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.
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.
Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine, Chicago, Illinois. Electronic address: ljennings@luriechildrens.org.
Lawrence J
LJ
Jennings
Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Memorial Sloan Kettering Cancer Center, New York, New York.
Maria E
ME
Arcila
Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Department of Pathology and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon.
Christopher
C
Corless
Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Department of Clinical Laboratory Genetics, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
Suzanne
S
Kamel-Reid
Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Centers for Disease Control and Prevention, Atlanta, Georgia.
Ira M
IM
Lubin
Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Washington University School of Medicine, St. Louis, Missouri.
John
J
Pfeifer
Association for Molecular Pathology, Bethesda, Maryland.
Robyn L
RL
Temple-Smolkin
Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; ARUP Laboratories, Salt Lake City, Utah; Department of Pathology, University of Utah, Salt Lake City, Utah.
Karl V
KV
Voelkerding
Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.
Marina N
MN
Nikiforova
D005820:Genetic Testing / Q000592:standards; D017408:Guidelines as Topic; D059014:High-Throughput Nucleotide Sequencing / Q000592:standards*; D006801:Humans; D057089:Pathology, Molecular / Q000592:standards*; D012955:Societies, Medical / Q000592:standards; D014481:United States