WXS of Mus musculus: Breast cancer PDX and PDX-derived cell line
WXS was performed by the Mayo Clinic Core facility using the Sure Select XT Whole Exon Capture v5 + UTRs 75 MB and the Illumina HiSeq 4000 Paired-End Sequencer. Paired-end libraries were prepared using 1.0 ug of genomic DNA following the manufacturers protocol (Agilent) using the Agilent Bravo liquid handler. Whole exon capture was carried out using 750 ng of the prepped library following the protocol for Agilents SureSelect Human All Exon v5 + UTRs 75 MB kit.  The purified capture products are then amplified using the SureSelect Post-Capture Indexing forward and Index PCR reverse primers (Agilent) for 12 cycles. The concentration and size distribution of the completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA). Libraries were sequenced at an average coverage of  about 250X following Illuminas standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cells were sequenced as 150 X 2 paired-end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kits and HCS v3.3.52 collection software. Base-calling was performed using Illuminas RTA version 2.7.3. (from Methods section of Zhuang et. al., npj Breast Cancer 2020)