Validation and implementation of a modular targeted capture assay for the detection of clinically significant molecular oncology alterations.

Autor:	Kuo AJ; Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA., Paulson VA; Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA., Hempelmann JA; Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA., Beightol M; Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA., Todhunter S; Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA., Colbert BG; Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA., Salipante SJ; Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA., Konnick EQ; Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA., Pritchard CC; Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA., Lockwood CM; Department of Laboratory Medicine, University of Washington Medical Center, 1959 NE Pacific Street, Seattle, WA, 98195, USA.
Jazyk:	angličtina
Zdroj:	Practical laboratory medicine [Pract Lab Med] 2020 Feb 03; Vol. 19, pp. e00153. Date of Electronic Publication: 2020 Feb 03 (Print Publication: 2020).
DOI:	10.1016/j.plabm.2020.e00153
Abstrakt:	Objectives: The rapid discovery of clinically significant genetic variants has translated to next-generation sequencing assays becoming out-of-date by the time they are designed, validated, and implemented. UW-OncoPlex addresses this through the adoption of a modular panel capable of redesign as significant alterations are identified. We describe the validation of OncoPlex version 6 (OPXv6) for the detection of single nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs), structural variants (SVs), microsatellite instability (MSI), and tumor mutational burden (TMB) in a panel of 340 genes. Design: One hundred twelve samples with diverse diagnoses were comprised of formalin-fixed-paraffin-embedded tissue, fresh-frozen tissue, plasma, peripheral blood, bone marrow, saliva, and cell-line DNA. Libraries were prepared from genomic and cell-free DNA, hybridized to a custom panel of xGen Lockdown probes, and sequenced on Illumina platforms. Sequences were processed through a custom bioinformatics pipeline, and variant calls were compared to prior orthogonal clinical results. Results: Accuracy was 99% for SNVs ≥5% allele frequency, 98% for indels, 97% for SVs, 99% for CNVs, 100% for MSI, and 100% for TMB (compared to previous OncoPlex versions). Library preparation turnaround time decreased by 40%, and sequencing quality improved with a 2.5-fold increase in average sequencing coverage and 4-fold increase in percent on-target. Conclusions: OPXv6 demonstrates improvements over prior UW-OncoPlex versions including reduced capture cost, improved sequencing quality, and decreased time to results. The modular capture probe design also provides a nimble laboratory response in addressing the expansions necessary to meet the needs of the continuously evolving field of molecular oncology. Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: CC Pritchard and SJ Salipante: consult for Promega EQ Konnick: Travel & honoraria – Ventana, Medscape, Roche, Genentech CM Lockwood: spouse is employed by Bayer. (© 2020 The Authors.)
Databáze:	MEDLINE
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