DNA extraction and whole-genome sequencing
DNA from saliva and FFPE samples was purified and extracted using Qiagen
Kit (Qiagen Systems) and Promega Kit, respectively. WGS libraries were
prepared for Illumina 150bp paired-end reads sequencing using the
NEBNext Ultra II DNA Library Prep Kit protocols. All libraries were
sequenced on the Novaseq 6000 platform (Illumina, San Diego, CA, USA)
using standard protocols. Whole-genome analysis was performed by the
Utah Center for Genomic Discovery (UCGD) at the University of Utah.
Germline SNVs and SVs for each sample (22 samples total) were detected
following a Genome Analysis Tool Kit (GATK) best practices equivalent
workflow for variant detection.18