Low-coverage whole genome sequencing of mouse cancer cell lines from the Mouse Cancer Cell line Atlas (MCCA).

The Mouse Cancer Cell line Atlas (MCCA) is a comprehensive resource of 590 murine cancer cell lines derived from 81 genetically engineered, inflammation-associated or irradiation-induced mouse models of malignancy, complemented by 38 widely used public cell lines. MCCA spans 22 cell lineages and 46 cancer entities and is designed to enable comparative, mechanistic and functional studies across diverse tissues and oncogenic contexts.
Low coverage whole genome sequencing (lcWGS) of 590 cell lines from MCCA was performed using 200 ng of gDNA from murine cell lines and matched normal samples from mouse tail biopsies when available. Libraries were prepared using the TruSeq DNA Nanokit (Illumina) following the manufacturer's instructions. Resulting libraries were analyzed on a 2100 Bioanalyzer instrument (Agilent Technologies) and sequenced on a NextSeq 550 (Illumina) or NovaSeq 6000 (Illumina) system. The analysis of low coverage whole genome sequencing data from mouse tumor/normal sample pairs was performed following the GATK best practice suggestions. The established MoCaSeq analysis pipeline (Lange et al. [Nat Protoc. 2020 Feb;15(2):266-315]) was used for processing all samples. Raw sequencing reads were trimmed using Trimmomatic (v0.39) (Bolger et al. [Bioinformatics. 2014 Aug 1;30(15):2114-20]), removing leading and trailing bases with Phred scores below 25 and reads with less than 50 nucleotides. In addition, an average base quality of 25 was enforced with a sliding window of 10 nucleotides for the reads. Passing reads were then aligned to the GRCm38.p6 reference genome using BWA-MEM (v0.7.17) (Li et al. [Bioinformatics. 2009 Jul 15;25(14):1754-60]) with default settings. The mapped reads were processed with samblaster (v0.1.26) (Faust et al. [Bioinformatics. 2014 Sep 1;30(17):2503-5]), sambamba (v0.7.0) (Tarasov et al. [Bioinformatics. 2015 Jun 15;31(12):2032-4]) and Picard tools (v2.20.0) [http://broadinstitute.github.io/picard]. Copy number calling was performed with CNVKit (Talevich et al. [PLoS Comput Biol. 2016 Apr 21;12(4):e1004873]) using the whole genome sequencing mode combined with the Agilent SureSelect XT Mouse All Exon Kit exon probe regions as on-target regions, following the CNVKit best practice suggestions.