Three transcripts cis-regulated by CNVs identified by whole genome sequencing data predict cellular sensitivity to functionally diverse chemotherapeutics. Through ENCODE/Gencode annotation, 376 genes were recently identified  to be cis-regulated by CNV deletions. At P < 0.05, we found 21 gene expression correlations with carboplatin, 15 with cisplatin, 23 with daunorubicin, and 21 with etoposide. Three transcripts (MOXD1 on chromosome 6, RCC1 on chromosome 1, SULF2I on chromosome 20) were significant after multiple testing adjustment (padj < 0.05) and were the only CNV deletions associated with all four agents at the nominal P < 0.05 threshold. The plots show level of expression (x axis) and IC50 (y axis).
Gamazon et al. Genome Biology 2011 12:R46 doi:10.1186/gb-2011-12-5-r46