Whole exome sequencing of primary colorectal cancers, brain metastases and associated brain metastasis stem cells cultures
DNA was extracted from paraffin-embedded tissue (CRC or BM of patients) with a tumor cellularity greater than 30%. Six  10 m formalin-fixed paraffin-embedded sections were subject to a deparaffinization protocol using Tween 20 detergent before DNA extraction with the Maxwell 16 FFPE Tissue LEV Purification kit. DNA was quantified by Quantus Fluorometer (Promega, Madison, WI). Genomic DNA from cell lines was extracted using the Maxwell 16 LEV DNA Purification kit (Promega). Library preparation was performed by using the SureSelectXTHS Enzymatic Fragmentation Kit and SureSelectXTHS Human All Exon V7 Target Enrichment System (Agilent, Santa Clara, CA), according to the manufacturers instructions. Library sequencing was performed by using a NextSeq 550 system (Illumina, San Diego, CA) high output run using v2 chemistry. Paired-end reads of 150 base pair lengths were generated in accordance with the supplied protocol. Samples were sequenced to median average depth of 150.