Autism Spectrum Disorder Genetic Profiling

Paired samples were obtained from the University of Maryland Brain and Tissue Bank as detailed in S1 Table. Individuals were diagnosed with ASD (n = 12) or were controls; criteria for diagnosing ASD included the Autism Diagnostic Interview-Revised (ADI-R), Childhood Autism Rating Scale (CARS), and Autism Diagnostic Observation Schedule (ADOS) as detailed S1 Table. DNA was extracted from tissue dissections according to protocols in the QIAGEN Genomic DNA Handbook. Exonic regions were selectively captured using Agilent SureSelectXT Human All Exon V5. Sequencing was performed at the Center for Inherited Disease Research at Johns Hopkins generating 100 bp sequence reads on an Illumina HiSeq. CIDRSeqSuite version 3.0.1 was used for processing of the raw data files. BCL files were converted to qseq format using Illumina’s BCL converter. qseq files were then demultiplexed and converted to FASTQ files using a custom demultiplexer. Paired-end alignment was performed using BWA aln to the 1000 genomes hg19/GRCh37 reference genome [34 (link)]. SAM files were sorted, converted to BAM, and duplicates were marked with Picard. GATK was used for local realignment and base quality score recalibration [35 (link),36 (link)]. Quality metrics for these data are provided in S2 Table.