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In this study, to identify new ER-negative susceptibility loci, we performed a meta-analysis of 11 genome-wide association studies (GWAS) consisting of 4,939 ER-negative cases and 14,352 controls, combined with 7,333 ER-negative cases and 42,468 controls and 15,252 <jats:italic>BRCA1<\/jats:italic> mutation carriers genotyped on the iCOGS array. We identify four previously unidentified loci including two loci at 13q22 near <jats:italic>KLF5<\/jats:italic>, a 2p23.2 locus near <jats:italic>WDR43<\/jats:italic> and a 2q33 locus near <jats:italic>PPIL3<\/jats:italic> that display genome-wide significant associations with ER-negative breast cancer. In addition, 19 known breast cancer risk loci have genome-wide significant associations and 40 had moderate associations (<jats:italic>P<\/jats:italic>&lt;0.05) with ER-negative disease. Using functional and eQTL studies we implicate <jats:italic>TRMT61B<\/jats:italic> and <jats:italic>WDR43<\/jats:italic> at 2p23.2 and <jats:italic>PPIL3<\/jats:italic> at 2q33 in ER-negative breast cancer aetiology. All ER-negative loci combined account for \u223c11% of familial relative risk for ER-negative disease and may contribute to improved ER-negative and <jats:italic>BRCA1<\/jats:italic> breast cancer risk prediction.<\/jats:p>","DOI":"10.1038\/ncomms11375","type":"journal-article","created":{"date-parts":[[2016,4,27]],"date-time":"2016-04-27T05:28:14Z","timestamp":1461734894000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":88,"title":["Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer"],"prefix":"10.1038","volume":"7","author":[{"given":"Fergus J.","family":"Couch","sequence":"first","affiliation":[]},{"given":"Karoline B.","family":"Kuchenbaecker","sequence":"additional","affiliation":[]},{"given":"Kyriaki","family":"Michailidou","sequence":"additional","affiliation":[]},{"given":"Gustavo A.","family":"Mendoza-Fandino","sequence":"additional","affiliation":[]},{"given":"Silje","family":"Nord","sequence":"additional","affiliation":[]},{"given":"Janna","family":"Lilyquist","sequence":"additional","affiliation":[]},{"given":"Curtis","family":"Olswold","sequence":"additional","affiliation":[]},{"given":"Emily","family":"Hallberg","sequence":"additional","affiliation":[]},{"given":"Simona","family":"Agata","sequence":"additional","affiliation":[]},{"given":"Habibul","family":"Ahsan","sequence":"additional","affiliation":[]},{"given":"Kristiina","family":"Aittom\u00e4ki","sequence":"additional","affiliation":[]},{"given":"Christine","family":"Ambrosone","sequence":"additional","affiliation":[]},{"given":"Irene L.","family":"Andrulis","sequence":"additional","affiliation":[]},{"given":"Hoda","family":"Anton-Culver","sequence":"additional","affiliation":[]},{"given":"Volker","family":"Arndt","sequence":"additional","affiliation":[]},{"given":"Banu K.","family":"Arun","sequence":"additional","affiliation":[]},{"given":"Brita","family":"Arver","sequence":"additional","affiliation":[]},{"given":"Monica","family":"Barile","sequence":"additional","affiliation":[]},{"given":"Rosa B.","family":"Barkardottir","sequence":"additional","affiliation":[]},{"given":"Daniel","family":"Barrowdale","sequence":"additional","affiliation":[]},{"given":"Lars","family":"Beckmann","sequence":"additional","affiliation":[]},{"given":"Matthias W.","family":"Beckmann","sequence":"additional","affiliation":[]},{"given":"Javier","family":"Benitez","sequence":"additional","affiliation":[]},{"given":"Stephanie V.","family":"Blank","sequence":"additional","affiliation":[]},{"given":"Carl","family":"Blomqvist","sequence":"additional","affiliation":[]},{"given":"Natalia V.","family":"Bogdanova","sequence":"additional","affiliation":[]},{"given":"Stig E.","family":"Bojesen","sequence":"additional","affiliation":[]},{"given":"Manjeet K.","family":"Bolla","sequence":"additional","affiliation":[]},{"given":"Bernardo","family":"Bonanni","sequence":"additional","affiliation":[]},{"given":"Hiltrud","family":"Brauch","sequence":"additional","affiliation":[]},{"given":"Hermann","family":"Brenner","sequence":"additional","affiliation":[]},{"given":"Barbara","family":"Burwinkel","sequence":"additional","affiliation":[]},{"given":"Saundra S.","family":"Buys","sequence":"additional","affiliation":[]},{"given":"Trinidad","family":"Caldes","sequence":"additional","affiliation":[]},{"given":"Maria A.","family":"Caligo","sequence":"additional","affiliation":[]},{"given":"Federico","family":"Canzian","sequence":"additional","affiliation":[]},{"given":"Jane","family":"Carpenter","sequence":"additional","affiliation":[]},{"given":"Jenny","family":"Chang-Claude","sequence":"additional","affiliation":[]},{"given":"Stephen J.","family":"Chanock","sequence":"additional","affiliation":[]},{"given":"Wendy K.","family":"Chung","sequence":"additional","affiliation":[]},{"given":"Kathleen B. 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