PALB2, CHEK2 and ATM rare variants and cancer risk : data from COGS

Southey, Melissa C.; Goldgar, David E.; Winqvist, Robert; Pylkäs, Katri; Couch, Fergus; Tischkowitz, Marc; Foulkes, William D.; Dennis, Joe; Michailidou, Kyriaki; van Rensburg, Elizabeth J.; Heikkinen, Tuomas; Nevanlinna, Heli; Hopper, John L.; Doerk, Thilo; Claes, Kathleen B. M.; Reis-Filho, Jorge; Teo, Zhi Ling; Radice, Paolo; Catucci, Irene; Peterlongo, Paolo; Tsimiklis, Helen; Odefrey, Fabrice A.; Dowty, James G.; Schmidt, Marjanka K.; Broeks, Annegien; Hogervorst, Frans B.; Verhoef, Senno; Carpenter, Jane; Clarke, Christine; Scott, Rodney J.; Fasching, Peter A.; Haeberle, Lothar; Ekici, Arif B.; Beckmann, Matthias W.; Peto, Julian; dos-Santos-Silva, Isabel; Fletcher, Olivia; Johnson, Nichola; Bolla, Manjeet K.; Sawyer, Elinor J.; Tomlinson, Ian; Kerin, Michael J.; Miller, Nicola; Marme, Federik; Burwinkel, Barbara; Yang, Rongxi; Guenel, Pascal; Therese Truong; Menegaux, Florence; Sanchez, Marie; Bojesen, Stig; Nielsen, Sune F.; Flyger, Henrik; Benitez, Javier; Pilar Zamora, M.; Arias Perez, Jose Ignacio; Menendez, Primitiva; Anton-Culver, Hoda; Neuhausen, Susan; Ziogas, Argyrios; Clarke, Christina A.; Brenner, Hermann; Arndt, Volker; Stegmaier, Christa; Brauch, Hiltrud; Bruening, Thomas; Ko, Yon-Dschun; Muranen, Taru A.; Aittomaki, Kristiina; Blomqvist, Carl; Bogdanova, Natalia V.; Antonenkova, Natalia N.; Lindblom, Annika; Margolin, Sara; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M.; Spurdle, Amanda B.; Wauters, Els; Smeets, Dominiek; Beuselinck, Benoit; Floris, Giuseppe; Chang-Claude, Jenny; Rudolph, Anja; Seibold, Petra; Flesch-Janys, Dieter; Olson, Janet E.; Vachon, Celine; Pankratz, Vernon S.; McLean, Catriona; Haiman, Christopher A.; Henderson, Brian E.; Schumacher, Fredrick; Le Marchand, Loic; Kristensen, Vessela; Alnaes, Grethe Grenaker; Zheng, Wei; Hunter, David J.; Lindstrom, Sara; Hankinson, Susan E.; Kraft, Peter; Andrulis, Irene; Knight, Julia A.; Glendon, Gord; Mulligan, Anna Marie; Jukkola-Vuorinen, Arja; Grip, Mervi; Kauppila, Saila; Devilee, Peter; Tollenaar, Robert A. E. M.; Seynaeve, Caroline; Hollestelle, Antoinette; Garcia-Closas, Montserrat; Figueroa, Jonine; Chanock, Stephen J.; Lissowska, Jolanta; Czene, Kamila; Darabi, Hatef; Eriksson, Mikael; Eccles, Diana M.; Rafiq, Sajjad; Tapper, William J.; Gerty, Sue M.; Hooning, Maartje J.; Martens, John W. M.; Collee, J. Margriet; Tilanus-Linthorst, Madeleine; Hall, Per; Li, Jingmei; Brand, Judith S.; Humphreys, Keith; Cox, Angela; Reed, Malcolm W. R.; Luccarini, Craig; Baynes, Caroline; Dunning, Alison M.; Hamann, Ute; Torres, Diana; Ulmer, Hans Ulrich; Ruediger, Thomas; Jakubowska, Anna; Lubinski, Jan; Jaworska, Katarzyna; Durda, Katarzyna; Slager, Susan; Toland, Amanda E.; Ambrosone, Christine B.; Yannoukakos, Drakoulis; Swerdlow, Anthony; Ashworth, Alan; Orr, Nick; Jones, Michael; Gonzalez-Neira, Anna; Pita, Guillermo; Rosario Alonso, M.; Alvarez, Nuria; Herrero, Daniel; Tessier, Daniel C.; Vincent, Daniel; Bacot, Francois; Simard, Jacques; Dumont, Martine; Soucy, Penny; Eeles, Rosalind; Muir, Kenneth; Wiklund, Fredrik; Gronberg, Henrik; Schleutker, Johanna; Nordestgaard, Borge G.; Weischer, Maren; Travis, Ruth C.; Neal, David; Donovan, Jenny L.; Hamdy, Freddie C.; Khaw, Kay-Tee; Stanford, Janet L.; Blot, William J.; Thibodeau, Stephen; Schaid, Daniel J.; Kelley, Joseph L.; Maier, Christiane; Kibel, Adam S.; Cybulski, Cezary; Cannon-Albright, Lisa; Butterbach, Katja; Park, Jong; Kaneva, Radka; Batra, Jyotsna; Teixeira, Manuel R.; Kote-Jarai, Zsofia; Al Olama, Ali Amin; Benlloch, Sara; Renner, Stefan P.; Hartmann, Arndt; Hein, Alexander; Ruebner, Matthias; Lambrechts, Diether; Van Nieuwenhuysen, Els; Vergote, Ignace; Lambretchs, Sandrina; Doherty, Jennifer A.; Rossing, Mary Anne; Nickels, Stefan; Eilber, Ursula; Wang-Gohrke, Shan; Odunsi, Kunle; Sucheston-Campbell, Lara E.; Friel, Grace; Lurie, Galina; Killeen, Jeffrey L.; Wilkens, Lynne R.; Goodman, Marc T.; Runnebaum, Ingo; Hillemanns, Peter A.; Pelttari, Liisa M.; Butzow, Ralf; Modugno, Francesmary; Edwards, Robert P.; Ness, Roberta B.; Moysich, Kirsten B.; du Bois, Andreas; Heitz, Florian; Harter, Philipp; Kommoss, Stefan; Karlan, Beth Y.; Walsh, Christine; Lester, Jenny; Jensen, Allan; Kjaer, Susanne Kruger; Hogdall, Estrid; Peissel, Bernard; Bonanni, Bernardo; Bernard, Loris; Goode, Ellen L.; Fridley, Brooke L.; Vierkant, Robert A.; Cunningham, Julie M.; Larson, Melissa C.; Fogarty, Zachary C.; Kalli, Kimberly R.; Liang, Dong; Lu, Karen H.; Hildebrandt, Michelle A. T.; Wu, Xifeng; Levine, Douglas A.; Dao, Fanny; Bisogna, Maria; Berchuck, Andrew; Iversen, Edwin S.; Marks, Jeffrey R.; Akushevich, Lucy; Cramer, Daniel W.; Schildkraut, Joellen; Terry, Kathryn L.; Poole, Elizabeth M.; Stampfer, Meir; Tworoger, Shelley S.; Bandera, Elisa V.; Orlow, Irene; Olson, Sara H.; Bjorge, Line; Salvesen, Helga B.; van Altena, Anne M.; Aben, Katja K. H.; Kiemeney, Lambertus A.; Massuger, Leon F. A. G.; Pejovic, Tanja; Bean, Yukie; Brooks-Wilson, Angela; Kelemen, Linda E.; Cook, Linda S.; Le, Nhu D.; Grski, Bohdan; Gronwald, Jacek; Menkiszak, Janusz; Hogdall, Claus K.; Lundvall, Lene; Nedergaard, Lotte; Engelholm, Svend Aage; Dicks, Ed; Tyrer, Jonathan; Campbell, Ian; McNeish, Iain; Paul, James; Siddiqui, Nadeem; Glasspool, Rosalind; Whittemore, Alice S.; Rothstein, Joseph H.; McGuire, Valerie; Sieh, Weiva; Cai, Hui; Shu, Xiao-Ou; Teten, Rachel T.; Sutphen, Rebecca; McLaughlin, John R.; Narod, Steven A.; Phelan, Catherine M.; Monteiro, Alvaro N.; Fenstermacher, David; Lin, Hui-Yi; Permuth, Jennifer B.; Sellers, Thomas A.; Chen, Y. Ann; Tsai, Ya-Yu; Chen, Zhihua; Gentry-Maharaj, Aleksandra; Gayther, Simon A.; Ramus, Susan J.; Menon, Usha; Wu, Anna H.; Pearce, Celeste L.; Van den Berg, David; Pike, Malcolm C.; Dansonka-Mieszkowska, Agnieszka; Plisiecka-Halasa, Joanna; Moes-Sosnowska, Joanna; Kupryjanczyk, Jolanta; Pharoah, Paul D. P.; Song, Honglin; Winship, Ingrid; Chenevix-Trench, Georgia; Giles, Graham G.; Tavtigian, Sean V.; Easton, Doug F.; Milne, Roger L.
 
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URL:
https://doi.org/10.1136/jmedgenet-2016-103839

Southey, Melissa C.
Goldgar, David E.
Winqvist, Robert
Pylkäs, Katri
Couch, Fergus
Tischkowitz, Marc
Foulkes, William D.
Dennis, Joe
Michailidou, Kyriaki
van Rensburg, Elizabeth J.
Heikkinen, Tuomas
Nevanlinna, Heli
Hopper, John L.
Doerk, Thilo
Claes, Kathleen B. M.
Reis-Filho, Jorge
Teo, Zhi Ling
Radice, Paolo
Catucci, Irene
Peterlongo, Paolo
Tsimiklis, Helen
Odefrey, Fabrice A.
Dowty, James G.
Schmidt, Marjanka K.
Broeks, Annegien
Hogervorst, Frans B.
Verhoef, Senno
Carpenter, Jane
Clarke, Christine
Scott, Rodney J.
Fasching, Peter A.
Haeberle, Lothar
Ekici, Arif B.
Beckmann, Matthias W.
Peto, Julian
dos-Santos-Silva, Isabel
Fletcher, Olivia
Johnson, Nichola
Bolla, Manjeet K.
Sawyer, Elinor J.
Tomlinson, Ian
Kerin, Michael J.
Miller, Nicola
Marme, Federik
Burwinkel, Barbara
Yang, Rongxi
Guenel, Pascal
Therese Truong
Menegaux, Florence
Sanchez, Marie
Bojesen, Stig
Nielsen, Sune F.
Flyger, Henrik
Benitez, Javier
Pilar Zamora, M.
Arias Perez, Jose Ignacio
Menendez, Primitiva
Anton-Culver, Hoda
Neuhausen, Susan
Ziogas, Argyrios
Clarke, Christina A.
Brenner, Hermann
Arndt, Volker
Stegmaier, Christa
Brauch, Hiltrud
Bruening, Thomas
Ko, Yon-Dschun
Muranen, Taru A.
Aittomaki, Kristiina
Blomqvist, Carl
Bogdanova, Natalia V.
Antonenkova, Natalia N.
Lindblom, Annika
Margolin, Sara
Mannermaa, Arto
Kataja, Vesa
Kosma, Veli-Matti
Hartikainen, Jaana M.
Spurdle, Amanda B.
Wauters, Els
Smeets, Dominiek
Beuselinck, Benoit
Floris, Giuseppe
Chang-Claude, Jenny
Rudolph, Anja
Seibold, Petra
Flesch-Janys, Dieter
Olson, Janet E.
Vachon, Celine
Pankratz, Vernon S.
McLean, Catriona
Haiman, Christopher A.
Henderson, Brian E.
Schumacher, Fredrick
Le Marchand, Loic
Kristensen, Vessela
Alnaes, Grethe Grenaker
Zheng, Wei
Hunter, David J.
Lindstrom, Sara
Hankinson, Susan E.
Kraft, Peter
Andrulis, Irene
Knight, Julia A.
Glendon, Gord
Mulligan, Anna Marie
Jukkola-Vuorinen, Arja
Grip, Mervi
Kauppila, Saila
Devilee, Peter
Tollenaar, Robert A. E. M.
Seynaeve, Caroline
Hollestelle, Antoinette
Garcia-Closas, Montserrat
Figueroa, Jonine
Chanock, Stephen J.
Lissowska, Jolanta
Czene, Kamila
Darabi, Hatef
Eriksson, Mikael
Eccles, Diana M.
Rafiq, Sajjad
Tapper, William J.
Gerty, Sue M.
Hooning, Maartje J.
Martens, John W. M.
Collee, J. Margriet
Tilanus-Linthorst, Madeleine
Hall, Per
Li, Jingmei
Brand, Judith S.
Humphreys, Keith
Cox, Angela
Reed, Malcolm W. R.
Luccarini, Craig
Baynes, Caroline
Dunning, Alison M.
Hamann, Ute
Torres, Diana
Ulmer, Hans Ulrich
Ruediger, Thomas
Jakubowska, Anna
Lubinski, Jan
Jaworska, Katarzyna
Durda, Katarzyna
Slager, Susan
Toland, Amanda E.
Ambrosone, Christine B.
Yannoukakos, Drakoulis
Swerdlow, Anthony
Ashworth, Alan
Orr, Nick
Jones, Michael
Gonzalez-Neira, Anna
Pita, Guillermo
Rosario Alonso, M.
Alvarez, Nuria
Herrero, Daniel
Tessier, Daniel C.
Vincent, Daniel
Bacot, Francois
Simard, Jacques
Dumont, Martine
Soucy, Penny
Eeles, Rosalind
Muir, Kenneth
Wiklund, Fredrik
Gronberg, Henrik
Schleutker, Johanna
Nordestgaard, Borge G.
Weischer, Maren
Travis, Ruth C.
Neal, David
Donovan, Jenny L.
Hamdy, Freddie C.
Khaw, Kay-Tee
Stanford, Janet L.
Blot, William J.
Thibodeau, Stephen
Schaid, Daniel J.
Kelley, Joseph L.
Maier, Christiane
Kibel, Adam S.
Cybulski, Cezary
Cannon-Albright, Lisa
Butterbach, Katja
Park, Jong
Kaneva, Radka
Batra, Jyotsna
Teixeira, Manuel R.
Kote-Jarai, Zsofia
Al Olama, Ali Amin
Benlloch, Sara
Renner, Stefan P.
Hartmann, Arndt
Hein, Alexander
Ruebner, Matthias
Lambrechts, Diether
Van Nieuwenhuysen, Els
Vergote, Ignace
Lambretchs, Sandrina
Doherty, Jennifer A.
Rossing, Mary Anne
Nickels, Stefan
Eilber, Ursula
Wang-Gohrke, Shan
Odunsi, Kunle
Sucheston-Campbell, Lara E.
Friel, Grace
Lurie, Galina
Killeen, Jeffrey L.
Wilkens, Lynne R.
Goodman, Marc T.
Runnebaum, Ingo
Hillemanns, Peter A.
Pelttari, Liisa M.
Butzow, Ralf
Modugno, Francesmary
Edwards, Robert P.
Ness, Roberta B.
Moysich, Kirsten B.
du Bois, Andreas
Heitz, Florian
Harter, Philipp
Kommoss, Stefan
Karlan, Beth Y.
Walsh, Christine
Lester, Jenny
Jensen, Allan
Kjaer, Susanne Kruger
Hogdall, Estrid
Peissel, Bernard
Bonanni, Bernardo
Bernard, Loris
Goode, Ellen L.
Fridley, Brooke L.
Vierkant, Robert A.
Cunningham, Julie M.
Larson, Melissa C.
Fogarty, Zachary C.
Kalli, Kimberly R.
Liang, Dong
Lu, Karen H.
Hildebrandt, Michelle A. T.
Wu, Xifeng
Levine, Douglas A.
Dao, Fanny
Bisogna, Maria
Berchuck, Andrew
Iversen, Edwin S.
Marks, Jeffrey R.
Akushevich, Lucy
Cramer, Daniel W.
Schildkraut, Joellen
Terry, Kathryn L.
Poole, Elizabeth M.
Stampfer, Meir
Tworoger, Shelley S.
Bandera, Elisa V.
Orlow, Irene
Olson, Sara H.
Bjorge, Line
Salvesen, Helga B.
van Altena, Anne M.
Aben, Katja K. H.
Kiemeney, Lambertus A.
Massuger, Leon F. A. G.
Pejovic, Tanja
Bean, Yukie
Brooks-Wilson, Angela
Kelemen, Linda E.
Cook, Linda S.
Le, Nhu D.
Grski, Bohdan
Gronwald, Jacek
Menkiszak, Janusz
Hogdall, Claus K.
Lundvall, Lene
Nedergaard, Lotte
Engelholm, Svend Aage
Dicks, Ed
Tyrer, Jonathan
Campbell, Ian
McNeish, Iain
Paul, James
Siddiqui, Nadeem
Glasspool, Rosalind
Whittemore, Alice S.
Rothstein, Joseph H.
McGuire, Valerie
Sieh, Weiva
Cai, Hui
Shu, Xiao-Ou
Teten, Rachel T.
Sutphen, Rebecca
McLaughlin, John R.
Narod, Steven A.
Phelan, Catherine M.
Monteiro, Alvaro N.
Fenstermacher, David
Lin, Hui-Yi
Permuth, Jennifer B.
Sellers, Thomas A.
Chen, Y. Ann
Tsai, Ya-Yu
Chen, Zhihua
Gentry-Maharaj, Aleksandra
Gayther, Simon A.
Ramus, Susan J.
Menon, Usha
Wu, Anna H.
Pearce, Celeste L.
Van den Berg, David
Pike, Malcolm C.
Dansonka-Mieszkowska, Agnieszka
Plisiecka-Halasa, Joanna
Moes-Sosnowska, Joanna
Kupryjanczyk, Jolanta
Pharoah, Paul D. P.
Song, Honglin
Winship, Ingrid
Chenevix-Trench, Georgia
Giles, Graham G.
Tavtigian, Sean V.
Easton, Doug F.
Milne, Roger L.
BMJ

Southey MC, Goldgar DE, Winqvist R, et al PALB2, CHEK2 and ATM rare variants and cancer risk: data from COGS Journal of Medical Genetics 2016;53:800-811.

https://creativecommons.org/licenses/by/4.0/
Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/ This is an Open Access article distributed in accordance with the terms of the Creative Commons Attribution (CC BY 4.0) license, which permits others to distribute, remix, adapt and build upon this work, for commercial use, provided the original work is properly cited. See: http://creativecommons.org/licenses/by/4.0/
https://creativecommons.org/licenses/by/4.0/
doi:https://doi.org/10.1136/jmedgenet-2016-103839
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Abstract

Background: The rarity of mutations in PALB2, CHEK2 and ATM make it difficult to estimate precisely associated cancer risks. Population-based family studies have provided evidence that at least some of these mutations are associated with breast cancer risk as high as those associated with rare BRCA2 mutations. We aimed to estimate the relative risks associated with specific rare variants in PALB2, CHEK2 and ATM via a multicentre case-control study.

Methods: We genotyped 10 rare mutations using the custom iCOGS array: PALB2 c.1592delT, c.2816T>G and c.3113G>A, CHEK2 c.349A>G, c.538C>T, c.715G>A, c.1036C>T, c.1312G>T, and c.1343T>G and ATM c.7271T>G. We assessed associations with breast cancer risk (42 671 cases and 42 164 controls), as well as prostate (22 301 cases and 22 320 controls) and ovarian (14 542 cases and 23 491 controls) cancer risk, for each variant.

Results: For European women, strong evidence of association with breast cancer risk was observed for PALB2 c.1592delT OR 3.44 (95% CI 1.39 to 8.52, p = 7.1 × 10⁻⁵), PALB2 c.3113G>A OR 4.21 (95% CI 1.84 to 9.60, p = 6.9 × 10⁻⁸) and ATM c.7271T>G OR 11.0 (95% CI 1.42 to 85.7, p = 0.0012). We also found evidence of association with breast cancer risk for three variants in CHEK2, c.349A>G OR 2.26 (95% CI 1.29 to 3.95), c.1036C>T OR 5.06 (95% CI 1.09 to 23.5) and c.538C>T OR 1.33 (95% CI 1.05 to 1.67) (p ≤ 0.017). Evidence for prostate cancer risk was observed for CHEK2 c.1343T>G OR 3.03 (95% CI 1.53 to 6.03, p = 0.0006) for African men and CHEK2 c.1312G>T OR 2.21 (95% CI 1.06 to 4.63, p = 0.030) for European men. No evidence of association with ovarian cancer was found for any of these variants.

Conclusions: This report adds to accumulating evidence that at least some variants in these genes are associated with an increased risk of breast cancer that is clinically important.

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