Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33

Bert Gold, Tomas Kirchhoff, Stefan Stefanov, James Lautenberger, Agnes Viale, Judy Garber, Eitan Friedman, Steven Narod, Adam B. Olshen, Peter Gregersen, Kristi Kosarin, Adam Olsh, Julie Bergeron, Nathan Ellis, Robert J. Klein, Andrew G. Clark, Larry Norton, Michael Dean, Jeff Boyd, Kenneth Offit

Research output: Contribution to journalArticle

254 Citations (Scopus)

Abstract

We performed a three-phase genome-wide association study (GWAS) using cases and controls from a genetically isolated population, Ashkenazi Jews (AJ), to identify loci associated with breast cancer risk. In the first phase, we compared allele frequencies of 150,080 SNPs in 249 high-risk, BRCA1/2 mutation-negative AJ familial cases and 299 cancer-free AJ controls using χ2 and the Cochran-Armitage trend tests. In the second phase, we genotyped 343 SNPs from 123 regions most significantly associated from stage 1, including 4 SNPs from the FGFR2 region, in 950 consecutive AJ breast cancer cases and 979 age-matched AJ controls. We replicated major associations in a third independent set of 243 AJ cases and 187 controls. We obtained a significant allele P value of association with AJ breast cancer in the FGFR2 region (P = 1.5 × 10-5, odds ratio (OR) 1.26, 95% confidence interval (CI) 1.13-1.40 at rs1078806 for all phases combined). In addition, we found a risk locus in a region of chromosome 6q22.33 (P = 2.9 × 10 -8, OR 1.41, 95% CI 1.25-1.59 at rs2180341). Using several SNPs at each implicated locus, we were able to verify associations and impute haplotypes. The major haplotype at the 6q22.33 locus conferred protection from disease, whereas the minor haplotype conferred risk. Candidate genes in the 6q22.33 region include ECHDC1, which encodes a protein involved in mitochondrial fatty acid oxidation, and also RNF146, which encodes a ubiquitin protein ligase, both known pathways in breast cancer pathogenesis.

Original languageEnglish (US)
Pages (from-to)4340-4345
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume105
Issue number11
DOIs
StatePublished - Mar 18 2008
Externally publishedYes

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Jews
Genome-Wide Association Study
Breast Neoplasms
Single Nucleotide Polymorphism
Haplotypes
Odds Ratio
Confidence Intervals
Ubiquitin-Protein Ligases
Gene Frequency
Fatty Acids
Chromosomes
Alleles
Mutation
Population
Genes

Keywords

  • Disease
  • Genomics
  • Mapping
  • Predisposition
  • SNP

ASJC Scopus subject areas

  • Genetics
  • General

Cite this

Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33. / Gold, Bert; Kirchhoff, Tomas; Stefanov, Stefan; Lautenberger, James; Viale, Agnes; Garber, Judy; Friedman, Eitan; Narod, Steven; Olshen, Adam B.; Gregersen, Peter; Kosarin, Kristi; Olsh, Adam; Bergeron, Julie; Ellis, Nathan; Klein, Robert J.; Clark, Andrew G.; Norton, Larry; Dean, Michael; Boyd, Jeff; Offit, Kenneth.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 11, 18.03.2008, p. 4340-4345.

Research output: Contribution to journalArticle

Gold, B, Kirchhoff, T, Stefanov, S, Lautenberger, J, Viale, A, Garber, J, Friedman, E, Narod, S, Olshen, AB, Gregersen, P, Kosarin, K, Olsh, A, Bergeron, J, Ellis, N, Klein, RJ, Clark, AG, Norton, L, Dean, M, Boyd, J & Offit, K 2008, 'Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33', Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 11, pp. 4340-4345. https://doi.org/10.1073/pnas.0800441105
Gold, Bert ; Kirchhoff, Tomas ; Stefanov, Stefan ; Lautenberger, James ; Viale, Agnes ; Garber, Judy ; Friedman, Eitan ; Narod, Steven ; Olshen, Adam B. ; Gregersen, Peter ; Kosarin, Kristi ; Olsh, Adam ; Bergeron, Julie ; Ellis, Nathan ; Klein, Robert J. ; Clark, Andrew G. ; Norton, Larry ; Dean, Michael ; Boyd, Jeff ; Offit, Kenneth. / Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33. In: Proceedings of the National Academy of Sciences of the United States of America. 2008 ; Vol. 105, No. 11. pp. 4340-4345.
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abstract = "We performed a three-phase genome-wide association study (GWAS) using cases and controls from a genetically isolated population, Ashkenazi Jews (AJ), to identify loci associated with breast cancer risk. In the first phase, we compared allele frequencies of 150,080 SNPs in 249 high-risk, BRCA1/2 mutation-negative AJ familial cases and 299 cancer-free AJ controls using χ2 and the Cochran-Armitage trend tests. In the second phase, we genotyped 343 SNPs from 123 regions most significantly associated from stage 1, including 4 SNPs from the FGFR2 region, in 950 consecutive AJ breast cancer cases and 979 age-matched AJ controls. We replicated major associations in a third independent set of 243 AJ cases and 187 controls. We obtained a significant allele P value of association with AJ breast cancer in the FGFR2 region (P = 1.5 × 10-5, odds ratio (OR) 1.26, 95{\%} confidence interval (CI) 1.13-1.40 at rs1078806 for all phases combined). In addition, we found a risk locus in a region of chromosome 6q22.33 (P = 2.9 × 10 -8, OR 1.41, 95{\%} CI 1.25-1.59 at rs2180341). Using several SNPs at each implicated locus, we were able to verify associations and impute haplotypes. The major haplotype at the 6q22.33 locus conferred protection from disease, whereas the minor haplotype conferred risk. Candidate genes in the 6q22.33 region include ECHDC1, which encodes a protein involved in mitochondrial fatty acid oxidation, and also RNF146, which encodes a ubiquitin protein ligase, both known pathways in breast cancer pathogenesis.",
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AU - Viale, Agnes

AU - Garber, Judy

AU - Friedman, Eitan

AU - Narod, Steven

AU - Olshen, Adam B.

AU - Gregersen, Peter

AU - Kosarin, Kristi

AU - Olsh, Adam

AU - Bergeron, Julie

AU - Ellis, Nathan

AU - Klein, Robert J.

AU - Clark, Andrew G.

AU - Norton, Larry

AU - Dean, Michael

AU - Boyd, Jeff

AU - Offit, Kenneth

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