Whole Exome Sequencing of Autism Spectrum Disorder

Genomic DNA was extracted from whole blood or saliva using a Qiagen QIAamp DNA blood kit or tissue kit (Qiagen, Hilden, Germany). Raw WES data were generated and processed to BAM files at three sites (Table S1): The Broad Institute (ASD = 256, HC = 299) [11 (link)] using Illumina HiSeq sequencers and an Illumina Nextera exome capture kit; Yokohama City University (ASD = 51) [14 (link)] using Illumina HiSeq with Agilent Sure Select v5; and Nagoya University (ASD = 2) using Illumina HiSeq with Agilent Sure Select v5. Detailed descriptions of each sequencing method are presented elsewhere [11 (link), 14 (link), 19 (link)]. Each sample’s sequencing reads were aligned onto the human genome build 37 (GRCh37/hg19) and then aggregated into a BAM file. Genomic variant call format (gVCF) files were generated using Haplotype Caller, version 4.1, in the Genome Analysis Toolkit (GATK) [20 (link)]. SNVs and insertions/deletions (indels) were jointly called across all samples (ASD = 309, HC = 299) using the GenotypeGVCF function.

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Kimura H., Nakatochi M., Aleksic B., Guevara J., Toyama M., Hayashi Y., Kato H., Kushima I., Morikawa M., Ishizuka K., Okada T., Tsurusaki Y., Fujita A., Miyake N., Ogi T., Takata A., Matsumoto N., Buxbaum J., Ozaki N, & Sebat J. (2022). Exome sequencing analysis of Japanese autism spectrum disorder case-control sample supports an increased burden of synaptic function-related genes. Translational Psychiatry, 12, 265.

Publication 2022

QIAamp DNA blood kit or tissue kit HiSeq sequencers

Blood Exome Genome Haplotype Human genome Indels Saliva Tissue

Corresponding Organization :

Other organizations : Nagoya University, University of California, San Diego, Nagoya University Hospital, Nagoya Institute of Technology, National Institute of Mental Health, National Center of Neurology and Psychiatry, Yokohama City University

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Variable analysis

independent variables

Study site (The Broad Institute, Yokohama City University, Nagoya University)

dependent variables

Genomic variants (Single Nucleotide Variants, insertions/deletions)

control variables

Whole blood or saliva samples
Qiagen QIAamp DNA blood kit or tissue kit for DNA extraction
Alignment of sequencing reads to human genome build 37 (GRCh37/hg19)
Joint variant calling across all samples (ASD = 309, HC = 299) using Haplotype Caller in GATK

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