Whole genome sequencing of canine osteosarcoma samples collected from COTC021/022 clinical trial
The Discovery cohort consisted of tumor and matched normal tissue samples from pet dogs enrolled in the COTC021/022 clinical trial (n = 55 tumor/normal paired samples). Samples were acquired at the time of standard-of-care amputation surgery. Tissue was placed in RNAlater and stored at -80 until processing. Normal tissue and tumor OS DNA samples that passed QA/QC (260/280 ratio > 1.8; >200 ng total DNA) were pooled and sequenced on NovaSeqStandard_S4 run using TruSeq Nano DNA library prep and paired-end sequencing mode. The samples were mapped, and variants were called using Dragen. Percent total mapping against reference canine genome (CanFam4, GSD_1.0) is about 99% and uniquely mapped reads are above 70%. Library complexity (i.e. percentage of non-duplicate reads) was determined by measuring the percentage of unique fragments in the mapped reads using MarkDuplicate utility. Coverage statistics were also measured using Dragen.