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

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    Authors
    Fachal, L
    Aschard, H
    Beesley, J
    Barnes, DR
    Allen, J
    Kar, S
    Pooley, KA
    Dennis, J
    Michailidou, K
    Turman, C
    Soucy, P
    Lemacon, A
    Lush, M
    Tyrer, JP
    Ghoussaini, M
    Marjaneh, MM
    Jiang, X
    Agata, S
    Aittomaki, K
    Alonso, MR
    Andrulis, IL
    Anton-Culver, H
    Antonenkova, NN
    Arason, A
    Arndt, V
    Aronson, KJ
    Arun, BK
    Auber, B
    Auer, PL
    Azzollini, J
    Balmana, J
    Barkardottir, RB
    Barrowdale, D
    Beeghly-Fadiel, A
    Benitez, J
    Bermisheva, M
    Bialkowska, K
    Blanco, AM
    Blomqvist, C
    Blot, W
    Bogdanova, NV
    Bojesen, SE
    Bolla, MK
    Bonanni, B
    Borg, A
    Bosse, K
    Brauch, H
    Brenner, H
    Briceno, I
    Brock, IW
    Brooks-Wilson, A
    Bruning, T
    Burwinkel, B
    Buys, SS
    Cai, Q
    Caldes, T
    Caligo, MA
    Camp, NJ
    Campbell, I
    Canzian, F
    Carroll, JS
    Carter, BD
    Castelao, JE
    Chiquette, J
    Christiansen, H
    Chung, WK
    Claes, KBM
    Clarke, CL
    Collee, JM
    Cornelissen, S
    Couch, FJ
    Cox, A
    Cross, SS
    Cybulski, C
    Czene, K
    Daly, MB
    de la Hoya, M
    Devilee, P
    Diez, O
    Ding, YC
    Dite, GS
    Domchek, SM
    Dork, T
    Dos-Santos-Silva, I
    Droit, A
    Dubois, S
    Dumont, M
    Duran, M
    Durcan, L
    Dwek, M
    Eccles, DM
    Engel, C
    Eriksson, M
    Evans, DG
    Fasching, PA
    Fletcher, O
    Floris, G
    Flyger, H
    Foretova, L
    Foulkes, WD
    Friedman, E
    Fritschi, L
    Frost, D
    Gabrielson, M
    Gago-Dominguez, M
    Gambino, G
    Ganz, PA
    Gapstur, SM
    Garber, J
    Garcia-Saenz, JA
    Gaudet, MM
    Georgoulias, V
    Giles, GG
    Glendon, G
    Godwin, AK
    Goldberg, MS
    Goldgar, DE
    Gonzalez-Neira, A
    Tibiletti, MG
    Greene, MH
    Grip, M
    Gronwald, J
    Grundy, A
    Guenel, P
    Hahnen, E
    Haiman, CA
    Hakansson, N
    Hall, P
    Hamann, U
    Harrington, PA
    Hartikainen, JM
    Hartman, M
    He, W
    Healey, CS
    Heemskerk-Gerritsen, BAM
    Heyworth, J
    Hillemanns, P
    Hogervorst, FBL
    Hollestelle, A
    Hooning, MJ
    Hopper, JL
    Howell, Anthony
    Huang, G
    Hulick, PJ
    Imyanitov, EN
    Isaacs, C
    Iwasaki, M
    Jager, A
    Jakimovska, M
    Jakubowska, A
    James, PA
    Janavicius, R
    Jankowitz, RC
    John, EM
    Johnson, N
    Jones, ME
    Jukkola-Vuorinen, A
    Jung, A
    Kaaks, R
    Kang, D
    Kapoor, PM
    Karlan, BY
    Keeman, R
    Kerin, MJ
    Khusnutdinova, E
    Kiiski, JI
    Kirk, J
    Kitahara, CM
    Ko, YD
    Konstantopoulou, I
    Kosma, VM
    Koutros, S
    Kubelka-Sabit, K
    Kwong, A
    Kyriacou, K
    Laitman, Y
    Lambrechts, D
    Lee, E
    Leslie, G
    Lester, J
    Lesueur, F
    Lindblom, A
    Lo, WY
    Long, J
    Lophatananon, A
    Loud, JT
    Lubinski, J
    MacInnis, RJ
    Maishman, T
    Makalic, E
    Mannermaa, A
    Manoochehri, M
    Manoukian, S
    Margolin, S
    Martinez, ME
    Matsuo, K
    Maurer, T
    Mavroudis, D
    Mayes, R
    McGuffog, L
    McLean, C
    Mebirouk, N
    Meindl, A
    Miller, A
    Miller, N
    Montagna, M
    Moreno, F
    Muir, K
    Mulligan, AM
    Munoz-Garzon, VM
    Muranen, TA
    Narod, SA
    Nassir, R
    Nathanson, KL
    Neuhausen, SL
    Nevanlinna, H
    Neven, P
    Nielsen, FC
    Nikitina-Zake, L
    Norman, A
    Offit, K
    Olah, E
    Olopade, OI
    Olsson, H
    Orr, N
    Osorio, A
    Pankratz, VS
    Papp, J
    Park, SK
    Park-Simon, TW
    Parsons, MT
    Paul, J
    Pedersen, IS
    Peissel, B
    Peshkin, B
    Peterlongo, P
    Peto, J
    Plaseska-Karanfilska, D
    Prajzendanc, K
    Prentice, R
    Presneau, N
    Prokofyeva, D
    Pujana, MA
    Pylkas, K
    Radice, P
    Ramus, SJ
    Rantala, J
    Rau-Murthy, R
    Rennert, G
    Risch, HA
    Robson, M
    Romero, A
    Rossing, M
    Saloustros, E
    Sanchez-Herrero, E
    Show allShow less
    Affiliation
    Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
    Issue Date
    2020
    
    Metadata
    Show full item record
    Abstract
    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.
    Citation
    Fachal L, Aschard H, Beesley J, Barnes DR, Allen J, Kar S, et al. Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes. Nat Genet. 2020;52(1):56-73.
    Journal
    Nature Genetics
    URI
    http://hdl.handle.net/10541/622711
    DOI
    10.1038/s41588-019-0537-1
    PubMed ID
    31911677
    Additional Links
    https://dx.doi.org/10.1038/s41588-019-0537-1
    Type
    Article
    Language
    en
    ae974a485f413a2113503eed53cd6c53
    10.1038/s41588-019-0537-1
    Scopus Count
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