Germline contamination and leakage in whole genome somatic single nucleotide variant detection

by Dorota H. Sendorek, Cristian Caloian, Kyle Ellrott, J. Christopher Bare, Takafumi N. Yamaguchi, Adam D. Ewing, Kathleen E. Houlahan, Thea C. Norman, Adam A. Margolin, Joshua M. Stuart, Paul C. Boutros
Published 2018-01-01

Cribriform and intraductal prostate cancer are associated with increased genomic instability and distinct genomic alterations

by René Böttcher, Charlotte F. Kweldam, Julie Livingstone, Emilie Lalonde, Takafumi N. Yamaguchi, Vincent Huang, Fouad Yousif, Michael Fraser, Robert G. Bristow, Theodorus van der Kwast, Paul C. Boutros, Guido Jenster, Geert J. L. H. van Leenders
Published 2018-01-01

Valection: design optimization for validation and verification studies

by Christopher I Cooper, Delia Yao, Dorota H Sendorek, Takafumi N Yamaguchi, Christine P’ng, Kathleen E Houlahan, Cristian Caloian, Michael Fraser, SMC-DNA Challenge Participants, Kyle Ellrott, Adam A Margolin, Robert G Bristow, Joshua M Stuart, Paul C Boutros
Published 2018-09-01

The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact

by Lisanne F. van Dessel, Job van Riet, Minke Smits, Yanyun Zhu, Paul Hamberg, Michiel S. van der Heijden, Andries M. Bergman, Inge M. van Oort, Ronald de Wit, Emile E. Voest, Neeltje Steeghs, Takafumi N. Yamaguchi, Julie Livingstone, Paul C. Boutros, John W. M. Martens, Stefan Sleijfer, Edwin Cuppen, Wilbert Zwart, Harmen J. G. van de Werken, Niven Mehra, Martijn P. Lolkema
Published 2019-11-01

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

by Anna Y. Lee, Adam D. Ewing, Kyle Ellrott, Yin Hu, Kathleen E. Houlahan, J. Christopher Bare, Shadrielle Melijah G. Espiritu, Vincent Huang, Kristen Dang, Zechen Chong, Cristian Caloian, Takafumi N. Yamaguchi, ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Michael R. Kellen, Ken Chen, Thea C. Norman, Stephen H. Friend, Justin Guinney, Gustavo Stolovitzky, David Haussler, Adam A. Margolin, Joshua M. Stuart, Paul C. Boutros
Published 2018-11-01

Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer

by Stanley Zhou, James R. Hawley, Fraser Soares, Giacomo Grillo, Mona Teng, Seyed Ali Madani Tonekaboni, Junjie Tony Hua, Ken J. Kron, Parisa Mazrooei, Musaddeque Ahmed, Christopher Arlidge, Hwa Young Yun, Julie Livingstone, Vincent Huang, Takafumi N. Yamaguchi, Shadrielle M. G. Espiritu, Yanyun Zhu, Tesa M. Severson, Alex Murison, Sarina Cameron, Wilbert Zwart, Theodorus van der Kwast, Trevor J. Pugh, Michael Fraser, Paul C. Boutros, Robert G. Bristow, Housheng Hansen He, Mathieu Lupien
Published 2020-01-01

Germline BRCA2 mutations drive prostate cancers with distinct evolutionary trajectories

by Renea A. Taylor, Michael Fraser, Julie Livingstone, Shadrielle Melijah G. Espiritu, Heather Thorne, Vincent Huang, Winnie Lo, Yu-Jia Shiah, Takafumi N. Yamaguchi, Ania Sliwinski, Sheri Horsburgh, Alice Meng, Lawrence E. Heisler, Nancy Yu, Fouad Yousif, Melissa Papargiris, Mitchell G. Lawrence, Lee Timms, Declan G. Murphy, Mark Frydenberg, Julia F. Hopkins, Damien Bolton, David Clouston, John D. McPherson, Theodorus van der Kwast, Paul C. Boutros, Gail P. Risbridger, Robert G. Bristow
Published 2017-01-01