title: Tissue Sources for Accurate Measurement of Germline DNA Genotypes in Prostate Cancer Patients Treated With Radical Prostatectomy.
abstract: 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.
  
  
  
  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.
  
  
  
  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).
  
  
  
  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. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Program in Biological and Medical Informatics, University of California, San Francisco, California.|Department of Epidemiology and Biostatistics, University of California, San Francisco, California.
authors.forename: Nima C
authors.initials: NC
authors.lastname: Emami
authors.affiliation: Department of Epidemiology and Biostatistics, University of California, San Francisco, California.
authors.forename: Lancelote
authors.initials: L
authors.lastname: Leong
authors.affiliation: Institute for Human Genetics, University of California, San Francisco, California.
authors.forename: Eunice
authors.initials: E
authors.lastname: Wan
authors.affiliation: Department of Epidemiology and Biostatistics, University of California, San Francisco, California.|Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.
authors.forename: Erin L
authors.initials: EL
authors.lastname: Van Blarigan
authors.affiliation: Department of Epidemiology and Biostatistics, University of California, San Francisco, California.|Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Cooperberg
authors.affiliation: Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.
authors.forename: Imelda
authors.initials: I
authors.lastname: Tenggara
authors.affiliation: Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.
authors.forename: Peter R
authors.initials: PR
authors.lastname: Carroll
authors.affiliation: Department of Epidemiology and Biostatistics, University of California, San Francisco, California.|Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.
authors.forename: June M
authors.initials: JM
authors.lastname: Chan
authors.affiliation: Program in Biological and Medical Informatics, University of California, San Francisco, California.|Department of Epidemiology and Biostatistics, University of California, San Francisco, California.|Institute for Human Genetics, University of California, San Francisco, California.|Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.
authors.forename: John S
authors.initials: JS
authors.lastname: Witte
authors.affiliation: Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.|Department of Anatomic Pathology, University of California, San Francisco, California.
authors.forename: Jeffry P
authors.initials: JP
authors.lastname: Simko
mesh_terms: D000072956:Adult Germline Stem Cells / Q000502:physiology; D000368:Aged; D004247:DNA / Q000235:genetics*; D005838:Genotype; D006801:Humans; D008297:Male; D008875:Middle Aged; D011468:Prostatectomy / Q000592:standards*; D011471:Prostatic Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000601:surgery*; D012669:Seminal Vesicles / Q000473:pathology / Q000502:physiology / Q000601:surgery; D016896:Treatment Outcome; D014521:Urethra / Q000473:pathology / Q000502:physiology / Q000601:surgery
chemical_list: D004247:DNA
keywords: archival FFPE tissue; genotype concordance; seminal vesicle; tumor-normal; urethra