A survey of current practices for genomic sequencing test interpretation and reporting processes in US laboratories.

• Type of Material: Article
• Authors: Julianne M. O'Daniel, University of North Carolina at Chapel Hill; Heather M. McLaughlin, Partners Healthcare Personalized Medicine; Laura M. Amendola, University of Washington; Sherri J. Bale, GeneDx, Inc.; Jonathan S. Berg, University of North Carolina at Chapel Hill; David Bick, Medical College of Wisconsin; Kevin M. Bowling, HudsonAlpha Institute for Biotechnology; Elizabeth C. Chao, Ambry Genetics; Wendy K. Chung, Columbia University; Laura K. Conlin, University of Pennsylvania; Gregory M. Cooper, HudsonAlpha Institute for Biotechnology; Soma Das, University of Chicago; Joshua L. Deignan, University of California Los Angeles; Michael O. Dorschner, University of Washington; James P. Evans, University of North Carolina at Chapel Hill; Arezou A. Ghazani, Dana Farber Cancer Institute; Katrina A. Goddard, Kaiser Permanente Northwest; Michele Gornick, University of Michigan; Kelly D. Farwell Hagman, Ambry Genetics; Tina Hambuch, Illumina, Inc.; Madhuri Hegde, Emory University; Lucia A. Hindorff, National Human Genome Research Institute; Ingrid A. Holm, Boston Children's Hospital; Gail P. Jarvik, University of Washington; Amy Knight Johnson, University of Chicago; Lindsey Mighion, Emory University; Massimo Morra, Personalis, Inc.; Sharon E. Plon, Baylor College of Medicine; Sumit Punj, Oregon Health & Science University; C. Sue Richards, Oregon Health & Science University; Avni Santani, The Children's Hospital of Philadelphia and Perelman School of Medicine at The University of Pennsylvania; Brian H. Shirts, University of Washington; Nancy B. Spinner, University of Pennsylvania; Sha Tang, Ambry Genetics; Karen E. Weck, University of North Carolina at Chapel Hill; Susan M. Wolf, University of Minnesota; Yaping Yang, Baylor College of Medicine and Baylor Miraca Genetics Laboratories; Heidi L/ Rehm, The Broad Institute of MIT and Harvard
• Language: English
• Date: 2016-11-03
• Publisher: Macmillan Publishers Limited
• Publication Version: Author Accepted Manuscript (After Peer Review)
• Copyright Statement: © 2017 Macmillan Publishers Limited
• Final Published Version (URL): http://dx.doi.org/10.1038/gim.2016.152
• Title of Journal or Parent Work: Genetics in Medicine
• Volume: 19
• Issue: 5
• Start Page: 575
• End Page: 582
• Keywords: clinical reporting; laboratory standards; exome sequencing; genome sequencing; genetic testing
• Research Categories: Biology, Genetics; Biology, Molecular

Abstract

PURPOSE: While the diagnostic success of genomic sequencing expands, the complexity of this testing should not be overlooked. Numerous laboratory processes are required to support the identification, interpretation, and reporting of clinically significant variants. This study aimed to examine the workflow and reporting procedures among US laboratories to highlight shared practices and identify areas in need of standardization. METHODS: Surveys and follow-up interviews were conducted with laboratories offering exome and/or genome sequencing to support a research program or for routine clinical services. The 73-item survey elicited multiple choice and free-text responses that were later clarified with phone interviews. RESULTS: Twenty-one laboratories participated. Practices highly concordant across all groups included consent documentation, multiperson case review, and enabling patient opt-out of incidental or secondary findings analysis. Noted divergence included use of phenotypic data to inform case analysis and interpretation and reporting of case-specific quality metrics and methods. Few laboratory policies detailed procedures for data reanalysis, data sharing, or patient access to data. C ONCLUSION: This study provides an overview of practices and policies of experienced exome and genome sequencing laboratories. The results enable broader consideration of which practices are becoming standard approaches, where divergence remains, and areas of development in best practice guidelines that may be helpful.