES9) at the Regeneron Genetics Center (RGC) and integrated together for this data release. All sequencing batches were processed using the same DNA extraction methods and sequencing machines, however two different exome capture panels were used, as described below. Genotyping was performed using a SNP genotyping array for WES1 through WES4 and using "genotyping-by-sequencing" (GxS) for WES5 through WES9. The first four sequencing batches were sequenced at Regeneron using custom NEB/Kapa reagents with the IDT (Integrated DNA Technologies) xGen capture platform, including custom exome capture regions. Samples starting with batch WES5 were sequenced using the Twist Bioscience Human Comprehensive Exome panel, combined with spike-ins for sequencing genotyping sites (see Genotyping Methods), the full mitochondrial genome, and coverage boosted at selected sites for assaying clonal hematopoiesis of indeterminate potential (CHIP). SFARI performed SNV/indel calling via DeepVariant and GATK to generate gVCFs, pairwise relatedness inferred using PLINK v1.9 IBD estimates from common SNPs (AF ≥ 0.01, dbSNP v151) with ≥15% relatedness flagged, and comprehensive individual- and family-level quality control executed using the internal GenomeCheckMate pipeline to exclude samples based on contamination (≥5%), insufficient coverage (<20x in <80% of targets), sex discordance, pedigree/IBD inconsistencies, unregistered relationships, unexpected duplicates, or excess relatedness, after which QC-passing individuals (selecting the most recent passing sample per person) were retained for variant calling and joint genotyping.

The complete, runnable command history for downloading, counting and annotating the SFARI data, alongside every other cohort in this collection, is in the makeDoc file; search it for "SFARI SPARK". The scripts it calls, including sparkMergeVcfAddCounts.sh (allele counts) and mergeAndAnnotate.sh (merge plus consequence annotation), are in the varFreqs scripts directory.

References

SPARK Consortium. Electronic address: pfeliciano@simonsfoundation.org, SPARK Consortium. SPARK: A US Cohort of 50,000 Families to Accelerate Autism Research. Neuron. 2018 Feb 7;97(3):488-493. PMID: 29420931; PMC: PMC7444276