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1. Ancestry-shift refinement mapping of the C6orf97-ESR1 breast cancer susceptibility locus.

Author

Stacey, Simon N, Sulem, Patrick, Zanon, Carlo, Gudjonsson, Sigurjon A, Thorleifsson, Gudmar, Helgason, Agnar, Jonasdottir, Aslaug, Besenbacher, Soren, Kostic, Jelena P, Fackenthal, James D, Huo, Dezheng, Adebamowo, Clement, Ogundiran, Temidayo, Olson, Janet E, Fredericksen, Zachary S, Wang, Xianshu, Look, Maxime P, Sieuwerts, Anieta M, Martens, John W M, Pajares, Isabel, Garcia-Prats, Maria D, Ramon-Cajal, Jose M, de Juan, Ana, Panadero, Angeles, Ortega, Eugenia, Aben, Katja K H, Vermeulen, Sita H, Asadzadeh, Fatemeh, van Engelenburg, K C Anton, Margolin, Sara, Shen, Chen-Yang, Wu, Pei-Ei, Försti, Asta, Lenner, Per, Henriksson, Roger, Johansson, Robert, Enquist, Kerstin, Hallmans, Göran, Jonsson, Thorvaldur, Sigurdsson, Helgi, Alexiusdottir, Kristin, Gudmundsson, Julius, Sigurdsson, Asgeir, Frigge, Michael L, Gudmundsson, Larus, Kristjansson, Kristleifur, Halldorsson, Bjarni V, Styrkarsdottir, Unnur, Gulcher, Jeffrey R, Hemminki, Kari, Lindblom, Annika, Kiemeney, Lambertus A, Mayordomo, Jose I, Foekens, John A, Couch, Fergus J, Olopade, Olufunmilayo I, Gudbjartsson, Daniel F, Thorsteinsdottir, Unnur, Rafnar, Thorunn, Johannsson, Oskar T, Stefansson, Kari, Stacey, Simon N, Sulem, Patrick, Zanon, Carlo, Gudjonsson, Sigurjon A, Thorleifsson, Gudmar, Helgason, Agnar, Jonasdottir, Aslaug, Besenbacher, Soren, Kostic, Jelena P, Fackenthal, James D, Huo, Dezheng, Adebamowo, Clement, Ogundiran, Temidayo, Olson, Janet E, Fredericksen, Zachary S, Wang, Xianshu, Look, Maxime P, Sieuwerts, Anieta M, Martens, John W M, Pajares, Isabel, Garcia-Prats, Maria D, Ramon-Cajal, Jose M, de Juan, Ana, Panadero, Angeles, Ortega, Eugenia, Aben, Katja K H, Vermeulen, Sita H, Asadzadeh, Fatemeh, van Engelenburg, K C Anton, Margolin, Sara, Shen, Chen-Yang, Wu, Pei-Ei, Försti, Asta, Lenner, Per, Henriksson, Roger, Johansson, Robert, Enquist, Kerstin, Hallmans, Göran, Jonsson, Thorvaldur, Sigurdsson, Helgi, Alexiusdottir, Kristin, Gudmundsson, Julius, Sigurdsson, Asgeir, Frigge, Michael L, Gudmundsson, Larus, Kristjansson, Kristleifur, Halldorsson, Bjarni V, Styrkarsdottir, Unnur, Gulcher, Jeffrey R, Hemminki, Kari, Lindblom, Annika, Kiemeney, Lambertus A, Mayordomo, Jose I, Foekens, John A, Couch, Fergus J, Olopade, Olufunmilayo I, Gudbjartsson, Daniel F, Thorsteinsdottir, Unnur, Rafnar, Thorunn, Johannsson, Oskar T, and Stefansson, Kari

Abstract

We used an approach that we term ancestry-shift refinement mapping to investigate an association, originally discovered in a GWAS of a Chinese population, between rs2046210[T] and breast cancer susceptibility. The locus is on 6q25.1 in proximity to the C6orf97 and estrogen receptor alpha (ESR1) genes. We identified a panel of SNPs that are correlated with rs2046210 in Chinese, but not necessarily so in other ancestral populations, and genotyped them in breast cancer case:control samples of Asian, European, and African origin, a total of 10,176 cases and 13,286 controls. We found that rs2046210[T] does not confer substantial risk of breast cancer in Europeans and Africans (OR = 1.04, P = 0.099, and OR = 0.98, P = 0.77, respectively). Rather, in those ancestries, an association signal arises from a group of less common SNPs typified by rs9397435. The rs9397435[G] allele was found to confer risk of breast cancer in European (OR = 1.15, P = 1.2 x 10(-3)), African (OR = 1.35, P = 0.014), and Asian (OR = 1.23, P = 2.9 x 10(-4)) population samples. Combined over all ancestries, the OR was 1.19 (P = 3.9 x 10(-7)), was without significant heterogeneity between ancestries (P(het) = 0.36) and the SNP fully accounted for the association signal in each ancestry. Haplotypes bearing rs9397435[G] are well tagged by rs2046210[T] only in Asians. The rs9397435[G] allele showed associations with both estrogen receptor positive and estrogen receptor negative breast cancer. Using early-draft data from the 1,000 Genomes project, we found that the risk allele of a novel SNP (rs77275268), which is closely correlated with rs9397435, disrupts a partially methylated CpG sequence within a known CTCF binding site. These studies demonstrate that shifting the analysis among ancestral populations can provide valuable resolution in association mapping.

Published
2010
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2. Ancestry-shift refinement mapping of the C6orf97-ESR1 breast cancer susceptibility locus.

Author

Stacey SN, Sulem P, Zanon C, Gudjonsson SA, Thorleifsson G, Helgason A, Jonasdottir A, Besenbacher S, Kostic JP, Fackenthal JD, Huo D, Adebamowo C, Ogundiran T, Olson JE, Fredericksen ZS, Wang X, Look MP, Sieuwerts AM, Martens JW, Pajares I, Garcia-Prats MD, Ramon-Cajal JM, de Juan A, Panadero A, Ortega E, Aben KK, Vermeulen SH, Asadzadeh F, van Engelenburg KC, Margolin S, Shen CY, Wu PE, Försti A, Lenner P, Henriksson R, Johansson R, Enquist K, Hallmans G, Jonsson T, Sigurdsson H, Alexiusdottir K, Gudmundsson J, Sigurdsson A, Frigge ML, Gudmundsson L, Kristjansson K, Halldorsson BV, Styrkarsdottir U, Gulcher JR, Hemminki K, Lindblom A, Kiemeney LA, Mayordomo JI, Foekens JA, Couch FJ, Olopade OI, Gudbjartsson DF, Thorsteinsdottir U, Rafnar T, Johannsson OT, and Stefansson K

Subjects
Breast Neoplasms epidemiology, Chromosomes, Human, Pair 6, Female, Genetic Loci, Genetic Predisposition to Disease epidemiology, Humans, Polymorphism, Single Nucleotide, Breast Neoplasms genetics, Estrogen Receptor alpha genetics, Genetic Predisposition to Disease genetics, Genome-Wide Association Study statistics & numerical data, Racial Groups genetics
Abstract

We used an approach that we term ancestry-shift refinement mapping to investigate an association, originally discovered in a GWAS of a Chinese population, between rs2046210[T] and breast cancer susceptibility. The locus is on 6q25.1 in proximity to the C6orf97 and estrogen receptor alpha (ESR1) genes. We identified a panel of SNPs that are correlated with rs2046210 in Chinese, but not necessarily so in other ancestral populations, and genotyped them in breast cancer case:control samples of Asian, European, and African origin, a total of 10,176 cases and 13,286 controls. We found that rs2046210[T] does not confer substantial risk of breast cancer in Europeans and Africans (OR = 1.04, P = 0.099, and OR = 0.98, P = 0.77, respectively). Rather, in those ancestries, an association signal arises from a group of less common SNPs typified by rs9397435. The rs9397435[G] allele was found to confer risk of breast cancer in European (OR = 1.15, P = 1.2 x 10(-3)), African (OR = 1.35, P = 0.014), and Asian (OR = 1.23, P = 2.9 x 10(-4)) population samples. Combined over all ancestries, the OR was 1.19 (P = 3.9 x 10(-7)), was without significant heterogeneity between ancestries (P(het) = 0.36) and the SNP fully accounted for the association signal in each ancestry. Haplotypes bearing rs9397435[G] are well tagged by rs2046210[T] only in Asians. The rs9397435[G] allele showed associations with both estrogen receptor positive and estrogen receptor negative breast cancer. Using early-draft data from the 1,000 Genomes project, we found that the risk allele of a novel SNP (rs77275268), which is closely correlated with rs9397435, disrupts a partially methylated CpG sequence within a known CTCF binding site. These studies demonstrate that shifting the analysis among ancestral populations can provide valuable resolution in association mapping., Competing Interests: All authors from deCODE have equity interests in the company.

Published
2010
Full Text
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