Infinium coreexome 24 array

Peripheral blood mononuclear cells were obtained from AllCells (USA). Genomic DNA was purified using the AllPrep kit (Qiagen, USA) and genotyped using the Infinium CoreExome 24 array (Illumina, USA) according to the manufacturer’s instructions.

Genomic DNA was prepared from 5 × 10⁵ cells with the DNeasy Blood and Tissue Kit (Qiagen) and submitted to the IGM Genomics Core at UCSD. CNA was determined by hybridizing 200 ng of DNA per sample onto an Infinium CoreExome-24 Array (Illumina) and analyzing with Nexus CN software (version 7.5). The log2 ratio of signal intensity were calculated for each SNP on the array and copy number segments identified using the Bioconductor copynumber package^{39 (link)}, including winsorization to remove outliers, imputation of missing value, and multi-sample copy number segmentation using multipcf. The differences in log2 ratio of all larger segments (more than 10 kb) were compared between control and KO BT549 cells.