Shallow Sequencing for Copy Number Analysis

The hybrid HSA3 and Neo3 cell lines were shallow sequenced to confirm copy number. Genomic DNA was prepared from cells and 500 ng DNA was fragmented using a Covaris sonicator. Genomic DNA libraries were prepared using Illumina TruSeq Nano DNA LT sample prep kit as per the manufacturer’s instructions and Illumina sequencing (50 bp, single-end reads) was performed on Illumina Hiseq 4000 (VUMC Cancer Centre, Amsterdam). FASTQ sequence files were obtained and reads were aligned to the human reference genome (hg19) using BWA and processed with Samtools v1.6^{85 (link)}. In R the BAM files were loaded into the Bioconductor package QDNAseq for copy number analysis. Human reference genome HG19 was used here as QDNAseq has pre-calculated bin annotations for genome build hg19. Sequence coverage was 0.23x coverage/base for HSA3 and 0.32x coverage/base for Neo3.