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Youssef O, Loukola A, Zidi-Mouaffak YHS, Tamlander M, Ruotsalainen S, Kilpeläinen E, Mars N, Ripatti S, Palotie A, Donner K, Carpén O. High-Resolution Genotyping of Formalin-Fixed Tissue Accurately Estimates Polygenic Risk Scores in Human Diseases. J Transl Med 2024; 104:100325. [PMID: 38220043 DOI: 10.1016/j.labinv.2024.100325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/11/2023] [Accepted: 01/05/2024] [Indexed: 01/16/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues stored in biobanks and pathology archives are a vast but underutilized source for molecular studies on different diseases. Beyond being the "gold standard" for preservation of diagnostic human tissues, FFPE samples retain similar genetic information as matching blood samples, which could make FFPE samples an ideal resource for genomic analysis. However, research on this resource has been hindered by the perception that DNA extracted from FFPE samples is of poor quality. Here, we show that germline disease-predisposing variants and polygenic risk scores (PRS) can be identified from FFPE normal tissue (FFPE-NT) DNA with high accuracy. We optimized the performance of FFPE-NT DNA on a genome-wide array containing 657,675 variants. Via a series of testing and validation phases, we established a protocol for FFPE-NT genotyping with results comparable with blood genotyping. The median call rate of FFPE-NT samples in the validation phase was 99.85% (range 98.26%-99.94%) and median concordance with matching blood samples was 99.79% (range 98.85%-99.9%). We also demonstrated that a rare pathogenic PALB2 genetic variant predisposing to cancer can be correctly identified in FFPE-NT samples. We further imputed the FFPE-NT genotype data and calculated the FFPE-NT genome-wide PRS in 3 diseases and 4 disease risk variables. In all cases, FFPE-NT and matching blood PRS were highly concordant (all Pearson's r > 0.95). The ability to precisely genotype FFPE-NT on a genome-wide array enables translational genomics applications of archived FFPE-NT samples with the possibility to link to corresponding phenotypes and longitudinal health data.
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Affiliation(s)
- Omar Youssef
- Department of Pathology, University of Helsinki, Helsinki, Finland; Clinical and Chemical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Anu Loukola
- Helsinki Biobank, Helsinki University Hospital (HUS), Helsinki, Finland
| | - Yossra H S Zidi-Mouaffak
- Department of Pathology, University of Helsinki, Helsinki, Finland; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Helsinki Biobank, Helsinki University Hospital (HUS), Helsinki, Finland
| | - Max Tamlander
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sanni Ruotsalainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Elina Kilpeläinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Nina Mars
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Clinicum, Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Analytic and Translational Genetics Unit, Department of Medicine, and the Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts
| | - Kati Donner
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Olli Carpén
- Department of Pathology, University of Helsinki, Helsinki, Finland; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Helsinki Biobank, Helsinki University Hospital (HUS), Helsinki, Finland
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Jiang Y, Meyers TJ, Emeka AA, Cooley LF, Cooper PR, Lancki N, Helenowski I, Kachuri L, Lin DW, Stanford JL, Newcomb LF, Kolb S, Finelli A, Fleshner NE, Komisarenko M, Eastham JA, Ehdaie B, Benfante N, Logothetis CJ, Gregg JR, Perez CA, Garza S, Kim J, Marks LS, Delfin M, Barsa D, Vesprini D, Klotz LH, Loblaw A, Mamedov A, Goldenberg SL, Higano CS, Spillane M, Wu E, Carter HB, Pavlovich CP, Mamawala M, Landis T, Carroll PR, Chan JM, Cooperberg MR, Cowan JE, Morgan TM, Siddiqui J, Martin R, Klein EA, Brittain K, Gotwald P, Barocas DA, Dallmer JR, Gordetsky JB, Steele P, Kundu SD, Stockdale J, Roobol MJ, Venderbos LD, Sanda MG, Arnold R, Patil D, Evans CP, Dall’Era MA, Vij A, Costello AJ, Chow K, Corcoran NM, Rais-Bahrami S, Phares C, Scherr DS, Flynn T, Karnes RJ, Koch M, Dhondt CR, Nelson JB, McBride D, Cookson MS, Stratton KL, Farriester S, Hemken E, Stadler WM, Pera T, Banionyte D, Bianco FJ, Lopez IH, Loeb S, Taneja SS, Byrne N, Amling CL, Martinez A, Boileau L, Gaylis FD, Petkewicz J, Kirwen N, Helfand BT, Xu J, Scholtens DM, Catalona WJ, Witte JS. Genetic Factors Associated with Prostate Cancer Conversion from Active Surveillance to Treatment. HGG ADVANCES 2022; 3:100070. [PMID: 34993496 PMCID: PMC8725988 DOI: 10.1016/j.xhgg.2021.100070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/12/2021] [Indexed: 12/18/2022] Open
Abstract
Men diagnosed with low-risk prostate cancer (PC) are increasingly electing active surveillance (AS) as their initial management strategy. While this may reduce the side effects of treatment for prostate cancer, many men on AS eventually convert to active treatment. PC is one of the most heritable cancers, and genetic factors that predispose to aggressive tumors may help distinguish men who are more likely to discontinue AS. To investigate this, we undertook a multi-institutional genome-wide association study (GWAS) of 5,222 PC patients and 1,139 other patients from replication cohorts, all of whom initially elected AS and were followed over time for the potential outcome of conversion from AS to active treatment. In the GWAS we detected 18 variants associated with conversion, 15 of which were not previously associated with PC risk. With a transcriptome-wide association study (TWAS), we found two genes associated with conversion (MAST3, p = 6.9×10-7 and GAB2, p = 2.0×10-6). Moreover, increasing values of a previously validated 269-variant genetic risk score (GRS) for PC was positively associated with conversion (e.g., comparing the highest to the two middle deciles gave a hazard ratio [HR] = 1.13; 95% Confidence Interval [CI]= 0.94-1.36); whereas, decreasing values of a 36-variant GRS for prostate-specific antigen (PSA) levels were positively associated with conversion (e.g., comparing the lowest to the two middle deciles gave a HR = 1.25; 95% CI, 1.04-1.50). These results suggest that germline genetics may help inform and individualize the decision of AS-or the intensity of monitoring on AS-versus treatment for the initial management of patients with low-risk PC.
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Affiliation(s)
- Yu Jiang
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Travis J. Meyers
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adaeze A. Emeka
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lauren Folgosa Cooley
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Phillip R. Cooper
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nicola Lancki
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Irene Helenowski
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel W. Lin
- Fred Hutchinson Cancer Research Center, Cancer Prevention Program, Public Health Sciences, Seattle, WA 98109, USA
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Janet L. Stanford
- Fred Hutchinson Cancer Research Center, Cancer Epidemiology Program, Public Health Sciences, Seattle, WA 98109, USA
- Department of Epidemiology, University of Washington, School of Public Health, Seattle, WA 98195, USA
| | - Lisa F. Newcomb
- Fred Hutchinson Cancer Research Center, Cancer Prevention Program, Public Health Sciences, Seattle, WA 98109, USA
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Suzanne Kolb
- Fred Hutchinson Cancer Research Center, Cancer Epidemiology Program, Public Health Sciences, Seattle, WA 98109, USA
- Department of Epidemiology, University of Washington, School of Public Health, Seattle, WA 98195, USA
| | - Antonio Finelli
- Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Neil E. Fleshner
- Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Maria Komisarenko
- Division of Urology, Department of Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - James A. Eastham
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Behfar Ehdaie
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicole Benfante
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher J. Logothetis
- Departments of Genitourinary Medical Oncology and Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Justin R. Gregg
- Departments of Genitourinary Medical Oncology and Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cherie A. Perez
- Departments of Genitourinary Medical Oncology and Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sergio Garza
- Departments of Genitourinary Medical Oncology and Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeri Kim
- Departments of Genitourinary Medical Oncology and Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Leonard S. Marks
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Merdie Delfin
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Danielle Barsa
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Danny Vesprini
- Odette Cancer Centre, Sunnybrook Health and Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Laurence H. Klotz
- Odette Cancer Centre, Sunnybrook Health and Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Andrew Loblaw
- Odette Cancer Centre, Sunnybrook Health and Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Alexandre Mamedov
- Odette Cancer Centre, Sunnybrook Health and Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - S. Larry Goldenberg
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Celestia S. Higano
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Maria Spillane
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Eugenia Wu
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - H. Ballentine Carter
- Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christian P. Pavlovich
- Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mufaddal Mamawala
- Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tricia Landis
- Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter R. Carroll
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - June M. Chan
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew R. Cooperberg
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Janet E. Cowan
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Todd M. Morgan
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Javed Siddiqui
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rabia Martin
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Eric A. Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Karen Brittain
- Glickman Urological and Kidney Institute, Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Paige Gotwald
- Glickman Urological and Kidney Institute, Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Daniel A. Barocas
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeremiah R. Dallmer
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jennifer B. Gordetsky
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Pam Steele
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shilajit D. Kundu
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jazmine Stockdale
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Monique J. Roobol
- Department of Urology, Erasmus Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Lionne D.F. Venderbos
- Department of Urology, Erasmus Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Martin G. Sanda
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Rebecca Arnold
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Dattatraya Patil
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Christopher P. Evans
- Department of Urologic Surgery, University of California, Davis Medical Center, Sacramento, CA, USA
| | - Marc A. Dall’Era
- Department of Urologic Surgery, University of California, Davis Medical Center, Sacramento, CA, USA
| | - Anjali Vij
- Department of Urologic Surgery, University of California, Davis Medical Center, Sacramento, CA, USA
| | - Anthony J. Costello
- Department of Urology, Royal Melbourne Hospital and University of Melbourne, Melbourne, VIC, Australia
| | - Ken Chow
- Department of Urology, Royal Melbourne Hospital and University of Melbourne, Melbourne, VIC, Australia
| | - Niall M. Corcoran
- Department of Urology, Royal Melbourne Hospital and University of Melbourne, Melbourne, VIC, Australia
| | - Soroush Rais-Bahrami
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Courtney Phares
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Douglas S. Scherr
- Department of Urology, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
| | - Thomas Flynn
- Department of Urology, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
| | | | - Michael Koch
- Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Courtney Rose Dhondt
- Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Joel B. Nelson
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Dawn McBride
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael S. Cookson
- Department of Urology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kelly L. Stratton
- Department of Urology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Stephen Farriester
- Department of Urology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Erin Hemken
- Department of Urology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | | | - Tuula Pera
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
| | | | | | | | - Stacy Loeb
- Departments of Urology and Population Health, New York University Langone Health and Manhattan Veterans Affairs Medical Center, New York, NY, USA
| | - Samir S. Taneja
- Departments of Urology and Population Health, New York University Langone Health and Manhattan Veterans Affairs Medical Center, New York, NY, USA
| | - Nataliya Byrne
- Departments of Urology and Population Health, New York University Langone Health and Manhattan Veterans Affairs Medical Center, New York, NY, USA
| | | | - Ann Martinez
- Department of Urology, Oregon Health and Science University, Portland, OR, USA
| | - Luc Boileau
- Department of Urology, Oregon Health and Science University, Portland, OR, USA
| | - Franklin D. Gaylis
- Genesis Healthcare Partners, Department of Urology, University of California, San Diego, CA, USA
| | | | - Nicholas Kirwen
- Division of Urology, NorthShore University Health System, Evanston, IL, USA
| | - Brian T. Helfand
- Division of Urology, NorthShore University Health System, Evanston, IL, USA
| | - Jianfeng Xu
- Division of Urology, NorthShore University Health System, Evanston, IL, USA
| | - Denise M. Scholtens
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - William J. Catalona
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - John S. Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Departments of Epidemiology and Population Health, Biomedical Data Science, and Genetics, Stanford University, Stanford, CA, USA
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