Shared and independent colorectal cancer risk alleles in TGFß-related genes in African and European Americans

Sonia S. Kupfer, Andrew D. Skol, Ellie Hong, Anton Ludvik, Rick A Kittles, Temitope O. Keku, Robert S. Sandler, Nathan Ellis

Research output: Contribution to journalArticle

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Abstract

Genome-wide association studies (GWAS) in colorectal cancer (CRC) identified five regions near transforming growth factor ß-related genes BMP4, GREM1, CDH1, SMAD7 and RPHN2. The true risk alleles remain to be identified in these regions, and their role in CRC risk in non-European populations has been understudied. Our previous work noted significant genetic heterogeneity between African Americans (AAs) and European Americans (EAs) for single nucleotide polymorphisms (SNPs) identified in GWAS. We hypothesized that associations may not have been replicated in AAs due to differential or independent genetic structures. In order to test this hypothesis, we genotyped 195 tagging SNPs across these five gene regions in 1194 CRC cases (795 AAs and 399 EAs) and 1352 controls (985 AAs and 367 EAs). Imputation was performed, and association testing of genotyped and imputed SNPs included ancestry, age and sex as covariates. In two of the five genes originally associated with CRC, we found evidence for association in AAs including rs1862748 in CDH1 (ORAdd = 0.82, P = 0.02) and in GREM1 the SNPs rs10318 (ORRec = 60.1, P = 0.01), rs11632715 (ORRec = 2.36; P = 0.004) and rs12902616 (ORRec = 1.28, P = 0.005), the latter which is in linkage disequilibrium with the previously identified SNP rs4779584. Testing more broadly for associations in these gene regions in AAs, we noted three statistically significant association peaks in GREM1 and RHPN2 that were not identified in EAs. We conclude that some CRC risk alleles are shared between EAs and AAs and others are population specific.

Original languageEnglish (US)
Article numberbgu088
Pages (from-to)2025-2030
Number of pages6
JournalCarcinogenesis
Volume35
Issue number9
DOIs
StatePublished - 2014

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African Americans
Colorectal Neoplasms
Alleles
Single Nucleotide Polymorphism
Genes
Genome-Wide Association Study
Genetic Heterogeneity
Genetic Structures
Linkage Disequilibrium
Transforming Growth Factors
Population

ASJC Scopus subject areas

  • Cancer Research

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Shared and independent colorectal cancer risk alleles in TGFß-related genes in African and European Americans. / Kupfer, Sonia S.; Skol, Andrew D.; Hong, Ellie; Ludvik, Anton; Kittles, Rick A; Keku, Temitope O.; Sandler, Robert S.; Ellis, Nathan.

In: Carcinogenesis, Vol. 35, No. 9, bgu088, 2014, p. 2025-2030.

Research output: Contribution to journalArticle

Kupfer, Sonia S. ; Skol, Andrew D. ; Hong, Ellie ; Ludvik, Anton ; Kittles, Rick A ; Keku, Temitope O. ; Sandler, Robert S. ; Ellis, Nathan. / Shared and independent colorectal cancer risk alleles in TGFß-related genes in African and European Americans. In: Carcinogenesis. 2014 ; Vol. 35, No. 9. pp. 2025-2030.
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abstract = "Genome-wide association studies (GWAS) in colorectal cancer (CRC) identified five regions near transforming growth factor {\ss}-related genes BMP4, GREM1, CDH1, SMAD7 and RPHN2. The true risk alleles remain to be identified in these regions, and their role in CRC risk in non-European populations has been understudied. Our previous work noted significant genetic heterogeneity between African Americans (AAs) and European Americans (EAs) for single nucleotide polymorphisms (SNPs) identified in GWAS. We hypothesized that associations may not have been replicated in AAs due to differential or independent genetic structures. In order to test this hypothesis, we genotyped 195 tagging SNPs across these five gene regions in 1194 CRC cases (795 AAs and 399 EAs) and 1352 controls (985 AAs and 367 EAs). Imputation was performed, and association testing of genotyped and imputed SNPs included ancestry, age and sex as covariates. In two of the five genes originally associated with CRC, we found evidence for association in AAs including rs1862748 in CDH1 (ORAdd = 0.82, P = 0.02) and in GREM1 the SNPs rs10318 (ORRec = 60.1, P = 0.01), rs11632715 (ORRec = 2.36; P = 0.004) and rs12902616 (ORRec = 1.28, P = 0.005), the latter which is in linkage disequilibrium with the previously identified SNP rs4779584. Testing more broadly for associations in these gene regions in AAs, we noted three statistically significant association peaks in GREM1 and RHPN2 that were not identified in EAs. We conclude that some CRC risk alleles are shared between EAs and AAs and others are population specific.",
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