5 results on '"Schumacher, Frederick R"'
Search Results
2. Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation.
- Author
-
Gusev, Alexander, Shi, Huwenbo, Kichaev, Gleb, Pomerantz, Mark, Li, Fugen, Long, Henry W, Ingles, Sue A, Kittles, Rick A, Strom, Sara S, Rybicki, Benjamin A, Nemesure, Barbara, Isaacs, William B, Zheng, Wei, Pettaway, Curtis A, Yeboah, Edward D, Tettey, Yao, Biritwum, Richard B, Adjei, Andrew A, Tay, Evelyn, Truelove, Ann, Niwa, Shelley, Chokkalingam, Anand P, John, Esther M, Murphy, Adam B, Signorello, Lisa B, Carpten, John, Leske, M Cristina, Wu, Suh-Yuh, Hennis, Anslem J M, Neslund-Dudas, Christine, Hsing, Ann W, Chu, Lisa, Goodman, Phyllis J, Klein, Eric A, Witte, John S, Casey, Graham, Kaggwa, Sam, Cook, Michael B, Stram, Daniel O, Blot, William J, Eeles, Rosalind A, Easton, Douglas, Kote-Jarai, ZSofia, Al Olama, Ali Amin, Benlloch, Sara, Muir, Kenneth, Giles, Graham G, Southey, Melissa C, Fitzgerald, Liesel M, Gronberg, Henrik, Wiklund, Fredrik, Aly, Markus, Henderson, Brian E, Schleutker, Johanna, Wahlfors, Tiina, Tammela, Teuvo L J, Nordestgaard, Børge G, Key, Tim J, Travis, Ruth C, Neal, David E, Donovan, Jenny L, Hamdy, Freddie C, Pharoah, Paul, Pashayan, Nora, Khaw, Kay-Tee, Stanford, Janet L, Thibodeau, Stephen N, McDonnell, Shannon K, Schaid, Daniel J, Maier, Christiane, Vogel, Walther, Luedeke, Manuel, Herkommer, Kathleen, Kibel, Adam S, Cybulski, Cezary, Wokolorczyk, Dominika, Kluzniak, Wojciech, Cannon-Albright, Lisa, Teerlink, Craig, Brenner, Hermann, Dieffenbach, Aida K, Arndt, Volker, Park, Jong Y, Sellers, Thomas A, Lin, Hui-Yi, Slavov, Chavdar, Kaneva, Radka, Mitev, Vanio, Batra, Jyotsna, Spurdle, Amanda, Clements, Judith A, Teixeira, Manuel R, Pandha, Hardev, Michael, Agnieszka, Paulo, Paula, Maia, Sofia, Kierzek, Andrzej, Conti, David V, Albanes, Demetrius, Berg, Christine, Berndt, Sonja I, Campa, Daniele, Crawford, E David, Diver, W Ryan, Gapstur, Susan M, Gaziano, J Michael, Giovannucci, Edward, Hoover, Robert, Hunter, David J, Johansson, Mattias, Kraft, Peter, Le Marchand, Loic, Lindström, Sara, Navarro, Carmen, Overvad, Kim, Riboli, Elio, Siddiq, Afshan, Stevens, Victoria L, Trichopoulos, Dimitrios, Vineis, Paolo, Yeager, Meredith, Trynka, Gosia, Raychaudhuri, Soumya, Schumacher, Frederick R, Price, Alkes L, Freedman, Matthew L, Haiman, Christopher A, Pasaniuc, Bogdan, Gusev, Alexander, Shi, Huwenbo, Kichaev, Gleb, Pomerantz, Mark, Li, Fugen, Long, Henry W, Ingles, Sue A, Kittles, Rick A, Strom, Sara S, Rybicki, Benjamin A, Nemesure, Barbara, Isaacs, William B, Zheng, Wei, Pettaway, Curtis A, Yeboah, Edward D, Tettey, Yao, Biritwum, Richard B, Adjei, Andrew A, Tay, Evelyn, Truelove, Ann, Niwa, Shelley, Chokkalingam, Anand P, John, Esther M, Murphy, Adam B, Signorello, Lisa B, Carpten, John, Leske, M Cristina, Wu, Suh-Yuh, Hennis, Anslem J M, Neslund-Dudas, Christine, Hsing, Ann W, Chu, Lisa, Goodman, Phyllis J, Klein, Eric A, Witte, John S, Casey, Graham, Kaggwa, Sam, Cook, Michael B, Stram, Daniel O, Blot, William J, Eeles, Rosalind A, Easton, Douglas, Kote-Jarai, ZSofia, Al Olama, Ali Amin, Benlloch, Sara, Muir, Kenneth, Giles, Graham G, Southey, Melissa C, Fitzgerald, Liesel M, Gronberg, Henrik, Wiklund, Fredrik, Aly, Markus, Henderson, Brian E, Schleutker, Johanna, Wahlfors, Tiina, Tammela, Teuvo L J, Nordestgaard, Børge G, Key, Tim J, Travis, Ruth C, Neal, David E, Donovan, Jenny L, Hamdy, Freddie C, Pharoah, Paul, Pashayan, Nora, Khaw, Kay-Tee, Stanford, Janet L, Thibodeau, Stephen N, McDonnell, Shannon K, Schaid, Daniel J, Maier, Christiane, Vogel, Walther, Luedeke, Manuel, Herkommer, Kathleen, Kibel, Adam S, Cybulski, Cezary, Wokolorczyk, Dominika, Kluzniak, Wojciech, Cannon-Albright, Lisa, Teerlink, Craig, Brenner, Hermann, Dieffenbach, Aida K, Arndt, Volker, Park, Jong Y, Sellers, Thomas A, Lin, Hui-Yi, Slavov, Chavdar, Kaneva, Radka, Mitev, Vanio, Batra, Jyotsna, Spurdle, Amanda, Clements, Judith A, Teixeira, Manuel R, Pandha, Hardev, Michael, Agnieszka, Paulo, Paula, Maia, Sofia, Kierzek, Andrzej, Conti, David V, Albanes, Demetrius, Berg, Christine, Berndt, Sonja I, Campa, Daniele, Crawford, E David, Diver, W Ryan, Gapstur, Susan M, Gaziano, J Michael, Giovannucci, Edward, Hoover, Robert, Hunter, David J, Johansson, Mattias, Kraft, Peter, Le Marchand, Loic, Lindström, Sara, Navarro, Carmen, Overvad, Kim, Riboli, Elio, Siddiq, Afshan, Stevens, Victoria L, Trichopoulos, Dimitrios, Vineis, Paolo, Yeager, Meredith, Trynka, Gosia, Raychaudhuri, Soumya, Schumacher, Frederick R, Price, Alkes L, Freedman, Matthew L, Haiman, Christopher A, and Pasaniuc, Bogdan
- Abstract
Although genome-wide association studies have identified over 100 risk loci that explain ∼33% of familial risk for prostate cancer (PrCa), their functional effects on risk remain largely unknown. Here we use genotype data from 59,089 men of European and African American ancestries combined with cell-type-specific epigenetic data to build a genomic atlas of single-nucleotide polymorphism (SNP) heritability in PrCa. We find significant differences in heritability between variants in prostate-relevant epigenetic marks defined in normal versus tumour tissue as well as between tissue and cell lines. The majority of SNP heritability lies in regions marked by H3k27 acetylation in prostate adenoc7arcinoma cell line (LNCaP) or by DNaseI hypersensitive sites in cancer cell lines. We find a high degree of similarity between European and African American ancestries suggesting a similar genetic architecture from common variation underlying PrCa risk. Our findings showcase the power of integrating functional annotation with genetic data to understand the genetic basis of PrCa.
- Published
- 2016
- Full Text
- View/download PDF
3. Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation
- Author
-
University of Helsinki, Clinicum, Gusev, Alexander, Shi, Huwenbo, Kichaev, Gleb, Pomerantz, Mark, Li, Fugen, Long, Henry W., Ingles, Sue A., Kittles, Rick A., Strom, Sara S., Rybicki, Benjamin A., Nemesure, Barbara, Isaacs, William B., Zheng, Wei, Pettaway, Curtis A., Yeboah, Edward D., Tettey, Yao, Biritwum, Richard B., Adjei, Andrew A., Tay, Evelyn, Truelove, Ann, Niwa, Shelley, Chokkalingam, Anand P., John, Esther M., Murphy, Adam B., Signorello, Lisa B., Carpten, John, Leske, M. Cristina, Wu, Suh-Yuh, Hennis, Anslem J. M., Neslund-Dudas, Christine, Hsing, Ann W., Chu, Lisa, Goodman, Phyllis J., Klein, Eric A., Witte, John S., Casey, Graham, Kaggwa, Sam, Cook, Michael B., Stram, Daniel O., Blot, William J., Eeles, Rosalind A., Easton, Douglas, Kote-Jarai, ZSofia, Al Olama, Ali Amin, Benlloch, Sara, Muir, Kenneth, Giles, Graham G., Southey, Melissa C., Fitzgerald, Liesel M., Gronberg, Henrik, Wiklund, Fredrik, Aly, Markus, Henderson, Brian E., Schleutker, Johanna, Wahlfors, Tiina, Tammela, Teuvo L. J., Nordestgaard, Borge G., Key, Tim J., Travis, Ruth C., Neal, David E., Donovan, Jenny L., Hamdy, Freddie C., Pharoah, Paul, Pashayan, Nora, Khaw, Kay-Tee, Stanford, Janet L., Thibodeau, Stephen N., McDonnell, Shannon K., Schaid, Daniel J., Maier, Christiane, Vogel, Walther, Luedeke, Manuel, Herkommer, Kathleen, Kibel, Adam S., Cybulski, Cezary, Wokolorczyk, Dominika, Kluzniak, Wojciech, Cannon-Albright, Lisa, Teerlink, Craig, Brenner, Hermann, Dieffenbach, Aida K., Arndt, Volker, Park, Jong Y., Sellers, Thomas A., Lin, Hui-Yi, Slavov, Chavdar, Kaneva, Radka, Mitev, Vanio, Batra, Jyotsna, Spurdle, Amanda, Clements, Judith A., Teixeira, Manuel R., Pandha, Hardev, Michael, Agnieszka, Paulo, Paula, Maia, Sofia, Kierzek, Andrzej, Conti, David V., Albanes, Demetrius, Berg, Christine, Berndt, Sonja I., Campa, Daniele, Crawford, E. David, Diver, W. Ryan, Gapstur, Susan M., Gaziano, J. Michael, Giovannucci, Edward, Hoover, Robert, Hunter, David J., Johansson, Mattias, Kraft, Peter, Le Marchand, Loic, Lindstrom, Sara, Navarro, Carmen, Overvad, Kim, Riboli, Elio, Siddiq, Afshan, Stevens, Victoria L., Trichopoulos, Dimitrios, Vineis, Paolo, Yeager, Meredith, Trynka, Gosia, Raychaudhuri, Soumya, Schumacher, Frederick R., Price, Alkes L., Freedman, Matthew L., Haiman, Christopher A., Pasaniuc, Bogdan, Cook, Margaret, Guy, Michelle, Govindasami, Koveela, Leongamornlert, Daniel, Sawyer, Emma J., Wilkinson, Rosemary, Saunders, Edward J., Tymrakiewicz, Malgorzata, Dadaev, Tokhir, Morgan, Angela, Fisher, Cyril, Hazel, Steve, Livni, Naomi, Lophatananon, Artitaya, Pedersen, John, Hopper, John L., Adolfson, Jan, Stattin, Paer, Johansson, Jan-Erik, Cavalli-Bjoerkman, Carin, Karlsson, Ami, Broms, Michael, Auvinen, Anssi, Kujala, Paula, Maattanen, Liisa, Murtola, Teemu, Taari, Kimmo, Weischer, Maren, Nielsen, Sune F., Klarskov, Peter, Roder, Andreas, Iversen, Peter, Wallinder, Hans, Gustafsson, Sven, Cox, Angela, Brown, Paul, George, Anne, Marsden, Gemma, Lane, Athene, Davis, Michael, Tillmans, Lori, Riska, Shaun, Wang, Liang, Rinckleb, Antje, Lubiski, Jan, Stegmaier, Christa, Pow-Sang, Julio, Park, Hyun, Radlein, Selina, Rincon, Maria, Haley, James, Zachariah, Babu, Kachakova, Darina, Popov, Elenko, Mitkova, Atanaska, Vlahova, Aleksandrina, Dikov, Tihomir, Christova, Svetlana, Heathcote, Peter, Wood, Glenn, Malone, Greg, Saunders, Pamela, Eckert, Allison, Yeadon, Trina, Kerr, Kris, Collins, Angus, Turner, Megan, Srinivasan, Srilakshmi, Kedda, Mary-Anne, Alexander, Kimberly, Omara, Tracy, Wu, Huihai, Henrique, Rui, Pinto, Pedro, Santos, Joana, Barros-Silva, Joao, PRACTICAL Consortium, University of Helsinki, Clinicum, Gusev, Alexander, Shi, Huwenbo, Kichaev, Gleb, Pomerantz, Mark, Li, Fugen, Long, Henry W., Ingles, Sue A., Kittles, Rick A., Strom, Sara S., Rybicki, Benjamin A., Nemesure, Barbara, Isaacs, William B., Zheng, Wei, Pettaway, Curtis A., Yeboah, Edward D., Tettey, Yao, Biritwum, Richard B., Adjei, Andrew A., Tay, Evelyn, Truelove, Ann, Niwa, Shelley, Chokkalingam, Anand P., John, Esther M., Murphy, Adam B., Signorello, Lisa B., Carpten, John, Leske, M. Cristina, Wu, Suh-Yuh, Hennis, Anslem J. M., Neslund-Dudas, Christine, Hsing, Ann W., Chu, Lisa, Goodman, Phyllis J., Klein, Eric A., Witte, John S., Casey, Graham, Kaggwa, Sam, Cook, Michael B., Stram, Daniel O., Blot, William J., Eeles, Rosalind A., Easton, Douglas, Kote-Jarai, ZSofia, Al Olama, Ali Amin, Benlloch, Sara, Muir, Kenneth, Giles, Graham G., Southey, Melissa C., Fitzgerald, Liesel M., Gronberg, Henrik, Wiklund, Fredrik, Aly, Markus, Henderson, Brian E., Schleutker, Johanna, Wahlfors, Tiina, Tammela, Teuvo L. J., Nordestgaard, Borge G., Key, Tim J., Travis, Ruth C., Neal, David E., Donovan, Jenny L., Hamdy, Freddie C., Pharoah, Paul, Pashayan, Nora, Khaw, Kay-Tee, Stanford, Janet L., Thibodeau, Stephen N., McDonnell, Shannon K., Schaid, Daniel J., Maier, Christiane, Vogel, Walther, Luedeke, Manuel, Herkommer, Kathleen, Kibel, Adam S., Cybulski, Cezary, Wokolorczyk, Dominika, Kluzniak, Wojciech, Cannon-Albright, Lisa, Teerlink, Craig, Brenner, Hermann, Dieffenbach, Aida K., Arndt, Volker, Park, Jong Y., Sellers, Thomas A., Lin, Hui-Yi, Slavov, Chavdar, Kaneva, Radka, Mitev, Vanio, Batra, Jyotsna, Spurdle, Amanda, Clements, Judith A., Teixeira, Manuel R., Pandha, Hardev, Michael, Agnieszka, Paulo, Paula, Maia, Sofia, Kierzek, Andrzej, Conti, David V., Albanes, Demetrius, Berg, Christine, Berndt, Sonja I., Campa, Daniele, Crawford, E. David, Diver, W. Ryan, Gapstur, Susan M., Gaziano, J. Michael, Giovannucci, Edward, Hoover, Robert, Hunter, David J., Johansson, Mattias, Kraft, Peter, Le Marchand, Loic, Lindstrom, Sara, Navarro, Carmen, Overvad, Kim, Riboli, Elio, Siddiq, Afshan, Stevens, Victoria L., Trichopoulos, Dimitrios, Vineis, Paolo, Yeager, Meredith, Trynka, Gosia, Raychaudhuri, Soumya, Schumacher, Frederick R., Price, Alkes L., Freedman, Matthew L., Haiman, Christopher A., Pasaniuc, Bogdan, Cook, Margaret, Guy, Michelle, Govindasami, Koveela, Leongamornlert, Daniel, Sawyer, Emma J., Wilkinson, Rosemary, Saunders, Edward J., Tymrakiewicz, Malgorzata, Dadaev, Tokhir, Morgan, Angela, Fisher, Cyril, Hazel, Steve, Livni, Naomi, Lophatananon, Artitaya, Pedersen, John, Hopper, John L., Adolfson, Jan, Stattin, Paer, Johansson, Jan-Erik, Cavalli-Bjoerkman, Carin, Karlsson, Ami, Broms, Michael, Auvinen, Anssi, Kujala, Paula, Maattanen, Liisa, Murtola, Teemu, Taari, Kimmo, Weischer, Maren, Nielsen, Sune F., Klarskov, Peter, Roder, Andreas, Iversen, Peter, Wallinder, Hans, Gustafsson, Sven, Cox, Angela, Brown, Paul, George, Anne, Marsden, Gemma, Lane, Athene, Davis, Michael, Tillmans, Lori, Riska, Shaun, Wang, Liang, Rinckleb, Antje, Lubiski, Jan, Stegmaier, Christa, Pow-Sang, Julio, Park, Hyun, Radlein, Selina, Rincon, Maria, Haley, James, Zachariah, Babu, Kachakova, Darina, Popov, Elenko, Mitkova, Atanaska, Vlahova, Aleksandrina, Dikov, Tihomir, Christova, Svetlana, Heathcote, Peter, Wood, Glenn, Malone, Greg, Saunders, Pamela, Eckert, Allison, Yeadon, Trina, Kerr, Kris, Collins, Angus, Turner, Megan, Srinivasan, Srilakshmi, Kedda, Mary-Anne, Alexander, Kimberly, Omara, Tracy, Wu, Huihai, Henrique, Rui, Pinto, Pedro, Santos, Joana, Barros-Silva, Joao, and PRACTICAL Consortium
- Abstract
Although genome-wide association studies have identified over 100 risk loci that explain similar to 33% of familial risk for prostate cancer (PrCa), their functional effects on risk remain largely unknown. Here we use genotype data from 59,089 men of European and African American ancestries combined with cell-type-specific epigenetic data to build a genomic atlas of single-nucleotide polymorphism (SNP) heritability in PrCa. We find significant differences in heritability between variants in prostate-relevant epigenetic marks defined in normal versus tumour tissue as well as between tissue and cell lines. The majority of SNP heritability lies in regions marked by H3k27 acetylation in prostate adenoc7arcinoma cell line (LNCaP) or by DNaseI hypersensitive sites in cancer cell lines. We find a high degree of similarity between European and African American ancestries suggesting a similar genetic architecture from common variation underlying PrCa risk. Our findings showcase the power of integrating functional annotation with genetic data to understand the genetic basis of PrCa.
- Published
- 2016
4. seXY: a tool for sex inference from genotype arrays
- Author
-
Qian, David C, primary, Busam, Jonathan A, additional, Xiao, Xiangjun, additional, O’Mara, Tracy A, additional, Eeles, Rosalind A, additional, Schumacher, Frederick R, additional, Phelan, Catherine M, additional, and Amos, Christopher I, additional
- Published
- 2016
- Full Text
- View/download PDF
5. seXY: a tool for sex inference from genotype arrays.
- Author
-
Qian, David C., Busam, Jonathan A., Xiangjun Xiao, O'Mara, Tracy A., Eeles, Rosalind A., Schumacher, Frederick R., Phelan, Catherine M., and Amos, Christopher I.
- Subjects
GENOTYPES ,GENOMES ,HUMAN sexuality ,X chromosome ,Y chromosome ,LOGISTIC regression analysis - Abstract
Motivation: Checking concordance between reported sex and genotype-inferred sex is a crucial quality control measure in genome-wide association studies (GWAS). However, limited insights exist regarding the true accuracy of software that infer sex from genotype array data. Results: We present seXY, a logistic regression model trained on both X chromosome heterozygosity and Y chromosome missingness, that consistently demonstrated>99.5% sex inference accuracy in cross-validation for 889 males and 5,361 females enrolled in prostate cancer and ovarian cancer GWAS. Compared to PLINK, one of the most popular tools for sex inference in GWAS that assesses only X chromosome heterozygosity, seXY achieved marginally better male classification and 3% more accurate female classification. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
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