Genomic sequencing

DNA sequencing was performed by core facilities at Cornell University and BCM. At Cornell Exome Sequencing Libraries were prepared using the Agilent SureSelect XT v6.0 Human kit. Sequencing was performed on an Illumina HiSeq 4000 machine (PE, 2 × 100 cycles, ∼133X estimated coverage per sample). At BCM, sequencing was performed on Illumina NovaSeq machine (PE, 2 × 100, ∼200M read pairs per sample). Separation of human and mouse reads, alignment to the reference genome, variant calling, and annotation were performed using the PDXNet ¹⁰⁵Tumor-Only Variant Calling pipeline developed by the Jackson Laboratory and hosted on the Cancer Genomics Cloud.