Additional file 5: Table 4. of Gene expression modules in primary breast cancers as risk factors for organotropic patterns of first metastatic spread: a case control study

Estimated ORs for molecular subtype representations based on logistic regression. (PDF 657 kb

Le Monde

15 janvier 18721872/01/15 (N13,A13)-1872/01/16.Appartient à l’ensemble documentaire : BbLevt

Minor allele frequencies WTCCC vs pooled NGS (24 pools combined).

<p>MAFs for 153 SNPs were compared between allele frequency estimates based on pooled NGS and genotyping data from the WTCCC [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004955#pgen.1004955.ref047" target="_blank">47</a>] for 634 individuals. MAFs are strongly correlated between both datasets (Spearman rank correlation coefficient R = 0.976), with only two SNPs showing substantial differences.</p

Summary of strategy for detecting rare variants associated with IBD.

<p>Overview of our rare variant screening strategy in IBD using DNA pools. We detected 3442 high quality variants in phase I based on stringent filtering criteria. We were able to validate 1252 of these variants using a) previously generated genotyping data for 153 SNPs in 634 of the individuals who were sequenced; b) case-control association p values for 1099 SNPs from CD Immunochip study [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004955#pgen.1004955.ref004" target="_blank">4</a>]. We then performed validation genotyping of 80 variants in phase II in 6335 IBD cases and 2974 controls and extended the analysis of the top 5 SNVs to a further 3662 IBD cases and 3639 controls (phase III) to allow a final combined analysis of 10,147 IBD cases and 7,008 controls.</p

SNPs associated with ILC (P<5×10⁻⁸) or LCIS (P<0.05) in a pooled lobular analysis (GLACIER and BCAC).

<p>SNPs associated with ILC (P<5×10⁻⁸) or LCIS (P<0.05) in a pooled lobular analysis (GLACIER and BCAC).</p

rs11977670, chromosome 7:139942304 G>A, and association ILC in populations of European ancestry.

<p>rs11977670, chromosome 7:139942304 G>A, and association ILC in populations of European ancestry.</p

SNPs showing differential lobular and ductal associations with breast cancer risk in BCAC subjects (ER+ tumours only).

<p>SNPs showing differential lobular and ductal associations with breast cancer risk in BCAC subjects (ER+ tumours only).</p

Association with risk of breast cancer for rs11977670 stratified by breast cancer tumour subtypes (Pooled analysis, BCAC, GLACIER, UK PHASE II).

<p>Association with risk of breast cancer for rs11977670 stratified by breast cancer tumour subtypes (Pooled analysis, BCAC, GLACIER, UK PHASE II).</p

Forest plot for rs11977670.

<p>Forest plot for rs11977670.</p

Lobular cancer study design.

<p>Lobular cancer study design.</p