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

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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Publication Details

Journal
Academic Pathology
Published
2026-09-16
DOI
https://doi.org/10.1016/j.acpath.2026.100299
Primary Topic
Cancer Genomics and Diagnostics
Type
article
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article

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

Eric Vail, Deqin Ma, Megan Parilla, Christopher D. Gocke et al.
Academic Pathology
Cancer Genomics and Diagnostics
article

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

Eric Vail, Deqin Ma, Megan Parilla, Christopher D. Gocke, Liqiang Xi, Karin E. Finberg, Somak Roy, Dara L. Aisner, Andrew C. Nelson, Adam D. Pfefferle, Noah A. Brown, Yulong Fu, Dan Jones, Audrey N. Jajosky, Georgios Deftereos, David Lieberman, Eric Konnick, Laura MacConaill, Jeffrey Gagan, Marjorie P. David, Erik Nohr, Thomas D. Lee, Christopher Mignogna, Peng Wang, Pamela Snyder, Fei Dong, Jennifer J.D. Morrissette
article en

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.

Academic PathologyVol. 13(4)
University of North Carolina at Chapel Hill (US), University of Iowa (US), Cedars-Sinai Medical Center (US), Brigham and Women's Hospital (US), Cincinnati Children's Hospital Medical Center (US), National Institutes of Health (US), University of Minnesota (US), NorthShore University HealthSystem (US), Johns Hopkins University (US), University of California, Los Angeles (US), The University of Texas at San Antonio Health Science Center (US), University of Calgary (CA), University of California, San Francisco (US), University of Washington (US), University of California, Irvine (US), University of Michigan (US), Hospital of the University of Pennsylvania (US), Johns Hopkins Medicine (US), University of Rochester Medical Center (US), Yale University (US), University of Chicago (US), Evanston Hospital (US), Computational Diagnostics (United States) (US), National Cancer Institute (US), Indiana University School of Medicine, The Ohio State University (US), Indiana University – Purdue University Indianapolis (US), University of Colorado Denver (US)
Openalex Percentile: Top 15%
Cancer Genomics and Diagnostics
DOIOpen Access PDFOpenAlex
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