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

Julianne M. O’Daniel, Heather M. McLaughlin, Laura M. Amendola, Sherri J. Bale, Jonathan S. Berg, David Bick, Kevin M. Bowling, Elizabeth C. Chao, Wendy K. Chung, Laura K. Conlin, Gregory M. Cooper, Soma Das, Joshua L. Deignan, Michael O. Dorschner, James P. Evans, Arezou A. Ghazani, Katrina A. Goddard, Michele Gornick, Kelly D. Farwell Hagman, Tina Hambuch, Madhuri Hegde, Lucia A. Hindorff, Ingrid A. Holm, Gail P. Jarvik, Amy Knight Johnson, Lindsey Mighion, Massimo Morra, Sharon E. Plon, Sumit Punj, C. Sue Richards, Avni Santani, Brian H. Shirts, Nancy B. Spinner, Sha Tang, Karen E. Weck, Susan M. Wolf, Yaping Yang, Heidi L. Rehm

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. 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. 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. 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.Genet Med advance online publication 03 Novemeber 2016Genetics in Medicine (2016); doi:10.1038/gim.2016.152.