Targeted-capture sequencing was performed using a Roche NimbleGen custom 385K capture array. Paired-end sequencing libraries were generated after capture and sequenced on an Illumina sequencer. Whole-exome sequencing libraries were prepared using the Sure-Select Human All Exon v2 kit (Agilent) and sequenced on an Illumina sequencer. Whole-genome sequencing was performed by Complete Genomics. Targeted-capture and whole-exome data were analyzed using GATK (Van der Auwera et al. 2013 (link)). Whole-genome sequencing data were analyzed using Complete Genomics software. Variants were annotated with ANNOVAR (Wang et al. 2010 (link)) and filtered if their allele frequency was ≥1% in any of the following public variant databases: ExAC (Lek et al. 2016 (link)), 1000 Genomes Project (The 1000 Genomes Project Consortium 2015 (link)), NHLBI Exome Sequencing Project (Tennessen et al. 2012 (link)), and Complete Genomics 69 control genomes (Drmanac et al. 2010 (link)). See Supplemental Methods for further details.
Other organizations :
Broad Institute, Harvard University, Howard Hughes Medical Institute, Boston Children's Hospital, Brigham and Women's Hospital, University College London, Wellcome Sanger Institute, German Cancer Research Center, Heidelberg University, University of Saskatchewan, Royal University Hospital, University of California, San Francisco, Massachusetts General Hospital, Saskatchewan Health
Targeted-capture sequencing using a Roche NimbleGen custom 385K capture array
Whole-exome sequencing using the SureSelect Human All Exon v2 kit (Agilent)
Whole-genome sequencing by Complete Genomics
dependent variables
Variants identified and annotated
control variables
Paired-end sequencing libraries generated after capture and sequenced on an Illumina sequencer
Whole-exome sequencing libraries sequenced on an Illumina sequencer
Whole-genome sequencing data analyzed using Complete Genomics software
Variants filtered if their allele frequency was ≥1% in any of the following public variant databases: ExAC, 1000 Genomes Project, NHLBI Exome Sequencing Project, and Complete Genomics 69 control genomes
positive controls
Not explicitly mentioned
negative controls
Not explicitly mentioned
Annotations
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