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125 results on '"Karyadi Danielle M"'

1. Genomic characterization of cervical lymph node metastases in papillary thyroid carcinoma following the Chornobyl accident

Author

Morton, Lindsay M., Lee, Olivia W., Karyadi, Danielle M., Bogdanova, Tetiana I., Stewart, Chip, Hartley, Stephen W., Breeze, Charles E., Schonfeld, Sara J., Cahoon, Elizabeth K., Drozdovitch, Vladimir, Masiuk, Sergii, Chepurny, Mykola, Zurnadzhy, Liudmyla Yu, Dai, Jieqiong, Krznaric, Marko, Yeager, Meredith, Hutchinson, Amy, Hicks, Belynda D., Dagnall, Casey L., Steinberg, Mia K., Jones, Kristine, Jain, Komal, Jordan, Ben, Machiela, Mitchell J., Dawson, Eric T., Vij, Vibha, Gastier-Foster, Julie M., Bowen, Jay, Mabuchi, Kiyohiko, Hatch, Maureen, Berrington de Gonzalez, Amy, Getz, Gad, Tronko, Mykola D., Thomas, Gerry A., and Chanock, Stephen J.

Published
2024
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3. Inflated expectations: Rare-variant association analysis using public controls

Author

Kim, Jung, Karyadi, Danielle M, Hartley, Stephen W, Zhu, Bin, Wang, Mingyi, Wu, Dongjing, Song, Lei, Armstrong, Gregory T, Bhatia, Smita, Robison, Leslie L, Yasui, Yutaka, Carter, Brian, Sampson, Joshua N, Freedman, Neal D, Goldstein, Alisa M, Mirabello, Lisa, Chanock, Stephen J, Morton, Lindsay M, Savage, Sharon A, and Stewart, Douglas R

Subjects
Epidemiology, Biological Sciences, Health Sciences, Genetics, Motivation, High-Throughput Nucleotide Sequencing, Polymorphism, Single Nucleotide, Software, General Science & Technology
Abstract

The use of publicly available sequencing datasets as controls (hereafter, "public controls") in studies of rare variant disease associations has great promise but can increase the risk of false-positive discovery. The specific factors that could contribute to inflated distribution of test statistics have not been systematically examined. Here, we leveraged both public controls, gnomAD v2.1 and several datasets sequenced in our laboratory to systematically investigate factors that could contribute to the false-positive discovery, as measured by λΔ95, a measure to quantify the degree of inflation in statistical significance. Analyses of datasets in this investigation found that 1) the significantly inflated distribution of test statistics decreased substantially when the same variant caller and filtering pipelines were employed, 2) differences in library prep kits and sequencers did not affect the false-positive discovery rate and, 3) joint vs. separate variant-calling of cases and controls did not contribute to the inflation of test statistics. Currently available methods do not adequately adjust for the high false-positive discovery. These results, especially if replicated, emphasize the risks of using public controls for rare-variant association tests in which individual-level data and the computational pipeline are not readily accessible, which prevents the use of the same variant-calling and filtering pipelines on both cases and controls. A plausible solution exists with the emergence of cloud-based computing, which can make it possible to bring containerized analytical pipelines to the data (rather than the data to the pipeline) and could avert or minimize these issues. It is suggested that future reports account for this issue and provide this as a limitation in reporting new findings based on studies that cannot practically analyze all data on a single pipeline.

Published
2023

4. Analysis of Xq27-28 linkage in the international consortium for prostate cancer genetics (ICPCG) families

Author

Bailey-Wilson Joan E, Childs Erica J, Cropp Cheryl D, Schaid Daniel J, Xu Jianfeng, Camp Nicola J, Cannon-Albright Lisa A, Farnham James M, George Asha, Powell Isaac, Carpten John D, Giles Graham G, Hopper John L, Severi Gianluca, English Dallas R, Foulkes William D, Mæhle Lovise, Møller Pål, Eeles Rosalind, Easton Douglas, Guy Michelle, Edwards Steve, Badzioch Michael D, Whittemore Alice S, Oakley-Girvan Ingrid, Hsieh Chih-Lin, Dimitrov Latchezar, Stanford Janet L, Karyadi Danielle M, Deutsch Kerry, McIntosh Laura, Ostrander Elaine A, Wiley Kathleen E, Isaacs Sarah D, Walsh Patrick C, Thibodeau Stephen N, McDonnell Shannon K, Hebbring Scott, Lange Ethan M, Cooney Kathleen A, Tammela Teuvo LJ, Schleutker Johanna, Maier Christiane, Bochum Sylvia, Hoegel Josef, Grönberg Henrik, Wiklund Fredrik, Emanuelsson Monica, Cancel-Tassin Geraldine, Valeri Antoine, Cussenot Olivier, and Isaacs William B

Subjects
Internal medicine, RC31-1245, Genetics, QH426-470
Abstract

Abstract Background Genetic variants are likely to contribute to a portion of prostate cancer risk. Full elucidation of the genetic etiology of prostate cancer is difficult because of incomplete penetrance and genetic and phenotypic heterogeneity. Current evidence suggests that genetic linkage to prostate cancer has been found on several chromosomes including the X; however, identification of causative genes has been elusive. Methods Parametric and non-parametric linkage analyses were performed using 26 microsatellite markers in each of 11 groups of multiple-case prostate cancer families from the International Consortium for Prostate Cancer Genetics (ICPCG). Meta-analyses of the resultant family-specific linkage statistics across the entire 1,323 families and in several predefined subsets were then performed. Results Meta-analyses of linkage statistics resulted in a maximum parametric heterogeneity lod score (HLOD) of 1.28, and an allele-sharing lod score (LOD) of 2.0 in favor of linkage to Xq27-q28 at 138 cM. In subset analyses, families with average age at onset less than 65 years exhibited a maximum HLOD of 1.8 (at 138 cM) versus a maximum regional HLOD of only 0.32 in families with average age at onset of 65 years or older. Surprisingly, the subset of families with only 2–3 affected men and some evidence of male-to-male transmission of prostate cancer gave the strongest evidence of linkage to the region (HLOD = 3.24, 134 cM). For this subset, the HLOD was slightly increased (HLOD = 3.47 at 134 cM) when families used in the original published report of linkage to Xq27-28 were excluded. Conclusions Although there was not strong support for linkage to the Xq27-28 region in the complete set of families, the subset of families with earlier age at onset exhibited more evidence of linkage than families with later onset of disease. A subset of families with 2–3 affected individuals and with some evidence of male to male disease transmission showed stronger linkage signals. Our results suggest that the genetic basis for prostate cancer in our families is much more complex than a single susceptibility locus on the X chromosome, and that future explorations of the Xq27-28 region should focus on the subset of families identified here with the strongest evidence of linkage to this region.

Published
2012
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5. ArCH: improving the performance of clonal hematopoiesis variant calling and interpretation

Author

Chan, Irenaeus C C, primary, Panchot, Alex, additional, Schmidt, Evelyn, additional, McNulty, Samantha, additional, Wiley, Brian J, additional, Liu, Jie, additional, Turner, Kimberly, additional, Moukarzel, Lea, additional, Wong, Wendy S W, additional, Tran, Duc, additional, Beeler, J Scott, additional, Batchi-Bouyou, Armel Landry, additional, Machiela, Mitchell J, additional, Karyadi, Danielle M, additional, Krajacich, Benjamin J, additional, Zhao, Junhua, additional, Kruglyak, Semyon, additional, Lajoie, Bryan, additional, Levy, Shawn, additional, Patel, Minal, additional, Kantoff, Philip W, additional, Mason, Christopher E, additional, Link, Daniel C, additional, Druley, Todd E, additional, Stopsack, Konrad H, additional, and Bolton, Kelly L, additional

Published
2024
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6. Supplementary Table 2 from Germline Missense Variants in the BTNL2 Gene Are Associated with Prostate Cancer Susceptibility

Author

FitzGerald, Liesel M., primary, Kumar, Akash, primary, Boyle, Evan A., primary, Zhang, Yuzheng, primary, McIntosh, Laura M., primary, Kolb, Suzanne, primary, Stott-Miller, Marni, primary, Smith, Tiffany, primary, Karyadi, Danielle M., primary, Ostrander, Elaine A., primary, Hsu, Li, primary, Shendure, Jay, primary, and Stanford, Janet L., primary

Published
2023
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7. Supplementary Data 1-9 from The MTAP-CDKN2A Locus Confers Susceptibility to a Naturally Occurring Canine Cancer

Author

Shearin, Abigail L., primary, Hedan, Benoit, primary, Cadieu, Edouard, primary, Erich, Suzanne A., primary, Schmidt, Emmett V., primary, Faden, Daniel L., primary, Cullen, John, primary, Abadie, Jerome, primary, Kwon, Erika M., primary, Gröne, Andrea, primary, Devauchelle, Patrick, primary, Rimbault, Maud, primary, Karyadi, Danielle M., primary, Lynch, Mary, primary, Galibert, Francis, primary, Breen, Matthew, primary, Rutteman, Gerard R., primary, André, Catherine, primary, Parker, Heidi G., primary, and Ostrander, Elaine A., primary

Published
2023
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8. Supplementary Table 3 from Germline Missense Variants in the BTNL2 Gene Are Associated with Prostate Cancer Susceptibility

Author

FitzGerald, Liesel M., primary, Kumar, Akash, primary, Boyle, Evan A., primary, Zhang, Yuzheng, primary, McIntosh, Laura M., primary, Kolb, Suzanne, primary, Stott-Miller, Marni, primary, Smith, Tiffany, primary, Karyadi, Danielle M., primary, Ostrander, Elaine A., primary, Hsu, Li, primary, Shendure, Jay, primary, and Stanford, Janet L., primary

Published
2023
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9. Supplementary Figure 1 from Germline Missense Variants in the BTNL2 Gene Are Associated with Prostate Cancer Susceptibility

Author

FitzGerald, Liesel M., primary, Kumar, Akash, primary, Boyle, Evan A., primary, Zhang, Yuzheng, primary, McIntosh, Laura M., primary, Kolb, Suzanne, primary, Stott-Miller, Marni, primary, Smith, Tiffany, primary, Karyadi, Danielle M., primary, Ostrander, Elaine A., primary, Hsu, Li, primary, Shendure, Jay, primary, and Stanford, Janet L., primary

Published
2023
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10. Data from Germline Missense Variants in the BTNL2 Gene Are Associated with Prostate Cancer Susceptibility

Author

FitzGerald, Liesel M., primary, Kumar, Akash, primary, Boyle, Evan A., primary, Zhang, Yuzheng, primary, McIntosh, Laura M., primary, Kolb, Suzanne, primary, Stott-Miller, Marni, primary, Smith, Tiffany, primary, Karyadi, Danielle M., primary, Ostrander, Elaine A., primary, Hsu, Li, primary, Shendure, Jay, primary, and Stanford, Janet L., primary

Published
2023
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11. Supplementary Figure Legend from Germline Missense Variants in the BTNL2 Gene Are Associated with Prostate Cancer Susceptibility

Author

FitzGerald, Liesel M., primary, Kumar, Akash, primary, Boyle, Evan A., primary, Zhang, Yuzheng, primary, McIntosh, Laura M., primary, Kolb, Suzanne, primary, Stott-Miller, Marni, primary, Smith, Tiffany, primary, Karyadi, Danielle M., primary, Ostrander, Elaine A., primary, Hsu, Li, primary, Shendure, Jay, primary, and Stanford, Janet L., primary

Published
2023
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12. Supplementary Table 1 from Germline Missense Variants in the BTNL2 Gene Are Associated with Prostate Cancer Susceptibility

Author

FitzGerald, Liesel M., primary, Kumar, Akash, primary, Boyle, Evan A., primary, Zhang, Yuzheng, primary, McIntosh, Laura M., primary, Kolb, Suzanne, primary, Stott-Miller, Marni, primary, Smith, Tiffany, primary, Karyadi, Danielle M., primary, Ostrander, Elaine A., primary, Hsu, Li, primary, Shendure, Jay, primary, and Stanford, Janet L., primary

Published
2023
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13. Abstract 980: Genomic characterization of lymph node metastases in papillary thyroid carcinoma following the Chernobyl accident reveals an expression profile specific to metastatic process

Author

Lee, Olivia W., primary, Karyadi, Danielle M., additional, Stewart, Chip, additional, Bogdanova, Tetiana I., additional, Dai, Jieqiong, additional, Hartley, Stephen W., additional, Schonfeld, Sara J., additional, Kapoor, Vidushi, additional, Krznaric, Marko, additional, Yeager, Meredith, additional, Hutchinson, Amy, additional, Hicks, Belynda D., additional, Dagnall, Casey L., additional, Gastier-Foster, Julie M., additional, Bowen, Jay, additional, Machiela, Mitchell J., additional, Cahoon, Elizabeth K., additional, Mabuchi, Kiyohiko, additional, Drozdovitch, Vladimir, additional, Masiuk, Sergii, additional, Chepurny, Mykola, additional, Zurnadzhy, Liudmyla Y., additional, de González, Amy Berrington, additional, Getz, Gad, additional, Thomas, Gerry A., additional, Tronko, Mykola D., additional, Morton, Lindsay M., additional, and Chanock, Stephen J., additional

Published
2022
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14. Joint effects of general population polygenic risk scores (PRS) and radiation treatment on subsequent neoplasm risk among childhood cancer survivors: A report from the Childhood Cancer Survivor Study (CCSS).

Author

Gibson, Todd M., primary, Karyadi, Danielle M, additional, Kapoor, Vidushi, additional, Arnold, Michael, additional, Berrington de González, Amy, additional, Bhatia, Smita, additional, Conces, Miriam, additional, Hartley, Stephen, additional, Howell, Rebecca M., additional, Leisenring, Wendy M., additional, Neglia, Joseph Philip, additional, Turcotte, Lucie Marie, additional, Yasui, Yutaka, additional, Chanock, Stephen J., additional, Armstrong, Gregory T., additional, and Morton, Lindsay M., additional

Published
2022
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16. Identification and characterization of novel SNPs in CHEK2 in Ashkenazi Jewish men with prostate cancer

Author

Tischkowitz, Marc D., Yilmaz, Ahmet, Chen, Long Q., Karyadi, Danielle M., Novak, David, Kirchhoff, Tomas, Hamel, Nancy, Tavtigian, Sean V., Kolb, Suzanne, Bismar, Tarek A., Aloyz, Raquel, Nelson, Peter S., Hood, Lee, Narod, Steven A., White, Kirsten A., Ostrander, Elaine A., Isaacs, William B., Offit, Kenneth, Cooney, Kathleen A., Stanford, Janet L., and Foulkes, William D.

Published
2008
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17. Radiation-related genomic profile of papillary thyroid carcinoma after the Chernobyl accident

Author

Morton, Lindsay M., primary, Karyadi, Danielle M., additional, Stewart, Chip, additional, Bogdanova, Tetiana I., additional, Dawson, Eric T., additional, Steinberg, Mia K., additional, Dai, Jieqiong, additional, Hartley, Stephen W., additional, Schonfeld, Sara J., additional, Sampson, Joshua N., additional, Maruvka, Yosef E., additional, Kapoor, Vidushi, additional, Ramsden, Dale A., additional, Carvajal-Garcia, Juan, additional, Perou, Charles M., additional, Parker, Joel S., additional, Krznaric, Marko, additional, Yeager, Meredith, additional, Boland, Joseph F., additional, Hutchinson, Amy, additional, Hicks, Belynda D., additional, Dagnall, Casey L., additional, Gastier-Foster, Julie M., additional, Bowen, Jay, additional, Lee, Olivia, additional, Machiela, Mitchell J., additional, Cahoon, Elizabeth K., additional, Brenner, Alina V., additional, Mabuchi, Kiyohiko, additional, Drozdovitch, Vladimir, additional, Masiuk, Sergii, additional, Chepurny, Mykola, additional, Zurnadzhy, Liudmyla Yu., additional, Hatch, Maureen, additional, Berrington de Gonzalez, Amy, additional, Thomas, Gerry A., additional, Tronko, Mykola D., additional, Getz, Gad, additional, and Chanock, Stephen J., additional

Published
2021
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18. In utero exposure to zidovudine-containing antiretroviral therapy and clonal hematopoiesis in HIV-exposed uninfected newborns

Author

Lin, Shu-Hong, primary, Wang, Youjin, additional, Hartley, Stephen W., additional, Karyadi, Danielle M., additional, Lee, Olivia W., additional, Zhu, Bin, additional, Zhou, Weiyin, additional, Brown, Derek W., additional, Beilstein-Wedel, Erin, additional, Hazra, Rohan, additional, Kacanek, Deborah, additional, Chadwick, Ellen G., additional, Marsit, Carmen J., additional, Poirier, Miriam C., additional, Brummel, Sean S., additional, Chanock, Stephen J., additional, Engels, Eric A., additional, and Machiela, Mitchell J., additional

Published
2021
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21. Frequency of Pathogenic Germline Variants in Cancer-Susceptibility Genes in the Childhood Cancer Survivor Study

Author

Kim, Jung, primary, Gianferante, Matthew, additional, Karyadi, Danielle M, additional, Hartley, Stephen W, additional, Frone, Megan N, additional, Luo, Wen, additional, Robison, Leslie L, additional, Armstrong, Gregory T, additional, Bhatia, Smita, additional, Dean, Michael, additional, Yeager, Meredith, additional, Zhu, Bin, additional, Song, Lei, additional, Sampson, Joshua N, additional, Yasui, Yutaka, additional, Leisenring, Wendy M, additional, Brodie, Seth A, additional, de Andrade, Kelvin C, additional, Fortes, Fernanda P, additional, Goldstein, Alisa M, additional, Khincha, Payal P, additional, Machiela, Mitchell J, additional, McMaster, Mary L, additional, Nickerson, Michael L, additional, Oba, Leatrisse, additional, Pemov, Alexander, additional, Pinheiro, Maisa, additional, Rotunno, Melissa, additional, Santiago, Karina, additional, Wegman-Ostrosky, Talia, additional, Diver, W Ryan, additional, Teras, Lauren, additional, Freedman, Neal D, additional, Hicks, Belynda D, additional, Wang, Mingyi, additional, Jones, Kristine, additional, Hutchinson, Amy A, additional, Dagnall, Casey, additional, Savage, Sharon A, additional, Tucker, Margaret A, additional, Chanock, Stephen J, additional, Morton, Lindsay M, additional, Stewart, Douglas R, additional, and Mirabello, Lisa, additional

Published
2021
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23. A meta-analysis of genome-wide association studies to identify prostate cancer susceptibility loci associated with aggressive and non-aggressive disease

Author

Amin Al Olama, Ali, Kote-Jarai, Zsofia, Schumacher, Fredrick R., Wiklund, Fredrik, Berndt, Sonja I., Benlloch, Sara, Giles, Graham G., Severi, Gianluca, Neal, David E., Hamdy, Freddie C., Donovan, Jenny L., Hunter, David J., Henderson, Brian E., Thun, Michael J., Gaziano, Michael, Giovannucci, Edward L., Siddiq, Afshan, Travis, Ruth C., Cox, David G., Canzian, Federico, Riboli, Elio, Key, Timothy J., Andriole, Gerald, Albanes, Demetrius, Hayes, Richard B., Schleutker, Johanna, Auvinen, Anssi, Tammela, Teuvo L.J., Weischer, Maren, Stanford, Janet L., Ostrander, Elaine A., Cybulski, Cezary, Lubinski, Jan, Thibodeau, Stephen N., Schaid, Daniel J., Sorensen, Karina D., Batra, Jyotsna, Clements, Judith A., Chambers, Suzanne, Aitken, Joanne, Gardiner, Robert A., Maier, Christiane, Vogel, Walther, Dörk, Thilo, Brenner, Hermann, Habuchi, Tomonori, Ingles, Sue, John, Esther M., Dickinson, Joanne L., Cannon-Albright, Lisa, Teixeira, Manuel R., Kaneva, Radka, Zhang, Hong-Wei, Lu, Yong-Jie, Park, Jong Y., Cooney, Kathleen A., Muir, Kenneth R., Leongamornlert, Daniel A., Saunders, Edward, Tymrakiewicz, Malgorzata, Mahmud, Nadiya, Guy, Michelle, Govindasami, Koveela, OʼBrien, Lynne T., Wilkinson, Rosemary A., Hall, Amanda L., Sawyer, Emma J., Dadaev, Tokhir, Morrison, Jonathan, Dearnaley, David P., Horwich, Alan, Huddart, Robert A., Khoo, Vincent S., Parker, Christopher C., Van As, Nicholas, Woodhouse, Christopher J., Thompson, Alan, Dudderidge, Tim, Ogden, Chris, Cooper, Colin S., Lophatonanon, Artitaya, Southey, Melissa C., Hopper, John L., English, Dallas, Virtamo, Jarmo, Le Marchand, Loic, Campa, Daniele, Kaaks, Rudolf, Lindstrom, Sara, Diver, W. Ryan, Gapstur, Susan, Yeager, Meredith, Cox, Angela, Stern, Mariana C., Corral, Roman, Aly, Markus, Isaacs, William, Adolfsson, Jan, Xu, Jianfeng, Zheng, S. Lilly, Wahlfors, Tiina, Taari, Kimmo, Kujala, Paula, Klarskov, Peter, Nordestgaard, Børge G., Røder, M. Andreas, Frikke-Schmidt, Ruth, Bojesen, Stig E., FitzGerald, Liesel M., Kolb, Suzanne, Kwon, Erika M., Karyadi, Danielle M., Orntoft, Torben Falck, Borre, Michael, Rinckleb, Antje, Luedeke, Manuel, Herkommer, Kathleen, Meyer, Andreas, Serth, Jürgen, Marthick, James R., Patterson, Briony, Wokolorczyk, Dominika, Spurdle, Amanda, Lose, Felicity, McDonnell, Shannon K., Joshi, Amit D., Shahabi, Ahva, Pinto, Pedro, Santos, Joana, Ray, Ana, Sellers, Thomas A., Lin, Hui-Yi, Stephenson, Robert A., Teerlink, Craig, Muller, Heiko, Rothenbacher, Dietrich, Tsuchiya, Norihiko, Narita, Shintaro, Cao, Guang-Wen, Slavov, Chavdar, Mitev, Vanio, Chanock, Stephen, Gronberg, Henrik, Haiman, Christopher A., Kraft, Peter, Easton, Douglas F., and Eeles, Rosalind A.

Published
2013
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25. Contributors

Author

Abbruzzese, James L., primary, Abeloff, Martin D., additional, Abou-Alfa, Ghassan K., additional, Abrahm, Janet L., additional, Abrams, Jeffery S., additional, Acs, Geza, additional, Aisner, Joseph, additional, Aisner, Seena C., additional, Alani, Rhoda M., additional, Alberts, Steven R., additional, Ambinder, Richard F., additional, Andritsos, Leslie A., additional, Appelbaum, Frederick R., additional, Apte, Sachin, additional, Armitage, James O., additional, Armstrong, Deborah, additional, Bagheri, Mamad M., additional, Balch, Charles M., additional, Balducci, Lodovico, additional, Beghé, Claudia, additional, Benjamin, Robert, additional, Bennett, Charles L., additional, Berkowitz, Ross Stuart, additional, Bernstein, Donna, additional, Bishop, Michael R., additional, Blot, William J., additional, Blumgart, Leslie, additional, Bommer, Guido T., additional, Borowitz, Michael J., additional, Brahmer, Julie R., additional, Bramwell, Viven H.C., additional, Brock, Malcom V., additional, Bydon, Ali, additional, Cairo, Mitchell S., additional, Campana, Dario, additional, Carbone, David P., additional, Carter, H. Ballentine, additional, Chadha, Manpreet K., additional, Chan, Daniel W., additional, Chang, Alfred E., additional, Cheung, Nai-Kong V., additional, Christian, Michaele, additional, Clarke, Michael F., additional, Cmelak, Anthony, additional, Coccia, Peter F., additional, Cohen, Alfred M., additional, Coleman, Robert E., additional, Compton, Carolyn, additional, Cooley, Linda D., additional, Cortes, Jorge, additional, Courtneidge, Sara A., additional, Cowan, Kenneth H., additional, Culkin, Daniel J., additional, Dalmau, Josep, additional, D'Angio, Giulio J., additional, Dawson, Laura, additional, Deitcher, Steven R., additional, DeMatteo, Ronald P., additional, DeSimone, Philip A., additional, DeWeese, Theodore L., additional, Digumarthy, Subba R., additional, Dispenzieri, Angela, additional, Dome, Jeffrey S., additional, Donohue, John H., additional, Doroshow, James H., additional, Drebin, Jeffery A., additional, Duda, Dan G., additional, Duffy, Austin, additional, Duska, Linda R., additional, Eisenberger, Mario A., additional, Elstrom, Rebecca L., additional, Erler, Janine T., additional, Ewer, Michael S., additional, Fearon, Eric R., additional, Fecher, Leslie A., additional, Fichera, Alessandro, additional, Filipovich, Alexandra H., additional, Fitzner, Karen A., additional, Foote, Robert L., additional, Foran, James M., additional, Forastiere, Arlene A., additional, Ford, James M., additional, Freifeld, Alison G., additional, Freter, Carl E., additional, Fuller, Arlan F., additional, Furth, Emma E., additional, Garofalo, Michael C., additional, Gebhardt, Mark C., additional, Gerber, N. Lynn, additional, Gharia, Manish, additional, Giaccia, Amato J., additional, Gilbert, Mark R., additional, Glaspy, John, additional, Glover, Katrina Y., additional, Gokaslan, Ziya L., additional, Gökbuget, Nicola, additional, Goldstein, Donald Peter, additional, Gonzalez, Adriana, additional, Goodman, Anne Kathryn, additional, Gordon, Ellen, additional, Green, Daniel M., additional, Grever, Michael R., additional, Grigg, Andrew, additional, Grochow, Louise, additional, Gross, Thomas G., additional, Grossman, Stuart A., additional, Gunderson, Leonard L., additional, Gunkel, Juliet, additional, Gutierrez, Martin, additional, Habermann, Thomas M., additional, Haik, Barrett G., additional, Hainsworth, John D., additional, Hallahan, Dennis, additional, Hanna, Nader N., additional, Harris, Eleanor E.R., additional, Hawk, Ernie, additional, Heideman, Nancy H., additional, Heideman, Richard L., additional, Helman, Lee J., additional, Hochberg, Jessica, additional, Hoelzer, Dieter, additional, Holen, Ingunn, additional, Horning, Sandra J., additional, Huang, Kim, additional, Illei, Peter B., additional, Jaffe, Elaine S., additional, Jagannath, Sanjay B., additional, Jain, Rakesh K., additional, Jarnagin, William, additional, Jhingran, Anuja, additional, Johnson, David H., additional, Jones, Heather, additional, Judy, Kevin D., additional, Juergens, Rosalyn A., additional, Kant, Jeffrey A., additional, Kantarjian, Hagop, additional, Karcioglu, Zeynel A., additional, Karyadi, Danielle M., additional, Kased, Norbert, additional, Kastan, Michael B., additional, Kaul, Daniel R., additional, Kawaoka, John, additional, Kemeny, Margaret, additional, Kemeny, Nancy, additional, Kensler, Thomas W., additional, Kleinberg, Lawrence R., additional, Kobrinsky, Boris, additional, Kowalski, Jeanne, additional, Kummar, Shivaani, additional, Lal, Geeta, additional, Lambert, Paul F., additional, Lange, Julie R., additional, Laskin, Janessa, additional, Lee, Fred, additional, Lee, Susanna I., additional, Lees, Jacqueline, additional, Lenzi, Renato, additional, Lerman, Caryn, additional, Lipton, Allan, additional, Loprinzi, Charles L., additional, Lozanski, Gerard, additional, Lustig, Robert, additional, Machtay, Mitchell, additional, Maity, Amit, additional, Malik, Uzma, additional, Manatt, C. Scott, additional, Mansour, John C., additional, Massion, Pierre P., additional, Mayer, R. Samuel, additional, McCormick, Beryl, additional, McDonald, Charles J., additional, McDougall, Ross, additional, McKenna, W. Gillies, additional, Meranze, Steven, additional, Metz, James M., additional, Meyskens, Frank L., additional, Michelassi, Fabrizio, additional, Mikkilineni, Radha, additional, Mock, Victoria, additional, Mohiuddin, Mohammed, additional, Montie, James, additional, Morton, A. Ross, additional, Murgo, Anthony J., additional, Neff, James R., additional, Nelson, William G., additional, Nesbit, Suzanne, additional, Niederhuber, John E., additional, O'Connor, Tracey, additional, O'Dorisio, Thomas, additional, Offit, Kenneth, additional, Onciu, Mihaela, additional, O'Reilly, Eileen M., additional, Ostrander, Elaine A., additional, O'Sullivan, Brian, additional, Pardoll, Drew M., additional, Park, Catherine K., additional, Patterson, Freda, additional, Pavletic, Steven Z., additional, Perry, Michael C., additional, Peterson, LoAnn C., additional, Phillips, Peter C., additional, Piantadosi, Steven, additional, Pili, Robert, additional, Pisters, Peter W.T., additional, Pittelkow, Mark R., additional, Plastaras, John P., additional, Platz, Elizabeth A., additional, Pribaz, Julian, additional, Pruitt, Amy A., additional, Pui, Ching-Hon, additional, Putnam, Joe Bill, additional, Quon, Harry, additional, Raber, Martin N., additional, Rajkumar, S. Vincent, additional, Regine, William F., additional, Ritter, Mark, additional, Roberts, John Robert, additional, Robinson-Bostom, Leslie, additional, Rodriguez, Ronald, additional, Rodriguez-Galindo, Carlos, additional, Rosenfeld, Myrna, additional, Rosenthal, Nadia, additional, Rubenstein, James L., additional, Rubin, Brian P., additional, Rupani, Reena, additional, Rusch, Valerie W., additional, Russell, Anthony H., additional, Ryan, Charles J., additional, Sacchini, Vergilio, additional, Sandler, Alan B., additional, Sandler, Howard, additional, Sandlund, John T., additional, Santana, Victor M., additional, Schnoll, Robert A., additional, Sciubba, Daniel M., additional, Seiden, Michael V., additional, Sekeres, Mikkael A., additional, Sharfman, William H., additional, Sharma, Ricky A., additional, Sideras, Kostandinos, additional, Silver, Kenneth, additional, Small, Eric J., additional, Smith, David C., additional, Sneed, Penny K., additional, Snow, Stephen N., additional, Sokoll, Lori J., additional, Sovak, Mika A., additional, Speyer, James L., additional, Spira, Alex I., additional, Springfield, Dempsey, additional, Spunt, Sheri L., additional, Stewart, Daniel, additional, Strickland, Paul T., additional, Sugden, Bill, additional, Sutcliffe, Siobhan, additional, Sun, Weijing, additional, Tallman, Martin S., additional, Talmadge, James E., additional, Tefferi, Ayalew, additional, Thom, Peter, additional, Thompson, Craig B., additional, Tisdale, Michael J., additional, Tobinai, Kensei, additional, Tomaszewski, Joseph E., additional, Topalian, Suzanne L., additional, Torti, Frank M., additional, Trump, Donald L., additional, Vallis, Katherine A., additional, Varadhachary, Gauri R., additional, Vemulapalli, Sreenivas, additional, Visvanathan, Kala, additional, Wagner-Johnston, Nina D., additional, Wahl, Richard L., additional, Watanabe, Toshiki, additional, Weber, Barbara L., additional, Weber, Sharon, additional, Weigel, Ronald J., additional, Weissman, Irving L., additional, Westra, William, additional, Wilson, Kathleen S., additional, Wilson, Wyndham H., additional, Wolff, Antonio C., additional, Wong, Sandra L., additional, Wood, Gary S., additional, Wyatt, Lance S., additional, Zakarija, Anaadriana, additional, Zaks, Tal Z., additional, and Zell, Jason A., additional

Published
2008
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26. Subsequent Neoplasm Risk Associated With Rare Variants in DNA Damage Response and Clinical Radiation Sensitivity Syndrome Genes in the Childhood Cancer Survivor Study

Author

Morton, Lindsay M., primary, Karyadi, Danielle M., additional, Hartley, Stephen W., additional, Frone, Megan N., additional, Sampson, Joshua N., additional, Howell, Rebecca M., additional, Neglia, Joseph P., additional, Arnold, Michael A., additional, Hicks, Belynda D., additional, Jones, Kristine, additional, Zhu, Bin, additional, Dagnall, Casey L., additional, Karlins, Eric, additional, Yeager, Meredith S., additional, Leisenring, Wendy M., additional, Yasui, Yutaka, additional, Turcotte, Lucie M., additional, Smith, Susan A., additional, Weathers, Rita E., additional, Miller, Jeremy, additional, Sigel, Byron S., additional, Merino, Diana M., additional, Berrington de Gonzalez, Amy, additional, Bhatia, Smita, additional, Robison, Leslie L., additional, Tucker, Margaret A., additional, Armstrong, Gregory T., additional, and Chanock, Stephen J., additional

Published
2020
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27. Family-based association analysis of 42 hereditary prostate cancer families identifies the Apolipoprotein L3 region on chromosome 22q12 as a risk locus

Author

Johanneson, Bo, McDonnell, Shannon K., Karyadi, Danielle M., Quignon, Pascale, McIntosh, Laura, Riska, Shaun M., FitzGerald, Liesel M., Johnson, Gregory, Deutsch, Kerry, Williams, Gabrielle, Tillmans, Lori S., Stanford, Janet L., Schaid, Daniel J., Thibodeau, Stephen N., and Ostrander, Elaine A.

Published
2010
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30. In-utero exposure to zidovudine-containing antiretroviral therapy and clonal hematopoiesis in HIV-exposed uninfected newborns.

Author

Shu-Hong Lin, Youjin Wang, Hartley, Stephen W., Karyadi, Danielle M., Lee, Olivia W., Bin Zhu, Weiyin Zhou, Brown, Derek W., Beilstein-Wedel, Erin, Hazra, Rohan, Kacanek, Deborah, Chadwick, Ellen G., Marsit, Carmen J., Poirier, Miriam C., Brummel, Sean S., Chanock, Stephen J., Engels, Eric A., Machiela, Mitchell J., Lin, Shu-Hong, and Wang, Youjin

Published
2021
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31. Subsequent neoplasm risk associated with rare variants in DNA repair and clinical radiation sensitivity syndrome genes: A report from the Childhood Cancer Survivor Study.

Author

Morton, Lindsay M., primary, Karyadi, Danielle M, additional, Hartley, Steven, additional, Frone, Megan, additional, Sampson, Joshua N, additional, Howell, Rebecca M., additional, Neglia, Joseph Philip, additional, Arnold, Michael A., additional, Dagnall, Casey L, additional, Hicks, Belynda, additional, Kristine, Jones, additional, Zhu, Bin, additional, Leisenring, Wendy M., additional, Yasui, Yutaka, additional, Bhatia, Smita, additional, Robison, Leslie L., additional, Tucker, Margaret A., additional, Armstrong, Gregory T., additional, and Chanock, Stephen J., additional

Published
2019
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33. Whole exome sequencing in 75 high-risk families with validation and replication in independent case-control studies identifies TANGO2, OR5H14, and CHAD as new prostate cancer susceptibility genes

Author

Karyadi, Danielle M., primary, Geybels, Milan S., additional, Karlins, Eric, additional, Decker, Brennan, additional, McIntosh, Laura, additional, Hutchinson, Amy, additional, Kolb, Suzanne, additional, McDonnell, Shannon K., additional, Hicks, Belynda, additional, Middha, Sumit, additional, FitzGerald, Liesel M., additional, DeRycke, Melissa S., additional, Yeager, Meredith, additional, Schaid, Daniel J., additional, Chanock, Stephen J., additional, Thibodeau, Stephen N., additional, Berndt, Sonja I., additional, Stanford, Janet L., additional, and Ostrander, Elaine A., additional

Published
2016
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35. Abstract B40: Rare variant discovery in known cancer genes from whole-exome sequencingof African American hereditary prostate cancer families

Author

Cropp, Cheryl D., primary, McDonnell, Shannon K., additional, Middha, Sumit, additional, DeRycke, Melissa, additional, Karyadi, Danielle M., additional, Schaid, Daniel, additional, Thibodeau, Stephen N., additional, Isaacs, William B., additional, Ostrander, Elaine A., additional, Stanford, Janet, additional, Cooney, Kathleen A., additional, Bailey-Wilson, Joan E., additional, and Carpten, John D., additional

Published
2016
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36. Analysis of Xq27-28 linkage in the international consortium for prostate cancer genetics (ICPCG) families

Author

Bailey-Wilson, Joan E, Childs, Erica J, Cropp, Cheryl D, Schaid, Daniel J, Xu, Jianfeng, Camp, Nicola J, Cannon-Albright, Lisa A, Farnham, James M, George, Asha, Powell, Isaac, Carpten, John D, Giles, Graham G, Hopper, John L, Severi, Gianluca, English, Dallas R, Foulkes, William D, Mæhle, Lovise, Møller, Pål, Eeles, Rosalind, Easton, Douglas, Guy, Michelle, Edwards, Steve, Badzioch, Michael D, Whittemore, Alice S, Oakley-Girvan, Ingrid, Hsieh, Chih-Lin, Dimitrov, Latchezar, Stanford, Janet L, Karyadi, Danielle M, Deutsch, Kerry, McIntosh, Laura, Ostrander, Elaine A, Wiley, Kathleen E, Isaacs, Sarah D, Walsh, Patrick C, Thibodeau, Stephen N, McDonnell, Shannon K, Hebbring, Scott, Lange, Ethan M, Cooney, Kathleen A, Tammela, Teuvo LJ, Schleutker, Johanna, Maier, Christiane, Bochum, Sylvia, Hoegel, Josef, Grönberg, Henrik, Wiklund, Fredrik, Emanuelsson, Monica, Cancel-Tassin, Geraldine, Valeri, Antoine, Cussenot, Olivier, Isaacs, William B, International Consortium for Prostate Cancer Genetics, Easton, Douglas [0000-0003-2444-3247], and Apollo - University of Cambridge Repository

Subjects
Male, Chromosomes, Human, X, Genetic Linkage, Humans, Prostatic Neoplasms, Alleles, Genome-Wide Association Study, Microsatellite Repeats
Abstract

BACKGROUND: Genetic variants are likely to contribute to a portion of prostate cancer risk. Full elucidation of the genetic etiology of prostate cancer is difficult because of incomplete penetrance and genetic and phenotypic heterogeneity. Current evidence suggests that genetic linkage to prostate cancer has been found on several chromosomes including the X; however, identification of causative genes has been elusive. METHODS: Parametric and non-parametric linkage analyses were performed using 26 microsatellite markers in each of 11 groups of multiple-case prostate cancer families from the International Consortium for Prostate Cancer Genetics (ICPCG). Meta-analyses of the resultant family-specific linkage statistics across the entire 1,323 families and in several predefined subsets were then performed. RESULTS: Meta-analyses of linkage statistics resulted in a maximum parametric heterogeneity lod score (HLOD) of 1.28, and an allele-sharing lod score (LOD) of 2.0 in favor of linkage to Xq27-q28 at 138 cM. In subset analyses, families with average age at onset less than 65 years exhibited a maximum HLOD of 1.8 (at 138 cM) versus a maximum regional HLOD of only 0.32 in families with average age at onset of 65 years or older. Surprisingly, the subset of families with only 2-3 affected men and some evidence of male-to-male transmission of prostate cancer gave the strongest evidence of linkage to the region (HLOD = 3.24, 134 cM). For this subset, the HLOD was slightly increased (HLOD = 3.47 at 134 cM) when families used in the original published report of linkage to Xq27-28 were excluded. CONCLUSIONS: Although there was not strong support for linkage to the Xq27-28 region in the complete set of families, the subset of families with earlier age at onset exhibited more evidence of linkage than families with later onset of disease. A subset of families with 2-3 affected individuals and with some evidence of male to male disease transmission showed stronger linkage signals. Our results suggest that the genetic basis for prostate cancer in our families is much more complex than a single susceptibility locus on the X chromosome, and that future explorations of the Xq27-28 region should focus on the subset of families identified here with the strongest evidence of linkage to this region.

Published
2012

37. Comparison against 186 canid whole-genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor

Author

Decker, Brennan, primary, Davis, Brian W., additional, Rimbault, Maud, additional, Long, Adrienne H., additional, Karlins, Eric, additional, Jagannathan, Vidhya, additional, Reiman, Rebecca, additional, Parker, Heidi G., additional, Drögemüller, Cord, additional, Corneveaux, Jason J., additional, Chapman, Erica S., additional, Trent, Jeffery M., additional, Leeb, Tosso, additional, Huentelman, Matthew J., additional, Wayne, Robert K., additional, Karyadi, Danielle M., additional, and Ostrander, Elaine A., additional

Published
2015
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40. Germline Missense Variants in the BTNL2 Gene Are Associated with Prostate Cancer Susceptibility

Author

FitzGerald, Liesel M., primary, Kumar, Akash, additional, Boyle, Evan A., additional, Zhang, Yuzheng, additional, McIntosh, Laura M., additional, Kolb, Suzanne, additional, Stott-Miller, Marni, additional, Smith, Tiffany, additional, Karyadi, Danielle M., additional, Ostrander, Elaine A., additional, Hsu, Li, additional, Shendure, Jay, additional, and Stanford, Janet L., additional

Published
2013
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43. The MTAP-CDKN2A Locus Confers Susceptibility to a Naturally Occurring Canine Cancer

Author

Shearin, Abigail L., primary, Hedan, Benoit, additional, Cadieu, Edouard, additional, Erich, Suzanne A., additional, Schmidt, Emmett V., additional, Faden, Daniel L., additional, Cullen, John, additional, Abadie, Jerome, additional, Kwon, Erika M., additional, Gröne, Andrea, additional, Devauchelle, Patrick, additional, Rimbault, Maud, additional, Karyadi, Danielle M., additional, Lynch, Mary, additional, Galibert, Francis, additional, Breen, Matthew, additional, Rutteman, Gerard R., additional, André, Catherine, additional, Parker, Heidi G., additional, and Ostrander, Elaine A., additional

Published
2012
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47. Fine mapping of familial prostate cancer families narrows the interval for a susceptibility locus on chromosome 22q12.3 to 1.36 Mb

Author

Johanneson, Bo, primary, McDonnell, Shannon K., additional, Karyadi, Danielle M., additional, Hebbring, Scott J., additional, Wang, Liang, additional, Deutsch, Kerry, additional, McIntosh, Laura, additional, Kwon, Erika M., additional, Suuriniemi, Miia, additional, Stanford, Janet L., additional, Schaid, Daniel J., additional, Ostrander, Elaine A., additional, and Thibodeau, Stephen N., additional

Published
2007
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48. The MTAP-CDKN2A Locus Confers Susceptibility to a Naturally Occurring Canine Cancer

Author

Karyadi, Danielle M., Shearin, Abigail L., Lynch, Mary, André, Catherine, Schmidt, Emmett V., Breen, Matthew, Galibert, Francis, Erich, Suzanne A., Devauchelle, Patrick, Rutteman, Gerard R., Gron̈e, Andrea, Faden, Daniel L., Abadie, Jerome, Hedan, Benoit, Cadieu, Edouard, Cullen, John, Ostrander, Elaine A., Parker, Heidi G., Kwon, Erika M., and Rimbault, Maud

Subjects
3. Good health
Abstract

Advantages offered by canine population substructure, combined with clinical presentations similar to human disorders, makes the dog an attractive system for studies of cancer genetics. Cancers that have been difficult to study in human families or populations are of particular interest. Histiocytic sarcoma is a rare and poorly understood neoplasm in humans that occurs in 15–25% of Bernese Mountain Dogs (BMD).

49. Whole exome sequencing in 75 high-risk families with validation and replication in independent case-control studies identifies TANGO2, OR5H14, and CHAD as new prostate cancer susceptibility genes.

Author

Karyadi DM, Geybels MS, Karlins E, Decker B, McIntosh L, Hutchinson A, Kolb S, McDonnell SK, Hicks B, Middha S, FitzGerald LM, DeRycke MS, Yeager M, Schaid DJ, Chanock SJ, Thibodeau SN, Berndt SI, Stanford JL, and Ostrander EA

Subjects
Aged, Aged, 80 and over, Case-Control Studies, Genetic Predisposition to Disease, Humans, Male, Middle Aged, Risk Factors, Exome Sequencing, Prostatic Neoplasms genetics
Abstract

Prostate cancer (PCa) susceptibility is defined by a continuum from rare, high-penetrance to common, low-penetrance alleles. Research to date has concentrated on identification of variants at the ends of that continuum. Taking an alternate approach, we focused on the important but elusive class of low-frequency, moderately penetrant variants by performing disease model-based variant filtering of whole exome sequence data from 75 hereditary PCa families. Analysis of 341 candidate risk variants identified nine variants significantly associated with increased PCa risk in a population-based, case-control study of 2,495 men. In an independent nested case-control study of 7,121 men, there was risk association evidence for TANGO2 p.Ser17Ter and the established HOXB13 p.Gly84Glu variant. Meta-analysis combining the case-control studies identified two additional variants suggestively associated with risk, OR5H14 p.Met59Val and CHAD p.Ala342Asp. The TANGO2 and HOXB13 variants co-occurred in cases more often than expected by chance and never in controls. Finally, TANGO2 p.Ser17Ter was associated with aggressive disease in both case-control studies separately. Our analyses identified three new PCa susceptibility alleles in the TANGO2, OR5H14 and CHAD genes that not only segregate in multiple high-risk families but are also of importance in altering disease risk for men from the general population. This is the first successful study to utilize sequencing in high-risk families for the express purpose of identifying low-frequency, moderately penetrant PCa risk mutations.

Published
2017
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50. Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.

Author

Eeles RA, Olama AA, Benlloch S, Saunders EJ, Leongamornlert DA, Tymrakiewicz M, Ghoussaini M, Luccarini C, Dennis J, Jugurnauth-Little S, Dadaev T, Neal DE, Hamdy FC, Donovan JL, Muir K, Giles GG, Severi G, Wiklund F, Gronberg H, Haiman CA, Schumacher F, Henderson BE, Le Marchand L, Lindstrom S, Kraft P, Hunter DJ, Gapstur S, Chanock SJ, Berndt SI, Albanes D, Andriole G, Schleutker J, Weischer M, Canzian F, Riboli E, Key TJ, Travis RC, Campa D, Ingles SA, John EM, Hayes RB, Pharoah PD, Pashayan N, Khaw KT, Stanford JL, Ostrander EA, Signorello LB, Thibodeau SN, Schaid D, Maier C, Vogel W, Kibel AS, Cybulski C, Lubinski J, Cannon-Albright L, Brenner H, Park JY, Kaneva R, Batra J, Spurdle AB, Clements JA, Teixeira MR, Dicks E, Lee A, Dunning AM, Baynes C, Conroy D, Maranian MJ, Ahmed S, Govindasami K, Guy M, Wilkinson RA, Sawyer EJ, Morgan A, Dearnaley DP, Horwich A, Huddart RA, Khoo VS, Parker CC, Van As NJ, Woodhouse CJ, Thompson A, Dudderidge T, Ogden C, Cooper CS, Lophatananon A, Cox A, Southey MC, Hopper JL, English DR, Aly M, Adolfsson J, Xu J, Zheng SL, Yeager M, Kaaks R, Diver WR, Gaudet MM, Stern MC, Corral R, Joshi AD, Shahabi A, Wahlfors T, Tammela TL, Auvinen A, Virtamo J, Klarskov P, Nordestgaard BG, Røder MA, Nielsen SF, Bojesen SE, Siddiq A, Fitzgerald LM, Kolb S, Kwon EM, Karyadi DM, Blot WJ, Zheng W, Cai Q, McDonnell SK, Rinckleb AE, Drake B, Colditz G, Wokolorczyk D, Stephenson RA, Teerlink C, Muller H, Rothenbacher D, Sellers TA, Lin HY, Slavov C, Mitev V, Lose F, Srinivasan S, Maia S, Paulo P, Lange E, Cooney KA, Antoniou AC, Vincent D, Bacot F, Tessier DC, Kote-Jarai Z, and Easton DF

Subjects
Case-Control Studies, Cooperative Behavior, Genome-Wide Association Study, Genotype, Humans, Male, Meta-Analysis as Topic, Oligonucleotide Array Sequence Analysis, Prostatic Neoplasms pathology, Risk Factors, Genetic Loci genetics, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide genetics, Prostatic Neoplasms etiology
Abstract

Prostate cancer is the most frequently diagnosed cancer in males in developed countries. To identify common prostate cancer susceptibility alleles, we genotyped 211,155 SNPs on a custom Illumina array (iCOGS) in blood DNA from 25,074 prostate cancer cases and 24,272 controls from the international PRACTICAL Consortium. Twenty-three new prostate cancer susceptibility loci were identified at genome-wide significance (P < 5 × 10(-8)). More than 70 prostate cancer susceptibility loci, explaining ∼30% of the familial risk for this disease, have now been identified. On the basis of combined risks conferred by the new and previously known risk loci, the top 1% of the risk distribution has a 4.7-fold higher risk than the average of the population being profiled. These results will facilitate population risk stratification for clinical studies.

Published
2013
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