Polymorphisms in the TOX3/LOC643714 Locus and Risk of Breast Cancer in African-American Women

Overview

Journal Cancer Epidemiol Biomarkers Prev

Specialties Biochemistry
Oncology
Public Health

Date 2010 Apr 22

PMID 20406955

Citations 34

Authors

Edward A Ruiz-Narvaez

Lynn Rosenberg

Yvette C Cozier

L Adrienne Cupples

Lucile L Adams-Campbell

Julie R Palmer

Affiliations

Soon will be listed here.

Abstract

Background: The rs3803662 single nucleotide polymorphism (SNP) in the TOX3/LOC643714 region was identified as a breast cancer susceptibility genetic variant in recent genome-wide association studies of women of European ancestry and has been replicated in other populations of European ancestry. The position of the causal variant tagged by the rs3803662 marker is still unknown. In fact, because the rs3803662 polymorphism is located between the TOX3 and the LOC643714 loci, it is unclear which gene is the one causally related to the risk of breast cancer. Because linkage disequilibrium blocks are smaller in populations of African ancestry, fine-mapping in African ancestry samples might be an effective approach to narrowing the position of the causal variant(s) in the TOX3/LOC643714 locus.

Methods: We evaluated a total of 60 tagging SNPs throughout the TOX3/LOC643714 region in a nested case-control study of breast cancer within the Black Women's Health Study, which included 906 cases and 1,111 controls.

Results: No significant association was found for the rs3803662 SNP. However, four other SNPs (rs3104746, rs3112562, rs3104793, and rs8046994), all of them located in the LOC643714 gene, were associated with risk of breast cancer. The strongest association was observed for rs3104746: each copy of the A-rs3104746 allele was associated with a 23% higher risk of breast cancer (odds ratios, 1.23; 95% confidence intervals, 1.05-1.44; P=0.009).

Conclusions: Our results confirm the association observed in genome-wide association studies of European ancestry populations.

Impact: The results narrow the locus to a smaller linkage disequilibrium block in the LOC643714 gene.

Citing Articles

Risk Association of and Gene Polymorphisms with Sporadic Breast Cancer in Mexican Women.

Solis-Coronado O, Villarreal-Vela M, Rodriguez-Gutierrez H, Gonzalez-Guerrero J, Cerda-Flores R, Alcorta-Nunez F Curr Oncol. 2022; 29(2):1008-1017.

PMID: 35200585 PMC: 8870835. DOI: 10.3390/curroncol29020086.

Quantitative assessment of the immune microenvironment in African American Triple Negative Breast Cancer: a case-control study.

Yaghoobi V, Moutafi M, Aung T, Pelekanou V, Yaghoubi S, Blenman K Breast Cancer Res. 2021; 23(1):113.

PMID: 34906209 PMC: 8670126. DOI: 10.1186/s13058-021-01493-w.

Correlation between and Polymorphisms and the Susceptibility to Breast Cancer.

Nourolahzadeh Z, Houshmand M, Mohammad F, Ghorbian S Rep Biochem Mol Biol. 2021; 9(3):291-296.

PMID: 33649722 PMC: 7816788. DOI: 10.29252/rbmb.9.3.291.

Genetic factors associated with cancer racial disparity - an integrative study across twenty-one cancer types.

Li Y, Pang X, Cui Z, Zhou Y, Mao F, Lin Y Mol Oncol. 2020; 14(11):2775-2786.

PMID: 32920960 PMC: 7607166. DOI: 10.1002/1878-0261.12799.

The association of CASC16 variants with breast Cancer risk in a northwest Chinese female population.

Zuo X, Wang H, Mi Y, Zhang Y, Wang X, Yang Y Mol Med. 2020; 26(1):11.

PMID: 31996122 PMC: 6988193. DOI: 10.1186/s10020-020-0137-7.

References

Valdes A, McWeeney S, Thomson G . HLA class II DR-DQ amino acids and insulin-dependent diabetes mellitus: application of the haplotype method. Am J Hum Genet. 1997; 60(3):717-28. PMC: 1712519. View

McKeigue P, Carpenter J, Parra E, Shriver M . Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African-American populations. Ann Hum Genet. 2001; 64(Pt 2):171-86. DOI: 10.1017/S0003480000008022. View

Reiner A, Ziv E, Lind D, Nievergelt C, Schork N, Cummings S . Population structure, admixture, and aging-related phenotypes in African American adults: the Cardiovascular Health Study. Am J Hum Genet. 2005; 76(3):463-77. PMC: 1196398. DOI: 10.1086/428654. View

Zheng W, Cai Q, Signorello L, Long J, Hargreaves M, Deming S . Evaluation of 11 breast cancer susceptibility loci in African-American women. Cancer Epidemiol Biomarkers Prev. 2009; 18(10):2761-4. PMC: 2759857. DOI: 10.1158/1055-9965.EPI-09-0624. View

Garcia-Closas M, Hall P, Nevanlinna H, Pooley K, Morrison J, Richesson D . Heterogeneity of breast cancer associations with five susceptibility loci by clinical and pathological characteristics. PLoS Genet. 2008; 4(4):e1000054. PMC: 2291027. DOI: 10.1371/journal.pgen.1000054. View

Hoggart C, Parra E, Shriver M, Bonilla C, Kittles R, Clayton D . Control of confounding of genetic associations in stratified populations. Am J Hum Genet. 2003; 72(6):1492-1504. PMC: 1180309. DOI: 10.1086/375613. View

Halder I, Yang B, Kranzler H, Stein M, Shriver M, Gelernter J . Measurement of admixture proportions and description of admixture structure in different U.S. populations. Hum Mutat. 2009; 30(9):1299-309. PMC: 2867064. DOI: 10.1002/humu.21045. View

de Bakker P, Yelensky R, Peer I, Gabriel S, Daly M, Altshuler D . Efficiency and power in genetic association studies. Nat Genet. 2005; 37(11):1217-23. DOI: 10.1038/ng1669. View

Stram D, Pearce C, Bretsky P, Freedman M, Hirschhorn J, Altshuler D . Modeling and E-M estimation of haplotype-specific relative risks from genotype data for a case-control study of unrelated individuals. Hum Hered. 2003; 55(4):179-90. DOI: 10.1159/000073202. View

10.

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M, Bender D . PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007; 81(3):559-75. PMC: 1950838. DOI: 10.1086/519795. View

11.

Pritchard J, Stephens M, Donnelly P . Inference of population structure using multilocus genotype data. Genetics. 2000; 155(2):945-59. PMC: 1461096. DOI: 10.1093/genetics/155.2.945. View

12.

. The International HapMap Project. Nature. 2003; 426(6968):789-96. DOI: 10.1038/nature02168. View

13.

Easton D, Pooley K, Dunning A, Pharoah P, Thompson D, Ballinger D . Genome-wide association study identifies novel breast cancer susceptibility loci. Nature. 2007; 447(7148):1087-93. PMC: 2714974. DOI: 10.1038/nature05887. View

14.

Zaykin D, Westfall P, Young S, Karnoub M, Wagner M, Ehm M . Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Hum Hered. 2002; 53(2):79-91. DOI: 10.1159/000057986. View

15.

Rosenberg L, Adams-Campbell L, Palmer J . The Black Women's Health Study: a follow-up study for causes and preventions of illness. J Am Med Womens Assoc (1972). 1995; 50(2):56-8. View

16.

Stacey S, Manolescu A, Sulem P, Rafnar T, Gudmundsson J, Gudjonsson S . Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet. 2007; 39(7):865-9. DOI: 10.1038/ng2064. View

17.

Barrett J, Fry B, Maller J, Daly M . Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2004; 21(2):263-5. DOI: 10.1093/bioinformatics/bth457. View

18.

Antoniou A, Spurdle A, Sinilnikova O, Healey S, Pooley K, Schmutzler R . Common breast cancer-predisposition alleles are associated with breast cancer risk in BRCA1 and BRCA2 mutation carriers. Am J Hum Genet. 2008; 82(4):937-48. PMC: 2427217. DOI: 10.1016/j.ajhg.2008.02.008. View

19.

Cozier Y, Palmer J, Rosenberg L . Comparison of methods for collection of DNA samples by mail in the Black Women's Health Study. Ann Epidemiol. 2004; 14(2):117-22. DOI: 10.1016/S1047-2797(03)00132-7. View

20.

Smith M, Patterson N, Lautenberger J, Truelove A, McDonald G, Waliszewska A . A high-density admixture map for disease gene discovery in african americans. Am J Hum Genet. 2004; 74(5):1001-13. PMC: 1181963. DOI: 10.1086/420856. View