Whole-Genome and Whole-Exome Sequencing in the BRIDGES Cohort

Whole-genome sequencing (WGS) was performed in the BRIDGES cohort using the Illumina HiSeq 2500 system. Library preparation was performed using Nimblegen SeqCap EZ Exome (RareBLISS and KPNC) or Agilent SureSelect Human All Exon v2 kit (Sweden), and whole-exome sequencing (WES) was performed using Illumina HiSeq 2000 or 2500 systems in RareBLISS, Sweden, and KPNC. Paired sequence reads were aligned to the human reference build hg19 using BWA ³⁹. Variant calling was performed using the GotCloud sequence analysis pipeline ^{40 (link)} for WGS data in BRIDGES, and joint variant calling was performed using the Genome Analysis ToolKit (GATK) ^{41 (link)} for WES data within each of RareBLISS, Sweden, and KPNC. Genotypes with low sequence coverage or poor call quality were removed. Samples that were identified as population outliers, duplicates or relatives, or that failed study-specific sequencing metrics were removed. Variants with high missingness across samples, poor average genotyping quality, or found to significantly deviate from Hardy-Weinberg equilibrium were removed. A full description of sequencing and data quality control is provided in supplemental materials.

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Jia X., Goes F.S., Locke A.E., Palmer D., Wang W., Cohen-Woods S., Genovese G., Jackson A.U., Jiang C., Kvale M., Mullins N., Nguyen H., Pirooznia M., Rivera M., Ruderfer D.M., Shen L., Thai K., Zawistowski M., Zhuang Y., Abecasis G., Akil H., Bergen S., Burmeister M., Chapman S., DelaBastide M., Juréus A., Kang H.M., Kwok P.Y., Li J.Z., Levy S.E., Monson E.T., Moran J., Sobell J., Watson S., Willour V., Zöllner S., Adolfsson R., Blackwood D., Boehnke M., Breen G., Corvin A., Craddock N., DiFlorio A., Hultman C.M., Landen M., Lewis C., McCarroll S.A., Richard McCombie W., McGuffin P., McIntosh A., McQuillin A., Morris D., Myers R.M., O’Donovan M., Ophoff R., Boks M., Kahn R., Ouwehand W., Owen M., Pato C., Pato M., Posthuma D., Potash J.B., Reif A., Sklar P., Smoller J., Sullivan P.F., Vincent J., Walters J., Neale B., Purcell S., Risch N., Schaefer C., Stahl E.A., Zandi P.P, & Scott L.J. (2021). Investigating rare pathogenic/likely pathogenic exonic variation in bipolar disorder. Molecular Psychiatry, 26(9), 5239-5250.

Publication 2020

HiSeq 2500 system SeqCap EZ Exome SureSelect Human All Exon v2 kit HiSeq 2000 or 2500 systems

Exome Exon Genome Human Joint Library

Corresponding Organization :

Other organizations : University of California, San Francisco, Johns Hopkins University, Broad Institute, Icahn School of Medicine at Mount Sinai, Flinders University, University of Michigan–Ann Arbor, Kaiser Permanente, National Heart Lung and Blood Institute, King's College London, Medical Research Council, Vanderbilt University Medical Center, Karolinska Institutet, Cold Spring Harbor Laboratory, HudsonAlpha Institute for Biotechnology, University of Iowa, Massachusetts General Hospital, University of Southern California, Umeå University, University of Edinburgh, Trinity College Dublin, Cardiff University, Harvard University, University College London, University of California, Los Angeles, University Medical Center Utrecht, University of Cambridge, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, University Hospital Frankfurt, Goethe University Frankfurt, University of North Carolina at Chapel Hill, Centre for Addiction and Mental Health, Brigham and Women's Hospital, Circadian (United States)

Top 5 similar protocols

Variable analysis

independent variables

Whole-genome sequencing (WGS) using Illumina HiSeq 2500 system
Whole-exome sequencing (WES) using Illumina HiSeq 2000 or 2500 systems
Library preparation using Nimblegen SeqCap EZ Exome (RareBLISS and KPNC) or Agilent SureSelect Human All Exon v2 kit (Sweden)

dependent variables

Variants in the sequenced genomes and exomes

control variables

Alignment of paired sequence reads to the human reference build hg19 using BWA
Variant calling using the GotCloud sequence analysis pipeline for WGS data in BRIDGES, and the Genome Analysis ToolKit (GATK) for WES data within each of RareBLISS, Sweden, and KPNC
Removal of genotypes with low sequence coverage or poor call quality
Removal of samples that were identified as population outliers, duplicates or relatives, or that failed study-specific sequencing metrics
Removal of variants with high missingness across samples, poor average genotyping quality, or found to significantly deviate from Hardy-Weinberg equilibrium

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