Abstract
Background: Breast cancer is a partially heritable trait and genome-wide association studies (GWAS) have identified over 180 common genetic variants associated with breast cancer. We have previously performed breast cancer GWAS in Latinas and identified a strongly protective single nucleotide polymorphism (SNP) at 6q25, with the protective minor allele originating from indigenous American ancestry. Here we report on fine mapping of the 6q25 locus in an expanded sample of Latinas. Methods: We performed GWAS in 2385 cases and 6416 controls who were either US Latinas or Mexican women. We replicated the top SNPs in 2412 cases and 1620 controls of US Latina, Mexican, and Colombian women. In addition, we validated the top novel variants in studies of African, Asian and European ancestry. In each dataset we used logistic regression models to test the association between SNPs and breast cancer risk and corrected for genetic ancestry using either principal components or genetic ancestry inferred from ancestry informative markers using a model-based approach. Results: We identified a novel set of SNPs at the 6q25 locus associated with genome-wide levels of significance (p = 3.3 × 10- 8 - 6.0 × 10- 9) not in linkage disequilibrium (LD) with variants previously reported at this locus. These SNPs were in high LD (r 2 > 0.9) with each other, with the top SNP, rs3778609, associated with breast cancer with an odds ratio (OR) and 95% confidence interval (95% CI) of 0.76 (0.70-0.84). In a replication in women of Latin American origin, we also observed a consistent effect (OR 0.88; 95% CI 0.78-0.99; p = 0.037). We also performed a meta-analysis of these SNPs in East Asians, African ancestry and European ancestry populations and also observed a consistent effect (rs3778609, OR 0.95; 95% CI 0.91-0.97; p = 0.0017). Conclusion: Our study adds to evidence about the importance of the 6q25 locus for breast cancer susceptibility. Our finding also highlights the utility of performing additional searches for genetic variants for breast cancer in non-European populations.
| Original language | English (US) |
|---|---|
| Article number | 3 |
| Journal | Breast Cancer Research |
| Volume | 21 |
| Issue number | 1 |
| DOIs | |
| State | Published - Jan 14 2019 |
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Keywords
- Fine mapping
- Genome wide association study
- Hispanic/Latino populations
ASJC Scopus subject areas
- Oncology
- Cancer Research
Cite this
Identification of novel common breast cancer risk variants at the 6q25 locus among Latinas 06 Biological Sciences. / Hoffman, Joshua; Fejerman, Laura; Hu, Donglei; Huntsman, Scott; Li, Min; John, Esther M.; Torres-Mejia, Gabriela; Kushi, Larry; Ding, Yuan Chun; Weitzel, Jeffrey; Neuhausen, Susan L.; Lott, Paul; Echeverry, Magdalena; Carvajal-Carmona, Luis; Burchard, Esteban; Eng, Celeste; Long, Jirong; Zheng, Wei; Olopade, Olufunmilayo; Huo, Dezheng; Haiman, Christopher; Ziv, Elad.
In: Breast Cancer Research, Vol. 21, No. 1, 3, 14.01.2019.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Identification of novel common breast cancer risk variants at the 6q25 locus among Latinas 06 Biological Sciences
AU - Hoffman, Joshua
AU - Fejerman, Laura
AU - Hu, Donglei
AU - Huntsman, Scott
AU - Li, Min
AU - John, Esther M.
AU - Torres-Mejia, Gabriela
AU - Kushi, Larry
AU - Ding, Yuan Chun
AU - Weitzel, Jeffrey
AU - Neuhausen, Susan L.
AU - Lott, Paul
AU - Echeverry, Magdalena
AU - Carvajal-Carmona, Luis
AU - Burchard, Esteban
AU - Eng, Celeste
AU - Long, Jirong
AU - Zheng, Wei
AU - Olopade, Olufunmilayo
AU - Huo, Dezheng
AU - Haiman, Christopher
AU - Ziv, Elad
PY - 2019/1/14
Y1 - 2019/1/14
N2 - Background: Breast cancer is a partially heritable trait and genome-wide association studies (GWAS) have identified over 180 common genetic variants associated with breast cancer. We have previously performed breast cancer GWAS in Latinas and identified a strongly protective single nucleotide polymorphism (SNP) at 6q25, with the protective minor allele originating from indigenous American ancestry. Here we report on fine mapping of the 6q25 locus in an expanded sample of Latinas. Methods: We performed GWAS in 2385 cases and 6416 controls who were either US Latinas or Mexican women. We replicated the top SNPs in 2412 cases and 1620 controls of US Latina, Mexican, and Colombian women. In addition, we validated the top novel variants in studies of African, Asian and European ancestry. In each dataset we used logistic regression models to test the association between SNPs and breast cancer risk and corrected for genetic ancestry using either principal components or genetic ancestry inferred from ancestry informative markers using a model-based approach. Results: We identified a novel set of SNPs at the 6q25 locus associated with genome-wide levels of significance (p = 3.3 × 10- 8 - 6.0 × 10- 9) not in linkage disequilibrium (LD) with variants previously reported at this locus. These SNPs were in high LD (r 2 > 0.9) with each other, with the top SNP, rs3778609, associated with breast cancer with an odds ratio (OR) and 95% confidence interval (95% CI) of 0.76 (0.70-0.84). In a replication in women of Latin American origin, we also observed a consistent effect (OR 0.88; 95% CI 0.78-0.99; p = 0.037). We also performed a meta-analysis of these SNPs in East Asians, African ancestry and European ancestry populations and also observed a consistent effect (rs3778609, OR 0.95; 95% CI 0.91-0.97; p = 0.0017). Conclusion: Our study adds to evidence about the importance of the 6q25 locus for breast cancer susceptibility. Our finding also highlights the utility of performing additional searches for genetic variants for breast cancer in non-European populations.
AB - Background: Breast cancer is a partially heritable trait and genome-wide association studies (GWAS) have identified over 180 common genetic variants associated with breast cancer. We have previously performed breast cancer GWAS in Latinas and identified a strongly protective single nucleotide polymorphism (SNP) at 6q25, with the protective minor allele originating from indigenous American ancestry. Here we report on fine mapping of the 6q25 locus in an expanded sample of Latinas. Methods: We performed GWAS in 2385 cases and 6416 controls who were either US Latinas or Mexican women. We replicated the top SNPs in 2412 cases and 1620 controls of US Latina, Mexican, and Colombian women. In addition, we validated the top novel variants in studies of African, Asian and European ancestry. In each dataset we used logistic regression models to test the association between SNPs and breast cancer risk and corrected for genetic ancestry using either principal components or genetic ancestry inferred from ancestry informative markers using a model-based approach. Results: We identified a novel set of SNPs at the 6q25 locus associated with genome-wide levels of significance (p = 3.3 × 10- 8 - 6.0 × 10- 9) not in linkage disequilibrium (LD) with variants previously reported at this locus. These SNPs were in high LD (r 2 > 0.9) with each other, with the top SNP, rs3778609, associated with breast cancer with an odds ratio (OR) and 95% confidence interval (95% CI) of 0.76 (0.70-0.84). In a replication in women of Latin American origin, we also observed a consistent effect (OR 0.88; 95% CI 0.78-0.99; p = 0.037). We also performed a meta-analysis of these SNPs in East Asians, African ancestry and European ancestry populations and also observed a consistent effect (rs3778609, OR 0.95; 95% CI 0.91-0.97; p = 0.0017). Conclusion: Our study adds to evidence about the importance of the 6q25 locus for breast cancer susceptibility. Our finding also highlights the utility of performing additional searches for genetic variants for breast cancer in non-European populations.
KW - Fine mapping
KW - Genome wide association study
KW - Hispanic/Latino populations
UR - http://www.scopus.com/inward/record.url?scp=85059952983&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85059952983&partnerID=8YFLogxK
U2 - 10.1186/s13058-018-1085-9
DO - 10.1186/s13058-018-1085-9
M3 - Article
C2 - 30642363
AN - SCOPUS:85059952983
VL - 21
JO - Breast Cancer Research
JF - Breast Cancer Research
SN - 1465-5411
IS - 1
M1 - 3
ER -