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Evidence Report/Technology Assessment Number 209 Multigene Panels in Prostate Cancer Risk Assessment Evidence-Based Practice Evidence Report/Technology Assessment Number 209 Multigene Panels in Prostate Cancer Risk Assessment Prepared for: Agency for Healthcare Research and Quality U.S. Department of Health and Human Services 540 Gaither Road Rockville, MD 20850 www.ahrq.gov Contract No. 290-2007-10060-1 Prepared by: McMaster University Evidence-based Practice Center Hamilton, ON, Canada Investigators: Julian Little, Ph.D. Brenda Wilson, M.B.Ch.B., M.Sc., M.R.C.P. (UK), FFPH Ron Carter, Ph.D. Kate Walker, M.Sc.PT. Pasqualina Santaguida, Ph.D. Eva Tomiak, M.D. Joseph Beyene, Ph.D. Parminder Raina, Ph.D. AHRQ Publication No. 12-E020-EF July 2012 This report is based on research conducted by the McMaster University Evidence-based Practice Center (EPC) under contract to the Agency for Healthcare Research and Quality (AHRQ), Rockville, MD (Contract No. 290-2007-10060-1). The findings and conclusions in this document are those of the authors, who are responsible for its contents; the findings and conclusions do not necessarily represent the views of AHRQ. Therefore, no statement in this report should be construed as an official position of AHRQ or of the U.S. Department of Health and Human Services. The information in this report is intended to help health care decisionmakers—patients and clinicians, health system leaders, and policymakers, among others—make well-informed decisions and thereby improve the quality of health care services. This report is not intended to be a substitute for the application of clinical judgment. Anyone who makes decisions concerning the provision of clinical care should consider this report in the same way as any medical reference and in conjunction with all other pertinent information, i.e., in the context of available resources and circumstances presented by individual patients. This report may be used, in whole or in part, as the basis for development of clinical practice guidelines and other quality enhancement tools, or as a basis for reimbursement and coverage policies. AHRQ or U.S. Department of Health and Human Services endorsement of such derivative products may not be stated or implied. This document is in the public domain and may be used and reprinted without permission except those copyrighted materials that are clearly noted in the document. Further reproduction of those copyrighted materials is prohibited without the specific permission of copyright holders. Persons using assistive technology may not be able to fully access information in this report. For assistance, contact [email protected]. None of the investigators have any affiliations or financial involvement that conflicts with the material presented in this report. Suggested citation: Little J, Wilson B, Carter R, Walker K, Santaguida P, Tomiak E, Beyene J, Raina P. Multigene Panels in Prostate Cancer Risk Assessment. Evidence Report No. 209. (Prepared by the McMaster University Evidence-based Practice Center under Contract No. 290- 2007-10060-1.) AHRQ Publication No.12-E020-EF. Rockville, MD: Agency for Healthcare Research and Quality. July 2012. www.effectivehealthcare.ahrq.gov/reports/final.cfm. ii Preface The Agency for Healthcare Research and Quality (AHRQ), through its Evidence-based Practice Centers (EPCs), sponsors the development of evidence reports and technology assessments to assist public- and private-sector organizations in their efforts to improve the quality of health care in the United States. The reports and assessments provide organizations with comprehensive, science-based information on common, costly medical conditions, and new health care technologies and strategies. The EPCs systematically review the relevant scientific literature on topics assigned to them by AHRQ and conduct additional analyses when appropriate prior to developing their reports and assessments. To bring the broadest range of experts into the development of evidence reports and health technology assessments, AHRQ encourages the EPCs to form partnerships and enter into collaborations with other medical and research organizations. The EPCs work with these partner organizations to ensure that the evidence reports and technology assessments they produce will become building blocks for health care quality improvement projects throughout the Nation. The reports undergo peer review and public comment prior to their release as a final report. AHRQ expects that the EPC evidence reports and technology assessments will inform individual health plans, providers, and purchasers as well as the health care system as a whole by providing important information to help improve health care quality. We welcome comments on this evidence report. Comments may be sent by mail to the Task Order Officer named in this report to: Agency for Healthcare Research and Quality, 540 Gaither Road, Rockville, MD 20850, or by email to [email protected]. Carolyn M. Clancy, M.D. Jean Slutsky, P.A., M.S.P.H. Director, Agency for Healthcare Research Director, Center for Outcomes and Evidence and Quality Agency for Healthcare Research and Quality Stephanie Chang M.D., M.P.H. Suchitra Iyer Director, EPC Program Task Order Officer Center for Outcomes and Evidence Center for Outcomes and Evidence Agency for Healthcare Research and Quality Agency for Healthcare Research and Quality iii Acknowledgments The researchers at the McMaster EPC would like to acknowledge the following people for their contributions. We are grateful to our Task Order Officer, Suchitra Iyer, for her support and guidance. Members of the technical expert panel were instrumental in the formation of the parameters and goals of this review. We would also like to thank those who worked so conscientiously, retrieving and screening citations, abstracting data, preparing figures, and editing the report: Una Adamcic-Bistrovoda, Julianna Beckett, Jan Brozek, Patricia Carson, Chris Carvalho, Bryan Cheeseman, Roxanne Cheeseman, Mary Gauld, Natalie Gallo, Inna Gong, Mahbubul Haq, Michael Knauer, Denise Landry, Leah Macdonald, Sohel Nazmul, Maureen Rice, and Jodi Wilson. Technical Expert Panel Rodney Breau, M.D. Urological Oncology Fellowship Mayo Clinic Rochester, MI Phillip Febbo, M.D. Department of Medicine, Leader, UCSF Helen Diller Family Comprehensive Cancer Center San Franscisco, CA Ted Ganiats, M.D. Department of Family and Preventitive Medicine Univeristy of California San Diego La Jolla, CA Roger Klein, M.D., J.D., FCAP Medical Director Molecular Oncology at BloodCenter of Wisconsin Milwaukee, WI Daniel Mercola, M.D., Ph.D. Pathology and Laboratory Medicine, Director, Translation Cancer Biology University of California Irvine, CA Ken Offit, M.D. Chief, Clinical Genetics Service Memorial Sloan-Kettering Cancer Center New York, NY Sue Richards, Ph.D. Oregon Health & Science Univeristy Portland, OR iv Multigene Panels in Prostate Cancer Risk Assessment Structured Abstract Objectives: The aim of this review is to identify, synthesize, and appraise the literature on the analytic validity, clinical validity, and clinical utility of commercially available single nucleotide polymorphism (SNP) panel tests for assessing the risk of prostate cancer. Data Sources: MEDLINE®, Cochrane CENTRAL, Cochrane Database of Systematic Reviews, and Embase, from the beginning of each database to October 2011. Search strategies used combinations of controlled vocabulary (medical subject headings, keywords) and text words. Grey literature was identified. Review Methods: Three Key Questions (KQs) encompassing broad aspects of the analytic validity, clinical validity, and clinical utility of SNP-based panels were developed with the input of a Technical Expert Panel assembled by the Evidence-based Practice Center and approved by the Agency for Healthcare Research and Quality. Standard systematic review methodology was applied, with eligibility criteria developed separately for each KQ. Results: From 1,998 unique citations, 14 were retained for data abstraction and quality assessment following title and abstract screening and full text screening. All focused on clinical validity (KQ2), and evaluated 15 individual panels with two to 35 SNPs. All had poor discriminative ability for predicting risk of prostate cancer and/or distinguishing between aggressive and asymptomatic/latent disease. The risk of bias of the studies was determined to be moderate. None of the panels had been evaluated in routine clinical settings. Conclusions: The evidence on currently available SNP panels does not permit meaningful assessment of analytic validity. The limited evidence on clinical validity is insufficient to conclude that the panels assessed would perform adequately as screening or risk stratification tests. No evidence is available on the clinical utility of current panels. v Contents Executive Summary .................................................................................................................ES-1 Introduction ....................................................................................................................................1 Prostate Cancer ..........................................................................................................................1 Risk Factors .........................................................................................................................1 Natural History.....................................................................................................................2
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  • A Genome-Wide Screen Reveals Functional Gene Clusters in the Cancer Genome and Identifies Epha2 As a Mitogen in Glioblastoma

    A Genome-Wide Screen Reveals Functional Gene Clusters in the Cancer Genome and Identifies Epha2 As a Mitogen in Glioblastoma

    Published OnlineFirst November 6, 2006; DOI: 10.1158/0008-5472.CAN-06-1408 Research Article A Genome-Wide Screen Reveals Functional Gene Clusters in the Cancer Genome and Identifies EphA2 as a Mitogen in Glioblastoma Fenghua Liu,1 Peter J. Park,3,7 Weil Lai,3 Elizabeth Maher,2,4,5 Arnab Chakravarti,1 Laura Durso,4,5 Xiuli Jiang,1 Yi Yu,1 Amanda Brosius,1 Meredith Thomas,1 Lynda Chin,4,6 Cameron Brennan,4,6 Ronald A. DePinho,4,5 Isaac Kohane,3,7 Rona S. Carroll,1 Peter M. Black,1,2 and Mark D. Johnson1,2 1Department of Neurological Surgery, Brigham and Women’s Hospital and Harvard Medical School; 2Program in Neuro-Oncology, Brigham and Women’s Hospital and Dana-Farber/Harvard Cancer Center; 3Harvard-Partners Center for Genetics and Genomics; 4Center for Applied Cancer Science, Belfer Foundation Institute for Innovative Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute; Departments of 5Medicine and Genetics and 6Dermatology, Harvard Medical School; and 7Children’s Hospital Informatics Program, Boston, Massachusetts Abstract human cancers (2–4). However, hundreds of genes with altered A novel genome-wide screen that combines patient outcome expression may be identified in such analyses, and it is often analysis with array comparative genomic hybridization and difficult to determine from these analyses alone which of the mRNA expression profiling was developed to identify genes changes in mRNA expression are upstream, initiating determinants with copy number alterations, aberrant mRNA expression, and of tumor phenotype and which ones represent secondary changes relevance to survival in glioblastoma.