Author Manuscript Published OnlineFirst on November 12, 2013; DOI: 10.1158/1055-9965.EPI-13-0818 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
A genome-wide association study of renal cell carcinoma among African Americans Mark P. Purdue, Yuanqing Ye, Zhaoming Wang, et al. Cancer Epidemiol Biomarkers Prev Published OnlineFirst November 12, 2013.
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A genome-wide association study of renal cell carcinoma among African Americans Running title: RCC GWAS among African Americans
Mark P. Purdue1*, Yuanqing Ye2*, Zhaoming Wang1*, Joanne S. Colt1, Kendra L. Schwartz3, Faith G. Davis4, Nathaniel Rothman1, Wong-Ho Chow2, Xifeng Wu2†, Stephen J. Chanock1†
1
Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD;
2
Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The
University of Texas M.D. Anderson Cancer Center, Houston, TX; 3Department of Family Medicine and Public Health Sciences and Barbara Ann Karmanos Institute, Wayne State University School of Medicine, Detroit, MI; 4Department of Public Health Sciences, University of Alberta, Edmonton, Alberta, Canada
*
Co-first authors; †Co-last authors
Funding: This research was supported by the Intramural Research Program of the NCI (NCI study) and NCI grant CA098897 and MD Anderson Research Trust (X.W.; MDACC study).
Address correspondence to: Mark Purdue, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Room 6E604, Rockville, MD 208509701; Tel (240) 276-7276; FAX (240) 276-7835; e-mail [email protected].
The authors have no potential conflicts of interest to disclose.
1
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Author Manuscript Published OnlineFirst on November 12, 2013; DOI: 10.1158/1055-9965.EPI-13-0818 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
ABSTRACT Genome-wide association studies (GWAS) of renal cell carcinoma (RCC) in populations of European ancestry have identified four susceptibility loci. No GWAS has been conducted among African Americans (AAs), who experience a higher incidence of RCC. We conducted a GWAS in which we analyzed 1,136,723 common single-nucleotide polymorphisms (SNPs) among 255 cases and 375 controls of African ancestry, and further investigated 16 SNPs in a replication set (140 cases, 543 controls). The 12p11.23 variant rs10771279, located 77kb from the European-ancestry RCC marker rs718314, was associated with RCC risk in the GWAS (P=1.2 x 10-7) but did not replicate (P=0.99). Consistent with European-ancestry findings, the A allele of rs7105934 on 11q13.3 was associated with decreased risk [odds ratio (OR)=0.76, 95% confidence interval (CI)=0.64-0.91; P=0.0022]. The frequency of this allele was higher than that observed in the European-ancestry GWAS (0.56 and 0.07 respectively among controls). The rs7105934 association was stronger for clear cell RCC (ccRCC: OR=0.56; P=7.4 x 10-7) and absent for cases of other or unknown histology (OR=1.02; P=0.86). Analyses of rs7105934 by subtype among European-ancestry participants from these studies yielded similar findings (ORs 0.69 and 0.92 respectively). This study provides, to our knowledge, the first evidence that rs7105934 is an RCC susceptibility locus among AAs. Our finding that the association with this SNP may be specific to ccRCC is novel and requires additional investigation. Additional investigation of rs10771279 and other suggestive GWAS findings is also needed.
2
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Author Manuscript Published OnlineFirst on November 12, 2013; DOI: 10.1158/1055-9965.EPI-13-0818 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
INTRODUCTION Renal cell carcinoma (RCC) is the deadliest type of urologic malignancy, with a five-year survival rate of approximately 65% (1). In the United States, the overall incidence rate of RCC is higher among African Americans than those of European descent (2), although African Americans have a lower incidence of clear cell RCC (ccRCC), the most common histologic subtype of this malignancy (3). There is a clear genetic component to RCC, with an approximate two-fold increased relative risk among individuals of European or African American descent reporting a first-degree relative with kidney cancer (4). In particular, dysregulation of the hypoxia-inducible factor (HIF) / von Hippel-Lindau (VHL) hypoxia-response pathway is a hallmark of ccRCC; very high rates of familial ccRCC are observed among patients with inherited mutations within the VHL tumor suppressor gene, and the majority of sporadic ccRCC cases exhibit VHL inactivation and constitutively high expression of HIF transcription factors (5).
Recent genome-wide association studies (GWAS) conducted among study populations of European ancestry have identified four susceptibility loci for RCC (6-8). The variant rs7579899 maps to EPAS1 on 2p21, which encodes HIF-2α, a critical factor in HIF/VHL-mediated development of ccRCC (5). The variants rs7105934, on 11q13.3, and rs12105918, mapping to ZEB2 on 2q22.3, are also suspected to influence RCC risk in a HIF-dependent manner (6, 8, 9). The biologic basis for the association with rs718314 (mapping to ITPR2 on 12p11.23) is unclear, although ITPR2 was associated with waist-to-hip ratio in an earlier GWAS (10); the latter is interesting because an elevated BMI is an established risk factor for RCC in all populations studied (2).
3
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Author Manuscript Published OnlineFirst on November 12, 2013; DOI: 10.1158/1055-9965.EPI-13-0818 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
To our knowledge, no GWAS of RCC among African Americans has been conducted to date, nor have the associations with established European-ancestry RCC loci been investigated in this racial group. Thus, we conducted a GWAS among African American participants in which we scanned one study and followed up promising loci in a second case-control study.
MATERIALS AND METHODS Study Populations Two case-control studies with comparatively large numbers of African American participants conducted by the National Cancer Institute (NCI) and the University of Texas MD Anderson Cancer Center (MDACC) were included in this investigation. The designs of these studies have been described (7, 11). Both studies were approved by Institutional Review Boards at all participating institutions, and written informed consent was obtained from all participants before interview and biospecimen collection.
Briefly, the NCI population-based case-control study of RCC was conducted between 2002 and 2007 in the metropolitan areas of Chicago (Cook County) and Detroit (Wayne, Macomb and Oakland Counties). The case series included residents between the ages of 20 and 79 years with histologically confirmed RCC. Control subjects aged 20 to 64 years were selected randomly from Department of Motor Vehicle (DMV) records in each state, and controls aged 65 to 79 years were selected from Medicare beneficiary records in the study area. Controls were frequency matched to the age-, race-, and gender-specific distributions of cases of RCC in each of the two study centers. Participating cases (843 European descent, 358 African American; 77%
4
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Author Manuscript Published OnlineFirst on November 12, 2013; DOI: 10.1158/1055-9965.EPI-13-0818 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
of contactable eligible individuals) and controls (707, 519; 54%) underwent interviews to collect information on lifestyle, medical and occupational risk factors. Copies of medical records were obtained from all cases to confirm diagnosis and collect information on histological and clinical factors. In addition, the original diagnostic slides were obtained for 706 cases (487 European descent, 219 African American) for central review by a single experienced pathologist. Germline DNA was extracted from blood (90%) or buccal cell (10%) specimens from 1,087 cases (774 European descent, 313 African American) and 1,091 controls (643, 448) using a phenol-chloroform protocol. We included 267 cases and 384 controls of African American race with genomic DNA in this investigation.
The MDACC study included newly diagnosed, histopathologically confirmed RCC patients recruited at the University of Texas MD Anderson Cancer Center from 2002 onward. Controls with no prior history of cancer (except non-melanoma skin cancer) were recruited through random digit dialing (RDD). The controls were frequency matched to the cases by age (±5 years), gender, ethnicity and county of residence. The overall response rate for RDD screening was 51% and, among those who agreed to participate, the response rate was 88%. The response rate for the eligible cases was 87%. RCC histology was ascertained through medical chart review. Genomic DNA was extracted from whole blood for all the samples by use of QIAamp DNA Mini kits (Qiagen, Valencia, CA).We included 140 cases and 543 controls of African American race with available genomic DNA in this investigation.
5
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Author Manuscript Published OnlineFirst on November 12, 2013; DOI: 10.1158/1055-9965.EPI-13-0818 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
Genotyping A total of 672 NCI study samples were genotyped using the Illumina 1M Duo BeadChip at the NCI Cancer Genomics Research Laboratory. Samples were excluded based on completion rates lower than 94% (n = 7 samples), abnormal heterozygosity values of 35% (n = 1), gender discordance (n = 2), and missing phenotype data (n=6). Genotypes for 20 pairs of duplicates were merged into unique individual level, and the overall concordance rate for this merging was greater than 99.9%. Using a set of 12,898 unlinked SNPs (12), 6 individuals with less than 20% African ancestry were excluded based on STRUCTURE analysis (13) and principal components analysis (PCA) (14). SNPs were excluded based on completion rates lower than 90% (N=62,464). After these exclusions, we had genotype data for 1,136,723 SNPs from 255 cases and 375 controls. Sixteen SNPs, listed in Table 1, were genotyped in the MDACC study using Taqman assays. These include 11 variants with NCI study associations approaching genome-wide significance (5 x 10-8), four variants with NCI study associations at P
A genome-wide association study of renal cell carcinoma among African Americans Mark P. Purdue, Yuanqing Ye, Zhaoming Wang, et al. Cancer Epidemiol Biomarkers Prev Published OnlineFirst November 12, 2013.
Updated version Supplementary Material Author Manuscript
E-mail alerts Reprints and Subscriptions Permissions
Access the most recent version of this article at: doi:10.1158/1055-9965.EPI-13-0818 Access the most recent supplemental material at: http://cebp.aacrjournals.org/content/suppl/2013/11/12/1055-9965.EPI-13-0818.DC1.html Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
Sign up to receive free email-alerts related to this article or journal. To order reprints of this article or to subscribe to the journal, contact the AACR Publications Department at [email protected]. To request permission to re-use all or part of this article, contact the AACR Publications Department at [email protected].
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Author Manuscript Published OnlineFirst on November 12, 2013; DOI: 10.1158/1055-9965.EPI-13-0818 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
A genome-wide association study of renal cell carcinoma among African Americans Running title: RCC GWAS among African Americans
Mark P. Purdue1*, Yuanqing Ye2*, Zhaoming Wang1*, Joanne S. Colt1, Kendra L. Schwartz3, Faith G. Davis4, Nathaniel Rothman1, Wong-Ho Chow2, Xifeng Wu2†, Stephen J. Chanock1†
1
Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD;
2
Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The
University of Texas M.D. Anderson Cancer Center, Houston, TX; 3Department of Family Medicine and Public Health Sciences and Barbara Ann Karmanos Institute, Wayne State University School of Medicine, Detroit, MI; 4Department of Public Health Sciences, University of Alberta, Edmonton, Alberta, Canada
*
Co-first authors; †Co-last authors
Funding: This research was supported by the Intramural Research Program of the NCI (NCI study) and NCI grant CA098897 and MD Anderson Research Trust (X.W.; MDACC study).
Address correspondence to: Mark Purdue, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Room 6E604, Rockville, MD 208509701; Tel (240) 276-7276; FAX (240) 276-7835; e-mail [email protected].
The authors have no potential conflicts of interest to disclose.
1
Downloaded from cebp.aacrjournals.org on November 16, 2013. © 2013 American Association for Cancer Research.
Author Manuscript Published OnlineFirst on November 12, 2013; DOI: 10.1158/1055-9965.EPI-13-0818 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
ABSTRACT Genome-wide association studies (GWAS) of renal cell carcinoma (RCC) in populations of European ancestry have identified four susceptibility loci. No GWAS has been conducted among African Americans (AAs), who experience a higher incidence of RCC. We conducted a GWAS in which we analyzed 1,136,723 common single-nucleotide polymorphisms (SNPs) among 255 cases and 375 controls of African ancestry, and further investigated 16 SNPs in a replication set (140 cases, 543 controls). The 12p11.23 variant rs10771279, located 77kb from the European-ancestry RCC marker rs718314, was associated with RCC risk in the GWAS (P=1.2 x 10-7) but did not replicate (P=0.99). Consistent with European-ancestry findings, the A allele of rs7105934 on 11q13.3 was associated with decreased risk [odds ratio (OR)=0.76, 95% confidence interval (CI)=0.64-0.91; P=0.0022]. The frequency of this allele was higher than that observed in the European-ancestry GWAS (0.56 and 0.07 respectively among controls). The rs7105934 association was stronger for clear cell RCC (ccRCC: OR=0.56; P=7.4 x 10-7) and absent for cases of other or unknown histology (OR=1.02; P=0.86). Analyses of rs7105934 by subtype among European-ancestry participants from these studies yielded similar findings (ORs 0.69 and 0.92 respectively). This study provides, to our knowledge, the first evidence that rs7105934 is an RCC susceptibility locus among AAs. Our finding that the association with this SNP may be specific to ccRCC is novel and requires additional investigation. Additional investigation of rs10771279 and other suggestive GWAS findings is also needed.
2
Downloaded from cebp.aacrjournals.org on November 16, 2013. © 2013 American Association for Cancer Research.
Author Manuscript Published OnlineFirst on November 12, 2013; DOI: 10.1158/1055-9965.EPI-13-0818 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
INTRODUCTION Renal cell carcinoma (RCC) is the deadliest type of urologic malignancy, with a five-year survival rate of approximately 65% (1). In the United States, the overall incidence rate of RCC is higher among African Americans than those of European descent (2), although African Americans have a lower incidence of clear cell RCC (ccRCC), the most common histologic subtype of this malignancy (3). There is a clear genetic component to RCC, with an approximate two-fold increased relative risk among individuals of European or African American descent reporting a first-degree relative with kidney cancer (4). In particular, dysregulation of the hypoxia-inducible factor (HIF) / von Hippel-Lindau (VHL) hypoxia-response pathway is a hallmark of ccRCC; very high rates of familial ccRCC are observed among patients with inherited mutations within the VHL tumor suppressor gene, and the majority of sporadic ccRCC cases exhibit VHL inactivation and constitutively high expression of HIF transcription factors (5).
Recent genome-wide association studies (GWAS) conducted among study populations of European ancestry have identified four susceptibility loci for RCC (6-8). The variant rs7579899 maps to EPAS1 on 2p21, which encodes HIF-2α, a critical factor in HIF/VHL-mediated development of ccRCC (5). The variants rs7105934, on 11q13.3, and rs12105918, mapping to ZEB2 on 2q22.3, are also suspected to influence RCC risk in a HIF-dependent manner (6, 8, 9). The biologic basis for the association with rs718314 (mapping to ITPR2 on 12p11.23) is unclear, although ITPR2 was associated with waist-to-hip ratio in an earlier GWAS (10); the latter is interesting because an elevated BMI is an established risk factor for RCC in all populations studied (2).
3
Downloaded from cebp.aacrjournals.org on November 16, 2013. © 2013 American Association for Cancer Research.
Author Manuscript Published OnlineFirst on November 12, 2013; DOI: 10.1158/1055-9965.EPI-13-0818 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
To our knowledge, no GWAS of RCC among African Americans has been conducted to date, nor have the associations with established European-ancestry RCC loci been investigated in this racial group. Thus, we conducted a GWAS among African American participants in which we scanned one study and followed up promising loci in a second case-control study.
MATERIALS AND METHODS Study Populations Two case-control studies with comparatively large numbers of African American participants conducted by the National Cancer Institute (NCI) and the University of Texas MD Anderson Cancer Center (MDACC) were included in this investigation. The designs of these studies have been described (7, 11). Both studies were approved by Institutional Review Boards at all participating institutions, and written informed consent was obtained from all participants before interview and biospecimen collection.
Briefly, the NCI population-based case-control study of RCC was conducted between 2002 and 2007 in the metropolitan areas of Chicago (Cook County) and Detroit (Wayne, Macomb and Oakland Counties). The case series included residents between the ages of 20 and 79 years with histologically confirmed RCC. Control subjects aged 20 to 64 years were selected randomly from Department of Motor Vehicle (DMV) records in each state, and controls aged 65 to 79 years were selected from Medicare beneficiary records in the study area. Controls were frequency matched to the age-, race-, and gender-specific distributions of cases of RCC in each of the two study centers. Participating cases (843 European descent, 358 African American; 77%
4
Downloaded from cebp.aacrjournals.org on November 16, 2013. © 2013 American Association for Cancer Research.
Author Manuscript Published OnlineFirst on November 12, 2013; DOI: 10.1158/1055-9965.EPI-13-0818 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
of contactable eligible individuals) and controls (707, 519; 54%) underwent interviews to collect information on lifestyle, medical and occupational risk factors. Copies of medical records were obtained from all cases to confirm diagnosis and collect information on histological and clinical factors. In addition, the original diagnostic slides were obtained for 706 cases (487 European descent, 219 African American) for central review by a single experienced pathologist. Germline DNA was extracted from blood (90%) or buccal cell (10%) specimens from 1,087 cases (774 European descent, 313 African American) and 1,091 controls (643, 448) using a phenol-chloroform protocol. We included 267 cases and 384 controls of African American race with genomic DNA in this investigation.
The MDACC study included newly diagnosed, histopathologically confirmed RCC patients recruited at the University of Texas MD Anderson Cancer Center from 2002 onward. Controls with no prior history of cancer (except non-melanoma skin cancer) were recruited through random digit dialing (RDD). The controls were frequency matched to the cases by age (±5 years), gender, ethnicity and county of residence. The overall response rate for RDD screening was 51% and, among those who agreed to participate, the response rate was 88%. The response rate for the eligible cases was 87%. RCC histology was ascertained through medical chart review. Genomic DNA was extracted from whole blood for all the samples by use of QIAamp DNA Mini kits (Qiagen, Valencia, CA).We included 140 cases and 543 controls of African American race with available genomic DNA in this investigation.
5
Downloaded from cebp.aacrjournals.org on November 16, 2013. © 2013 American Association for Cancer Research.
Author Manuscript Published OnlineFirst on November 12, 2013; DOI: 10.1158/1055-9965.EPI-13-0818 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
Genotyping A total of 672 NCI study samples were genotyped using the Illumina 1M Duo BeadChip at the NCI Cancer Genomics Research Laboratory. Samples were excluded based on completion rates lower than 94% (n = 7 samples), abnormal heterozygosity values of 35% (n = 1), gender discordance (n = 2), and missing phenotype data (n=6). Genotypes for 20 pairs of duplicates were merged into unique individual level, and the overall concordance rate for this merging was greater than 99.9%. Using a set of 12,898 unlinked SNPs (12), 6 individuals with less than 20% African ancestry were excluded based on STRUCTURE analysis (13) and principal components analysis (PCA) (14). SNPs were excluded based on completion rates lower than 90% (N=62,464). After these exclusions, we had genotype data for 1,136,723 SNPs from 255 cases and 375 controls. Sixteen SNPs, listed in Table 1, were genotyped in the MDACC study using Taqman assays. These include 11 variants with NCI study associations approaching genome-wide significance (5 x 10-8), four variants with NCI study associations at P
