Landscape of approaches for streamlining pre-analytical and early analytical variables for solid tumor next-generation sequencing: A Genomics Organization for Academic Laboratories consortium report
Abstract
The scope of pre-analytical and early analytical methods used in clinical molecular laboratories can have vast effects on the quality and turnaround time for solid tumor next-generation sequencing assays. To learn more about various approaches, a survey of 24 academic laboratories within the Genomics Organization for Academic Laboratories consortium was administered, focusing on pre-analytical and early analytical issues in next-generation sequencing clinical assays that may affect patient care. The survey revealed the landscape of clinical laboratory practices for use of cytopathology smears, block selection, histology practices and protocols, sample transport, slide imaging, sample adequacy assessment, tumor cell enrichment, and deparaffinization methods. Most laboratories reported that they either accepted cytopathology smears for next-generation sequencing testing or had a plan to accept them soon. All laboratories surveyed performed micro- or macro-dissection on unstained formalin-fixed, paraffin-embedded slides for tumor cell enrichment. Several laboratories reported sectioning blocks within the molecular laboratory. While most respondents used an organic solvent for deparaffinization, several laboratories used mineral oil as an alternative. The approaches of other laboratories reported here are expected to be an impactful resource to address pre-analytical issues that may improve assay quality and turnaround time.
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Authors: Marjorie P. David, Jennifer J.D. Morrissette, Noah A. Brown, Georgios Deftereos, Fei Dong, Karin E. Finberg, Yulong Fu, Jeffrey Gagan, Christopher D. Gocke, Audrey N. Jajosky, Eric Konnick, Thomas D. Lee, David Lieberman, Deqin Ma, Laura MacConaill, Christopher Mignogna, Andrew C. Nelson, Erik Nohr, Megan Parilla, Adam D. Pfefferle, Somak Roy, Pamela Snyder, Eric Vail, Peng Wang, Liqiang Xi, Dan Jones, Dara L. Aisner
Institutions: Brigham and Women's Hospital, University of California, Los Angeles, University of Chicago, University of Washington, University of Colorado Denver, Johns Hopkins University, The Ohio State University, University of North Carolina at Chapel Hill, Cincinnati Children's Hospital Medical Center, University of California, San Francisco, University of Michigan, University of Iowa, University of Calgary, Cedars-Sinai Medical Center, University of Minnesota, Yale University, Indiana University School of Medicine, Indiana University – Purdue University Indianapolis, Johns Hopkins Medicine, The University of Texas at San Antonio Health Science Center, University of California, Irvine, National Cancer Institute, University of Rochester Medicine, National Institutes of Health, Hospital of the University of Pennsylvania, Endeavor Health, Evanston Hospital, Computational Diagnostics (United States)