Genome-wide local ancestry approach identifies genes and variants associated with chemotherapeutic susceptibility in African Americans

Abstract

Chemotherapeutic agents are used in the treatment of many cancers, yet variable resistance and toxicities among individuals limit successful outcomes. Several studies have indicated outcome differences associated with ancestry among patients with various cancer types. Using both traditional SNP-based and newly developed gene-based genome-wide approaches, we investigated the genetics of chemotherapeutic susceptibility in lymphoblastoid cell lines derived from 83 African Americans, a population for which there is a disparity in the number of genome-wide studies performed. To account for population structure in this admixed population, we incorporated local ancestry information into our association model. We tested over 2 million SNPs and identified 325, 176, 240, and 190 SNPs that were suggestively associated with cytarabine-, 5'-deoxyfluorouridine (5'-DFUR)-, carboplatin-, and cisplatin-induced cytotoxicity, respectively (p≤10(-4)). Importantly, some of these variants are found only in populations of African descent. We also show that cisplatin-susceptibility SNPs are enriched for carboplatin-susceptibility SNPs. Using a gene-based genome-wide association approach, we identified 26, 11, 20, and 41 suggestive candidate genes for association with cytarabine-, 5'-DFUR-, carboplatin-, and cisplatin-induced cytotoxicity, respectively (p≤10(-3)). Fourteen of these genes showed evidence of association with their respective chemotherapeutic phenotypes in the Yoruba from Ibadan, Nigeria (p<0.05), including TP53I11, COPS5 and GAS8, which are known to be involved in tumorigenesis. Although our results require further study, we have identified variants and genes associated with chemotherapeutic susceptibility in African Americans by using an approach that incorporates local ancestry information.

Figure 1. Global ancestry and local ancestry estimates.

(A) The first two principal components (PCs), a measure of global ancestry, are plotted from the results of the genotype comparison of unrelated individuals in the four populations using EIGENSTRAT . Two ASW individuals (NA19701 and NA19704) have similar PCs. (B) Shown are the predicted numbers of European chromosome copies, a measure of local ancestry, from the HAPMIX analysis at each SNP locus for ASW individuals NA19701 and NA19704 at chromosome 1.

Figure 2. Genome-wide association results for chemotherapeutic-induced cytotoxicity in the ASW.

Each point represents a SNP. Blue lines are at the suggestive significance threshold of p = 10⁻⁴. Red lines are at the genome-wide significance threshold of p = 5×10⁻⁸.

Figure 3. Genomic regions associated with chemotherapeutic-induced cytotoxicity in the ASW population.

(A) rs1543175, which is 42 kb upstream of non-protein coding RNA 295 (NCRNA00295), associated with ASW 5′-DFUR AUC (p = 3.4×10⁻⁷) and is a trans eQTL in YRI (Table S1). (B) rs417245, which is 546 kb upstream of F-box only protein 33 (FBXO33), associated with ASW 5′-DFUR AUC (p = 9.6×10⁻⁷) and the expression of two genes in YRI (Table S1). (C) The SNP rs9828664 in the first intron of calcium channel, voltage-dependent, alpha 2/delta subunit 3 (CACNA2D3) associated with ASW carboplatin IC₅₀ (p = 2.5×10⁻⁶) and the expression of two genes in YRI (Table S1). Plots were made with LocusZoom and the color of each dot represents the SNP's linkage disequilibrium r² in the YRI with the labeled SNP (purple diamond).

Figure 4. Overall ASW GWAS p-value distributions compared to the p-value distributions of the top cisplatin-associated SNPs.

The p-values for the top 190 cisplatin IC₅₀-associated SNPs (p≤10⁻⁴) were pulled from the overall list of ∼2 million SNPs tested for association with each drug-induced phenotype (cytarabine AUC, 5′-DFUR AUC, carboplatin IC₅₀). The mean p-value in each class is listed across the top. The boxes define the interquartile range and the thick line is the median. Open dots are possible outliers. The means of the “All SNPs” classes differed from the means of the “Top cisplatin SNPs” classes for all three drugs (cytarabine p = 4.5×10⁻²⁴, 5′-DFUR p = 4.4×10⁻²⁴, carboplatin p = 2.2×10⁻¹⁹¹, Student's t-test).

Figure 5. Gene-based genome-wide association results for chemotherapeutic-induced cytotoxicity in the ASW.

Each point represents a gene. Blue lines are at the suggestive significance threshold of p = 10⁻³. Red lines are at the Bonferroni-adjusted genome-wide significance threshold of p = 2.8×10⁻⁶ for 17,723 tests.

Figure 6. Chromosome 8 cluster of linked genes associated with cisplatin IC₅₀ in ASW and YRI.

The four genes associated with cisplatin IC₅₀ were detected using a gene-based analysis . They are COPS5 (ASW p = 1.8×10⁻⁴, YRI p = 0.020), ARFGEF1 (ASW p = 8.6×10⁻⁵, YRI p = 0.017), CSPP1 (ASW p = 2.4×10⁻⁴, YRI p = 0.017), and LRRC67 (ASW p = 3.1×10⁻⁴, YRI p = 0.020). Plots were made with LocusZoom and the position of each dot corresponds to the SNP's p-value for association with carboplatin IC₅₀ in the ASW and the color of each dot represents the SNP's linkage disequilibrium r² in the YRI with the labeled SNP (purple diamond).