Whole Genome Sequencing of Mouse Tumors

Raw whole genome sequencing data from mouse tumors was previously obtained^{28 (link)}. Briefly, three samples from each group (total of 12) were used, DNA from flash frozen extracted following manufacture’s protocol for Qiagen Genomic-tip 20/G kit. Sequencing was completed at a depth of 40 × with paired end, 150 base pair reads. DNA was prepared and sequenced using Illumina TruSeq Nano DNA library preparation and an Illumina HiSeq 2500. For this study, raw fastq files were assessed for quality control using FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using Trimmomatic^{41 (link)}. Files were aligned to mm10 mouse reference using BWA MEM⁴² with standard parameters. Picard tools (“Picard Toolkit.” 2019) was used to add read groups and remove duplicates. Samtools^{43 (link)} was used to sort and index files.