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1. Adaptation of the socioecological model to address disparities in engagement of Black men in prostate cancer genetic testing

Author

Leader, Amy E., Rebbeck, Timothy R., Oh, William K., Patel, Alpa V., Winer, Eric P., Bailey, LeeAnn O., Gomella, Leonard G., Lumpkins, Crystal Y., Garraway, Isla P., Aiello, Lisa B., Baskin, Monica L., Cheng, Heather H., Cooney, Kathleen A., Ganzak, Amanda, George, Daniel J., Halabi, Susan, Hathaway, Feighanne, Healy, Claire, Kim, Joseph W., Leapman, Michael S., Loeb, Stacy, Maxwell, Kara N., McNair, Christopher, Morgan, Todd M., Prindeville, Breanne, Soule, Howard R., Steward, Whitney L., Suttiratana, Sakinah C., Taplin, Mary-Ellen, Yamoah, Kosj, Fortune, Thierry, Bennett, Kris, Blanding-Godbolt, Joshua, Gross, Laura, and Giri, Veda N.

Published
2024
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2. Two-stage Study of Familial Prostate Cancer by Whole-exome Sequencing and Custom Capture Identifies 10 Novel Genes Associated with the Risk of Prostate Cancer.

Author

Schaid, Daniel, McDonnell, Shannon, FitzGerald, Liesel, DeRycke, Lissa, Fogarty, Zachary, Giles, Graham, MacInnis, Robert, Southey, Melissa, Nguyen-Dumont, Tu, Cancel-Tassin, Geraldine, Cussenot, Oliver, Whittemore, Alice, Sieh, Weiva, Hsieh, Chih-Lin, Stanford, Janet, Schleutker, Johanna, Cropp, Cheryl, Carpten, John, Hoegel, Josef, Eeles, Rosalind, Kote-Jarai, Zsofia, Ackerman, Michael, Klein, Christopher, Mandal, Diptasri, Cooney, Kathleen, Bailey-Wilson, Joan, Helfand, Brian, Catalona, William, Wiklund, Fredrick, Riska, Shaun, Bahetti, Saurabh, Larson, Melissa, Cannon Albright, Lisa, Teerlink, Craig, Xu, Jianfeng, Isaacs, William, Ostrander, Elaine, Thibodeau, Stephen, and Ioannidis, Nilah

Subjects
Custom-capture sequencing, Familial prostate cancer, Genetic risk variants, Whole-exome sequencing, Genes, BRCA2, Guanine Nucleotide Exchange Factors, Humans, Male, Neoplasm Grading, Prostatic Neoplasms, Protein Serine-Threonine Kinases, Trypsin, Exome Sequencing
Abstract

BACKGROUND: Family history of prostate cancer (PCa) is a well-known risk factor, and both common and rare genetic variants are associated with the disease. OBJECTIVE: To detect new genetic variants associated with PCa, capitalizing on the role of family history and more aggressive PCa. DESIGN, SETTING, AND PARTICIPANTS: A two-stage design was used. In stage one, whole-exome sequencing was used to identify potential risk alleles among affected men with a strong family history of disease or with more aggressive disease (491 cases and 429 controls). Aggressive disease was based on a sum of scores for Gleason score, node status, metastasis, tumor stage, prostate-specific antigen at diagnosis, systemic recurrence, and time to PCa death. Genes identified in stage one were screened in stage two using a custom-capture design in an independent set of 2917 cases and 1899 controls. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Frequencies of genetic variants (singly or jointly in a gene) were compared between cases and controls. RESULTS AND LIMITATIONS: Eleven genes previously reported to be associated with PCa were detected (ATM, BRCA2, HOXB13, FAM111A, EMSY, HNF1B, KLK3, MSMB, PCAT1, PRSS3, and TERT), as well as an additional 10 novel genes (PABPC1, QK1, FAM114A1, MUC6, MYCBP2, RAPGEF4, RNASEH2B, ULK4, XPO7, and THAP3). Of these 10 novel genes, all but PABPC1 and ULK4 were primarily associated with the risk of aggressive PCa. CONCLUSIONS: Our approach demonstrates the advantage of gene sequencing in the search for genetic variants associated with PCa and the benefits of sampling patients with a strong family history of disease or an aggressive form of disease. PATIENT SUMMARY: Multiple genes are associated with prostate cancer (PCa) among men with a strong family history of this disease or among men with an aggressive form of PCa.

Published
2021

3. Implementation of Germline Testing for Prostate Cancer: Philadelphia Prostate Cancer Consensus Conference 2019.

Author

Giri, Veda N, Knudsen, Karen E, Kelly, William K, Cheng, Heather H, Cooney, Kathleen A, Cookson, Michael S, Dahut, William, Weissman, Scott, Soule, Howard R, Petrylak, Daniel P, Dicker, Adam P, AlDubayan, Saud H, Toland, Amanda E, Pritchard, Colin C, Pettaway, Curtis A, Daly, Mary B, Mohler, James L, Parsons, J Kellogg, Carroll, Peter R, Pilarski, Robert, Blanco, Amie, Woodson, Ashley, Rahm, Alanna, Taplin, Mary-Ellen, Polascik, Thomas J, Helfand, Brian T, Hyatt, Colette, Morgans, Alicia K, Feng, Felix, Mullane, Michael, Powers, Jacqueline, Concepcion, Raoul, Lin, Daniel W, Wender, Richard, Mark, James Ryan, Costello, Anthony, Burnett, Arthur L, Sartor, Oliver, Isaacs, William B, Xu, Jianfeng, Weitzel, Jeffrey, Andriole, Gerald L, Beltran, Himisha, Briganti, Alberto, Byrne, Lindsey, Calvaresi, Anne, Chandrasekar, Thenappan, Chen, David YT, Den, Robert B, Dobi, Albert, Crawford, E David, Eastham, James, Eggener, Scott, Freedman, Matthew L, Garnick, Marc, Gomella, Patrick T, Handley, Nathan, Hurwitz, Mark D, Izes, Joseph, Karnes, R Jeffrey, Lallas, Costas, Languino, Lucia, Loeb, Stacy, Lopez, Ana Maria, Loughlin, Kevin R, Lu-Yao, Grace, Malkowicz, S Bruce, Mann, Mark, Mille, Patrick, Miner, Martin M, Morgan, Todd, Moreno, Jose, Mucci, Lorelei, Myers, Ronald E, Nielsen, Sarah M, O'Neil, Brock, Pinover, Wayne, Pinto, Peter, Poage, Wendy, Raj, Ganesh V, Rebbeck, Timothy R, Ryan, Charles, Sandler, Howard, Schiewer, Matthew, Scott, E Michael D, Szymaniak, Brittany, Tester, William, Trabulsi, Edouard J, Vapiwala, Neha, Yu, Evan Y, Zeigler-Johnson, Charnita, and Gomella, Leonard G

Subjects
Biotechnology, Aging, Genetics, Prevention, Clinical Research, Cancer, Prostate Cancer, Genetic Testing, Urologic Diseases, Health Services, Good Health and Well Being, Germ-Line Mutation, History, 20th Century, Humans, Male, Prostatic Neoplasms, Clinical Sciences, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

PurposeGermline testing (GT) is a central feature of prostate cancer (PCA) treatment, management, and hereditary cancer assessment. Critical needs include optimized multigene testing strategies that incorporate evolving genetic data, consistency in GT indications and management, and alternate genetic evaluation models that address the rising demand for genetic services.MethodsA multidisciplinary consensus conference that included experts, stakeholders, and national organization leaders was convened in response to current practice challenges and to develop a genetic implementation framework. Evidence review informed questions using the modified Delphi model. The final framework included criteria with strong (> 75%) agreement (Recommend) or moderate (50% to 74%) agreement (Consider).ResultsLarge germline panels and somatic testing were recommended for metastatic PCA. Reflex testing-initial testing of priority genes followed by expanded testing-was suggested for multiple scenarios. Metastatic disease or family history suggestive of hereditary PCA was recommended for GT. Additional family history and pathologic criteria garnered moderate consensus. Priority genes to test for metastatic disease treatment included BRCA2, BRCA1, and mismatch repair genes, with broader testing, such as ATM, for clinical trial eligibility. BRCA2 was recommended for active surveillance discussions. Screening starting at age 40 years or 10 years before the youngest PCA diagnosis in a family was recommended for BRCA2 carriers, with consideration in HOXB13, BRCA1, ATM, and mismatch repair carriers. Collaborative (point-of-care) evaluation models between health care and genetic providers was endorsed to address the genetic counseling shortage. The genetic evaluation framework included optimal pretest informed consent, post-test discussion, cascade testing, and technology-based approaches.ConclusionThis multidisciplinary, consensus-driven PCA genetic implementation framework provides novel guidance to clinicians and patients tailored to the precision era. Multiple research, education, and policy needs remain of importance.

Published
2020

8. Targeting Androgen Receptor and DNA Repair in Metastatic Castration-Resistant Prostate Cancer: Results From NCI 9012

Author

Hussain, Maha, Daignault-Newton, Stephanie, Twardowski, Przemyslaw W, Albany, Costantine, Stein, Mark N, Kunju, Lakshmi P, Siddiqui, Javed, Wu, Yi-Mi, Robinson, Dan, Lonigro, Robert J, Cao, Xuhong, Tomlins, Scott A, Mehra, Rohit, Cooney, Kathleen A, Montgomery, Bruce, Antonarakis, Emmanuel S, Shevrin, Daniel H, Corn, Paul G, Whang, Young E, Smith, David C, Caram, Megan V, Knudsen, Karen E, Stadler, Walter M, Feng, Felix Y, and Chinnaiyan, Arul M

Subjects
Genetics, Prostate Cancer, Cancer, Urologic Diseases, Aged, Aged, 80 and over, Androstenes, Antineoplastic Combined Chemotherapy Protocols, Benzimidazoles, Biomarkers, Tumor, DNA Repair, Humans, Male, Middle Aged, Molecular Targeted Therapy, Neoplasm Metastasis, Poly(ADP-ribose) Polymerase Inhibitors, Prednisone, Prostatic Neoplasms, Castration-Resistant, Proto-Oncogene Proteins c-ets, Receptors, Androgen, Clinical Sciences, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

Purpose To determine whether cotargeting poly (ADP-ribose) polymerase-1 plus androgen receptor is superior to androgen receptor inhibition in metastatic castration-resistant prostate cancer (mCRPC) and whether ETS fusions predict response. Patients and Methods Patients underwent metastatic site biopsy and were stratified by ETS status and randomly assigned to abiraterone plus prednisone without (arm A) or with veliparib (arm B). Primary objectives were: confirmed prostate-specific antigen (PSA) response rate (RR) and whether ETS fusions predicted response. Secondary objectives were: safety, measurable disease RR (mRR), progression-free survival (PFS), and molecular biomarker analysis. A total of 148 patients were randomly assigned to detect a 20% PSA RR improvement. Results A total of 148 patients with mCRPC were randomly assigned: arm A, n = 72; arm B, n = 76. There were no differences in PSA RR (63.9% v 72.4%; P = .27), mRR (45.0% v 52.2%; P = .51), or median PFS (10.1 v 11 months; P = .99). ETS fusions did not predict response. Exploratory analysis of tumor sequencing (80 patients) revealed: 41 patients (51%) were ETS positive, 20 (25%) had DNA-damage repair defect (DRD), 41 (51%) had AR amplification or copy gain, 34 (43%) had PTEN mutation, 33 (41%) had TP53 mutation, 39 (49%) had PIK3CA pathway activation, and 12 (15%) had WNT pathway alteration. Patients with DRD had significantly higher PSA RR (90% v 56.7%; P = .007) and mRR (87.5% v 38.6%; P = .001), PSA decline ≥ 90% (75% v 25%; P = .001), and longer median PFS (14.5 v 8.1 months; P = .025) versus those with wild-type tumors. Median PFS was longer in patients with normal PTEN (13.5 v 6.7 months; P = .02), TP53 (13.5 v 7.7 months; P = .01), and PIK3CA (13.8 v 8.3 months; P = .03) versus those with mutation or activation. In multivariable analysis adjusting for clinical covariates, DRD association with PFS remained significant. Conclusion Veliparib and ETS status did not affect response. Exploratory analysis identified a novel DRD association with mCRPC outcomes.

Published
2018

9. Role of Genetic Testing for Inherited Prostate Cancer Risk: Philadelphia Prostate Cancer Consensus Conference 2017.

Author

Giri, Veda N, Knudsen, Karen E, Kelly, William K, Abida, Wassim, Andriole, Gerald L, Bangma, Chris H, Bekelman, Justin E, Benson, Mitchell C, Blanco, Amie, Burnett, Arthur, Catalona, William J, Cooney, Kathleen A, Cooperberg, Matthew, Crawford, David E, Den, Robert B, Dicker, Adam P, Eggener, Scott, Fleshner, Neil, Freedman, Matthew L, Hamdy, Freddie C, Hoffman-Censits, Jean, Hurwitz, Mark D, Hyatt, Colette, Isaacs, William B, Kane, Christopher J, Kantoff, Philip, Karnes, R Jeffrey, Karsh, Lawrence I, Klein, Eric A, Lin, Daniel W, Loughlin, Kevin R, Lu-Yao, Grace, Malkowicz, S Bruce, Mann, Mark J, Mark, James R, McCue, Peter A, Miner, Martin M, Morgan, Todd, Moul, Judd W, Myers, Ronald E, Nielsen, Sarah M, Obeid, Elias, Pavlovich, Christian P, Peiper, Stephen C, Penson, David F, Petrylak, Daniel, Pettaway, Curtis A, Pilarski, Robert, Pinto, Peter A, Poage, Wendy, Raj, Ganesh V, Rebbeck, Timothy R, Robson, Mark E, Rosenberg, Matt T, Sandler, Howard, Sartor, Oliver, Schaeffer, Edward, Schwartz, Gordon F, Shahin, Mark S, Shore, Neal D, Shuch, Brian, Soule, Howard R, Tomlins, Scott A, Trabulsi, Edouard J, Uzzo, Robert, Vander Griend, Donald J, Walsh, Patrick C, Weil, Carol J, Wender, Richard, and Gomella, Leonard G

Subjects
Humans, Prostatic Neoplasms, Genetic Predisposition to Disease, Prognosis, Risk Factors, Predictive Value of Tests, Pedigree, Age Factors, Heredity, Phenotype, Adult, Aged, Middle Aged, Male, Genetic Testing, Biomarkers, Tumor, Clinical Decision-Making, Genetics, Aging, Cancer, Prevention, Prostate Cancer, Urologic Diseases, 4.1 Discovery and preclinical testing of markers and technologies, Detection, screening and diagnosis, Clinical Sciences, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

Purpose Guidelines are limited for genetic testing for prostate cancer (PCA). The goal of this conference was to develop an expert consensus-driven working framework for comprehensive genetic evaluation of inherited PCA in the multigene testing era addressing genetic counseling, testing, and genetically informed management. Methods An expert consensus conference was convened including key stakeholders to address genetic counseling and testing, PCA screening, and management informed by evidence review. Results Consensus was strong that patients should engage in shared decision making for genetic testing. There was strong consensus to test HOXB13 for suspected hereditary PCA, BRCA1/2 for suspected hereditary breast and ovarian cancer, and DNA mismatch repair genes for suspected Lynch syndrome. There was strong consensus to factor BRCA2 mutations into PCA screening discussions. BRCA2 achieved moderate consensus for factoring into early-stage management discussion, with stronger consensus in high-risk/advanced and metastatic setting. Agreement was moderate to test all men with metastatic castration-resistant PCA, regardless of family history, with stronger agreement to test BRCA1/2 and moderate agreement to test ATM to inform prognosis and targeted therapy. Conclusion To our knowledge, this is the first comprehensive, multidisciplinary consensus statement to address a genetic evaluation framework for inherited PCA in the multigene testing era. Future research should focus on developing a working definition of familial PCA for clinical genetic testing, expanding understanding of genetic contribution to aggressive PCA, exploring clinical use of genetic testing for PCA management, genetic testing of African American males, and addressing the value framework of genetic evaluation and testing men at risk for PCA-a clinically heterogeneous disease.

Published
2018

10. A prospective prostate cancer screening programme for men with pathogenic variants in mismatch repair genes (IMPACT): initial results from an international prospective study

Author

Adams, Lisa, Adlard, Julian, Alfonso, Rosa, Ali, Saira, Andrew, Angela, Araújo, Luís, Azam, Nazya, Ball, Darran, Barker, Queenstone, Basevitch, Alon, Benton, Barbara, Berlin, Cheryl, Bermingham, Nicola, Biller, Leah, Bloss, Angela, Bradford, Matilda, Bradshaw, Nicola, Branson, Amy, Brendler, Charles, Brennan, Maria, Bulman, Barbara, Burgess, Lucy, Cahill, Declan, Callard, Alice, Calvo Verges, Nuria, Cardoso, Marta, Carter, Vanda, Catanzaro, Mario, Chamberlain, Anthony, Chapman, Cyril, Chong, Michael, Clark, Caroline, Clowes, Virginia, Cogley, Lyn, Cole, Trevor, Compton, Cecilia, Conner, Tom, Cookson, Sandra, Cornford, Philip, Costello, Philandra, Coulier, Laura, Davies, Michaela, Dechet, Christopher, DeSouza, Bianca, Devlin, Gemma, Douglas, Fiona, Douglas, Emma, Dudakia, Darshna, Duncan, Alexis, Ellery, Natalie, Everest, Sarah, Freemantle, Sue, Frydenberg, Mark, Fuller, Debbie, Gabriel, Camila, Gale, Madeline, Garcia, Lynda, Gay, Simona, Genova, Elena, George, Angela, Georgiou, Demetra, Gisbert, Alexandra, Gleeson, Margaret, Glover, Wayne, Gnanapragasam, Vincent, Goff, Sally, Goldgar, David, Gonçalves, Nuno, Goodman, Selina, Gorrie, Jennifer, Gott, Hannah, Grant, Anna, Gray, Catherine, Griffiths, Julie, Gupwell, Karin, Gurasashvili, Jana, Hanslien, Eldbjørg, Haraldsdottir, Sigurdis, Hart, Rachel, Hartigan, Catherine, Hawkes, Lara, Heaton, Tricia, Henderson, Alex, Henrique, Rui, Hilario, Kathrine, Hill, Kathryn, Hulick, Peter, Hunt, Clare, Hutchings, Melanie, Ibitoye, Rita, Inglehearn, Thomas, Ireland, Joanna, Islam, Farah, Ismail, Siti, Jacobs, Chris, James, Denzil, Jenkins, Sharon, Jobson, Irene, Johnstone, Anne, Jones, Oliver, Josefsberg Ben-Yehoshua, Sagi, Kaemba, Beckie, Kaul, Karen, Kemp, Zoe, Kinsella, Netty, Klehm, Margaret, Kockelbergh, Roger, Kohut, Kelly, Kosicka-Slawinska, Monika, Kulkarni, Anjana, Kumar, Pardeep, Lam, Jimmy, LeButt, Mandy, Leibovici, Dan, Lim, Ramona, Limb, Lauren, Lomas, Claire, Longmuir, Mark, López, Consol, Magnani, Tiziana, Maia, Sofia, Maiden, Jessica, Male, Alison, Manalo, Merrie, Martin, Phoebe, McBride, Donna, McGuire, Michael, McMahon, Romayne, McNally, Claire, McVeigh, Terri, Melzer, Ehud, Mencias, Mark, Mercer, Catherine, Mitchell, Gillian, Mora, Josefina, Morton, Catherine, Moss, Cathryn, Murphy, Morgan, Murphy, Declan, Mzazi, Shumi, Nadolski, Maria, Newlin, Anna, Nogueira, Pedro, O'Keefe, Rachael, O'Toole, Karen, O'Connell, Shona, Ogden, Chris, Okoth, Linda, Oliveira, Jorge, Paez, Edgar, Palou, Joan, Park, Linda, Patel, Nafisa, Paulo Souto, João, Pearce, Allison, Peixoto, Ana, Perez, Kimberley, Petelin, Lara, Pichert, Gabriella, Poile, Charlotte, Potter, Alison, Preitner, Nadia, Purnell, Helen, Quinn, Ellen, Radice, Paolo, Rankin, Brigette, Rees, Katie, Renton, Caroline, Richardson, Kate, Risby, Peter, Rogers, Jason, Ruderman, Maggie, Ruiz, April, Sajoo, Anaar, Salvatore, Natale, Sands, Victoria, Sanguedolce, Francesco, Sattar, Ayisha, Saunders, Kathryn, Schofield, Lyn, Scott, Rodney, Searle, Anne, Sehra, Ravinder, Selkirk, Christina, Shackleton, Kylie, Shanley, Sue, Shaw, Adam, Shevrin, Daniel, Shipman, Hannah, Sidat, Zahirah, Siguake, Kas, Simon, Kate, Smyth, Courtney, Snadden, Lesley, Solanky, Nita, Solomons, Joyce, Sorrentino, Margherita, Stayner, Barbara, Stephenson, Robert, Stoffel, Elena, Thomas, Maggie, Thompson, Alan, Tidey, Lizzie, Tischkowitz, Marc, Torokwa, Audrey, Townshend, Sharron, Treherne, Katy, Tricker, Karen, Trinh, Quoc-Dien, Tripathi, Vishakha, Turnbull, Clare, Valdagni, Riccardo, Van As, Nicholas, Venne, Vickie, Verdon, Lizzie, Vitellaro, Marco, Vogel, Kristen, Walker, Lisa, Watford, Amy, Watt, Cathy, Weintroub, Ilana, Weiss, Shelly, Weissman, Scott, Weston, Michelle, Wiggins, Jennifer, Wise, Gillian, Woodhouse, Christopher, Yesildag, Pembe, Youngs, Alice, Yurgelun, Matthew, Zollo, Fabiana, Bancroft, Elizabeth K, Page, Elizabeth C, Brook, Mark N, Thomas, Sarah, Taylor, Natalie, Pope, Jennifer, McHugh, Jana, Jones, Ann-Britt, Karlsson, Questa, Merson, Susan, Ong, Kai Ren, Hoffman, Jonathan, Huber, Camilla, Maehle, Lovise, Grindedal, Eli Marie, Stormorken, Astrid, Evans, D Gareth, Rothwell, Jeanette, Lalloo, Fiona, Brady, Angela F, Bartlett, Marion, Snape, Katie, Hanson, Helen, James, Paul, McKinley, Joanne, Mascarenhas, Lyon, Syngal, Sapna, Ukaegbu, Chinedu, Side, Lucy, Thomas, Tessy, Barwell, Julian, Teixeira, Manuel R, Izatt, Louise, Suri, Mohnish, Macrae, Finlay A, Poplawski, Nicola, Chen-Shtoyerman, Rakefet, Ahmed, Munaza, Musgrave, Hannah, Nicolai, Nicola, Greenhalgh, Lynn, Brewer, Carole, Pachter, Nicholas, Spigelman, Allan D, Azzabi, Ashraf, Helfand, Brian T, Halliday, Dorothy, Buys, Saundra, Ramon y Cajal, Teresa, Donaldson, Alan, Cooney, Kathleen A, Harris, Marion, McGrath, John, Davidson, Rosemarie, Taylor, Amy, Cooke, Peter, Myhill, Kathryn, Hogben, Matthew, Aaronson, Neil K, Ardern-Jones, Audrey, Bangma, Chris H, Castro, Elena, Dearnaley, David, Dias, Alexander, Dudderidge, Tim, Eccles, Diana M, Green, Kate, Eyfjord, Jorunn, Falconer, Alison, Foster, Christopher S, Gronberg, Henrik, Hamdy, Freddie C, Johannsson, Oskar, Khoo, Vincent, Lilja, Hans, Lindeman, Geoffrey J, Lubinski, Jan, Axcrona, Karol, Mikropoulos, Christos, Mitra, Anita V, Moynihan, Clare, Ni Raghallaigh, Holly, Rennert, Gad, Collier, Rebecca, Offman, Judith, Kote-Jarai, Zsofia, and Eeles, Rosalind A

Published
2021
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15. REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants.

Author

Rothstein, Joseph, Pejaver, Vikas, Middha, Sumit, McDonnell, Shannon, Baheti, Saurabh, Musolf, Anthony, Li, Qing, Holzinger, Emily, Karyadi, Danielle, Cannon-Albright, Lisa, Teerlink, Craig, Stanford, Janet, Isaacs, William, Xu, Jianfeng, Cooney, Kathleen, Lange, Ethan, Schleutker, Johanna, Carpten, John, Powell, Isaac, Cussenot, Olivier, Cancel-Tassin, Geraldine, Giles, Graham, MacInnis, Robert, Maier, Christiane, Hsieh, Chih-Lin, Wiklund, Fredrik, Catalona, William, Foulkes, William, Mandal, Diptasri, Eeles, Rosalind, Kote-Jarai, Zsofia, Bustamante, Carlos, Schaid, Daniel, Hastie, Trevor, Ostrander, Elaine, Bailey-Wilson, Joan, Radivojac, Predrag, Thibodeau, Stephen, Whittemore, Alice, Sieh, Weiva, and Ioannidis, Nilah

Subjects
Area Under Curve, DNA Mutational Analysis, Disease, Exome, Gene Frequency, Humans, Mutation, Missense, ROC Curve, Software
Abstract

The vast majority of coding variants are rare, and assessment of the contribution of rare variants to complex traits is hampered by low statistical power and limited functional data. Improved methods for predicting the pathogenicity of rare coding variants are needed to facilitate the discovery of disease variants from exome sequencing studies. We developed REVEL (rare exome variant ensemble learner), an ensemble method for predicting the pathogenicity of missense variants on the basis of individual tools: MutPred, FATHMM, VEST, PolyPhen, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP, SiPhy, phyloP, and phastCons. REVEL was trained with recently discovered pathogenic and rare neutral missense variants, excluding those previously used to train its constituent tools. When applied to two independent test sets, REVEL had the best overall performance (p < 10-12) as compared to any individual tool and seven ensemble methods: MetaSVM, MetaLR, KGGSeq, Condel, CADD, DANN, and Eigen. Importantly, REVEL also had the best performance for distinguishing pathogenic from rare neutral variants with allele frequencies

Published
2016

17. How pet owners define a 'good death': New study reveals some surprising facts

Author

Cooney, Kathleen and Kogan, Lori

Subjects
Euthanasia -- Social aspects -- Surveys -- Methods, Pet owners -- Surveys, Veterinary medicine -- Methods -- Ethical aspects, Health, Zoology and wildlife conservation
Abstract

Euthanasia is a procedure that most veterinarians perform frequently. It is chosen for many reasons, most commonly to relieve pain and suffering when further treatment is no longer in the [...]

Published
2022

19. Associations of prostate cancer risk variants with disease aggressiveness: results of the NCI-SPORE Genetics Working Group analysis of 18,343 cases.

Author

Helfand, Brian T, Roehl, Kimberly A, Cooper, Phillip R, McGuire, Barry B, Fitzgerald, Liesel M, Cancel-Tassin, Geraldine, Cornu, Jean-Nicolas, Bauer, Scott, Van Blarigan, Erin L, Chen, Xin, Duggan, David, Ostrander, Elaine A, Gwo-Shu, Mary, Zhang, Zuo-Feng, Chang, Shen-Chih, Jeong, Somee, Fontham, Elizabeth TH, Smith, Gary, Mohler, James L, Berndt, Sonja I, McDonnell, Shannon K, Kittles, Rick, Rybicki, Benjamin A, Freedman, Matthew, Kantoff, Philip W, Pomerantz, Mark, Breyer, Joan P, Smith, Jeffrey R, Rebbeck, Timothy R, Mercola, Dan, Isaacs, William B, Wiklund, Fredrick, Cussenot, Olivier, Thibodeau, Stephen N, Schaid, Daniel J, Cannon-Albright, Lisa, Cooney, Kathleen A, Chanock, Stephen J, Stanford, Janet L, Chan, June M, Witte, John, Xu, Jianfeng, Bensen, Jeannette T, Taylor, Jack A, and Catalona, William J

Subjects
Humans, Prostatic Neoplasms, Neoplasm Invasiveness, Genetic Predisposition to Disease, Risk Factors, Cohort Studies, Polymorphism, Single Nucleotide, Adult, Aged, Aged, 80 and over, Middle Aged, United States, Male, National Cancer Institute (U.S.), Genetic Association Studies, Polymorphism, Single Nucleotide, and over, National Cancer Institute, Urologic Diseases, Prostate Cancer, Human Genome, Genetics, Cancer, Prevention, Aging, 2.1 Biological and endogenous factors, Genetics & Heredity, Complementary and Alternative Medicine, Paediatrics and Reproductive Medicine
Abstract

Genetic studies have identified single nucleotide polymorphisms (SNPs) associated with the risk of prostate cancer (PC). It remains unclear whether such genetic variants are associated with disease aggressiveness. The NCI-SPORE Genetics Working Group retrospectively collected clinicopathologic information and genotype data for 36 SNPs which at the time had been validated to be associated with PC risk from 25,674 cases with PC. Cases were grouped according to race, Gleason score (Gleason ≤ 6, 7, ≥ 8) and aggressiveness (non-aggressive, intermediate, and aggressive disease). Statistical analyses were used to compare the frequency of the SNPs between different disease cohorts. After adjusting for multiple testing, only PC-risk SNP rs2735839 (G) was significantly and inversely associated with aggressive (OR = 0.77; 95 % CI 0.69-0.87) and high-grade disease (OR = 0.77; 95 % CI 0.68-0.86) in European men. Similar associations with aggressive (OR = 0.72; 95 % CI 0.58-0.89) and high-grade disease (OR = 0.69; 95 % CI 0.54-0.87) were documented in African-American subjects. The G allele of rs2735839 was associated with disease aggressiveness even at low PSA levels (

Published
2015

23. Global Patterns of Prostate Cancer Incidence, Aggressiveness, and Mortality in Men of African Descent

Author

Rebbeck, Timothy R, Devesa, Susan S, Chang, Bao-Li, Bunker, Clareann H, Cheng, Iona, Cooney, Kathleen, Eeles, Rosalind, Fernandez, Pedro, Giri, Veda N, Gueye, Serigne M, Haiman, Christopher A, Henderson, Brian E, Heyns, Chris F, Hu, Jennifer J, Ingles, Sue Ann, Isaacs, William, Jalloh, Mohamed, John, Esther M, Kibel, Adam S, Kidd, LaCreis R, Layne, Penelope, Leach, Robin J, Neslund-Dudas, Christine, Okobia, Michael N, Ostrander, Elaine A, Park, Jong Y, Patrick, Alan L, Phelan, Catherine M, Ragin, Camille, Roberts, Robin A, Rybicki, Benjamin A, Stanford, Janet L, Strom, Sara, Thompson, Ian M, Witte, John, Xu, Jianfeng, Yeboah, Edward, Hsing, Ann W, and Zeigler-Johnson, Charnita M

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Clinical Research, Aging, Cancer, Urologic Diseases, Prostate Cancer, Good Health and Well Being, Clinical sciences, Oncology and carcinogenesis
Abstract

Prostate cancer (CaP) is the leading cancer among men of African descent in the USA, Caribbean, and Sub-Saharan Africa (SSA). The estimated number of CaP deaths in SSA during 2008 was more than five times that among African Americans and is expected to double in Africa by 2030. We summarize publicly available CaP data and collected data from the men of African descent and Carcinoma of the Prostate (MADCaP) Consortium and the African Caribbean Cancer Consortium (AC3) to evaluate CaP incidence and mortality in men of African descent worldwide. CaP incidence and mortality are highest in men of African descent in the USA and the Caribbean. Tumor stage and grade were highest in SSA. We report a higher proportion of T1 stage prostate tumors in countries with greater percent gross domestic product spent on health care and physicians per 100,000 persons. We also observed that regions with a higher proportion of advanced tumors reported lower mortality rates. This finding suggests that CaP is underdiagnosed and/or underreported in SSA men. Nonetheless, CaP incidence and mortality represent a significant public health problem in men of African descent around the world.

Published
2013

24. Genome-wide association study of prostate cancer in men of African ancestry identifies a susceptibility locus at 17q21

Author

Haiman, Christopher A, Chen, Gary K, Blot, William J, Strom, Sara S, Berndt, Sonja I, Kittles, Rick A, Rybicki, Benjamin A, Isaacs, William B, Ingles, Sue A, Stanford, Janet L, Diver, W Ryan, Witte, John S, Hsing, Ann W, Nemesure, Barbara, Rebbeck, Timothy R, Cooney, Kathleen A, Xu, Jianfeng, Kibel, Adam S, Hu, Jennifer J, John, Esther M, Gueye, Serigne M, Watya, Stephen, Signorello, Lisa B, Hayes, Richard B, Wang, Zhaoming, Yeboah, Edward, Tettey, Yao, Cai, Qiuyin, Kolb, Suzanne, Ostrander, Elaine A, Zeigler-Johnson, Charnita, Yamamura, Yuko, Neslund-Dudas, Christine, Haslag-Minoff, Jennifer, Wu, William, Thomas, Venetta, Allen, Glenn O, Murphy, Adam, Chang, Bao-Li, Zheng, S Lilly, Leske, M Cristina, Wu, Suh-Yuh, Ray, Anna M, Hennis, Anselm JM, Thun, Michael J, Carpten, John, Casey, Graham, Carter, Erin N, Duarte, Edder R, Xia, Lucy Y, Sheng, Xin, Wan, Peggy, Pooler, Loreall C, Cheng, Iona, Monroe, Kristine R, Schumacher, Fredrick, Le Marchand, Loic, Kolonel, Laurence N, Chanock, Stephen J, Berg, David Van Den, Stram, Daniel O, and Henderson, Brian E

Subjects
Biological Sciences, Genetics, Human Genome, Aging, Urologic Diseases, Prevention, Prostate Cancer, Cancer, 2.1 Biological and endogenous factors, Aetiology, Black or African American, Chromosomes, Human, Pair 17, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Male, Polymorphism, Single Nucleotide, Prostatic Neoplasms, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

In search of common risk alleles for prostate cancer that could contribute to high rates of the disease in men of African ancestry, we conducted a genome-wide association study, with 1,047,986 SNP markers examined in 3,425 African-Americans with prostate cancer (cases) and 3,290 African-American male controls. We followed up the most significant 17 new associations from stage 1 in 1,844 cases and 3,269 controls of African ancestry. We identified a new risk variant on chromosome 17q21 (rs7210100, odds ratio per allele = 1.51, P = 3.4 × 10(-13)). The frequency of the risk allele is ∼5% in men of African descent, whereas it is rare in other populations (

Published
2011

29. Data from Risk Analysis of Prostate Cancer in PRACTICAL, a Multinational Consortium, Using 25 Known Prostate Cancer Susceptibility Loci

Author

Amin Al Olama, Ali, primary, Benlloch, Sara, primary, Antoniou, Antonis C., primary, Giles, Graham G., primary, Severi, Gianluca, primary, Neal, David E., primary, Hamdy, Freddie C., primary, Donovan, Jenny L., primary, Muir, Kenneth, primary, Schleutker, Johanna, primary, Henderson, Brian E., primary, Haiman, Christopher A., primary, Schumacher, Fredrick R., primary, Pashayan, Nora, primary, Pharoah, Paul D.P., primary, Ostrander, Elaine A., primary, Stanford, Janet L., primary, Batra, Jyotsna, primary, Clements, Judith A., primary, Chambers, Suzanne K., primary, Weischer, Maren, primary, Nordestgaard, Børge G., primary, Ingles, Sue A., primary, Sorensen, Karina D., primary, Orntoft, Torben F., primary, Park, Jong Y., primary, Cybulski, Cezary, primary, Maier, Christiane, primary, Doerk, Thilo, primary, Dickinson, Joanne L., primary, Cannon-Albright, Lisa, primary, Brenner, Hermann, primary, Rebbeck, Timothy R., primary, Zeigler-Johnson, Charnita, primary, Habuchi, Tomonori, primary, Thibodeau, Stephen N., primary, Cooney, Kathleen A., primary, Chappuis, Pierre O., primary, Hutter, Pierre, primary, Kaneva, Radka P., primary, Foulkes, William D., primary, Zeegers, Maurice P., primary, Lu, Yong-Jie, primary, Zhang, Hong-Wei, primary, Stephenson, Robert, primary, Cox, Angela, primary, Southey, Melissa C., primary, Spurdle, Amanda B., primary, FitzGerald, Liesel, primary, Leongamornlert, Daniel, primary, Saunders, Edward, primary, Tymrakiewicz, Malgorzata, primary, Guy, Michelle, primary, Dadaev, Tokhir, primary, Little, Sarah J., primary, Govindasami, Koveela, primary, Sawyer, Emma, primary, Wilkinson, Rosemary, primary, Herkommer, Kathleen, primary, Hopper, John L., primary, Lophatonanon, Aritaya, primary, Rinckleb, Antje E., primary, Kote-Jarai, Zsofia, primary, Eeles, Rosalind A., primary, and Easton, Douglas F., primary

Published
2023
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30. Supplementary Figure 1 from Risk Analysis of Prostate Cancer in PRACTICAL, a Multinational Consortium, Using 25 Known Prostate Cancer Susceptibility Loci

Author

Amin Al Olama, Ali, primary, Benlloch, Sara, primary, Antoniou, Antonis C., primary, Giles, Graham G., primary, Severi, Gianluca, primary, Neal, David E., primary, Hamdy, Freddie C., primary, Donovan, Jenny L., primary, Muir, Kenneth, primary, Schleutker, Johanna, primary, Henderson, Brian E., primary, Haiman, Christopher A., primary, Schumacher, Fredrick R., primary, Pashayan, Nora, primary, Pharoah, Paul D.P., primary, Ostrander, Elaine A., primary, Stanford, Janet L., primary, Batra, Jyotsna, primary, Clements, Judith A., primary, Chambers, Suzanne K., primary, Weischer, Maren, primary, Nordestgaard, Børge G., primary, Ingles, Sue A., primary, Sorensen, Karina D., primary, Orntoft, Torben F., primary, Park, Jong Y., primary, Cybulski, Cezary, primary, Maier, Christiane, primary, Doerk, Thilo, primary, Dickinson, Joanne L., primary, Cannon-Albright, Lisa, primary, Brenner, Hermann, primary, Rebbeck, Timothy R., primary, Zeigler-Johnson, Charnita, primary, Habuchi, Tomonori, primary, Thibodeau, Stephen N., primary, Cooney, Kathleen A., primary, Chappuis, Pierre O., primary, Hutter, Pierre, primary, Kaneva, Radka P., primary, Foulkes, William D., primary, Zeegers, Maurice P., primary, Lu, Yong-Jie, primary, Zhang, Hong-Wei, primary, Stephenson, Robert, primary, Cox, Angela, primary, Southey, Melissa C., primary, Spurdle, Amanda B., primary, FitzGerald, Liesel, primary, Leongamornlert, Daniel, primary, Saunders, Edward, primary, Tymrakiewicz, Malgorzata, primary, Guy, Michelle, primary, Dadaev, Tokhir, primary, Little, Sarah J., primary, Govindasami, Koveela, primary, Sawyer, Emma, primary, Wilkinson, Rosemary, primary, Herkommer, Kathleen, primary, Hopper, John L., primary, Lophatonanon, Aritaya, primary, Rinckleb, Antje E., primary, Kote-Jarai, Zsofia, primary, Eeles, Rosalind A., primary, and Easton, Douglas F., primary

Published
2023
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31. Supplementary Tables 1-8 from Risk Analysis of Prostate Cancer in PRACTICAL, a Multinational Consortium, Using 25 Known Prostate Cancer Susceptibility Loci

Author

Amin Al Olama, Ali, primary, Benlloch, Sara, primary, Antoniou, Antonis C., primary, Giles, Graham G., primary, Severi, Gianluca, primary, Neal, David E., primary, Hamdy, Freddie C., primary, Donovan, Jenny L., primary, Muir, Kenneth, primary, Schleutker, Johanna, primary, Henderson, Brian E., primary, Haiman, Christopher A., primary, Schumacher, Fredrick R., primary, Pashayan, Nora, primary, Pharoah, Paul D.P., primary, Ostrander, Elaine A., primary, Stanford, Janet L., primary, Batra, Jyotsna, primary, Clements, Judith A., primary, Chambers, Suzanne K., primary, Weischer, Maren, primary, Nordestgaard, Børge G., primary, Ingles, Sue A., primary, Sorensen, Karina D., primary, Orntoft, Torben F., primary, Park, Jong Y., primary, Cybulski, Cezary, primary, Maier, Christiane, primary, Doerk, Thilo, primary, Dickinson, Joanne L., primary, Cannon-Albright, Lisa, primary, Brenner, Hermann, primary, Rebbeck, Timothy R., primary, Zeigler-Johnson, Charnita, primary, Habuchi, Tomonori, primary, Thibodeau, Stephen N., primary, Cooney, Kathleen A., primary, Chappuis, Pierre O., primary, Hutter, Pierre, primary, Kaneva, Radka P., primary, Foulkes, William D., primary, Zeegers, Maurice P., primary, Lu, Yong-Jie, primary, Zhang, Hong-Wei, primary, Stephenson, Robert, primary, Cox, Angela, primary, Southey, Melissa C., primary, Spurdle, Amanda B., primary, FitzGerald, Liesel, primary, Leongamornlert, Daniel, primary, Saunders, Edward, primary, Tymrakiewicz, Malgorzata, primary, Guy, Michelle, primary, Dadaev, Tokhir, primary, Little, Sarah J., primary, Govindasami, Koveela, primary, Sawyer, Emma, primary, Wilkinson, Rosemary, primary, Herkommer, Kathleen, primary, Hopper, John L., primary, Lophatonanon, Aritaya, primary, Rinckleb, Antje E., primary, Kote-Jarai, Zsofia, primary, Eeles, Rosalind A., primary, and Easton, Douglas F., primary

Published
2023
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32. Data from Validation of Genome-Wide Prostate Cancer Associations in Men of African Descent

Author

Chang, Bao-Li, primary, Spangler, Elaine, primary, Gallagher, Stephen, primary, Haiman, Christopher A., primary, Henderson, Brian, primary, Isaacs, William, primary, Benford, Marnita L., primary, Kidd, LaCreis R., primary, Cooney, Kathleen, primary, Strom, Sara, primary, Ingles, Sue Ann, primary, Stern, Mariana C., primary, Corral, Roman, primary, Joshi, Amit D., primary, Xu, Jianfeng, primary, Giri, Veda N., primary, Rybicki, Benjamin, primary, Neslund-Dudas, Christine, primary, Kibel, Adam S., primary, Thompson, Ian M., primary, Leach, Robin J., primary, Ostrander, Elaine A., primary, Stanford, Janet L., primary, Witte, John, primary, Casey, Graham, primary, Eeles, Rosalind, primary, Hsing, Ann W., primary, Chanock, Stephen, primary, Hu, Jennifer J., primary, John, Esther M., primary, Park, Jong, primary, Stefflova, Klara, primary, Zeigler-Johnson, Charnita, primary, and Rebbeck, Timothy R., primary

Published
2023
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33. Supplementary Notes from Risk Analysis of Prostate Cancer in PRACTICAL, a Multinational Consortium, Using 25 Known Prostate Cancer Susceptibility Loci

Author

Amin Al Olama, Ali, primary, Benlloch, Sara, primary, Antoniou, Antonis C., primary, Giles, Graham G., primary, Severi, Gianluca, primary, Neal, David E., primary, Hamdy, Freddie C., primary, Donovan, Jenny L., primary, Muir, Kenneth, primary, Schleutker, Johanna, primary, Henderson, Brian E., primary, Haiman, Christopher A., primary, Schumacher, Fredrick R., primary, Pashayan, Nora, primary, Pharoah, Paul D.P., primary, Ostrander, Elaine A., primary, Stanford, Janet L., primary, Batra, Jyotsna, primary, Clements, Judith A., primary, Chambers, Suzanne K., primary, Weischer, Maren, primary, Nordestgaard, Børge G., primary, Ingles, Sue A., primary, Sorensen, Karina D., primary, Orntoft, Torben F., primary, Park, Jong Y., primary, Cybulski, Cezary, primary, Maier, Christiane, primary, Doerk, Thilo, primary, Dickinson, Joanne L., primary, Cannon-Albright, Lisa, primary, Brenner, Hermann, primary, Rebbeck, Timothy R., primary, Zeigler-Johnson, Charnita, primary, Habuchi, Tomonori, primary, Thibodeau, Stephen N., primary, Cooney, Kathleen A., primary, Chappuis, Pierre O., primary, Hutter, Pierre, primary, Kaneva, Radka P., primary, Foulkes, William D., primary, Zeegers, Maurice P., primary, Lu, Yong-Jie, primary, Zhang, Hong-Wei, primary, Stephenson, Robert, primary, Cox, Angela, primary, Southey, Melissa C., primary, Spurdle, Amanda B., primary, FitzGerald, Liesel, primary, Leongamornlert, Daniel, primary, Saunders, Edward, primary, Tymrakiewicz, Malgorzata, primary, Guy, Michelle, primary, Dadaev, Tokhir, primary, Little, Sarah J., primary, Govindasami, Koveela, primary, Sawyer, Emma, primary, Wilkinson, Rosemary, primary, Herkommer, Kathleen, primary, Hopper, John L., primary, Lophatonanon, Aritaya, primary, Rinckleb, Antje E., primary, Kote-Jarai, Zsofia, primary, Eeles, Rosalind A., primary, and Easton, Douglas F., primary

Published
2023
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34. Supplementary Figure 3 from Risk Analysis of Prostate Cancer in PRACTICAL, a Multinational Consortium, Using 25 Known Prostate Cancer Susceptibility Loci

Author

Amin Al Olama, Ali, primary, Benlloch, Sara, primary, Antoniou, Antonis C., primary, Giles, Graham G., primary, Severi, Gianluca, primary, Neal, David E., primary, Hamdy, Freddie C., primary, Donovan, Jenny L., primary, Muir, Kenneth, primary, Schleutker, Johanna, primary, Henderson, Brian E., primary, Haiman, Christopher A., primary, Schumacher, Fredrick R., primary, Pashayan, Nora, primary, Pharoah, Paul D.P., primary, Ostrander, Elaine A., primary, Stanford, Janet L., primary, Batra, Jyotsna, primary, Clements, Judith A., primary, Chambers, Suzanne K., primary, Weischer, Maren, primary, Nordestgaard, Børge G., primary, Ingles, Sue A., primary, Sorensen, Karina D., primary, Orntoft, Torben F., primary, Park, Jong Y., primary, Cybulski, Cezary, primary, Maier, Christiane, primary, Doerk, Thilo, primary, Dickinson, Joanne L., primary, Cannon-Albright, Lisa, primary, Brenner, Hermann, primary, Rebbeck, Timothy R., primary, Zeigler-Johnson, Charnita, primary, Habuchi, Tomonori, primary, Thibodeau, Stephen N., primary, Cooney, Kathleen A., primary, Chappuis, Pierre O., primary, Hutter, Pierre, primary, Kaneva, Radka P., primary, Foulkes, William D., primary, Zeegers, Maurice P., primary, Lu, Yong-Jie, primary, Zhang, Hong-Wei, primary, Stephenson, Robert, primary, Cox, Angela, primary, Southey, Melissa C., primary, Spurdle, Amanda B., primary, FitzGerald, Liesel, primary, Leongamornlert, Daniel, primary, Saunders, Edward, primary, Tymrakiewicz, Malgorzata, primary, Guy, Michelle, primary, Dadaev, Tokhir, primary, Little, Sarah J., primary, Govindasami, Koveela, primary, Sawyer, Emma, primary, Wilkinson, Rosemary, primary, Herkommer, Kathleen, primary, Hopper, John L., primary, Lophatonanon, Aritaya, primary, Rinckleb, Antje E., primary, Kote-Jarai, Zsofia, primary, Eeles, Rosalind A., primary, and Easton, Douglas F., primary

Published
2023
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35. Supplementary Figure 2 from Risk Analysis of Prostate Cancer in PRACTICAL, a Multinational Consortium, Using 25 Known Prostate Cancer Susceptibility Loci

Author

Amin Al Olama, Ali, primary, Benlloch, Sara, primary, Antoniou, Antonis C., primary, Giles, Graham G., primary, Severi, Gianluca, primary, Neal, David E., primary, Hamdy, Freddie C., primary, Donovan, Jenny L., primary, Muir, Kenneth, primary, Schleutker, Johanna, primary, Henderson, Brian E., primary, Haiman, Christopher A., primary, Schumacher, Fredrick R., primary, Pashayan, Nora, primary, Pharoah, Paul D.P., primary, Ostrander, Elaine A., primary, Stanford, Janet L., primary, Batra, Jyotsna, primary, Clements, Judith A., primary, Chambers, Suzanne K., primary, Weischer, Maren, primary, Nordestgaard, Børge G., primary, Ingles, Sue A., primary, Sorensen, Karina D., primary, Orntoft, Torben F., primary, Park, Jong Y., primary, Cybulski, Cezary, primary, Maier, Christiane, primary, Doerk, Thilo, primary, Dickinson, Joanne L., primary, Cannon-Albright, Lisa, primary, Brenner, Hermann, primary, Rebbeck, Timothy R., primary, Zeigler-Johnson, Charnita, primary, Habuchi, Tomonori, primary, Thibodeau, Stephen N., primary, Cooney, Kathleen A., primary, Chappuis, Pierre O., primary, Hutter, Pierre, primary, Kaneva, Radka P., primary, Foulkes, William D., primary, Zeegers, Maurice P., primary, Lu, Yong-Jie, primary, Zhang, Hong-Wei, primary, Stephenson, Robert, primary, Cox, Angela, primary, Southey, Melissa C., primary, Spurdle, Amanda B., primary, FitzGerald, Liesel, primary, Leongamornlert, Daniel, primary, Saunders, Edward, primary, Tymrakiewicz, Malgorzata, primary, Guy, Michelle, primary, Dadaev, Tokhir, primary, Little, Sarah J., primary, Govindasami, Koveela, primary, Sawyer, Emma, primary, Wilkinson, Rosemary, primary, Herkommer, Kathleen, primary, Hopper, John L., primary, Lophatonanon, Aritaya, primary, Rinckleb, Antje E., primary, Kote-Jarai, Zsofia, primary, Eeles, Rosalind A., primary, and Easton, Douglas F., primary

Published
2023
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36. Supplementary Materials from Validation of Genome-Wide Prostate Cancer Associations in Men of African Descent

Author

Chang, Bao-Li, primary, Spangler, Elaine, primary, Gallagher, Stephen, primary, Haiman, Christopher A., primary, Henderson, Brian, primary, Isaacs, William, primary, Benford, Marnita L., primary, Kidd, LaCreis R., primary, Cooney, Kathleen, primary, Strom, Sara, primary, Ingles, Sue Ann, primary, Stern, Mariana C., primary, Corral, Roman, primary, Joshi, Amit D., primary, Xu, Jianfeng, primary, Giri, Veda N., primary, Rybicki, Benjamin, primary, Neslund-Dudas, Christine, primary, Kibel, Adam S., primary, Thompson, Ian M., primary, Leach, Robin J., primary, Ostrander, Elaine A., primary, Stanford, Janet L., primary, Witte, John, primary, Casey, Graham, primary, Eeles, Rosalind, primary, Hsing, Ann W., primary, Chanock, Stephen, primary, Hu, Jennifer J., primary, John, Esther M., primary, Park, Jong, primary, Stefflova, Klara, primary, Zeigler-Johnson, Charnita, primary, and Rebbeck, Timothy R., primary

Published
2023
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40. Using gene and gene-set association tests to identify lethal prostate cancer genes

Author

Feng, Bing-Jian, Boyle, Julie L., Wei, Jun, Carroll, Courtney, Snyder, Nathan A., Shi, Zhuqing, Zheng, S. Lilly, Xu, Jianfeng, Isaacs, William B., and Cooney, Kathleen A.

Abstract

Background: Recent advances in the detection and treatment of prostate cancer (PCa) have reduced morbidity and mortality from this common cancer. Despite these improvements, PCa remains the second leading cause of cancer death in men in the United States. Further understanding of the genetic underpinnings of lethal PCa is required to drive risk detection and prevention and ultimately reduce mortality. We therefore set out to identify germline variants associated with cases of lethal prostate cancer (LPCa). Methods: Using a two-stage study design, we compared whole-exome sequencing data of 550 LPCa patients to 488 healthy male controls. Men were classified as having LPCa based on medical record review. Candidate genes were identified using gene- and gene-set-based rare truncating variant association tests. Case-control burden testing through Firth’s penalized logistic regression and case-gnomAD allelic burden testing through a one-sided mid-p Fisher’s exact test were conducted. Each gene’s p-values from these tests were combined into an omnibus p-value for candidate gene selection. In the subsequent validation stage, genes were assessed using the UK Biobank and Firth’s penalized logistic regression for each ancestry, combined through meta-analysis. Results: Gene-based rare variant association tests identified 12 genes nominally associated with LPCa. Rare-variant association tests identified a gene set with a significantly higher burden of truncating germline mutations in LPCa patients than controls. Combining gene- and gene-set test results, four nominally significant genes (PPP1R3A, TG, PPFIBP2, and BTN3A3) were selected as candidates. Subsequent validation using the UK Biobank found that PPP1R3Awas significantly associated with LPCa risk (odds ratio 2.34, CI 1.20–4.59). Specifically, pGln662ArgfsTer7 was identified as the predominant variant in PPP1R3Aamong LPCa patients in our dataset. Conclusions: Both individual gene and gene-set analyses identified candidates associated with LPCa. The novel association of PPP1R3Aand LPCa risk merits further investigation.

Published
2024
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43. Development and Validation of a Scalable Next-Generation Sequencing System for Assessing Relevant Somatic Variants in Solid Tumors

Author

Hovelson, Daniel H., McDaniel, Andrew S., Cani, Andi K., Johnson, Bryan, Rhodes, Kate, Williams, Paul D., Bandla, Santhoshi, Bien, Geoffrey, Choppa, Paul, Hyland, Fiona, Gottimukkala, Rajesh, Liu, Guoying, Manivannan, Manimozhi, Schageman, Jeoffrey, Ballesteros-Villagrana, Efren, Grasso, Catherine S., Quist, Michael J., Yadati, Venkata, Amin, Anmol, Siddiqui, Javed, Betz, Bryan L., Knudsen, Karen E., Cooney, Kathleen A., Feng, Felix Y., Roh, Michael H., Nelson, Peter S., Liu, Chia-Jen, Beer, David G., Wyngaard, Peter, Chinnaiyan, Arul M., Sadis, Seth, Rhodes, Daniel R., and Tomlins, Scott A.

Published
2015
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44. Association of rare, recurrent nonsynonymous variants in the germline of prostate cancer patients of African ancestry

Author

Wei, Jun, primary, Beebe‐Dimmer, Jennifer, additional, Shi, Zhuqing, additional, Sample, Christopher, additional, Yan, Guifang, additional, Rifkin, Andrew S., additional, Sadeghpour, Azita, additional, Gielzak, Marta, additional, Choi, Sodam, additional, Moon, David, additional, Zheng, S. Lilly, additional, Helfand, Brian T., additional, Walsh, Patrick C., additional, Xu, Jianfeng, additional, Cooney, Kathleen A., additional, and Isaacs, William B., additional

Published
2022
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45. Association of rare, recurrent nonsynonymous variants in the germline of prostate cancer patients of African ancestry

Author

Xu, Jianfeng, primary, Wei, Jun, additional, Beebe-Dimmer, Jennifer, additional, Shi, Zhuqing, additional, Sample, Christopher, additional, Yan, Guifang, additional, Rifkin, Andrew, additional, Sadeghpour, Azita, additional, Gielzak, Marta, additional, Choi, Sodam, additional, Moon, David, additional, Zheng, S. Lilly, additional, Helfand, Brian, additional, Walsh, Patrick, additional, Cooney, Kathleen, additional, and Isaacs, William, additional

Published
2022
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46. Euthanasia attendants in modern practice: Provide more compassionate support by having 1 person guide grieving clients through the appointment from beginning to end

Author

Cooney, Kathleen

Subjects
Euthanasia -- Social aspects -- Quality management, Terminal care -- Quality management -- Social aspects, Health, Zoology and wildlife conservation
Abstract

On times of sadness, we need someone we can rely on to carry us through. During a euthanasia appointment, various personnel commonly interact with the client and patient, but rarely [...]

Published
2022

49. Genome-wide association of familial prostate cancer cases identifies evidence for a rare segregating haplotype at 8q24.21

Author

Teerlink, Craig C., Leongamornlert, Daniel, Dadaev, Tokhir, Thomas, Alun, Farnham, James, Stephenson, Robert A., Riska, Shaun, McDonnell, Shannon K., Schaid, Daniel J., Catalona, William J., Zheng, S. Lilly, Cooney, Kathleen A., Ray, Anna M., Zuhlke, Kimberly A., Lange, Ethan M., Giles, Graham G., Southey, Melissa C., Fitzgerald, Liesel M., Rinckleb, Antje, Luedeke, Manuel, Maier, Christiane, Stanford, Janet L., Ostrander, Elaine A., Kaikkonen, Elina M., Sipeky, Csilla, Tammela, Teuvo, Schleutker, Johanna, Wiley, Kathleen E., Isaacs, Sarah D., Walsh, Patrick C., Isaacs, William B., Xu, Jianfeng, Cancel-Tassin, Geraldine, Cussenot, Olivier, Mandal, Diptasri, Laurie, Cecelia, Laurie, Cathy, Thibodeau, Stephen N., Eeles, Rosalind A., Kote-Jarai, Zsofia, Cannon-Albright, Lisa, The PRACTICAL consortium, and International Consortium for Prostate Cancer Genetics

Published
2016
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