Genomic library preparation
DNA extractions for supernatant, formalin-fixed and pellet samples were sent directly to Arbor Biosciences for library preparation, capture, and sequencing. Samples arrived at Arbor Biosciences fully dried and were resuspended in 50 μl of Buffer EBT. Fragment distributions of a subset of the gDNA samples were checked via Bioanalyzer (Agilent, Santa Clara, CA). Samples were quantified via an intercalating dye assay, and gDNA samples were sonicated and size-selected to a fragment length < 300 bp. Up to 200 ng of sonicated gDNA, where available, was taken into Illumina TruSeq-style library preparation. Samples received 5–7 cycles of indexing amplification to add unique dual-indexes. Capture pools of five samples were prepared with 150 ng of gDNA libraries. Captures were performed at 62°C (to account for potential divergence of hDNA samples from bait sequence) overnight according to the myBaits v4 manual. After clean-up, capture pools were amplified for 12 cycles followed by a second round of capture with 3x the recommended amount of Block C (human cot-1; following McCartnery-Melstad et al. 2016) with the rest of the parameters remaining the same. The final post-capture material was amplified for 10 cycles and sequenced on a partial lane of a NovaSeq 6000 S4 PE150 run, resulting in 113.6 million PE reads (~3.8 million reads per library).