Integration of Technical, Bioinformatic, and Variant Assessment Approaches in the Validation of a Targeted Next-Generation Sequencing Panel for Myeloid Malignancies.
Context.--Detection of variants in hematologic malignancies is increasingly important because of a growing number of variants impacting diagnosis, prognosis, and treatment response, and as potential therapeutic targets. The use of next-generation sequencing technologies to detect variants in hematol...
| Published in: | Archives of Pathology & Laboratory Medicine Vol. 141; no. 6; pp. 759 - 776 |
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| Main Authors: | , , , , , , , , , |
| Format: | research tables/charts Journal Article |
| Published: |
College of American Pathologists
Jun2017
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| Online Access: | View this record in EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=123400135&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 123400135 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 00039985 1FS jtl: Archives of Pathology & Laboratory Medicine issn: 00039985 maglogo: N pubinfo: dt: Jun2017 vid: 141 iid: 6 pid: 2550 pub: College of American Pathologists place: Northfield, Illinois artinfo: ui: 123400135 123400135 123400135 10.5858/arpa.2016-0547-RA 123400135 ppf: 759 ppct: 17 formats: fmt: @attributes: type: P tig: atl: Integration of Technical, Bioinformatic, and Variant Assessment Approaches in the Validation of a Targeted Next-Generation Sequencing Panel for Myeloid Malignancies. aug: au: Thomas, Mariam Sukhai, Mahadeo A. Zhang, Tong Dolatshahi, Roozbeh Harbi, Djamel Garg, Swati Misyura, Maksym Pugh, Trevor Stockley, Tracy L. Kamel-Reid, Suzanne affil: Laboratory Medicine Program, Advanced Molecular Diagnostics Laboratory, Departments of Pathology and Genetics, University Health Network, Toronto, Ontario, Canada sug: subj: Bioinformatics Technology Leukemia, Myeloid Genetic Screening Methods Sequence Analysis Hematologic Neoplasms Diagnosis Hematologic Neoplasms Physiopathology Outcomes (Health Care) Tumor Markers, Biological Diffusion of Innovation Genes Data Collection Data Analysis Software Funding Source ab: Context.--Detection of variants in hematologic malignancies is increasingly important because of a growing number of variants impacting diagnosis, prognosis, and treatment response, and as potential therapeutic targets. The use of next-generation sequencing technologies to detect variants in hematologic malignancies in a clinical diagnostic laboratory setting allows for efficient identification of routinely tested markers in multiple genes simultaneously, as well as the identification of novel and rare variants in other clinically relevant genes. Objective.--To apply a systematic approach to evaluate and validate a commercially available next-generation sequencing panel (TruSight Myeloid Sequencing Panel, Illumina, San Diego, California) targeting 54 genes. In this manuscript, we focused on the parameters that were used to evaluate assay performance characteristics. Data Sources.--Analytical validation was performed using samples containing known variants that had been identified previously. Cases were selected from different disease types, with variants in a range of genes. Panel performance characteristics were assessed and genomic regions requiring additional analysis or wet-bench approaches identified. Conclusions.--We validated the performance characteristics of a myeloid next-generation sequencing panel for detection of variants. The TruSight Myeloid Sequencing Panel covers more than 95% of target regions with depth greater than 5003. However, because of unique variant types such as large insertions or deletions or genomic regions of high GC content, variants in CEBPA, FLT3, and CALR required supplementation with non--next-generation sequencing assays or with informatics approaches to address deficiencies in performance. The use of multiple bioinformatics approaches (2 variant callers and informatics scripts) allows for maximizing calling of true positives, while identifying limitations in using either method alone. pubtype: Academic Journal doctype: research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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