Associations between SNPs in 9p22.2 with ovarian cancer risk for <i>BRCA1</i> and <i>BRCA2</i> mutation carriers.

<p>In each plot, the purple diamond corresponds to the strongest associated SNP and the colour code indicates the linkage disequilibrium with respect to this variant. Horizontal lines indicate the -log₁₀ p-value such that the SNPs above the line are the potential causal ones. This set was defined based on a likelihood ratio for a particular SNP as being less or equal than 100, relative to the most likely variant and r²>0.1. (A) <i>BRCA1</i> mutation carriers, (B) <i>BRCA2</i> mutation carriers.</p

Pairwise correlations (r²) between selected SNPs.

<p>SNPs correspond to: rs10124837, the strongest associated in <i>BRCA1</i>; rs62543583, the strongest associated in <i>BRCA2</i> mutation carriers; rs7046326, the strongest associated in <i>BRCA1/2</i> meta-analysis; rs3814113, was the strongest associated variant in the initial GWAS analysis.</p

Associations between SNPs in 9p22.2 with ovarian cancer risk for the meta-analysis of <i>BRCA1</i> and <i>BRCA2</i> mutation carriers.

<p>(A) The purple diamond corresponds to the strongest associated SNP and the colour code indicates the linkage disequilibrium with respect to this variant. Horizontal lines indicate the -log₁₀ p-value such that the SNPs above the line are the potential causal ones. This set was defined based on a likelihood ratio for a particular SNP as being less or equal than 100, relative to the most likely variant and r²>0.1. (B) Haplotype block indicating relevant SNPs. From left to right the indicated SNPs correspond to: the strongest associated in <i>BRCA1/2</i> meta-analysis, the strongest in <i>BRCA1</i> and the strongest in <i>BRCA2</i>.</p

Genomic features surrounding the 9p22.2 locus.

<p>Illustration of the genomic region (chr9:16,839,835–16,924,468) encompassing peaks (shaded areas) containing candidate causal variants associated with ovarian cancer risk in <i>BRCA1</i> and <i>BRCA2</i> mutation carriers. Epigenomic data from Coetzee et al., (2015) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158801#pone.0158801.ref020" target="_blank">20</a>] representing potential regulatory elements in ovarian cells (iOSE4 and iOSE11) and fallopian tube (FTSEC33) cells derived from formaldehyde assisted identification of regulatory elements sequencing (FAIRE-seq) and histone modification ChIP-seq are shown as black bars. Variants which overlap one of these features are coloured red. Data from the ENCODE project including histone modification ChIP-seq for three modifications (H3K4me1, H3K4me3, and H3K27ac) are shown as coloured histograms, as well as DNaseI hypersensitive site mapping and transcription factor ChIP-seq. The positions of all common SNPs from dbSNP build 142 are shown in the lowest track.</p

Conditional associations for <i>BRCA1</i> and <i>BRCA2</i> top SNPs.

<p><b>The table shows the HR estimate. 95% CI and p-value for the conditional analysis adjusting for the lead SNP in the univariate analysis for <i>BRCA1</i> (left hand side) or <i>BRCA2</i> mutation carriers (right had side).</b> SNPs correspond to: rs10124837, the strongest associated in <i>BRCA1</i>; rs62543583, the strongest associated in <i>BRCA2</i> mutation carriers; rs7046326, the strongest associated in <i>BRCA1/2</i> meta-analysis; rs3814113, was the strongest associated variant in the initial GWAS analysis. “HR”, hazard ratio; “CI”, confidence interval.</p