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- Title
Reference Samples to Compare Next-Generation Sequencing Test Performance for Oncology Therapeutics and Diagnostics.
- Authors
Pfeifer, John D; Loberg, Robert; Lofton-Day, Catherine; Zehnbauer, Barbara A
- Abstract
<bold>Objectives: </bold>Diversity of laboratory-developed tests (LDTs) using next-generation sequencing (NGS) raises concerns about their accuracy for selection of targeted therapies. A working group developed a pilot study of traceable reference samples to measure NGS LDT performance among a cohort of clinical laboratories.<bold>Methods: </bold>Human cell lines were engineered via CRISPR/Cas9 and prepared as formalin-fixed, paraffin-embedded cell pellets ("wet" samples) to assess the entire NGS test cycle. In silico mutagenized NGS sequence files ("dry" samples) were used to assess the bioinformatics component of the NGS test cycle. Single and multinucleotide variants (n = 36) of KRAS and NRAS were tested at 5% or 15% variant allele fraction to determine eligibility for therapy with the EGFR inhibitor panitumumab in the setting of metastatic colorectal cancer.<bold>Results: </bold>Twenty-one (21/21) laboratories tested wet samples; 19 of 21 analyzed dry samples. Of the laboratories that tested both the wet and dry samples, 7 (37%) of 19 laboratories correctly reported all variants, 3 (16%) of 19 had fewer than five errors, and 9 (47%) of 19 had five or more errors. Most errors were false negatives.<bold>Conclusions: </bold>Genetically engineered cell lines and mutagenized sequence files are complementary reference samples for evaluating NGS test performance among clinical laboratories using LDTs. Variable accuracy in detection of genetic variants among some LDTs may identify different patient populations for targeted therapy.
- Subjects
COLON tumors; PILOT projects; SEQUENCE analysis; GENETIC mutation; RESEARCH funding
- Publication
American Journal of Clinical Pathology, 2022, Vol 157, Issue 4, p628
- ISSN
0002-9173
- Publication type
journal article
- DOI
10.1093/ajcp/aqab164