African American populations are underrepresented in genetic studies, especially those performed on a genome-wide scale. Several studies have indicated an ancestry difference in outcome among patients with various cancer types 
. We investigated the genetics of chemotherapeutic susceptibility in 83 LCLs derived from the HapMap ASW population. Using local ancestry covariates 
to account for population structure in the ASW, we tested over 2 million SNPs and identified 325 that were associated with cytarabine AUC, 176 with 5′-DFUR AUC, 240 with carboplatin IC50
, and 190 with cisplatin IC50
). Using a gene-based GWA approach, we identified several suggestive candidate genes: 26 genes for cytarabine, 11 genes for 5′-DFUR, 20 genes for carboplatin and 41 genes for cisplatin susceptibility (p≤10−3
). Fourteen of these genes showed evidence of replication in the YRI (p<0.05).
One important reason for studying populations of African descent is that common alleles present in African populations may be rare or absent in other populations. For example, the minor allele of the highlighted SNP rs9828664, which has a frequency of 0.29 and associated with increased carboplatin sensitivity in ASW (), is not present in the HapMap population of European ancestry from Utah (CEU). Of the 919 unique SNPs suggestively associated with one or more chemotherapeutic-induced phenotypes in ASW (p≤10−4), 237 (25.8%) of them have a minor allele frequency less than 0.05 in the CEU. The minor allele frequency in the CEU is zero for 116 (12.6%) of the ASW-associated SNPs. All of these potential associations would have been missed if only European populations were studied.
As might be expected based on the observation that carboplatin and cisplatin phenotypes were correlated, we observed an enrichment of carboplatin-associated SNPs in the results of cisplatin-associated SNPs. Both carboplatin and cisplatin are platinating agents that act through the formation of intrastrand and interstrand cross-links on DNA, which result in DNA strand breaks leading to cell death 
. The two agents are often used interchangeably, especially in the treatment of ovarian and lung cancers 
. These results support that common genetic mechanisms may influence the effects of both drugs. In contrast, a smaller shift in mean p-value was found when comparing the overall p-value distribution to the cisplatin-SNP p-value distribution for unrelated drugs cytarabine and 5′-DFUR even though both phenotypes are also correlated with cisplatin, albeit to a lesser degree (). Studies in larger cohorts are needed to define common genetic mechanisms within and among chemotherapeutic classes.
The VEGAS gene-based method revealed two linked genes associated with both carboplatin- and cisplatin-induced cytotoxicity in ASW and YRI. One of these genes, COPS5
, is also know as JAB1
(Jun activation domain-binding protein 1) and encodes a protein involved in multiple signaling pathways 
. Overexpression of COPS5
has been implicated in the pathogenesis of several types of cancer in humans and in some cases has correlated with poor prognosis 
. In one study, loss of COPS5
expression sensitized both mouse primary embryonic fibroblasts and osteosarcoma cells to radiation-induced apoptosis 
is linked to three other genes on chromosome 8 that also associated with cisplatin IC50
in the gene-based analysis (). The p-values of two of these three genes for association with carboplatin IC50
were just above our suggestive threshold of p≤10−3
. Although COPS5
is the only gene of these four known to be involved in tumorigenesis, the possibility that the others are involved in susceptibility to platinating agents cannot be ruled out due to the strong linkage disequilibrium in the region.
Two of the genes that associated with chemotherapeutic-induced cytotocity in the gene-based analysis in both populations are candidate tumor suppressors. TP53I11
associated with cytarabine AUC and overexpression of the gene promotes apoptosis in hepatocellular carcinoma cells 
, which associated with cisplatin IC50
, is sometimes deleted in breast and prostate cancer 
. Further studies are needed to elucidate how the function of all fourteen of the genes identified in our gene-based genome-wide analysis may affect tumor cell response to their associated chemotherapeutic agents.
Our approach to correct for population structure in the admixed ASW population differs from that taken in other African American GWA studies 
. Rather than using principal components to infer global ancestry, we used HAPMIX to infer local ancestry at each SNP locus and included this value as a covariate in the association test 
. Similar local ancestry approaches were taken in candidate gene studies using Ancestry Informative Markers 
. Using local ancestry rather than global ancestry for African Americans more accurately reflects the structure of the population at each SNP locus and is thus useful for the single-marker tests of GWA studies. Recently, it was shown that combining local ancestry and admixture association signals into a test statistic had more power to map disease loci than case-control studies correcting for global ancestry only in African American populations 
. HAPMIX is one of several methods for detecting chromosomal segments of distinct ancestry 
and determining the best way to apply local ancestry in genetic association tests in admixed populations remains an open question.
Currently, GWA studies in populations of African descent are limited by SNP genotyping arrays, which were designed to capture genetic variation in European populations where LD blocks are larger 
. Thus, SNP tagging does not work as well in populations of African ancestry compared to non-African populations. It is also more difficult to impute genotypes for African American samples than more genetically homogeneous populations, although using a pooled reference panel as was done here with YRI and CEU has been shown to boost performance 
. Furthermore, because the LD patterns among variants are less consistent between African subgroups, it can be more difficult to replicate associations once they have been detected, unless the causal variant has been identified 
. Therefore, we took a gene-based approach to attempt to replicate our initial ASW findings in the YRI. We found evidence of replication for 14 of the 98 genes identified in the ASW using the gene-based GWA approach, but larger sample sizes are need to confirm these associations.
Whole genome sequencing will shift association studies from LD-tagged variation to directly genotyped variation, which will benefit populations with African ancestry. The ASW population is in the pipeline to be sequenced by the 1000 Genomes Project 
. In our gene-based analysis, we only considered SNPs within a gene region, but trans
eQTLs are also known to affect gene activity 
. In future analyses, we plan to extend the VEGAS method to incorporate additional SNPs discovered by the 1000 Genomes Project and SNPs associated with gene expression in relevant tissues into the gene-based test. Our results highlight the importance of studying populations of African descent and we eventually hope to clinically validate both genes and variants in a cohort of African American patients treated with one or more of the chemotherapeutic agents studied to determine their roles in patient response and toxicity.