Genomic DNA (1 μg) was fragmented by sonication. Illumina paired-end libraries from genomic DNA samples were constructed (Lupski et al., 2013 (link)). Pre-capture libraries were pooled and hybridized in solution to the BCM-HGSC CORE exome capture design (Bainbridge et al., 2011 (link)) (52Mb; NimbleGen). Captured DNA fragments were sequenced on an Illumina HiSeq 2000 platform, producing 9–10 gigabase-pairs (Gb) of sequence for each personal genome and achieving an average of 95% of the targeted exome bases covered to an average depth of 20x or greater, with mean coverage of target bases of over 100x. Raw sequence reads were mapped and aligned to the GRCh37 (hg19) human genome reference assembly using the HGSC Mercury analysis pipeline (http://www.tinyurl.com/HGSC-Mercury/ ) (Reid et al., 2014 (link)) or the Baylor Genetics analysis pipeline (Liu et al., 2019 (link)).
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Whole Exome Sequencing Approach
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Corresponding Organization : Neurological Research Institute
Other organizations : University of Colorado Denver, Wroclaw Medical University, Centre Hospitalier de Luxembourg, University of Arkansas for Medical Sciences, Vivantes Klinikum, Charité - Universitätsmedizin Berlin, Ghent University Hospital, University of Alabama at Birmingham, Children's Hospital of Philadelphia, Baylor Genetics, Génétique Médicale & Génomique Fonctionelle, Centre Hospitalier Universitaire de Nantes, Royal Brisbane and Women's Hospital, North York General Hospital, University of Toronto, Aalborg University, Baylor University Medical Center
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Variable analysis
independent variables
- Fragmentation of genomic DNA by sonication
- Coverage of the targeted exome bases (average depth of 20x or greater, with mean coverage of target bases of over 100x)
- Sequence reads mapped and aligned to the GRCh37 (hg19) human genome reference assembly
- Genomic DNA (1 μg) used as input
- Illumina paired-end libraries constructed from genomic DNA samples
- Pre-capture libraries pooled and hybridized in solution to the BCM-HGSC CORE exome capture design (52Mb; NimbleGen)
- Captured DNA fragments sequenced on an Illumina HiSeq 2000 platform
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