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. 2017 Dec;49(12):1767-1778.
doi: 10.1038/ng.3785. Epub 2017 Oct 23.

Identification of Ten Variants Associated With Risk of Estrogen-Receptor-Negative Breast Cancer

Roger L Milne  1   2 Karoline B Kuchenbaecker  3   4 Kyriaki Michailidou  3   5 Jonathan Beesley  6 Siddhartha Kar  7 Sara Lindström  8   9 Shirley Hui  10 Audrey Lemaçon  11 Penny Soucy  11 Joe Dennis  3 Xia Jiang  9 Asha Rostamianfar  10 Hilary Finucane  9   12 Manjeet K Bolla  3 Lesley McGuffog  3 Qin Wang  3 Cora M Aalfs  13 ABCTB InvestigatorsMarcia Adams  14 Julian Adlard  15 Simona Agata  16 Shahana Ahmed  7 Habibul Ahsan  17 Kristiina Aittomäki  18 Fares Al-Ejeh  19 Jamie Allen  3 Christine B Ambrosone  20 Christopher I Amos  21 Irene L Andrulis  22   23 Hoda Anton-Culver  24 Natalia N Antonenkova  25 Volker Arndt  26 Norbert Arnold  27 Kristan J Aronson  28 Bernd Auber  29 Paul L Auer  30   31 Margreet G E M Ausems  32 Jacopo Azzollini  33 François Bacot  34 Judith Balmaña  35 Monica Barile  36 Laure Barjhoux  37 Rosa B Barkardottir  38   39 Myrto Barrdahl  40 Daniel Barnes  3 Daniel Barrowdale  3 Caroline Baynes  7 Matthias W Beckmann  41 Javier Benitez  42   43   44 Marina Bermisheva  45 Leslie Bernstein  46 Yves-Jean Bignon  47 Kathleen R Blazer  48 Marinus J Blok  49 Carl Blomqvist  50 William Blot  51   52 Kristie Bobolis  53 Bram Boeckx  54   55 Natalia V Bogdanova  25   56   57 Anders Bojesen  58 Stig E Bojesen  59   60   61 Bernardo Bonanni  36 Anne-Lise Børresen-Dale  62 Aniko Bozsik  63 Angela R Bradbury  64 Judith S Brand  65 Hiltrud Brauch  66   67   68 Hermann Brenner  26   68   69 Brigitte Bressac-de Paillerets  70 Carole Brewer  71 Louise Brinton  72 Per Broberg  73 Angela Brooks-Wilson  74   75 Joan Brunet  76 Thomas Brüning  77 Barbara Burwinkel  78   79 Saundra S Buys  80 Jinyoung Byun  21 Qiuyin Cai  51 Trinidad Caldés  81 Maria A Caligo  82 Ian Campbell  83   84 Federico Canzian  85 Olivier Caron  70 Angel Carracedo  86   87 Brian D Carter  88 J Esteban Castelao  89 Laurent Castera  90 Virginie Caux-Moncoutier  91 Salina B ChanJenny Chang-Claude  40   92 Stephen J Chanock  72 Xiaoqing Chen  6 Ting-Yuan David Cheng  93 Jocelyne Chiquette  94 Hans Christiansen  56 Kathleen B M Claes  95 Christine L Clarke  96 Thomas Conner  97 Don M Conroy  7 Jackie Cook  98 Emilie Cordina-Duverger  99 Sten Cornelissen  100 Isabelle Coupier  101 Angela Cox  102 David G Cox  103   104 Simon S Cross  105 Katarina Cuk  26 Julie M Cunningham  106 Kamila Czene  65 Mary B Daly  107 Francesca Damiola  37 Hatef Darabi  65 Rosemarie Davidson  108 Kim De Leeneer  95 Peter Devilee  109   110 Ed Dicks  7 Orland Diez  111 Yuan Chun Ding  46 Nina Ditsch  112 Kimberly F Doheny  14 Susan M Domchek  64 Cecilia M Dorfling  113 Thilo Dörk  57 Isabel Dos-Santos-Silva  114 Stéphane Dubois  11 Pierre-Antoine Dugué  1   2 Martine Dumont  11 Alison M Dunning  7 Lorraine Durcan  115   116 Miriam Dwek  117 Bernd Dworniczak  118 Diana Eccles  116 Ros Eeles  119 Hans Ehrencrona  120 Ursula Eilber  40 Bent Ejlertsen  121 Arif B Ekici  122 A Heather Eliassen  123   124 EMBRACEChristoph Engel  125   126 Mikael Eriksson  65 Laura Fachal  7 Laurence Faivre  127   128 Peter A Fasching  41   129 Ulrike Faust  130 Jonine Figueroa  72   131 Dieter Flesch-Janys  132   133 Olivia Fletcher  134 Henrik Flyger  135 William D Foulkes  136 Eitan Friedman  137   138 Lin Fritschi  139 Debra Frost  3 Marike Gabrielson  65 Pragna Gaddam  140 Marilie D Gammon  141 Patricia A Ganz  142 Susan M Gapstur  88 Judy Garber  143 Vanesa Garcia-Barberan  81 José A García-Sáenz  81 Mia M Gaudet  88 Marion Gauthier-Villars  91 Andrea Gehrig  144 GEMO Study CollaboratorsVassilios Georgoulias  145 Anne-Marie Gerdes  146 Graham G Giles  1   2 Gord Glendon  22 Andrew K Godwin  147 Mark S Goldberg  148   149 David E Goldgar  150 Anna González-Neira  42 Paul Goodfellow  151 Mark H Greene  152 Grethe I Grenaker Alnæs  62 Mervi Grip  153 Jacek Gronwald  154 Anne Grundy  155 Daphne Gschwantler-Kaulich  156 Pascal Guénel  99 Qi Guo  157 Lothar Haeberle  41 Eric Hahnen  158   159   160 Christopher A Haiman  161 Niclas Håkansson  162 Emily Hallberg  163 Ute Hamann  164 Nathalie Hamel  34 Susan Hankinson  165 Thomas V O Hansen  166 Patricia Harrington  7 Steven N Hart  163 Jaana M Hartikainen  167   168   169 Catherine S Healey  7 HEBONAlexander Hein  41 Sonja Helbig  57 Alex Henderson  170 Jane Heyworth  171 Belynda Hicks  172 Peter Hillemanns  57 Shirley Hodgson  173 Frans B Hogervorst  174 Antoinette Hollestelle  175 Maartje J Hooning  175 Bob Hoover  72 John L Hopper  2 Chunling Hu  106 Guanmengqian Huang  164 Peter J Hulick  176   177 Keith Humphreys  65 David J Hunter  9   124 Evgeny N Imyanitov  178 Claudine Isaacs  179 Motoki Iwasaki  180 Louise Izatt  181 Anna Jakubowska  154 Paul James  84   182 Ramunas Janavicius  183 Wolfgang Janni  184 Uffe Birk Jensen  185 Esther M John  186   187 Nichola Johnson  134 Kristine Jones  172 Michael Jones  188 Arja Jukkola-Vuorinen  189 Rudolf Kaaks  40 Maria Kabisch  164 Katarzyna Kaczmarek  154 Daehee Kang  190   191   192 Karin Kast  193 kConFab/AOCS InvestigatorsRenske Keeman  100 Michael J Kerin  194 Carolien M Kets  195 Machteld Keupers  196 Sofia Khan  197 Elza Khusnutdinova  45   198 Johanna I Kiiski  197 Sung-Won Kim  156 Julia A Knight  199   200 Irene Konstantopoulou  201 Veli-Matti Kosma  167   168   169 Vessela N Kristensen  62   202   203 Torben A Kruse  204 Ava Kwong  205   206   207 Anne-Vibeke Lænkholm  208 Yael Laitman  137 Fiona Lalloo  209 Diether Lambrechts  54   55 Keren Landsman  210 Christine Lasset  211 Conxi Lazaro  212 Loic Le Marchand  213 Julie Lecarpentier  3 Andrew Lee  3 Eunjung Lee  161 Jong Won Lee  214 Min Hyuk Lee  215 Flavio Lejbkowicz  210 Fabienne Lesueur  216   217   218   219 Jingmei Li  65 Jenna Lilyquist  220 Anne Lincoln  221 Annika Lindblom  222 Jolanta Lissowska  223 Wing-Yee Lo  66   67 Sibylle Loibl  224 Jirong Long  51 Jennifer T Loud  152 Jan Lubinski  154 Craig Luccarini  7 Michael Lush  3 Robert J MacInnis  1   2 Tom Maishman  115   116 Enes Makalic  2 Ivana Maleva Kostovska  225 Kathleen E Malone  226 Siranoush Manoukian  33 JoAnn E Manson  227 Sara Margolin  228 John W M Martens  175 Maria Elena Martinez  229   230 Keitaro Matsuo  231   232 Dimitrios Mavroudis  145 Sylvie Mazoyer  233 Catriona McLean  234 Hanne Meijers-Heijboer  13   235 Primitiva Menéndez  236 Jeffery Meyer  106 Hui Miao  237 Austin Miller  238 Nicola Miller  194 Gillian Mitchell  84   182 Marco Montagna  16 Kenneth Muir  239   240 Anna Marie Mulligan  241   242 Claire Mulot  243 Sue Nadesan  53 Katherine L Nathanson  64 NBSC CollaboratorsSusan L Neuhausen  46 Heli Nevanlinna  197 Ines Nevelsteen  196 Dieter Niederacher  244 Sune F Nielsen  59   60 Børge G Nordestgaard  59   60   61 Aaron Norman  163 Robert L Nussbaum  245 Edith Olah  63 Olufunmilayo I Olopade  246 Janet E Olson  163 Curtis Olswold  163 Kai-Ren Ong  247 Jan C Oosterwijk  248 Nick Orr  134 Ana Osorio  43   44 V Shane Pankratz  249 Laura Papi  250 Tjoung-Won Park-Simon  57 Ylva Paulsson-Karlsson  251 Rachel Lloyd  252 Inge Søkilde Pedersen  253 Bernard Peissel  33 Ana Peixoto  254 Jose I A Perez  255 Paolo Peterlongo  256 Julian Peto  114 Georg Pfeiler  157 Catherine M Phelan  257 Mila Pinchev  210 Dijana Plaseska-Karanfilska  225 Bruce Poppe  95 Mary E Porteous  258 Ross Prentice  30 Nadege Presneau  117 Darya Prokofieva  198 Elizabeth Pugh  14 Miquel Angel Pujana  259 Katri Pylkäs  260   261 Brigitte Rack  112   184 Paolo Radice  262 Nazneen Rahman  263 Johanna Rantala  264 Christine Rappaport-Fuerhauser  156 Gad Rennert  210   265 Hedy S Rennert  210   265 Valerie Rhenius  7 Kerstin Rhiem  158   159   160 Andrea Richardson  266 Gustavo C Rodriguez  267 Atocha Romero  81   268 Jane Romm  14 Matti A Rookus  269 Anja Rudolph  40 Thomas Ruediger  270 Emmanouil Saloustros  271 Joyce Sanders  272 Dale P Sandler  273 Suleeporn Sangrajrang  274 Elinor J Sawyer  275 Daniel F Schmidt  2 Minouk J Schoemaker  188 Fredrick Schumacher  276 Peter Schürmann  57 Lukas Schwentner  184 Christopher Scott  163 Rodney J Scott  277   278 Sheila Seal  263 Leigha Senter  279 Caroline Seynaeve  175 Mitul Shah  7 Priyanka Sharma  280 Chen-Yang Shen  281   282 Xin Sheng  161 Hermela Shimelis  106 Martha J Shrubsole  51 Xiao-Ou Shu  51 Lucy E Side  283 Christian F Singer  156 Christof Sohn  284 Melissa C Southey  285 John J Spinelli  286   287 Amanda B Spurdle  6 Christa Stegmaier  288 Dominique Stoppa-Lyonnet  91 Grzegorz Sukiennicki  154 Harald Surowy  78   79 Christian Sutter  289 Anthony Swerdlow  188   290 Csilla I Szabo  291 Rulla M Tamimi  9   123   124 Yen Y Tan  156 Jack A Taylor  273   292 Maria-Isabel Tejada  293 Maria Tengström  167   294   295 Soo H Teo  296   297 Mary B Terry  298 Daniel C Tessier  34 Alex Teulé  299 Kathrin Thöne  133 Darcy L Thull  300 Maria Grazia Tibiletti  301 Laima Tihomirova  302 Marc Tischkowitz  136   303 Amanda E Toland  304 Rob A E M Tollenaar  305 Ian Tomlinson  306 Ling Tong  17 Diana Torres  164   307 Martine Tranchant  11 Thérèse Truong  99 Kathy Tucker  308 Nadine Tung  309 Jonathan Tyrer  7 Hans-Ulrich Ulmer  310 Celine Vachon  163 Christi J van Asperen  311 David Van Den Berg  161 Ans M W van den Ouweland  312 Elizabeth J van Rensburg  113 Liliana Varesco  313 Raymonda Varon-Mateeva  314 Ana Vega  315   316 Alessandra Viel  317 Joseph Vijai  221 Daniel Vincent  34 Jason Vollenweider  106 Lisa Walker  318 Zhaoming Wang  72   319 Shan Wang-Gohrke  184 Barbara Wappenschmidt  158   159   160 Clarice R Weinberg  320 Jeffrey N Weitzel  48 Camilla Wendt  228 Jelle Wesseling  100   272 Alice S Whittemore  187   321 Juul T Wijnen  110   312 Walter Willett  124   322 Robert Winqvist  260   261 Alicja Wolk  162 Anna H Wu  161 Lucy Xia  161 Xiaohong R Yang  72 Drakoulis Yannoukakos  201 Daniela Zaffaroni  33 Wei Zheng  51 Bin Zhu  172 Argyrios Ziogas  24 Elad Ziv  323 Kristin K Zorn  301 Manuela Gago-Dominguez  86   229 Arto Mannermaa  167   168   169 Håkan Olsson  73 Manuel R Teixeira  254   324 Jennifer Stone  252   325 Kenneth Offit  326   327 Laura Ottini  328 Sue K Park  190   192 Mads Thomassen  204 Per Hall  65   329 Alfons Meindl  330 Rita K Schmutzler  158   160 Arnaud Droit  11 Gary D Bader  10 Paul D P Pharoah  3   7 Fergus J Couch  106 Douglas F Easton  3   7 Peter Kraft  9   124 Georgia Chenevix-Trench  6 Montserrat García-Closas  72 Marjanka K Schmidt  100   331 Antonis C Antoniou  3 Jacques Simard  11
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Free PMC article

Identification of Ten Variants Associated With Risk of Estrogen-Receptor-Negative Breast Cancer

Roger L Milne et al. Nat Genet. .
Free PMC article

Abstract

Most common breast cancer susceptibility variants have been identified through genome-wide association studies (GWAS) of predominantly estrogen receptor (ER)-positive disease. 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 × 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.

Conflict of interest statement

COMPETING FINANCIAL INTERESTS

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1
Genomic region around the independent ER-negative risk-associated variants 11_108345515_G_A (rs11374964) and 11_108357137_G_A (rs74911261). A 1-Mb regional association plot shows the statistical significance of all genotyped and imputed SNPs with the genome-wide significance level (P = 5 × 10−8) represented by the dashed red line. The positions of candidate causal variants for two independent signals (depicted as red and blue ticks) are shown in relation to RefSeq genes. Missense variants are labeled with asterisks. Mammary cell enhancers overlapping candidate SNPs predicted to target nearby genes by IM-PET46 are depicted as black bars. Chromatin interactions from ENCODE ChIA-PET data in MCF7 cells overlapping candidate variants are shaded to reflect interaction confidence scores with darker shading indicating greater confidence. Epigenomic features (derived from publicly available ChIP–seq and DNase–seq data sets) that overlap candidate variants are shown as red or blue segments, depending on the intersected signal. Density tracks show the summed occurrence of ChIP–seq and DNase–seq peak signals at each position. Roadmap Epigenomics Project chromatin state models for HMECs and myoepithelial cells grouped into enhancer, promoter or transcribed annotations are shown as yellow, red and green segments, respectively. Transcript levels in MCF7 cells and HMECs are represented by histograms depicting mean normalized RNA-seq expression. All MCF7 ChIA-PET (ENCODE) and HMEC Hi-C47 chromatin interactions are represented by black and blue arcs, respectively. NHGRI GWAS catalog SNPs are shown as green ticks. All OncoArray SNPs (genotyped or imputed) are shown as black ticks, and uninterrogated, common SNPs (dbSNP138, European (EUR) MAF > 1%) are shown as red ticks. Features may be examined in detail via exploration of a custom UCSC Genome Browser session accessible via hyperlinks within Supplementary Table 5. TF, transcription factor; DHS, DNase I–hypersensitive site.

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  • Analysis of mitochondrial m1A/G RNA modification reveals links to nuclear genetic variants and associated disease processes.
    Ali AT, Idaghdour Y, Hodgkinson A. Ali AT, et al. Commun Biol. 2020 Mar 27;3(1):147. doi: 10.1038/s42003-020-0879-3. Commun Biol. 2020. PMID: 32221480 Free PMC article.
  • Update Breast Cancer 2020 Part 1 - Early Breast Cancer: Consolidation of Knowledge About Known Therapies.
    Schneeweiss A, Hartkopf AD, Müller V, Wöckel A, Lux MP, Janni W, Ettl J, Belleville E, Huober J, Thill M, Fasching PA, Kolberg HC, Pöschke P, Welslau M, Overkamp F, Tesch H, Fehm TN, Lüftner D, Schütz F. Schneeweiss A, et al. Geburtshilfe Frauenheilkd. 2020 Mar;80(3):277-287. doi: 10.1055/a-1111-2431. Epub 2020 Mar 4. Geburtshilfe Frauenheilkd. 2020. PMID: 32139917 Free PMC article.
  • Clinical applications of polygenic breast cancer risk: a critical review and perspectives of an emerging field.
    Yanes T, Young MA, Meiser B, James PA. Yanes T, et al. Breast Cancer Res. 2020 Feb 17;22(1):21. doi: 10.1186/s13058-020-01260-3. Breast Cancer Res. 2020. PMID: 32066492 Free PMC article. Review.
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