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Results: 4

1.
Figure 4

Figure 4. From: Copy number polymorphisms and anticancer pharmacogenomics.

The relationship between CCND1 expression and etoposide IC50 in the discovery set and in an independent replication set of 52 CEPH LCLs. (a) Discovery set; (b) independent replication set of 52 CEPH LCLs. Panel (b) describes the expression- IC50 relationship using real-time expression; the relationship is consistent with that in the discovery set of CEU samples.

Eric R Gamazon, et al. Genome Biol. 2011;12(5):R46-R46.
2.
Figure 2

Figure 2. From: Copy number polymorphisms and anticancer pharmacogenomics.

A schematic of the approach to the discovery of drug susceptibility-associated CNVs. We added to PACdb the CNV associations with cellular sensitivity to the chemotherapeutic agents. Note that some drug-associated CNVs (dCNVs) are poorly interrogated by SNPs and are thus independent of drug-associated SNPs (dSNPs). SCAN includes the results of eQTL mapping of CNVs to transcriptional expression.

Eric R Gamazon, et al. Genome Biol. 2011;12(5):R46-R46.
3.
Figure 3

Figure 3. From: Copy number polymorphisms and anticancer pharmacogenomics.

A CNV associated with cellular sensitivity to both carboplatin and cisplatin. We identified an amplification CNV, CNVR7826_full on chromosome 20, that is associated with both carboplatin sensitivity (a) (P = 0.0056) and cisplatin sensitivity (b) (P = 0.0023). The x-axis is the copy number (3 or 4) for the CNV; the y-axis is the log2-transformed IC50.

Eric R Gamazon, et al. Genome Biol. 2011;12(5):R46-R46.
4.
Figure 1

Figure 1. From: Copy number polymorphisms and anticancer pharmacogenomics.

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 [12] 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).

Eric R Gamazon, et al. Genome Biol. 2011;12(5):R46-R46.

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