Supplemental Methods Table 1. Participating Institutions Providing Genotype & Phenotype Information.

SNP / Location / AAHPC / FHCRC / France / Harvard / HFH / Hopkins / Mayo / Michigan / Northwestern / PCaP / PLCO / Sweden / UCI / UCLA / UCSF_Chan / UCSF_Witte / Upenn / Utah / Vanderbilt
rs721048 / 2p15 / X / X / X / X / X / X / X / X / X / X / X
rs1465618 / 2p21 / X / X / X / X / X / X / X / X / X / X / X
rs12621278 / 2q31.1 / X / X / X / X / X / X / X / X / X / X / X / X
rs2660753 / 3p12.1 / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X
rs10934853 / 3q21 / X / X / X / X / X / X / X / X / X / X
rs12500426 / 4q22.3 / X / X / X / X / X / X / X / X / X / X / X / X
rs17021918 / 4q22.3 / X / X / X / X / X / X / X / X / X / X / X
rs7679673 / 4q24 / X / X / X / X / X / X / X / X / X / X
rs2736098 / 5p15 / X / X / X
rs401681 / 5p16 / X / X / X / X / X / X / X / X
rs9364554 / 6q25.3 / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X
rs10486567 / 7p15.2 / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X
rs6465657 / 7q21.3 / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X
rs1512268 / 8p21.2 / X / X / X / X / X / X / X / X / X / X / X / X
rs16901979 / 8q24 / X / X / X / X / X / X / X / X / X / X / X / X / X
rs6983267 / 8q24 / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X
rs1447295 / 8q24 / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X
rs16902094 / 8q24 / X / X / X / X / X / X / X
rs445114 / 8q24 / X / X / X / X / X / X / X
rs10086908 / 8q24 / X / X / X / X / X / X / X / X / X
rs1571801 / 9q33.2 / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X
rs10993994 (MSMB) / 10q11 / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X
rs4962416 / 10q26.13 / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X
rs7127900 / 11p15.5 / X / X / X / X / X / X / X / X / X / X / X / X
rs11228565 / 11q13 / X / X / X / X / X / X / X / X
rs10896450 / 11q13 / X / X / X / X / X / X
rs12418451 / 11q13.3 / X / X / X / X
rs4054823 / 17p12 / X / X / X / X / X / X / X / X / X
rs4430796 / 17q12 / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X
rs11649743 / 17q12 / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X
rs1859962 / 17q24 / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X
rs8102476 / 19q13 / X / X / X / X / X / X / X / X / X / X / X
rs2735839 / 19q13.3 / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X / X
rs9623117 / 22q13.1 / X / X / X / X / X / X / X / X
rs5759167 / 22q13.2 / X / X / X / X / X / X / X / X / X / X
rs5945572 / Xp11 / X / X / X / X / X / X / X / X / X / X / X
No. of SNPs / 15 / 20 / 15 / 29 / 34 / 12 / 23 / 28 / 36 / 15 / 29 / 33 / 30 / 3 / 24 / 34 / 20 / 15 / 12
No. of Cases / 75 / 1140 / 376 / 4043 / 401 / 5401 / 829 / 193 / 1729 / 2147 / 1643 / 2725 / 68 / 192 / 568 / 511 / 2104 / 218 / 1311

Supplemental Methods Table 2. Genotyping Methodologies, Funding, and Authorship by Institution.

  • Northwestern University/ NorthShore University
  • Authors: Brian T. Helfand, William J. Catalona, Phillip R. Cooper, Kimberly A. Roehl
  • Disclosures: NONE
  • Affiliations: (BTH) Department of Surgery, Division of Urology, NorthShore University HealthSystem, Evanston, IL 60201; (WJC, PRC, KAR) Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611
  • Funding/Acknowledgements:
  • (BTH) John and Carol Walter Center for Urological Health and The National Institutes of Health (U01 CA89600); (WJC) Urologic Research Foundation, The National Institutes of Health (U01 CA89600 and P50CA090386)
  • Cohort: Institutional review board approval was obtained. All participants provided written informed consent. 1729 men diagnosed with prostate cancer between 2003 and 2012 were consented for genetic studies. Of these patients, 1248 underwent radical prostatectomy (RP) by a single surgeon, and the remaining underwent surgical treatment by other urologists from the Northwestern University Specialized Program of Research Excellence (SPORE) group. The patients were enrolled from a prospective database. All participants filled out a questionnaire including race and provided a blood sample for genotype analyses. The clinical and pathological characteristics were recorded, including preoperative PSA level, clinical and pathological tumor stage, and presence of extracapsular tumor extension, seminal vesicle invasion and lymph node metastases.
  • Genotyping: DNA was extracted from whole blood at deCODE® genetics Inc., in Reykjavik, Iceland. Each sample was genotyped for 36 prostate cancer risk SNPs; the Centaurus (Nanogen) genotyping methods were employed, and their accuracy has been evaluated as previously described(Gudmundsson et al. 2010; Helfand et al. 2011; Helfand et al. 2008; Helfand et al. 2010).
  • The North Carolina-Louisiana Prostate Cancer Project (PCaP)
  • Authors: Elizabeth T.H. Fontham, Gary, Smith, James L. Mohler, Jeanette T. Bensen, Jack A. Taylor
  • Disclosures: None
  • Affiliations:(ETHF) School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA; (GS, JLM) Department of Urology, Roswell Park Cancer Institute, Buffalo, NY;(JTB) Gillings School of Global Public HealthDepartment of Epidemiology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7435; (JAT) Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
  • Funding/Acknowledgements:The North Carolina –Louisiana Prostate Cancer Project (PCaP) is carried out as a collaborative study supported by the Department of Defense contract DAMD 17-03-2-0052. The authors thank the staff, advisory committees and research subjects participating in the PCaP study for their important contributions. We would like to acknowledge the UNC Tissue Culture Facility ( and BioSpecimenProcessing Facility ( the LSUHSC Pathology Lab for our lymphocyte immortalizations, DNA extractions, blood processing, storage and sample disbursement.
  • Cohort:PCaP ( is a multi-disciplinary, population-based, case-only study designed to investigate racial differences in prostate cancer that has been previously described(Bensen et al. 2013; Schroeder et al. 2006). Briefly, in North Carolina (NC), prostate cancer cases were diagnosed between July 2004 and October 2007. In total 1,655 NC men were eligible and 1,031 NC men participated (62.3%) in the PCaP study including 505 AA (62.1% participation rate) and 526 EA (64.9% participation rate). In Louisiana (LA), prostate cancer cases were diagnosed between May 2004 and June 2005 (Pre- Hurricane Katrina PCaP cohort) and between January 2006 and July 2009 (Post-Hurricane Katrina PCaP cohort). In total, 293 LA men were eligible for the Pre-Katrina cohort and 213 participated (72.7%) in PCaP including 119 AA (70.8% participation rate) and 94 EA (79.0% participation rate). In total, 1,614 LA men were eligible for the Post-Katrina cohort and 1,014 participated (70.7%) in PCaP including 506 AA (62.6% participation rate) and 508 EA (70.7% participation rate). In summary, 1,130 men self-reporting as black/African American (AA) and 1,128 men self-reporting as white/Caucasian/Caucasian American/ European American (EA) between 40–79 years of age with newly diagnosed, histologically- confirmed, adenocarcinoma of the prostate were enrolled in North Carolina (NC) or Louisiana (LA). Study questionnaire information was collected via a structured in-home interview conducted by trained study nurses that included information on date of birth, self- described race and ethnicity, family history of prostate cancer, and detailed information on demographic characteristics, diet, and health history. Medical records were abstracted for information related to the prostate cancer screening and diagnosis including total serum prostate- specific antigen (PSA) (defined as the PSA value closest and within 1 year prior to diagnosis date), tumor stage at diagnosis (stage number was derived from stage as reported in the medical record) and clinical Gleason score (sum of primary and secondary Gleason grade). Prostate cancer treatment was also abstracted from the medical records.
  • Genotyping: DNA was extracted from blood samples (n=1,785) or buccal cells (n=140) by the UNC- Chapel Hill Biospecimen Processing Facility, or from lymphocytes immortalized by the UNC-Chapel Hill Tissue Culture Facility (n=222). Genotyping was performed by the NIH Center for Inherited Disease Research (CIDR)using a custom designed 1,536 SNP IlluminaGoldenGate array (Bensen et al. 2013). Genotyping took place in 2 phases (phase 1: 933 samples and phase 2: 1,315 samples) as samples became available. Genotyping in phase 1 included a set of 22 blinded PCaP sample duplicates, 29 HapMap sample duplicates and 19 HapMap trios. Phase 2 included a set of 29 blinded PCaP sample duplicates, 19 HapMap sample duplicates and 11 HapMap sample trios. A total of 100 PCaP samples overlapped between phase 1 and phase 2 to monitor genotyping quality. For both phases the HapMap samples included representation of CEU and YRI ancestral groups. Allele calling was conducted using Illumina’s Genotyping Module version 1.0.10 in GenomeStudio 1.0.2.20706. The genotype intensity cluster plots were visually inspected for each SNP. Genotypes with an IlluminaGenCall (GC) score below 0.25 were assigned as missing. The overall subject genotyping call rate was 99.95%. The reproducibility rate was 99.99% based on blind duplicates and the overall P–P–C heritability based on HapMap trios was 99.95%.
  • University of California San Francisco
  • Authors: Dr. John Witte
  • Affiliations: Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California.
  • Disclosures: NONE
  • Funding/Acknowledgements:None
  • Cohort: The institutional review board of University of California, San Francisco approved this study. All participants provided written consent. Need description
  • Genotyping: We evaluated 34 single nucleotide polymorphisms identified by recent GWAS of prostate cancer susceptibility. All SNPs were genotyped using the TaqMan allelic discrimination assay as previously described. The average genotyping success rate across the 34 SNPs was 98.7%, and the average genotype concordance rate for 2% duplicates was 99.0%.
  • University of California San Francisco
  • Authors: Drs. June M. Chan, Scott Bauer, Erin L. Van Blarigan
  • Affiliations: Departments of Epidemiology and Biostatistics and Urology, University of California San Francisco, San Francisco, California
  • Disclosures:None
  • Funding/Acknowledgements: The authors would like to acknowledge the Genome Analysis Core Facility, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco for their help and assistance in this work.

NIH/NCI R01CA106947

  • Cohort: Under supervision of the UCSF institutional review board, consenting patients with available blood samples for genotyping were identified from the UCSF Helen Diller Family Comprehensive Cancer Center Urologic Oncology Data Base (UODB). A cohort of 568 consecutive patients with prostate cancer who underwent radical prostatectomy between 1997 and 2011 at UCSF were identified for this study.
  • Genotyping: Genotyping was performed as previously described. Briefly, single PCR reactions were conducted with 5ul reaction volumes of 2mM PCR buffer, 2mM MgCl2, 500M of each deoxynucleotide triphosphate (dNTP), 0.1M of each forward and reverse SNP specific PCR primer, 1unit of PCR enzyme (for groups/plexes below 24 SNPs Taq was reduced to 0.5 units per reaction), and 10-30ng of DNA. A large master mix of the above-mentioned components (minus DNA) was made for each group (plex) of SNPs and 3ul was pipetted into each well of a 384-well plate. 2L of DNA was then added. PCR was conducted on the GeneAmp PCR system 9700 (Applied Biosystems) using the following cycling parameters: 95° for 2 minutes; 45 cycles of 95° for 30 seconds, 56° for 30 seconds, 72° for 1 minute; and 72° for 5 minutes. Shrimp Alkaline Phosphatase (SAP) master mix consisting of 10x SAP Buffer and SAP enzyme was mixed and 2L was added to each PCR reaction. The PCR/SAP mixture was cycled with the following conditions: 37° for 40 minutes; 85° for 5 minutes.iPLEX extend reactions were conducted with 0.222x iPLEX Buffer, 1x iPLEX termination mix (for plexes below 18 SNPs Termination Mix is reduced to 0.5x), 1x iPLEX Enzyme (for groups/plexes below 18 SNPs iPLEX Enzyme was reduced to 0.5x), and 0.74M-1.75M of each SNP specific extend primer. 2l of the extend mix was added to each PCR/SAP mixture and cycled. Sample clean-up and transfer: 16µl of Millipore filtered water was added to each reaction well of the 384-well sample plate. Then 6mg of clean resin was added to each sample reaction and shaken for 20 minutes. The plate was centrifuged for 5 minutes at 3200 rpm. Sample was dispensed from the 384-well sample plate to a 384 SpectroCHIP using a Nanodispenser and fired on a Sequenom MALDI-TOF mass spectrometer. Data was analyzed using MassArrayTyper Version 4.0.2.0.
  • University of California at Irvine
  • Authors: Dr. Dan Mercola, Dr. Xin Chen, Dr. David Duggan [note that Dr. David Duggan collaborated from TGEN so his address is Translational Genomics Research Institute, 445 N. Fifth Street, 6th Floor, Phoenix, AZ 85004, Business Phone: +1 (602) 343-8400, Business Fax: +1 (602) 343-8440
  • Affiliations:Department of Pathology & Laboratory Medicine, University of California Irvine, Irvine, California 92697
  • Disclosures: D. Mercola is a stock holder of Proveri Inc. which holds a license from the Regents of the University of California on intellectual property for the development of biomarkers of prostate cancer.
  • Cohort: A total of 68 patients treated by radical prostatectomy (RP) for prostate cancer were analyzed for this study. Informed consents were obtained in all cases following IRB-approved protocols as part of the NCI “SPECS” consortium at UCI (formerly at the Sidney Kimmel Cancer Center in San Diego) for Strategic Partners for the Evaluation of Cancer Signatures for Prostate Cancer. The frozen non tumor tissue of each subject was manually microdissected while mounted in a cryostat into multiple sections for DNA preparation.
  • Genotyping: DNA was prepared from prostate tissue remote from tumor for hybridization to Illumina Human 1M-Duov3 B arrays. A total of 1199187 SNPs were extracted from the array data.
  • University of California, Los Angeles
  • Authors: Dr. Zuo-Feng Zhang, Dr. Shen-Chih Cheng, SomeeJeong
  • Affiliations: Department of Molecular Epidemiology, UCLA Fielding School of Public Health Los Angeles, California 90095
  • Disclosures: NONE
  • Cohort: The University of California Los Angeles (UCLA) prostate cancer study was conducted at Memorial Sloan-Kettering Cancer Center (MSKCC). The study was approved by the Institutional Research Board on Human Subjects of MSKCC and UCLA, and study participants were asked to sign an informed consent form stating they agreed to participate in the study. Eligible cases were patients seen at MSKCC from1993 to1997 with pathologically confirmed diagnoses of prostate adenocarcinoma. Cases were either newly diagnosed or undergoing prostatectomy. A total of 192 cases (125 prostate cancer patients and 67 prostate cancer patients with concurrent bladder cancer diagnosis) with DNA isolated from either blood or prostate normal tissue were recruited. Eligible controls were healthy and cancer-free males, recruited from the blood bank at MSKCC. They were approached and interviewed by the same nurse who interviewed cases, and met the same eligibility criteria, except for never having a diagnosis or history of cancer.All men included in this study self-reported either European or African ancestry.
  • Genotyping: SNP genotyping for 3 prostate cancer risk SNPs were performed using the TaqMan allelic discrimination method with the ABI 7900HT Real-time PCR System (Applied Biosystems, Foster City, CA). We randomly genotyped 5% duplicated samples to evaluate reproducibility and the concordance rate was >99%. The call rates were >96% for all three SNPs.
  • Johns Hopkins Hospital (JHH)
  • Authors: William B Isaacs
  • Affiliations:Department of Urology, Johns Hopkins Medical Institutions, Baltimore, MD 21205
  • Disclosures: NONE
  • Cohort:The cohort includes 5401 men who underwent radical prostatectomy for treatment of clinically localized prostate cancer at the JHH from 1993 to 2001 and who were prospectively followed. All men were consented for genotyping studies for the IRB approved study. All subjects completed questionnaire including race and provided a blood sample for genotype analyses. The clinical and pathological characteristics were recorded in the database.
  • Genotyping: Genotyping was performed as previously described(Sun et al. 2008; Xu et al. 2009). SNP genotyping in the JHH cohort were performed using the MassARRAYiPLEX genotyping system (Sequenom) at Wake Forest University. Duplicate test samples and two water samples (PCR negative controls) that were blinded to the technician were included in each 96-well plate. The rate of concordant results between 100 duplicate samples was >99%.
  • Centre for Educational Research in Equalities, Policy and Pedagogy (CeRePP)
  • Authors: Geraldine Cancel-Tassin, Jean-Nicolas Cornu and Olivier Cussenot;
  • Affiliations: (1) CeRePP, HopitalTenon, 75020 Paris, France; (2) UPMC Univ Paris 06, GRC n°5, 75020 Paris, France; (3) AP-HP, Urology Department, HopitalTenon, 75020 Paris, France. Only 1 &2 for me, and 1, 2 and 3 for Jean-Nicolas Cornu and Olivier Cussenot.
  • Disclosures: NONE
  • Cohort: The information for the supplemental table including details of patient recruitment and genotype methods are the followings: The Centre de Recherche pour les Pathologies Prostatiques Paris (CeRePP) population consisted of 376 PCa cases. These cases were recruited, in three French Departments of Urology (Paris, Brest and Nancy) for the French Prostate Cancer Case Control Study (CeRePP), also known as ProGene study, which began in July 1994. Patients who had histologically confirmed prostate cancer were included after receiving their informed consent. All men included in this study self-reported either European or African descent.
  • Genotyping: Study protocols were approved by the Institutional Review Board Paris Ile de France IV.For the French Prostate Cancer Case Control Study, the genotypes were generated during the follow-up stage of the CGEMS genome wide association study using the custom iSelectInfinium platform from Illumina at the Core Genotyping Facilities of the National Cancer Institute.
  • University of Pennsylvania
  • Authors: Timothy R. Rebbeck, PhD
  • Affiliations: Department of Epidemiology University ofPennsylvania, Philadelphia, PA. 19104
  • Disclosures: NONE
  • Cohort: Incident prostate cancer cases were identified through Urologic Oncology Clinics at multiple hospitals of the University of Pennsylvania Health System (UPHS) between 1995 and 2008. All study participants provided informed consents. Our final study population consisted of 2104 individuals were included. Age was defined as age. Self-identified race was reported by each study participant during the study interview. All study procedures involving human subjects were approved by the University of Pennsylvania Institutional Review Board.
  • Genotyping: A custom Illumina SNP panel including 20 prostate cancer risk SNPs was used for genotyping as previously described.(Barnholtz-Sloan et al. 2011)
  • Vanderbilt University
  • Authors: Dr. Joan P. Breyer, Dr. Jeffrey R. Smith
  • Affiliations: Department of Medicine, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, TN. 37232
  • Disclosures: NONE
  • Cohort:The Familial Prostate Cancer Study was initiated as an observational hospital-based study of familial prostate cancer at Vanderbilt University in 2003. Incident familial prostate cancer case probands (≥ 2 affected 1st or 2nd degree relatives in the pedigree) were recruited at the time of treatment for the principal diagnosis of prostate cancer (confirmed by review of pathology), Approximately 95% of eligible subjects agreed to participate, with written informed consent under Institutional Review Board governance. All subjects completed a structured questionnaire of family cancer history, demographics, and grandparental ancestry. The date, age, and PSA level at diagnosis of adenocarcinoma was recorded for each subject. The initial clinical staging (clinical TNM), biopsy Gleason score, treatment modality and date(s) were recorded. Over 97% of case subjects underwent radical prostatectomy, providing definitive histopathologic diagnoses. For these, surgical pathology staging (pathological TNM), seminal vesicle invasion, margin status, left and right lobe Gleason scores and sum, and capsular penetration were recorded. In addition, a series of independent singleton cases, without a family history of prostate cancer among first- or second-degree relatives, was also accrued. Collectively, data for 846 familial cases and for 293 singleton cases were evaluated in this study. Of these, 13% were of African descent and the remainder were of European descent.
  • Genotyping: DNA was extracted from whole blood on an Autopure LS robot using the Puregene DNA Purification System Standard Protocol (Qiagen, Valencia, CA). DNA was quantified using the PicoGreen dsDNA Quantitation Kit (Invitrogen, Carlsbad, CA), imaged with a Molecular Devices / LJL Analyst HT (Molecular Devices, Union City, CA). SNP genotyping was conducted using TaqMan (Applied Biosystems, Foster City, CA), GoldenGate (Illumina, San Diego, CA) or Centaurus (Nanogen, Bothell, WA) SNP genotyping assay. Methods have been previously described(Breyer et al. 2012; Breyer et al. 2014; Gudmundsson et al. 2009; Gudmundsson et al. 2008).
  • Mayo Clinic
  • Authors: Stephen N.