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      • Association of breast cancer risk in <i>BRCA1</i> and <i>BRCA2</i> mutation carriers with genetic variants showing differential allelic expression: identification of a modifier of breast cancer risk at locus 11q22.3

        Hamdi, Yosr,Soucy, Penny,Kuchenbaeker, Karoline B.,Pastinen, Tomi,Droit, Arnaud,Lemaç,on, Audrey,Adlard, Julian,Aittomä,ki, Kristiina,Andrulis, Irene L.,Arason, Adalgeir,Arnold, Norbert,Arun Springer US 2017 Breast cancer research and treatment Vol.161 No.1

        <P><B>Purpose</B></P><P><I>Cis</I>-acting regulatory SNPs resulting in differential allelic expression (DAE) may, in part, explain the underlying phenotypic variation associated with many complex diseases. To investigate whether common variants associated with DAE were involved in breast cancer susceptibility among <I>BRCA1</I> and <I>BRCA2</I> mutation carriers, a list of 175 genes was developed based of their involvement in cancer-related pathways.</P><P><B>Methods</B></P><P>Using data from a genome-wide map of SNPs associated with allelic expression, we assessed the association of ~320 SNPs located in the vicinity of these genes with breast and ovarian cancer risks in 15,252 <I>BRCA1</I> and 8211 <I>BRCA2</I> mutation carriers ascertained from 54 studies participating in the Consortium of Investigators of Modifiers of <I>BRCA1/2</I>.</P><P><B>Results</B></P><P>We identified a region on 11q22.3 that is significantly associated with breast cancer risk in <I>BRCA1</I> mutation carriers (most significant SNP rs228595 <I>p</I> = 7 × 10<SUP>−6</SUP>). This association was absent in <I>BRCA2</I> carriers (<I>p</I> = 0.57). The 11q22.3 region notably encompasses genes such as <I>ACAT1</I>, <I>NPAT</I>, and <I>ATM</I>. Expression quantitative trait loci associations were observed in both normal breast and tumors across this region, namely for <I>ACAT1</I>, <I>ATM</I>, and other genes. In silico analysis revealed some overlap between top risk-associated SNPs and relevant biological features in mammary cell data, which suggests potential functional significance.</P><P><B>Conclusion</B></P><P>We identified 11q22.3 as a new modifier locus in <I>BRCA1</I> carriers. Replication in larger studies using estrogen receptor (ER)-negative or triple-negative (i.e., ER-, progesterone receptor-, and HER2-negative) cases could therefore be helpful to confirm the association of this locus with breast cancer risk.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1007/s10549-016-4018-2) contains supplementary material, which is available to authorized users.</P>

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        Association analysis identifies 65 new breast cancer risk loci

        Michailidou, Kyriaki,Lindströ,m, Sara,Dennis, Joe,Beesley, Jonathan,Hui, Shirley,Kar, Siddhartha,Lemaç,on, Audrey,Soucy, Penny,Glubb, Dylan,Rostamianfar, Asha,Bolla, Manjeet K.,Wang, Qin,Tyr Macmillan Publishers Limited, part of Springer Nat 2017 Nature Vol.551 No.7678

        <P>Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as BRCA1, and many common, mostly non-coding variants. However, much of the genetic contribution to breast cancer risk remains unknown. Here we report the results of a genome-wide association study of breast cancer in 122,977 cases and 105,974 controls of European ancestry and 14,068 cases and 13,104 controls of East Asian ancestry(1). We identified 65 new loci that are associated with overall breast cancer risk at P < 5 x 10(-8). The majority of credible risk single-nucleotide polymorphisms in these loci fall in distal regulatory elements, and by integrating in silico data to predict target genes in breast cells at each locus, we demonstrate a strong overlap between candidate target genes and somatic driver genes in breast tumours. We also find that heritability of breast cancer due to all single-nucleotide polymorphisms in regulatory features was 2-5-fold enriched relative to the genome-wide average, with strong enrichment for particular transcription factor binding sites. These results provide further insight into genetic susceptibility to breast cancer and will improve the use of genetic risk scores for individualized screening and prevention.</P>

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        Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

        Milne, Roger L,Kuchenbaecker, Karoline B,Michailidou, Kyriaki,Beesley, Jonathan,Kar, Siddhartha,Lindströ,m, Sara,Hui, Shirley,Lemaç,on, Audrey,Soucy, Penny,Dennis, Joe,Jiang, Xia,Rostamianfa Nature Pub. Co 2017 Nature genetics Vol.49 No.12

        <P>Most common breast cancer susceptibility variants have been identified through genome-wide association studies (GWAS) of predominantly estrogen receptor (ER)-positive disease(1). We conducted a GWAS using 21,468 ER-negative cases and 100,594 controls combined with 18,908 BRCA1 mutation carriers (9,414 with breast cancer), all of European origin. We identified independent associations at P < 5 x 10(-8) with ten variants at nine new loci. At P < 0.05, we replicated associations with 10 of 11 variants previously reported in ER-negative disease or BRCA1 mutation carrier GWAS and observed consistent associations with ER-negative disease for 105 susceptibility variants identified by other studies. These 125 variants explain approximately 16% of the familial risk of this breast cancer subtype. There was high genetic correlation (0.72) between risk of ER-negative breast cancer and breast cancer risk for BRCA1 mutation carriers. These findings may lead to improved risk prediction and inform further fine-mapping and functional work to better understand the biological basis of ER-negative breast cancer.</P>

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