| Literature DB >> 21424380 |
Badan Sehrawat1, Malinee Sridharan, Sunita Ghosh, Paula Robson, Carol E Cass, John R Mackey, Russell Greiner, Sambasivarao Damaraju.
Abstract
Previous genome-wide association studies (GWAS) have shown several risk alleles to be associated with breast cancer. However, the variants identified so far contribute to only a small proportion of disease risk. The objective of our GWAS was to identify additional novel breast cancer susceptibility variants and to replicate these findings in an independent cohort. We performed a two-stage association study in a cohort of 3,064 women from Alberta, Canada. In Stage I, we interrogated 906,600 single nucleotide polymorphisms (SNPs) on Affymetrix SNP 6.0 arrays using 348 breast cancer cases and 348 controls. We used single-locus association tests to determine statistical significance for the observed differences in allele frequencies between cases and controls. In Stage II, we attempted to replicate 35 significant markers identified in Stage I in an independent study of 1,153 cases and 1,215 controls. Genotyping of Stage II samples was done using Sequenom Mass-ARRAY iPlex platform. Six loci from four different gene regions (chromosomes 4, 5, 16 and 19) showed statistically significant differences between cases and controls in both Stage I and Stage II testing, and also in joint analysis. The identified variants were from EDNRA, ROPN1L, C16orf61 and ZNF577 gene regions. The presented joint analyses from the two-stage study design were not significant after genome-wide correction. The SNPs identified in this study may serve as potential candidate loci for breast cancer risk in a further replication study in Stage III from Alberta population or independent validation in Caucasian cohorts elsewhere.Entities:
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Year: 2011 PMID: 21424380 PMCID: PMC3178778 DOI: 10.1007/s00439-011-0973-1
Source DB: PubMed Journal: Hum Genet ISSN: 0340-6717 Impact factor: 4.132
Fig. 1Manhattan plot for Stage I association study showing 35,589 markers (p < 0.05) distributed across chromosomes. This graph is plotted against allelic χ2 p values on –log10 scale to indicate polygenic nature of breast cancer susceptibility
Six novel loci showing consistent association with breast cancer in both stages of the study
| dbSNP rs# | Polymorphism | Chr | Associated gene | Relative location | Stage I | Stage II χ2
| Joint analysis | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
| χ2 FDR | OR (95% CI) | CR | MA | MAF | Cases | Controls | |||||||||||||
| AA | AB | BB |
| AA | AB | BB |
| |||||||||||||
| rs1092913 | C>T | 5p15.2 |
| 2.5 kb Downstream | 7.00E−04 | 2.17E−04 | 1.89E−06 | 3.30E−05 | 1.45 (1.24, 1.69) | 0.99 | T | 0.13 | 1,054 | 333 | 48 | 1,435 | 1,228 | 275 | 28 | 1,531 |
| rs10411161 | C>T | 19q13.33 |
| 3′ UTR | 1.08E−03 | 6.16E−04 | 7.09E−06 | 8.27E−05 | 1.42 (1.22, 1.65) | 0.99 | T | 0.13 | 1,068 | 306 | 64 | 1,438 | 1,232 | 251 | 45 | 1,528 |
| rs3848562 | C>T | 19q13.33 |
| Intron | 8.01E−04 | 9.78E−04 | 9.23E−06 | 8.08E−05 | 1.42 (1.22, 1.66) | 1.00 | C | 0.12 | 1,078 | 336 | 38 | 1,452 | 1,238 | 274 | 23 | 1,535 |
| rs11878583 | C>T | 19q13.33 |
| Intron | 1.25E−03 | 7.59E−03 | 1.35E−04 | 9.45E−04 | 1.35 (1.16, 1.57) | 1.00 | C | 0.13 | 1,077 | 332 | 42 | 1,451 | 1,214 | 301 | 19 | 1,534 |
| rs1429142 | C>T | 4q31.23 |
| 112.5 kb Upstream | 2.80E−03 | 1.28E−02 | 3.59E−04 | 2.10E−03 | 1.27 (1.11, 1.45) | 1.00 | C | 0.18 | 926 | 466 | 57 | 1,449 | 1,074 | 417 | 44 | 1,535 |
| rs1981867 | A>G | 16q23.2 |
| 85.9 kb Downstream | 3.70E−04 | 3.17E−02 | 4.32E−04 | 2.16E−03 | 1.22 (1.09, 1.36) | 1.00 | A | 0.31 | 664 | 611 | 171 | 1,446 | 769 | 651 | 116 | 1,536 |
Chr chromosome, UTR untranslated region, χ chi-square, FDR false discovery rate, OR odds ratio, CI confidence interval, CR call rate, MA minor allele, MAF minor allele frequency; genotypes: AA wild-type homozygous, AB heterozygous, BB variant homozygous, n sample size