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Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes

生物 计算生物学 基因 连锁不平衡 表达数量性状基因座 全基因组关联研究 遗传关联 遗传学 单核苷酸多态性 等位基因 单倍型 基因型
作者
Laura Fachal,Hugues Aschard,Jonathan Beesley,Daniel R. Barnes,Jamie Allen,Siddhartha Kar,Karen A. Pooley,Joe Dennis,Kyriaki Michailidou,Constance Turman,Penny Soucy,Audrey Lemaçon,Michael Lush,Jonathan Tyrer,Maya Ghoussaini,Mahdi Moradi Marjaneh,Xia Jiang,Simona Agata,Conxi Lázaro,­Rosario ­Tumino,Irene L. Andrulis,Hoda Anton‐Culver,Natalia Antonenkova,Aðalgeir Arason,Volker Arndt,Kristan J. Aronson,Banu Arun,Bernd Auber,Paul L. Auer,Brita Arver,Judith Balmañà,Rosa B. Barkardottir,Daniel Barrowdale,Javier Benı́tez,Javier Benı́tez,Marina Bermisheva,Katarzyna Białkowska,Amie Blanco,Carl Blomqvist,William J. Blot,Natalia Bogdanova,Stig E. Bojesen,Manjeet K. Bolla,Bernardo Bonanni,Kathleen Claes,K Bosse,Hiltrud Brauch,Hermann Brenner,Ignacio Briceño,Simon S. Cross,Angela Brooks‐Wilson,Thomas Brüning,Barbara Burwinkel,Saundra S. Buys,Qiuyin Cai,Trinidad Caldés,Maria Adelaide Caligo,Nicola J. Camp,Ian Campbell,Federico Canzian,Jason S. Carroll,Brian D. Carter,Jose E. Castelao,Jocelyne Chiquette,Hans Christiansen,Wendy K. Chung,Kathleen Claes,Christine L. Clarke,Margriet Collée,Sten Cornelissen,Fergus J. Couch,Angela Cox,Simon S. Cross,Cezary Cybulski,Kamila Czene,Mary Beth Terry,Geertruida H. de Bock,Peter Devilee,Orland Díez,Yuan Chun Ding,Gillian S. Dite,Susan M. Domchek,Thilo Dörk,Isabel dos‐Santos‐Silva,Arnaud Droit,Stéphane Dubois,Martine Dumont,M. Durán,Lorraine Durcan,Miriam Dwek,Diana Eccles,Christoph Engel,Mikael Eriksson,D. Gareth Evans,Peter A. Fasching,Olivia Fletcher,Giuseppe Floris,Daehee Kang,Lenka Foretová,William D. Foulkes,Eitan Friedman,Lin Fritschi,Debra Frost,Marike Gabrielson,Manuela Gago-Domínguez,Andrea Gehrig,Patricia A. Ganz,William Tapper,Judy E. Garber,José Á. García-Sáenz,Mia M. Gaudet,V. Georgoulias,Graham J. Mann,Gord Glendon,Andrew K. Godwin,Mark S. Goldberg,David E. Goldgar,Anna González‐Neira,Maria Grazia Tibiletti,Mark H. Greene,Mervi Grip,Jacek Gronwald,Anne Grundy,Pascal Guénel,Eric Hahnen,Christopher A. Haiman,Torben F. Ørntoft,Per Hall,Ute Hamann,Alexander Hein,Jaana M. Hartikainen,Mikael Hartman,Wei He,Catherine S. Healey,Bernadette A.M. Heemskerk-Gerritsen,Jane Heyworth,Peter Hillemanns,Sofia Khan,Antoinette Hollestelle,Maartje J. Hooning,John L. Hopper,Anthony Howell,Guanmengqian Huang,Peter J. Hulick,Evgeny N. Imyanitov,Claudine Isaacs,Motoki Iwasaki,Agnes Jager,Camilla Wendt,Anna Jakubowska,Paul James,Muna Abbas Ahmed,Rachel C. Jankowitz,Esther M. John,Nichola Johnson,Michael Jones,Arja Jukkola‐Vuorinen,Audrey Jung,Rudolf Kaaks,Daehee Kang,Pooja Middha Kapoor,Beth Y. Karlan,Renske Keeman,Michael J. Kerin,Э. К. Хуснутдинова,Jonathan Beesley,Sandrine M. Caputo,Cari M. Kitahara,Yon-Dschun Ko,Irene Konstantopoulou,Veli‐Matti Kosma,Stella Koutros,Katerina Kubelka-Sabit,Ava Kwong,Kyriacos Kyriacou,Gad Rennert,Diether Lambrechts,Eunjung Lee,Goska Leslie,Jenny Lester,Fabienne Lesueur,Annika Lindblom,Wing‐Yee Lo,Jirong Long,Artitaya Lophatananon,Jennifer T. Loud,Jan Lubiński,Robert J. MacInnis,Tom Maishman,Enes Makalic,Arto Mannermaa,Miriam Dwek,Siranoush Manoukian,Annika Lindblom,Maria Elena Martinez,Keitaro Matsuo,Tabea Maurer,Dimitrios Mavroudis,Rebecca Mayes,Christoph Engel,Catriona McLean,Noura Mebirouk,Alfons Meindl,Austin Miller,Austin Miller,Marco Montagna,Fernando Moreno,Kenneth Muir,Anna Marie Mulligan,Victor M. Muñoz-Garzon,Taru Muranen,Usha Menon,Rami Nassir,Katherine L. Nathanson,Susan L. Neuhausen,Heli Nevanlinna,Patrick Neven,Finn Cilius Nielsen,Liene Ņikitina-Zaķe,Aaron D. Norman,Conxi Lázaro,Edith Oláh,Olufunmilayo I. Olopade,Håkan Olsson,Nick Orr,Ana Osório,V. Shane Pankratz,J. Papp,Sue K. Park,Tjoung‐Won Park‐Simon,Michael T. Parsons,James Paul,Inge Søkilde Pedersen,Bernard Peissel,Beth N. Peshkin,Paolo Peterlongo,Julian Peto,Dijana Plaseska‐Karanfilska,Karolina Prajzendanc,Ross L. Prentice,Nadège Presneau,Darya Prokofyeva,Á. Izquierdo,Katri Pylkäs,Paolo Radice,Susan J. Ramus,Susan J. Ramus,Rohini Rau‐Murthy,Gad Rennert,Álvaro N.A. Monteiro,Mark E. Robson,Atocha Romero,Maria Rossing,Emmanouil Saloustros,Estela Sánchez‐Herrero,Dale P. Sandler,Marta Santamariña,Christobel Saunders,Elinor J. Sawyer,Maren T. Scheuner,Daniel F. Schmidt,David M. O’Malley,Andreas Schneeweiß,Mary Anne Rossing,Ben Schöttker,Peter Schürmann,Christopher G. Scott,Rodney J. Scott,Leigha Senter,Caroline Seynaeve,Mitul Shah,Helga B. Salvesen,Chen‐Yang Shen,Xiang Shu,Christian F. Singer,Thomas P. Slavin,Snezhana Smichkoska,Melissa C. Southey,John J. Spinelli,Amanda B. Spurdle,Jennifer Stone,Dominique Stoppa‐Lyonnet,Christian Sutter,Anthony J. Swerdlow,Rulla M. Tamimi,Yen Tan,William Tapper,Jack A. Taylor,Manuel R. Teixeira,Maria Tengström,Soo‐Hwang Teo,Mary Beth Terry,Àlex Teulé,Mads Thomassen,Darcy L. Thull,Marc Tischkowitz,Amanda E. Toland,Rob A.�E.�M. Tollenaar,Ian Tomlinson,Diana Torres,Gabriela Torres-Mejía,Melissa A. Troester,Thérèse Truong,Nadine Tung,Maria Tzardi,Hans-Ulrich Ulmer,Celine M. Vachon,Christi J. van Asperen,Lizet E. van der Kolk,Elizabeth J. van Rensburg,Ana Vega,Alessandra Viel,Joseph Vijai,Maartje J. Vogel,Qin Wang,Barbara Wappenschmidt,Clarice R. Weinberg,Jeffrey N. Weitzel,Camilla Wendt,Hans Wildiers,Robert Winqvist,Alicja Wolk,Anna H. Wu,Drakoulis Yannoukakos,Yan Zhang,Wei Zheng,David Wyld,Paul D.P. Pharoah,Jenny Chang‐Claude,Montserrat García‐Closas,Marjanka K. Schmidt,Roger L. Milne,Vessela N. Kristensen,Juliet D. French,Stacey L. Edwards,Antonis C. Antoniou,Georgia Chenevix‐Trench,Jacques Simard,Douglas F. Easton,Peter Kraft,Alison M. Dunning
出处
期刊:Nature Genetics [Nature Portfolio]
卷期号:52 (1): 56-73 被引量:138
标识
DOI:10.1038/s41588-019-0537-1
摘要

Genome-wide association studies have identified breast cancer risk variants in over 150 genomic regions, but the mechanisms underlying risk remain largely unknown. These regions were explored by combining association analysis with in silico genomic feature annotations. We defined 205 independent risk-associated signals with the set of credible causal variants in each one. In parallel, we used a Bayesian approach (PAINTOR) that combines genetic association, linkage disequilibrium and enriched genomic features to determine variants with high posterior probabilities of being causal. Potentially causal variants were significantly over-represented in active gene regulatory regions and transcription factor binding sites. We applied our INQUSIT pipeline for prioritizing genes as targets of those potentially causal variants, using gene expression (expression quantitative trait loci), chromatin interaction and functional annotations. Known cancer drivers, transcription factors and genes in the developmental, apoptosis, immune system and DNA integrity checkpoint gene ontology pathways were over-represented among the highest-confidence target genes. Fine-mapping of causal variants and integration of epigenetic and chromatin conformation data identify likely target genes for 150 breast cancer risk regions.

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