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Borate U, Yang F, Press R, Ruppert AS, Jones D, Caruthers S, Zhao W, Vergilio JA, Pavlick DC, Juckett L, Norris B, Bucy T, Burd A, Stein EM, Patel P, Baer MR, Stock W, Schiller G, Blum W, Kovacsovics T, Litzow M, Foran J, Heerema NA, Rosenberg L, Marcus S, Yocum A, Stefanos M, Druker B, Byrd JC, Levine RL, Mims A. Samples from patients with AML show high concordance in detection of mutations by NGS at local institutions vs central laboratories. Blood Adv 2023; 7:6048-6054. [PMID: 37459200 PMCID: PMC10582272 DOI: 10.1182/bloodadvances.2022009008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/20/2023] [Indexed: 10/12/2023] Open
Abstract
Next-generation sequencing (NGS) to identify pathogenic mutations is an integral part of acute myeloid leukemia (AML) therapeutic decision-making. The concordance in identifying pathogenic mutations among different NGS platforms at different diagnostic laboratories has been studied in solid tumors but not in myeloid malignancies to date. To determine this interlaboratory concordance, we collected a total of 194 AML bone marrow or peripheral blood samples from newly diagnosed patients with AML enrolled in the Beat AML Master Trial (BAMT) at 2 academic institutions. We analyzed the diagnostic samples from patients with AML for the detection of pathogenic myeloid mutations in 8 genes (DNMT3A, FLT3, IDH1, IDH2, NPM1, TET2, TP53, and WT1) locally using the Hematologic Neoplasm Mutation Panel (50-gene myeloid indication filter) (site 1) or the GeneTrails Comprehensive Heme Panel (site 2) at the 2 institutions and compared them with the central results from the diagnostic laboratory for the BAMT, Foundation Medicine, Inc. The overall percent agreement was over 95% each in all 8 genes, with almost perfect agreement (κ > 0.906) in all but WT1, which had substantial agreement (κ = 0.848) when controlling for site. The minimal discrepancies were due to reporting variants of unknown significance (VUS) for the WT1 and TP53 genes. These results indicate that the various NGS methods used to analyze samples from patients with AML enrolled in the BAMT show high concordance, a reassuring finding given the wide use of NGS for therapeutic decision-making in AML.
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Affiliation(s)
- Uma Borate
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Fei Yang
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - Richard Press
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - Amy S. Ruppert
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Dan Jones
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Sean Caruthers
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Weiqiang Zhao
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | | | | | | | - Brianna Norris
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - Taylor Bucy
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - Amy Burd
- Leukemia and Lymphoma Society, Rye Brook, NY
| | | | - Prapti Patel
- The University of Texas Southwestern Medical Center, Dallas, TX
| | - Maria R. Baer
- University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD
| | - Wendy Stock
- Division of Hematology-Oncology, Department of Internal Medicine, University of Chicago, Chicago, IL
| | - Gary Schiller
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - William Blum
- Winship Cancer Institute of Emory University, Atlanta, GA
| | - Tibor Kovacsovics
- Division of Hematology and Hematologic Malignancies, Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT
| | - Mark Litzow
- Division of Hematology, Mayo Clinic, Rochester, MN
| | - James Foran
- Division of Hematology, Mayo Clinic Florida, Jacksonville, FL
| | - Nyla A. Heerema
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | | | | | | | - Mona Stefanos
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Brian Druker
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - John C. Byrd
- Division of Hematology-Oncology, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH
| | | | - Alice Mims
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH
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Willey JC, Morrison TB, Austermiller B, Crawford EL, Craig DJ, Blomquist TM, Jones WD, Wali A, Lococo JS, Haseley N, Richmond TA, Novoradovskaya N, Kusko R, Chen G, Li QZ, Johann DJ, Deveson IW, Mercer TR, Wu L, Xu J. Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA. CELL REPORTS METHODS 2021; 1:100106. [PMID: 35475002 PMCID: PMC9017191 DOI: 10.1016/j.crmeth.2021.100106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/31/2021] [Accepted: 10/11/2021] [Indexed: 11/25/2022]
Abstract
The primary objective of the FDA-led Sequencing and Quality Control Phase 2 (SEQC2) project is to develop standard analysis protocols and quality control metrics for use in DNA testing to enhance scientific research and precision medicine. This study reports a targeted next-generation sequencing (NGS) method that will enable more accurate detection of actionable mutations in circulating tumor DNA (ctDNA) clinical specimens. To accomplish this, a synthetic internal standard spike-in was designed for each actionable mutation target, suitable for use in NGS following hybrid capture enrichment and unique molecular index (UMI) or non-UMI library preparation. When mixed with contrived ctDNA reference samples, internal standards enabled calculation of technical error rate, limit of blank, and limit of detection for each variant at each nucleotide position in each sample. True-positive mutations with variant allele fraction too low for detection by current practice were detected with this method, thereby increasing sensitivity.
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Affiliation(s)
- James C. Willey
- College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
| | - Tom B. Morrison
- AccuGenomics Inc., The Atrium, Suite 105, 1410 Commonwealth Drive, Wilmington, NC 28403, USA
| | - Bradley Austermiller
- AccuGenomics Inc., The Atrium, Suite 105, 1410 Commonwealth Drive, Wilmington, NC 28403, USA
| | - Erin L. Crawford
- College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
| | - Daniel J. Craig
- College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
| | - Thomas M. Blomquist
- College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
| | | | - Aminah Wali
- Q Solutions, EA Genomics, Morrisville, NC 27560, USA
| | | | - Nathan Haseley
- Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | | | | | | | - Guangchun Chen
- University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Quan-Zhen Li
- University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Donald J. Johann
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W Markham Street, Little Rock, AR 72205, USA
| | - Ira W. Deveson
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Timothy R. Mercer
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- St. Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Leihong Wu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
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3
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Wood DE, White JR, Georgiadis A, Van Emburgh B, Parpart-Li S, Mitchell J, Anagnostou V, Niknafs N, Karchin R, Papp E, McCord C, LoVerso P, Riley D, Diaz LA, Jones S, Sausen M, Velculescu VE, Angiuoli SV. A machine learning approach for somatic mutation discovery. Sci Transl Med 2019; 10:10/457/eaar7939. [PMID: 30185652 DOI: 10.1126/scitranslmed.aar7939] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 05/26/2018] [Accepted: 08/16/2018] [Indexed: 12/19/2022]
Abstract
Variability in the accuracy of somatic mutation detection may affect the discovery of alterations and the therapeutic management of cancer patients. To address this issue, we developed a somatic mutation discovery approach based on machine learning that outperformed existing methods in identifying experimentally validated tumor alterations (sensitivity of 97% versus 90 to 99%; positive predictive value of 98% versus 34 to 92%). Analysis of paired tumor-normal exome data from 1368 TCGA (The Cancer Genome Atlas) samples using this method revealed concordance for 74% of mutation calls but also identified likely false-positive and false-negative changes in TCGA data, including in clinically actionable genes. Determination of high-quality somatic mutation calls improved tumor mutation load-based predictions of clinical outcome for melanoma and lung cancer patients previously treated with immune checkpoint inhibitors. Integration of high-quality machine learning mutation detection in clinical next-generation sequencing (NGS) analyses increased the accuracy of test results compared to other clinical sequencing analyses. These analyses provide an approach for improved identification of tumor-specific mutations and have important implications for research and clinical management of cancer patients.
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Affiliation(s)
| | - James R White
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | | | | | | | | | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Noushin Niknafs
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Rachel Karchin
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Eniko Papp
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | | | - Peter LoVerso
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - David Riley
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Luis A Diaz
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Siân Jones
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Mark Sausen
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Victor E Velculescu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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4
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Kuderer NM, Burton KA, Blau S, Rose AL, Parker S, Lyman GH, Blau CA. Comparison of 2 Commercially Available Next-Generation Sequencing Platforms in Oncology. JAMA Oncol 2019; 3:996-998. [PMID: 27978570 DOI: 10.1001/jamaoncol.2016.4983] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Nicole M Kuderer
- Department of Medicine, University of Washington, Seattle2Center for Cancer Innovation, University of Washington, Seattle
| | - Kimberly A Burton
- Department of Medicine, University of Washington, Seattle2Center for Cancer Innovation, University of Washington, Seattle
| | - Sibel Blau
- Center for Cancer Innovation, University of Washington, Seattle3Northwest Medical Specialties, Puyallup, Washington
| | - Andrea L Rose
- Center for Cancer Innovation, University of Washington, Seattle3Northwest Medical Specialties, Puyallup, Washington
| | - Stephanie Parker
- Center for Cancer Innovation, University of Washington, Seattle3Northwest Medical Specialties, Puyallup, Washington
| | - Gary H Lyman
- Department of Medicine, University of Washington, Seattle4 Hutchinson Institute for Cancer Outcomes Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - C Anthony Blau
- Department of Medicine, University of Washington, Seattle2Center for Cancer Innovation, University of Washington, Seattle5Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle
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Performance of next-generation sequencing on small tumor specimens and/or low tumor content samples using a commercially available platform. PLoS One 2018; 13:e0196556. [PMID: 29702695 PMCID: PMC5922576 DOI: 10.1371/journal.pone.0196556] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/16/2018] [Indexed: 11/30/2022] Open
Abstract
Background Next generation sequencing tests (NGS) are usually performed on relatively small core biopsy or fine needle aspiration (FNA) samples. Data is limited on what amount of tumor by volume or minimum number of FNA passes are needed to yield sufficient material for running NGS. We sought to identify the amount of tumor for running the PCDx NGS platform. Methods 2,723 consecutive tumor tissues of all cancer types were queried and reviewed for inclusion. Information on tumor volume, success of performing NGS, and results of NGS were compiled. Assessment of sequence analysis, mutation calling and sensitivity, quality control, drug associations, and data aggregation and analysis were performed. Results 6.4% of samples were rejected from all testing due to insufficient tumor quantity. The number of genes with insufficient sensitivity make definitive mutation calls increased as the percentage of tumor decreased, reaching statistical significance below 5% tumor content. The number of drug associations also decreased with a lower percentage of tumor, but this difference only became significant between 1–3%. The number of drug associations did decrease with smaller tissue size as expected. Neither specimen size or percentage of tumor affected the ability to pass mRNA quality control. A tumor area of 10 mm2 provides a good margin of error for specimens to yield adequate drug association results. Conclusions Specimen suitability remains a major obstacle to clinical NGS testing. We determined that PCR-based library creation methods allow the use of smaller specimens, and those with a lower percentage of tumor cells to be run on the PCDx NGS platform.
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Khodakov D, Wang C, Zhang DY. Diagnostics based on nucleic acid sequence variant profiling: PCR, hybridization, and NGS approaches. Adv Drug Deliv Rev 2016; 105:3-19. [PMID: 27089811 DOI: 10.1016/j.addr.2016.04.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/21/2016] [Accepted: 04/06/2016] [Indexed: 12/22/2022]
Abstract
Nucleic acid sequence variations have been implicated in many diseases, and reliable detection and quantitation of DNA/RNA biomarkers can inform effective therapeutic action, enabling precision medicine. Nucleic acid analysis technologies being translated into the clinic can broadly be classified into hybridization, PCR, and sequencing, as well as their combinations. Here we review the molecular mechanisms of popular commercial assays, and their progress in translation into in vitro diagnostics.
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