Guidelines for Validation of Next-Generation Sequencing–Based Oncology Panels: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists

Lawrence J. Jennings, Maria E. Arcila, Christopher Corless, Suzanne Kamel-Reid, Ira M. Lubin, John Pfeifer, Robyn L. Temple-Smolkin, Karl V. Voelkerding, Marina N. Nikiforova

Research output: Contribution to journalReview article

114 Citations (Scopus)

Abstract

Next-generation sequencing (NGS) methods for cancer testing have been rapidly adopted by clinical laboratories. To establish analytical validation best practice guidelines for NGS gene panel testing of somatic variants, a working group was convened by the Association of Molecular Pathology with liaison representation from the College of American Pathologists. These joint consensus recommendations address NGS test development, optimization, and validation, including recommendations on panel content selection and rationale for optimization and familiarization phase conducted before test validation; utilization of reference cell lines and reference materials for evaluation of assay performance; determining of positive percentage agreement and positive predictive value for each variant type; and requirements for minimal depth of coverage and minimum number of samples that should be used to establish test performance characteristics. The recommendations emphasize the role of laboratory director in using an error-based approach that identifies potential sources of errors that may occur throughout the analytical process and addressing these potential errors through test design, method validation, or quality controls so that no harm comes to the patient. The recommendations contained herein are intended to assist clinical laboratories with the validation and ongoing monitoring of NGS testing for detection of somatic variants and to ensure high quality of sequencing results.

Original languageEnglish (US)
Pages (from-to)341-365
Number of pages25
JournalJournal of Molecular Diagnostics
Volume19
Issue number3
DOIs
StatePublished - May 1 2017

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Molecular Pathology
Joints
Guidelines
Practice Guidelines
Quality Control
Research Design
Cell Line
Genes
Pathologists
Neoplasms

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Molecular Medicine

Cite this

Guidelines for Validation of Next-Generation Sequencing–Based Oncology Panels : A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. / Jennings, Lawrence J.; Arcila, Maria E.; Corless, Christopher; Kamel-Reid, Suzanne; Lubin, Ira M.; Pfeifer, John; Temple-Smolkin, Robyn L.; Voelkerding, Karl V.; Nikiforova, Marina N.

In: Journal of Molecular Diagnostics, Vol. 19, No. 3, 01.05.2017, p. 341-365.

Research output: Contribution to journalReview article

Jennings, Lawrence J. ; Arcila, Maria E. ; Corless, Christopher ; Kamel-Reid, Suzanne ; Lubin, Ira M. ; Pfeifer, John ; Temple-Smolkin, Robyn L. ; Voelkerding, Karl V. ; Nikiforova, Marina N. / Guidelines for Validation of Next-Generation Sequencing–Based Oncology Panels : A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. In: Journal of Molecular Diagnostics. 2017 ; Vol. 19, No. 3. pp. 341-365.
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