Whole exome sequencing of MPA/DMBA-induced mouse mammary tumors

Mammary tumors were induced in FVNB/NJ mice using medroxyprogesterone acetate (MPA) and 7,12-dimethylbenzanthracene (DMBA) according to established protocol [1]. 18 mammary tumors were harvested from 14 mice, with matched normal. DNA isolation and whole exome sequencing was carried out at Theragen Etex Bio Institute (Seoul, South-Korea). DNA was isolated using QIAamp DNA Mini Kit (Qiagen #51306) per manufacturer's protocol. DNA from two samples (S159_14_11 and S176_14_11) was isolated using CTAB Extraction Solution (Biosesang #C2007) per manufacturer's protocol. DNA integrity was assessed by electrophoresis and concentration was determined using Nanodrop spectrophotometry and Qubit. Library preparation and target enrichment was carried out using the SureSelect XT Mouse All Exon Kit (Agilent #5190-4641) per manufacturer's instructions. Sequencing was performed on an Illumina HiSeq 2500 (Illumina #SY–401–2501). DNA was sequenced to a mean depth of 58. Quality control was performed with FastQC [2]. Adapter sequences were removed using CutAdapt, version 1.10 [3]. Low quality reads were trimmed using Sickle version 1.33 [4], in paired end mode with quality threshold set to 20 and length threshold set to 50 bp. Reads were aligned to the mm10 reference genome using the Burrows-Wheeler MEM aligner (BWA-MEM), version 0.7.12 [5]. [1] Aldaz CM, Liao QY, LaBate M, Johnston DA. Medroxyprogesterone acetate accelerates the development and increases the incidence of mouse mammary tumors induced by dimethylbenzanthracene. Carcinogenesis. 1996;17:2069–72. [2] Andrews S. FastQC: A quality control tool for high throughput sequence data. Ref Source. 2010. [3]. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBNet.journal. 2011;17 [4] Joshi NA FJN. Sickle: A sliding-window, adaptive, quality-based tool for FastQ files. 2011. https://github.com/najoshi/sickle. [5] Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:13033997. 2013.