Nima C Emami1,2, Lancelote Leong2, Eunice Wan3, Erin L Van Blarigan2,4, Matthew R Cooperberg2,4, Imelda Tenggara4, Peter R Carroll4, June M Chan2,4, John S Witte1,2,3,4, Jeffry P Simko4,5. 1. Program in Biological and Medical Informatics, University of California, San Francisco, California. 2. Department of Epidemiology and Biostatistics, University of California, San Francisco, California. 3. Institute for Human Genetics, University of California, San Francisco, California. 4. Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California. 5. Department of Anatomic Pathology, University of California, San Francisco, California.
Abstract
BACKGROUND: Benign tissue from a tumor-containing organ is commonly the only available source for obtaining a patient's unmutated genome for use in cancer research. While it is critical to identify histologically normal tissue that is independent of the tumor lineage, few additional considerations are applied to the choice of this material for such measurements. METHODS: Normal formalin-fixed, paraffin-embedded seminal vesicle, and urethral tissues, in addition to whole blood, were collected from 31 prostate cancer patients having undergone radical prostatectomy. Genotype concordance was evaluated for DNA from each tissue source in relation to whole blood. RESULTS: Overall, there was a greater genotype call rate for DNA derived from urethral tissue (97.0%) in comparison with patient-matched seminal vesicle tissues (95.9%, P = 0.0015). Furthermore, with reference to patient-matched whole blood, urethral samples exhibited higher genotype concordance (94.1%) than that of seminal vesicle samples (92.5%, P = 0.035). CONCLUSIONS: These findings highlight the heterogeneity between diverse sources of DNA in genotype measurement and motivate the consideration of normal tissue biases in tumor-normal analyses. Prostate 77: 425-434, 2017.
BACKGROUND: Benign tissue from a tumor-containing organ is commonly the only available source for obtaining a patient's unmutated genome for use in cancer research. While it is critical to identify histologically normal tissue that is independent of the tumor lineage, few additional considerations are applied to the choice of this material for such measurements. METHODS: Normal formalin-fixed, paraffin-embedded seminal vesicle, and urethral tissues, in addition to whole blood, were collected from 31 prostate cancerpatients having undergone radical prostatectomy. Genotype concordance was evaluated for DNA from each tissue source in relation to whole blood. RESULTS: Overall, there was a greater genotype call rate for DNA derived from urethral tissue (97.0%) in comparison with patient-matched seminal vesicle tissues (95.9%, P = 0.0015). Furthermore, with reference to patient-matched whole blood, urethral samples exhibited higher genotype concordance (94.1%) than that of seminal vesicle samples (92.5%, P = 0.035). CONCLUSIONS: These findings highlight the heterogeneity between diverse sources of DNA in genotype measurement and motivate the consideration of normal tissue biases in tumor-normal analyses. Prostate 77: 425-434, 2017.
Authors: Hanneke I Vos; Tahar van der Straaten; Marieke J H Coenen; Uta Flucke; D Maroeska W M te Loo; Henk-Jan Guchelaar Journal: J Mol Diagn Date: 2015-01 Impact factor: 5.568
Authors: Mark N Kvale; Stephanie Hesselson; Thomas J Hoffmann; Yang Cao; David Chan; Sheryl Connell; Lisa A Croen; Brad P Dispensa; Jasmin Eshragh; Andrea Finn; Jeremy Gollub; Carlos Iribarren; Eric Jorgenson; Lawrence H Kushi; Richard Lao; Yontao Lu; Dana Ludwig; Gurpreet K Mathauda; William B McGuire; Gangwu Mei; Sunita Miles; Michael Mittman; Mohini Patil; Charles P Quesenberry; Dilrini Ranatunga; Sarah Rowell; Marianne Sadler; Lori C Sakoda; Michael Shapero; Ling Shen; Tanu Shenoy; David Smethurst; Carol P Somkin; Stephen K Van Den Eeden; Lawrence Walter; Eunice Wan; Teresa Webster; Rachel A Whitmer; Simon Wong; Chia Zau; Yiping Zhan; Catherine Schaefer; Pui-Yan Kwok; Neil Risch Journal: Genetics Date: 2015-06-19 Impact factor: 4.562
Authors: Karla J Lindquist; Pamela L Paris; Thomas J Hoffmann; Niall J Cardin; Rémi Kazma; Joel A Mefford; Jeffrey P Simko; Vy Ngo; Yalei Chen; Albert M Levin; Dhananjay Chitale; Brian T Helfand; William J Catalona; Benjamin A Rybicki; John S Witte Journal: Cancer Res Date: 2016-02-26 Impact factor: 12.701
Authors: Celine M Vachon; V Shane Pankratz; Christopher G Scott; Lothar Haeberle; Elad Ziv; Matthew R Jensen; Kathleen R Brandt; Dana H Whaley; Janet E Olson; Katharina Heusinger; Carolin C Hack; Sebastian M Jud; Matthias W Beckmann; Ruediger Schulz-Wendtland; Jeffrey A Tice; Aaron D Norman; Julie M Cunningham; Kristen S Purrington; Douglas F Easton; Thomas A Sellers; Karla Kerlikowske; Peter A Fasching; Fergus J Couch Journal: J Natl Cancer Inst Date: 2015-03-04 Impact factor: 13.506
Authors: Henrik Grönberg; Jan Adolfsson; Markus Aly; Tobias Nordström; Peter Wiklund; Yvonne Brandberg; James Thompson; Fredrik Wiklund; Johan Lindberg; Mark Clements; Lars Egevad; Martin Eklund Journal: Lancet Oncol Date: 2015-11-10 Impact factor: 41.316
Authors: Huixiao Hong; Lei Xu; Jie Liu; Wendell D Jones; Zhenqiang Su; Baitang Ning; Roger Perkins; Weigong Ge; Kelci Miclaus; Li Zhang; Kyunghee Park; Bridgett Green; Tao Han; Hong Fang; Christophe G Lambert; Silvia C Vega; Simon M Lin; Nadereh Jafari; Wendy Czika; Russell D Wolfinger; Federico Goodsaid; Weida Tong; Leming Shi Journal: PLoS One Date: 2012-09-07 Impact factor: 3.240
Authors: Jean E Abraham; Mel J Maranian; Inmaculada Spiteri; Roslin Russell; Susan Ingle; Craig Luccarini; Helena M Earl; Paul P D Pharoah; Alison M Dunning; Carlos Caldas Journal: BMC Med Genomics Date: 2012-05-30 Impact factor: 3.063
Authors: Adam Auton; Lisa D Brooks; Richard M Durbin; Erik P Garrison; Hyun Min Kang; Jan O Korbel; Jonathan L Marchini; Shane McCarthy; Gil A McVean; Gonçalo R Abecasis Journal: Nature Date: 2015-10-01 Impact factor: 49.962
Authors: Yuker Wang; Victoria E H Carlton; George Karlin-Neumann; Ronald Sapolsky; Li Zhang; Martin Moorhead; Zhigang C Wang; Andrea L Richardson; Robert Warren; Axel Walther; Melissa Bondy; Aysegul Sahin; Ralf Krahe; Musaffe Tuna; Patricia A Thompson; Paul T Spellman; Joe W Gray; Gordon B Mills; Malek Faham Journal: BMC Med Genomics Date: 2009-02-19 Impact factor: 3.063
Authors: Andrew E Teschendorff; Yang Gao; Allison Jones; Matthias Ruebner; Matthias W Beckmann; David L Wachter; Peter A Fasching; Martin Widschwendter Journal: Nat Commun Date: 2016-01-29 Impact factor: 14.919
Authors: Yu Jiang; Travis J Meyers; Adaeze A Emeka; Lauren Folgosa Cooley; Phillip R Cooper; Nicola Lancki; Irene Helenowski; Linda Kachuri; Daniel W Lin; Janet L Stanford; Lisa F Newcomb; Suzanne Kolb; Antonio Finelli; Neil E Fleshner; Maria Komisarenko; James A Eastham; Behfar Ehdaie; Nicole Benfante; Christopher J Logothetis; Justin R Gregg; Cherie A Perez; Sergio Garza; Jeri Kim; Leonard S Marks; Merdie Delfin; Danielle Barsa; Danny Vesprini; Laurence H Klotz; Andrew Loblaw; Alexandre Mamedov; S Larry Goldenberg; Celestia S Higano; Maria Spillane; Eugenia Wu; H Ballentine Carter; Christian P Pavlovich; Mufaddal Mamawala; Tricia Landis; Peter R Carroll; June M Chan; Matthew R Cooperberg; Janet E Cowan; Todd M Morgan; Javed Siddiqui; Rabia Martin; Eric A Klein; Karen Brittain; Paige Gotwald; Daniel A Barocas; Jeremiah R Dallmer; Jennifer B Gordetsky; Pam Steele; Shilajit D Kundu; Jazmine Stockdale; Monique J Roobol; Lionne D F Venderbos; Martin G Sanda; Rebecca Arnold; Dattatraya Patil; Christopher P Evans; Marc A Dall'Era; Anjali Vij; Anthony J Costello; Ken Chow; Niall M Corcoran; Soroush Rais-Bahrami; Courtney Phares; Douglas S Scherr; Thomas Flynn; R Jeffrey Karnes; Michael Koch; Courtney Rose Dhondt; Joel B Nelson; Dawn McBride; Michael S Cookson; Kelly L Stratton; Stephen Farriester; Erin Hemken; Walter M Stadler; Tuula Pera; Deimante Banionyte; Fernando J Bianco; Isabel H Lopez; Stacy Loeb; Samir S Taneja; Nataliya Byrne; Christopher L Amling; Ann Martinez; Luc Boileau; Franklin D Gaylis; Jacqueline Petkewicz; Nicholas Kirwen; Brian T Helfand; Jianfeng Xu; Denise M Scholtens; William J Catalona; John S Witte Journal: HGG Adv Date: 2021-11-19