Whole Exome Sequencing with Mitochondrial Genome Capture

DNA was extracted from peripheral blood using a commercially available kit (Promega Maxwell RSC DNA Extraction Kit). The WES library was generated using the Agilent SureSelect Human All Exon V6 plus a custom mitochondrial genome capture kit, designed in collaboration with Agilent for consistent coverage across the mitochondrial genome (Falk et al. 2012 (link)). Paired-end 2 × 100 bp sequencing was performed using the Illumina NextSeq 500 sequencing system. The overall exome sequencing workflow is illustrated in Figure 2, and the bioinformatics methodologies are detailed in the Supplemental Information. In brief, we used a combination of the bcbio pipeline (https://github.com/chapmanb/bcbio-nextgen), custom scripts and open-source bioinformatics tools to fully automate quality control (QC), sequence alignment, coverage analysis, variant calling, and initial filtering based on ExAC (Exome Aggregation Consortium, http://exac.broadinstitute.org/) allele frequencies. The coverage statistics are summarized in Supplemental Figure 1 and detailed in Supplemental Table 3. The variant statistics are detailed in Supplemental Information.