51
|
Lagunas-Rangel FA, Chávez-Valencia V. FLT3–ITD and its current role in acute myeloid leukaemia. Med Oncol 2017; 34:114. [DOI: 10.1007/s12032-017-0970-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 04/25/2017] [Indexed: 01/20/2023]
|
52
|
Patel JL, Schumacher JA, Frizzell K, Sorrells S, Shen W, Clayton A, Jattani R, Kelley TW. Coexisting and cooperating mutations in NPM1-mutated acute myeloid leukemia. Leuk Res 2017; 56:7-12. [PMID: 28152414 DOI: 10.1016/j.leukres.2017.01.027] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/17/2017] [Accepted: 01/22/2017] [Indexed: 11/30/2022]
Abstract
NPM1 insertion mutations represent a common recurrent genetic abnormality in acute myeloid leukemia (AML) patients. The frequency of these mutations varies from approximately 30% overall up to 50% in patients with a normal karyotype. Several recent studies have exploited advances in massively parallel sequencing technology to shed light on the complex genomic landscape of AML. We hypothesize that variant allele fraction (VAF) data derived from massively parallel sequencing studies may provide further insights into the clonal architecture and pathogenesis of NPM1-driven leukemogenesis. Diagnostic peripheral blood or bone marrow samples from NPM1-mutated AML patients (n=120) were subjected to targeted sequencing using a panel of fifty-seven genes known to be commonly mutated in myeloid malignancies. NPM1 mutations were always accompanied by additional mutations and NPM1 had the highest VAF in only one case. Nearly all NPM1-mutated AML patients showed concurrent mutations in genes involved in regulation of DNA methylation (DNMT3A, TET2, IDH1, IDH2), RNA splicing (SRSF2, SF3B1), or in the cohesin complex (RAD21, SMC1A, SMC3, STAG2). Mutations in these genes had higher median VAFs that were higher (40% or greater) than the co-existing NPM1 mutations (median VAF 16.8%). Mutations associated with cell signaling pathways (FLT3, NRAS, and PTPN11) are also frequently encountered in NPM1-mutated AML cases, but had relatively low VAFs (7.0-11.9%). No cases of NPM1-mutated AML with a concurrent IDH2R172 mutation were observed, suggesting that these variants are mutually exclusive. Overall, these data suggest that NPM1 mutations are a secondary or late event in the pathogenesis of AML and are preceded by founder mutations in genes that may be associated with recently described preclinical states such as clonal hematopoiesis of indeterminate potential or clonal cytopenias of undetermined significance.
Collapse
Affiliation(s)
- Jay L Patel
- Department of Pathology, University of Utah, Salt Lake City, UT, USA; ARUP Laboratories, Salt Lake City, UT, USA.
| | | | | | | | - Wei Shen
- ARUP Laboratories, Salt Lake City, UT, USA
| | | | | | - Todd W Kelley
- Department of Pathology, University of Utah, Salt Lake City, UT, USA; ARUP Laboratories, Salt Lake City, UT, USA
| |
Collapse
|
53
|
Jennings LJ, Arcila ME, Corless C, Kamel-Reid S, Lubin IM, Pfeifer J, Temple-Smolkin RL, Voelkerding KV, Nikiforova MN. 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. J Mol Diagn 2017; 19:341-365. [PMID: 28341590 DOI: 10.1016/j.jmoldx.2017.01.011] [Citation(s) in RCA: 433] [Impact Index Per Article: 61.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 01/24/2017] [Indexed: 02/07/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Lawrence J Jennings
- 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.
| | - Maria E Arcila
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christopher Corless
- 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
| | - Suzanne Kamel-Reid
- 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
| | - Ira M Lubin
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John Pfeifer
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Washington University School of Medicine, St. Louis, Missouri
| | | | - Karl V Voelkerding
- 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
| | - Marina N Nikiforova
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| |
Collapse
|
54
|
Lin PH, Li HY, Fan SC, Yuan TH, Chen M, Hsu YH, Yang YH, Li LY, Yeh SP, Bai LY, Liao YM, Lin CY, Hsieh CY, Lin CC, Lin CH, Lien MY, Chen TT, Ni YH, Chiu CF. A targeted next-generation sequencing in the molecular risk stratification of adult acute myeloid leukemia: implications for clinical practice. Cancer Med 2017; 6:349-360. [PMID: 28070990 PMCID: PMC5313641 DOI: 10.1002/cam4.969] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 09/12/2016] [Accepted: 10/26/2016] [Indexed: 12/19/2022] Open
Abstract
Conventional cytogenetics can categorize patients with acute myeloid leukemia (AML) into favorable, intermediate, and unfavorable-risk groups; however, patients with intermediate-risk cytogenetics represent the major population with variable outcomes. Because molecular profiling can assist with AML prognosis and next-generation sequencing allows simultaneous sequencing of many target genes, we analyzed 260 genes in 112 patients with de novo AML who received standard treatment. Multivariate analysis showed that karyotypes and mutation status of TET2, PHF6, KIT, and NPM1mutation /FLT3- internal tandem duplication (ITD)negative were independent prognostic factors for the entire cohort. Among patients with intermediate-risk cytogenetics, patients with mutations in CEBPAdouble mutation , IDH2, and NPM1 in the absence of FLT3-ITD were associated with improved Overall survival (OS), similar to those with favorable-risk cytogenetics; patients with mutations in TET2, RUNX1, ASXL1, and DNMT3A were associated with reduced OS, similar to those with unfavorable-risk cytogenetics. We concluded that integration of cytogenetic and molecular profiling improves prognostic stratification of patients into three groups with more distinct prognoses (P < 0.001) and significantly reduces the number of patients classified as intermediate risk. In addition, our study demonstrates that next-generation sequencing (NGS)-based multi-gene sequencing is clinically applicable in establishing an accurate risk stratification system for guiding therapeutic decisions.
Collapse
Affiliation(s)
- Po-Han Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, China Medical University, Taichung, Taiwan
| | - Huei-Ying Li
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Sheng-Chih Fan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Tzu-Hang Yuan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Ming Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Department of Genomic Medicine, Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan
| | - Yu-Hua Hsu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Hsuan Yang
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Long-Yuan Li
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Su-Peng Yeh
- Division of Hematology and Oncology, Department of Internal Medicine, China Medical University Hospital.,Department of Internal Medicine, Graduate Institute of Clinical Medicine, China Medical University, Taichung, Taiwan
| | - Li-Yuan Bai
- Division of Hematology and Oncology, Department of Internal Medicine, China Medical University Hospital.,Department of Internal Medicine, Graduate Institute of Clinical Medicine, China Medical University, Taichung, Taiwan
| | - Yu-Min Liao
- Division of Hematology and Oncology, Department of Internal Medicine, China Medical University Hospital
| | - Chen-Yuan Lin
- Division of Hematology and Oncology, Department of Internal Medicine, China Medical University Hospital
| | - Ching-Yun Hsieh
- Division of Hematology and Oncology, Department of Internal Medicine, China Medical University Hospital
| | - Ching-Chan Lin
- Division of Hematology and Oncology, Department of Internal Medicine, China Medical University Hospital
| | - Che-Hung Lin
- Division of Hematology and Oncology, Department of Internal Medicine, China Medical University Hospital
| | - Ming-Yu Lien
- Division of Hematology and Oncology, Department of Internal Medicine, China Medical University Hospital
| | - Tzu-Ting Chen
- Division of Hematology and Oncology, Department of Internal Medicine, China Medical University Hospital
| | - Yen-Hsuan Ni
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Chang-Fang Chiu
- Division of Hematology and Oncology, Department of Internal Medicine, China Medical University Hospital.,Department of Internal Medicine, Graduate Institute of Clinical Medicine, China Medical University, Taichung, Taiwan
| |
Collapse
|
55
|
Mutational analysis of disease relapse in patients allografted for acute myeloid leukemia. Blood Adv 2016; 1:193-204. [PMID: 29296935 DOI: 10.1182/bloodadvances.2016000760] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/31/2016] [Indexed: 01/27/2023] Open
Abstract
Disease relapse is the major cause of treatment failure after allogeneic stem cell transplantation (allo-SCT) in acute myeloid leukemia (AML). To identify AML-associated genes prognostic of AML relapse post-allo-SCT, we resequenced 35 genes in 113 adults at diagnosis, 49 of whom relapsed. Two hundred sixty-two mutations were detected in 102/113 (90%) patients. An increased risk of relapse was observed in patients with mutations in WT1 (P = .018), DNMT3A (P = .045), FLT3 ITD (P = .071), and TP53 (P = .06), whereas mutations in IDH1 were associated with a reduced risk of disease relapse (P = .018). In 29 patients, we additionally compared mutational profiles in bone marrow at diagnosis and relapse to study changes in clonal structure at relapse. In 13/29 patients, mutational profiles altered at relapse. In 9 patients, mutations present at relapse were not detected at diagnosis. In 15 patients, additional available pre-allo-SCT samples demonstrated that mutations identified posttransplant but not at diagnosis were detectable immediately prior to transplant in 2 of 15 patients. Taken together, these observations, if confirmed in larger studies, have the potential to inform the design of novel strategies to reduce posttransplant relapse highlighting the potential importance of post-allo-SCT interventions with a broad antitumor specificity in contrast to targeted therapies based on mutational profile at diagnosis.
Collapse
|
56
|
Hansen MC, Herborg LL, Hansen M, Roug AS, Hokland P. Combination of RNA- and exome sequencing: Increasing specificity for identification of somatic point mutations and indels in acute leukaemia. Leuk Res 2016; 51:27-31. [DOI: 10.1016/j.leukres.2016.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 10/15/2016] [Accepted: 10/18/2016] [Indexed: 02/03/2023]
|
57
|
Sholl LM, Do K, Shivdasani P, Cerami E, Dubuc AM, Kuo FC, Garcia EP, Jia Y, Davineni P, Abo RP, Pugh TJ, van Hummelen P, Thorner AR, Ducar M, Berger AH, Nishino M, Janeway KA, Church A, Harris M, Ritterhouse LL, Campbell JD, Rojas-Rudilla V, Ligon AH, Ramkissoon S, Cleary JM, Matulonis U, Oxnard GR, Chao R, Tassell V, Christensen J, Hahn WC, Kantoff PW, Kwiatkowski DJ, Johnson BE, Meyerson M, Garraway LA, Shapiro GI, Rollins BJ, Lindeman NI, MacConaill LE. Institutional implementation of clinical tumor profiling on an unselected cancer population. JCI Insight 2016; 1:e87062. [PMID: 27882345 DOI: 10.1172/jci.insight.87062] [Citation(s) in RCA: 339] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND. Comprehensive genomic profiling of a patient's cancer can be used to diagnose, monitor, and recommend treatment. Clinical implementation of tumor profiling in an enterprise-wide, unselected cancer patient population has yet to be reported. METHODS. We deployed a hybrid-capture and massively parallel sequencing assay (OncoPanel) for all adult and pediatric patients at our combined cancer centers. Results were categorized by pathologists based on actionability. We report the results for the first 3,727 patients tested. RESULTS. Our cohort consists of cancer patients unrestricted by disease site or stage. Across all consented patients, half had sufficient and available (>20% tumor) material for profiling; once specimens were received in the laboratory for pathology review, 73% were scored as adequate for genomic testing. When sufficient DNA was obtained, OncoPanel yielded a result in 96% of cases. 73% of patients harbored an actionable or informative alteration; only 19% of these represented a current standard of care for therapeutic stratification. The findings recapitulate those of previous studies of common cancers but also identify alterations, including in AXL and EGFR, associated with response to targeted therapies. In rare cancers, potentially actionable alterations suggest the utility of a "cancer-agnostic" approach in genomic profiling. Retrospective analyses uncovered contextual genomic features that may inform therapeutic response and examples where diagnoses revised by genomic profiling markedly changed clinical management. CONCLUSIONS. Broad sequencing-based testing deployed across an unselected cancer cohort is feasible. Genomic results may alter management in diverse scenarios; however, additional barriers must be overcome to enable precision cancer medicine on a large scale. FUNDING. This work was supported by DFCI, BWH, and the National Cancer Institute (5R33CA155554 and 5K23CA157631).
Collapse
Affiliation(s)
- Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Khanh Do
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Early Drug Discovery Center
| | - Priyanka Shivdasani
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ethan Cerami
- Department of Biostatistics and Computational Biology, and
| | - Adrian M Dubuc
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Frank C Kuo
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Elizabeth P Garcia
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Yonghui Jia
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Phani Davineni
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ryan P Abo
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Center for Cancer Genome Discovery, DFCI, Boston, Massachusetts, USA
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | | | - Aaron R Thorner
- Center for Cancer Genome Discovery, DFCI, Boston, Massachusetts, USA
| | - Matthew Ducar
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Center for Cancer Genome Discovery, DFCI, Boston, Massachusetts, USA
| | - Alice H Berger
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Mizuki Nishino
- Department of Radiology, DFCI and Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Katherine A Janeway
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Alanna Church
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Marian Harris
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Joshua D Campbell
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Vanesa Rojas-Rudilla
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Azra H Ligon
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Shakti Ramkissoon
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - James M Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Early Drug Discovery Center
| | - Ursula Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Geoffrey R Oxnard
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | | | | | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Center for Cancer Genome Discovery, DFCI, Boston, Massachusetts, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Lank Center for Genitourinary Oncology and
| | | | - David J Kwiatkowski
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Bruce E Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Matthew Meyerson
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Center for Cancer Genome Discovery, DFCI, Boston, Massachusetts, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Center for Cancer Precision Medicine, DFCI, Boston, Massachusetts, USA
| | - Geoffrey I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Early Drug Discovery Center
| | - Barrett J Rollins
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Laura E MacConaill
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Center for Cancer Genome Discovery, DFCI, Boston, Massachusetts, USA
| |
Collapse
|
58
|
Duncavage EJ, Abel HJ, Pfeifer JD. In Silico Proficiency Testing for Clinical Next-Generation Sequencing. J Mol Diagn 2016; 19:35-42. [PMID: 27863262 DOI: 10.1016/j.jmoldx.2016.09.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/09/2016] [Accepted: 09/13/2016] [Indexed: 12/18/2022] Open
Abstract
Quality assurance for clinical next-generation sequencing (NGS)-based assays is difficult given the complex methods and the range of sequence variants such assays can detect. As the number and range of mutations detected by clinical NGS assays has increased, it is difficult to apply standard analyte-specific proficiency testing (PT). Most current proficiency testing challenges for NGS are methods-based PT surveys that use DNA from reference samples engineered to harbor specific mutations that test both sequence generation and bioinformatics analysis. These methods-based PTs are limited by the number and types of mutations that can be physically introduced into a single DNA sample. In silico proficiency testing, which evaluates only the bioinformatics component of NGS assays, is a recently introduced PT method that allows for evaluation of numerous mutations spanning a range of variant classes. In silico PT data sets can be generated from simulated or actual sequencing data and are used to test alignment through variant detection and annotation steps. In silico PT has several advantages over the use of physical samples, including greater flexibility in tested variants, the ability to design laboratory-specific challenges, and lower costs. Herein, we review the use of in silico PT as an alternative to traditional methods-based PT as it is evolving in oncology applications and discuss how the approach is applicable more broadly.
Collapse
Affiliation(s)
- Eric J Duncavage
- Department of Pathology, Washington University School of Medicine, St. Louis, Missouri
| | - Haley J Abel
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - John D Pfeifer
- Department of Pathology, Washington University School of Medicine, St. Louis, Missouri.
| |
Collapse
|
59
|
Minimal Residual Disease in Acute Myeloid Leukemia of Adults: Determination, Prognostic Impact and Clinical Applications. Mediterr J Hematol Infect Dis 2016; 8:e2016052. [PMID: 27872732 PMCID: PMC5111512 DOI: 10.4084/mjhid.2016.052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 09/12/2016] [Indexed: 02/06/2023] Open
Abstract
Pretreatment assessment of cytogenetic/genetic signature of acute myeloid leukemia (AML) has been consistently shown to play a major prognostic role but also to fail at predicting outcome on individual basis, even in low-risk AML. Therefore, we are in need of further accurate methods to refine the patients’ risk allocation process, distinguishing more adequately those who are likely to recur from those who are not. In this view, there is now evidence that the submicroscopic amounts of leukemic cells (called minimal residual disease, MRD), measured during the course of treatment, indicate the quality of response to therapy. Therefore, MRD might serve as an independent, additional biomarker to help to identify patients at higher risk of relapse. Detection of MRD requires the use of highly sensitive ancillary techniques, such as polymerase chain reaction (PCR) and multiparametric flow cytometry(MPFC). In the present manuscript, we will review the current approaches to investigate MRD and its clinical applications in AML management.
Collapse
|
60
|
Lin MT, Tseng LH, Dudley JC, Riel S, Tsai H, Zheng G, Pratz KW, Levis MJ, Gocke CD. A Novel Tandem Duplication Assay to Detect Minimal Residual Disease in FLT3/ITD AML. Mol Diagn Ther 2016; 19:409-17. [PMID: 26446915 DOI: 10.1007/s40291-015-0170-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Internal tandem duplication (ITD) of the fms-related tyrosine kinase 3 (FLT3) gene is associated with a poor prognosis in acute myeloid leukemia (AML) patients with a normal karyotype. The current standard polymerase chain reaction (PCR) assay for FLT3/ITD detection is not sufficiently sensitive to monitor minimal residual disease (MRD). Clone-specific assays may have sufficient sensitivity but are not practical to implement, since each clone-specific primer/probe requires clinical validation. OBJECTIVE To develop an assay for clinical molecular diagnostics laboratories to monitor MRD in FLT3/ITD AMLs. METHODS We designed a simple novel assay, tandem duplication PCR (TD-PCR), and tested its sensitivity, specificity, and clinical utility in FLT3/ITD AML patients. RESULTS TD-PCR was capable of detecting a single ITD molecule and was applicable to 75 % of ITD mutants tested. TD-PCR detected MRD in bone marrow prior to patient relapse. TD-PCR also identified low-level ITD mutants not only in FLT3/ITD AMLs but also in initial diagnostic specimens that were reportedly negative by the standard assay in patients who progressed with the same ITDs detected by the TD-PCR assay. CONCLUSION Detection of MRD by TD-PCR may guide patient selection for early clinical intervention. In contrast to clone-specific approaches, the TD-PCR assay can be more easily validated for MRD detection in clinical laboratories because it uses standardized primers and a universal positive control. In addition, our findings on multi-clonality and low-level ITDs suggest that further studies are warranted to elucidate their clinical/biological significance.
Collapse
Affiliation(s)
- Ming-Tseh Lin
- Division of Molecular Pathology, Department of Pathology, Johns Hopkins University School of Medicine, Park SB202, 600 North Wolfe Street, Baltimore, MD, 21287, USA
| | - Li-Hui Tseng
- Division of Molecular Pathology, Department of Pathology, Johns Hopkins University School of Medicine, Park SB202, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Jonathan C Dudley
- Division of Molecular Pathology, Department of Pathology, Johns Hopkins University School of Medicine, Park SB202, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Stacey Riel
- Division of Molecular Pathology, Department of Pathology, Johns Hopkins University School of Medicine, Park SB202, 600 North Wolfe Street, Baltimore, MD, 21287, USA
| | - Harrison Tsai
- Division of Molecular Pathology, Department of Pathology, Johns Hopkins University School of Medicine, Park SB202, 600 North Wolfe Street, Baltimore, MD, 21287, USA
| | - Gang Zheng
- Division of Molecular Pathology, Department of Pathology, Johns Hopkins University School of Medicine, Park SB202, 600 North Wolfe Street, Baltimore, MD, 21287, USA
| | - Keith W Pratz
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mark J Levis
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher D Gocke
- Division of Molecular Pathology, Department of Pathology, Johns Hopkins University School of Medicine, Park SB202, 600 North Wolfe Street, Baltimore, MD, 21287, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
61
|
Kuhn M, Stange T, Herold S, Thiede C, Roeder I. Finding small somatic structural variants in exome sequencing data: a machine learning approach. Comput Stat 2016. [DOI: 10.1007/s00180-016-0674-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
62
|
Next-generation sequencing of FLT3 internal tandem duplications for minimal residual disease monitoring in acute myeloid leukemia. Oncotarget 2016; 6:22812-21. [PMID: 26078355 PMCID: PMC4673201 DOI: 10.18632/oncotarget.4333] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 05/25/2015] [Indexed: 11/25/2022] Open
Abstract
Minimal Residual Disease (MRD) detection can be used for early intervention in relapse, risk stratification, and treatment guidance. FLT3 ITD is the most common mutation found in AML patients with normal karyotype. We evaluated the feasibility of NGS with high coverage (up to 2.4.10(6) PE fragments) for MRD monitoring on FLT3 ITD. We sequenced 37 adult patients at diagnosis and various times of their disease (64 samples) and compared the results with FLT3 ITD ratios measured by fragment analysis. We found that NGS could detect variable insertion sites and lengths in a single test for several patients. We also showed mutational shifts between diagnosis and relapse, with the outgrowth of a clone at relapse different from that dominant at diagnosis. Since NGS is scalable, we were able to adapt sensitivity by increasing the number of reads obtained for follow-up samples, compared to diagnosis samples. This technique could be applied to detect biological relapse before its clinical consequences and to better tailor treatments through the use of FLT3 inhibitors. Larger cohorts should be assessed in order to validate this approach.
Collapse
|
63
|
Roy S, Pfeifer JD, LaFramboise WA, Pantanowitz L. Molecular digital pathology: progress and potential of exchanging molecular data. Expert Rev Mol Diagn 2016; 16:941-7. [PMID: 27471996 DOI: 10.1080/14737159.2016.1206472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Many of the demands to perform next generation sequencing (NGS) in the clinical laboratory can be resolved using the principles of telepathology. Molecular telepathology can allow facilities to outsource all or a portion of their NGS operation such as cloud computing, bioinformatics pipelines, variant data management, and knowledge curation. Clinical pathology laboratories can electronically share diverse types of molecular data with reference laboratories, technology service providers, and/or regulatory agencies. Exchange of electronic molecular data allows laboratories to perform validation of rare diseases using foreign data, check the accuracy of their test results against benchmarks, and leverage in silico proficiency testing. This review covers the emerging subject of molecular telepathology, describes clinical use cases for the appropriate exchange of molecular data, and highlights key issues such as data integrity, interoperable formats for massive genomic datasets, security, malpractice and emerging regulations involved with this novel practice.
Collapse
Affiliation(s)
- Somak Roy
- a Department of Pathology , University of Pittsburgh Medical Center , Pittsburgh , PA , USA
| | - John D Pfeifer
- b Department of Pathology , Washington University , St Louis , MO , USA
| | - William A LaFramboise
- a Department of Pathology , University of Pittsburgh Medical Center , Pittsburgh , PA , USA
| | - Liron Pantanowitz
- a Department of Pathology , University of Pittsburgh Medical Center , Pittsburgh , PA , USA
| |
Collapse
|
64
|
Duncavage EJ, Abel HJ, Merker JD, Bodner JB, Zhao Q, Voelkerding KV, Pfeifer JD. A Model Study of In Silico Proficiency Testing for Clinical Next-Generation Sequencing. Arch Pathol Lab Med 2016; 140:1085-91. [PMID: 27388684 DOI: 10.5858/arpa.2016-0194-cp] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT -Most current proficiency testing challenges for next-generation sequencing assays are methods-based proficiency testing surveys that use DNA from characterized reference samples to test both the wet-bench and bioinformatics/dry-bench aspects of the tests. Methods-based proficiency testing surveys are limited by the number and types of mutations that either are naturally present or can be introduced into a single DNA sample. OBJECTIVE -To address these limitations by exploring a model of in silico proficiency testing in which sequence data from a single well-characterized specimen are manipulated electronically. DESIGN -DNA from the College of American Pathologists reference genome was enriched using the Illumina TruSeq and Life Technologies AmpliSeq panels and sequenced on the MiSeq and Ion Torrent platforms, respectively. The resulting data were mutagenized in silico and 26 variants, including single-nucleotide variants, deletions, and dinucleotide substitutions, were added at variant allele fractions (VAFs) from 10% to 50%. Participating clinical laboratories downloaded these files and analyzed them using their clinical bioinformatics pipelines. RESULTS -Laboratories using the AmpliSeq/Ion Torrent and/or the TruSeq/MiSeq participated in the 2 surveys. On average, laboratories identified 24.6 of 26 variants (95%) overall and 21.4 of 22 variants (97%) with VAFs greater than 15%. No false-positive calls were reported. The most frequently missed variants were single-nucleotide variants with VAFs less than 15%. Across both challenges, reported VAF concordance was excellent, with less than 1% median absolute difference between the simulated VAF and mean reported VAF. CONCLUSIONS -The results indicate that in silico proficiency testing is a feasible approach for methods-based proficiency testing, and demonstrate that the sensitivity and specificity of current next-generation sequencing bioinformatics across clinical laboratories are high.
Collapse
Affiliation(s)
- Eric J Duncavage
- From the Departments of Pathology (Drs Duncavage and Pfeifer) and Genetics (Dr Abel), Washington University School of Medicine, St Louis, Missouri; the Department of Pathology (Dr Merker), Stanford University School of Medicine, Stanford, California; Product Development, Laboratory Improvement Program (Mr Bodner), and the Surveys Department (Dr Zhao), College of American Pathologists, Northfield, Illinois; and the Department of Pathology and ARUP Laboratories, University of Utah, Salt Lake City (Dr Voelkerding)
| | | | | | | | | | | | | |
Collapse
|
65
|
Quek L, Otto GW, Garnett C, Lhermitte L, Karamitros D, Stoilova B, Lau IJ, Doondeea J, Usukhbayar B, Kennedy A, Metzner M, Goardon N, Ivey A, Allen C, Gale R, Davies B, Sternberg A, Killick S, Hunter H, Cahalin P, Price A, Carr A, Griffiths M, Virgo P, Mackinnon S, Grimwade D, Freeman S, Russell N, Craddock C, Mead A, Peniket A, Porcher C, Vyas P. Genetically distinct leukemic stem cells in human CD34- acute myeloid leukemia are arrested at a hemopoietic precursor-like stage. J Exp Med 2016; 213:1513-35. [PMID: 27377587 PMCID: PMC4986529 DOI: 10.1084/jem.20151775] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 05/19/2016] [Indexed: 12/16/2022] Open
Abstract
Quek and colleagues identify human leukemic stem cells (LSCs) present in CD34− AML. In-depth characterization of the functional and clonal aspects of CD34− LSCs indicates that most are similar to myeloid precursors. Our understanding of the perturbation of normal cellular differentiation hierarchies to create tumor-propagating stem cell populations is incomplete. In human acute myeloid leukemia (AML), current models suggest transformation creates leukemic stem cell (LSC) populations arrested at a progenitor-like stage expressing cell surface CD34. We show that in ∼25% of AML, with a distinct genetic mutation pattern where >98% of cells are CD34−, there are multiple, nonhierarchically arranged CD34+ and CD34− LSC populations. Within CD34− and CD34+ LSC–containing populations, LSC frequencies are similar; there are shared clonal structures and near-identical transcriptional signatures. CD34− LSCs have disordered global transcription profiles, but these profiles are enriched for transcriptional signatures of normal CD34− mature granulocyte–macrophage precursors, downstream of progenitors. But unlike mature precursors, LSCs express multiple normal stem cell transcriptional regulators previously implicated in LSC function. This suggests a new refined model of the relationship between LSCs and normal hemopoiesis in which the nature of genetic/epigenetic changes determines the disordered transcriptional program, resulting in LSC differentiation arrest at stages that are most like either progenitor or precursor stages of hemopoiesis.
Collapse
Affiliation(s)
- Lynn Quek
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX1 2JD, England, UK Department of Hematology, Oxford University Hospital National Health Service Trust, Oxford OX3 9DU, England, UK
| | - Georg W Otto
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX1 2JD, England, UK
| | - Catherine Garnett
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX1 2JD, England, UK
| | - Ludovic Lhermitte
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX1 2JD, England, UK
| | - Dimitris Karamitros
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX1 2JD, England, UK
| | - Bilyana Stoilova
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX1 2JD, England, UK
| | - I-Jun Lau
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX1 2JD, England, UK Department of Hematology, Oxford University Hospital National Health Service Trust, Oxford OX3 9DU, England, UK
| | - Jessica Doondeea
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX1 2JD, England, UK
| | - Batchimeg Usukhbayar
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX1 2JD, England, UK
| | - Alison Kennedy
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX1 2JD, England, UK
| | - Marlen Metzner
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX1 2JD, England, UK
| | - Nicolas Goardon
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX1 2JD, England, UK
| | - Adam Ivey
- Department of Genetics, King's College London, London WC2R 2LS, England, UK
| | - Christopher Allen
- Cancer Institute, University College London, London WC1E 6BT, England, UK
| | - Rosemary Gale
- Cancer Institute, University College London, London WC1E 6BT, England, UK
| | - Benjamin Davies
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Oxford University Hospital National Health Service Trust, Oxford OX3 9DU, England, UK
| | - Alexander Sternberg
- Department of Hematology, Great Western Hospital National Health Service Foundation Trust, Swindon SN3 6BB, England, UK
| | - Sally Killick
- Department of Hematology, Royal Bournemouth and Christchurch Hospital National Health Service Trust, Bournemouth BH7 7DW, England, UK
| | - Hannah Hunter
- Department of Hematology, Plymouth Hospitals National Health Service Trust, Plymouth PL6 8DH, England, UK
| | - Paul Cahalin
- Department of Hematology, Blackpool, Fylde and Wyre Hospitals National Health Service Trust, Blackpool FY3 8NR, England, UK
| | - Andrew Price
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Oxford University Hospital National Health Service Trust, Oxford OX3 9DU, England, UK
| | - Andrew Carr
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Oxford University Hospital National Health Service Trust, Oxford OX3 9DU, England, UK
| | - Mike Griffiths
- West Midlands Regional Genetics Laboratory, Birmingham B15 2TG, England, UK
| | - Paul Virgo
- Department of Immunology, North Bristol National Health Service Trust, Bristol BS10 5NB, England, UK
| | - Stephen Mackinnon
- Cancer Institute, University College London, London WC1E 6BT, England, UK Department of Hematology, University College London Hospital National Health Service Foundation Trust, London NW1 2BU, England, UK
| | - David Grimwade
- Department of Genetics, King's College London, London WC2R 2LS, England, UK
| | - Sylvie Freeman
- School of Immunity and Infection, University of Birmingham, Birmingham B15 2TT, England, UK Department of Haematology, University Hospitals Birmingham National Health Service Foundation Trust, Birmingham B15 2TH, England, UK
| | - Nigel Russell
- Centre for Clinical Hematology, Nottingham University Hospitals National Health Service Trust, Nottingham NG5 1PB, England, UK
| | - Charles Craddock
- Department of Clinical Haematology, University of Birmingham, Birmingham B15 2TT, England, UK Department of Clinical Haematology, University Hospitals Birmingham National Health Service Foundation Trust, Birmingham B15 2TH, England, UK
| | - Adam Mead
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX1 2JD, England, UK Department of Hematology, Oxford University Hospital National Health Service Trust, Oxford OX3 9DU, England, UK
| | - Andrew Peniket
- Department of Hematology, Oxford University Hospital National Health Service Trust, Oxford OX3 9DU, England, UK
| | - Catherine Porcher
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX1 2JD, England, UK
| | - Paresh Vyas
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX1 2JD, England, UK Department of Hematology, Oxford University Hospital National Health Service Trust, Oxford OX3 9DU, England, UK
| |
Collapse
|
66
|
Development and validation of a comprehensive genomic diagnostic tool for myeloid malignancies. Blood 2016; 128:e1-9. [PMID: 27121471 DOI: 10.1182/blood-2015-11-683334] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 04/21/2016] [Indexed: 12/22/2022] Open
Abstract
The diagnosis of hematologic malignancies relies on multidisciplinary workflows involving morphology, flow cytometry, cytogenetic, and molecular genetic analyses. Advances in cancer genomics have identified numerous recurrent mutations with clear prognostic and/or therapeutic significance to different cancers. In myeloid malignancies, there is a clinical imperative to test for such mutations in mainstream diagnosis; however, progress toward this has been slow and piecemeal. Here we describe Karyogene, an integrated targeted resequencing/analytical platform that detects nucleotide substitutions, insertions/deletions, chromosomal translocations, copy number abnormalities, and zygosity changes in a single assay. We validate the approach against 62 acute myeloid leukemia, 50 myelodysplastic syndrome, and 40 blood DNA samples from individuals without evidence of clonal blood disorders. We demonstrate robust detection of sequence changes in 49 genes, including difficult-to-detect mutations such as FLT3 internal-tandem and mixed-lineage leukemia (MLL) partial-tandem duplications, and clinically significant chromosomal rearrangements including MLL translocations to known and unknown partners, identifying the novel fusion gene MLL-DIAPH2 in the process. Additionally, we identify most significant chromosomal gains and losses, and several copy neutral loss-of-heterozygosity mutations at a genome-wide level, including previously unreported changes such as homozygosity for DNMT3A R882 mutations. Karyogene represents a dependable genomic diagnosis platform for translational research and for the clinical management of myeloid malignancies, which can be readily adapted for use in other cancers.
Collapse
|
67
|
Rustagi N, Hampton OA, Li J, Xi L, Gibbs RA, Plon SE, Kimmel M, Wheeler DA. ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data. BMC Bioinformatics 2016; 17:188. [PMID: 27121965 PMCID: PMC4847212 DOI: 10.1186/s12859-016-1031-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 04/12/2016] [Indexed: 11/13/2022] Open
Abstract
Background Detection of tandem duplication within coding exons, referred to as internal tandem duplication (ITD), remains challenging due to inefficiencies in alignment of ITD-containing reads to the reference genome. There is a critical need to develop efficient methods to recover these important mutational events. Results In this paper we introduce ITD Assembler, a novel approach that rapidly evaluates all unmapped and partially mapped reads from whole exome NGS data using a De Bruijn graphs approach to select reads that harbor cycles of appropriate length, followed by assembly using overlap-layout-consensus. We tested ITD Assembler on The Cancer Genome Atlas AML dataset as a truth set. ITD Assembler identified the highest percentage of reported FLT3-ITDs when compared to other ITD detection algorithms, and discovered additional ITDs in FLT3, KIT, CEBPA, WT1 and other genes. Evidence of polymorphic ITDs in 54 genes were also found. Novel ITDs were validated by analyzing the corresponding RNA sequencing data. Conclusions ITD Assembler is a very sensitive tool which can detect partial, large and complex tandem duplications. This study highlights the need to more effectively look for ITD’s in other cancers and Mendelian diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1031-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Navin Rustagi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA. .,Department of Statistics, Rice University, Houston, TX, USA.
| | - Oliver A Hampton
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jie Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Dermatology, Xiangya Hospital, Central South University, Hunan, China
| | - Liu Xi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sharon E Plon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics/Hematology-Oncology, Texas Children's Hospital, Houston, TX, USA
| | - Marek Kimmel
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
68
|
Building a Robust Tumor Profiling Program: Synergy between Next-Generation Sequencing and Targeted Single-Gene Testing. PLoS One 2016; 11:e0152851. [PMID: 27043212 PMCID: PMC4820127 DOI: 10.1371/journal.pone.0152851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/21/2016] [Indexed: 12/25/2022] Open
Abstract
Next-generation sequencing (NGS) is a powerful platform for identifying cancer mutations. Routine clinical adoption of NGS requires optimized quality control metrics to ensure accurate results. To assess the robustness of our clinical NGS pipeline, we analyzed the results of 304 solid tumor and hematologic malignancy specimens tested simultaneously by NGS and one or more targeted single-gene tests (EGFR, KRAS, BRAF, NPM1, FLT3, and JAK2). For samples that passed our validated tumor percentage and DNA quality and quantity thresholds, there was perfect concordance between NGS and targeted single-gene tests with the exception of two FLT3 internal tandem duplications that fell below the stringent pre-established reporting threshold but were readily detected by manual inspection. In addition, NGS identified clinically significant mutations not covered by single-gene tests. These findings confirm NGS as a reliable platform for routine clinical use when appropriate quality control metrics, such as tumor percentage and DNA quality cutoffs, are in place. Based on our findings, we suggest a simple workflow that should facilitate adoption of clinical oncologic NGS services at other institutions.
Collapse
|
69
|
Duncavage EJ, Tandon B. The utility of next-generation sequencing in diagnosis and monitoring of acute myeloid leukemia and myelodysplastic syndromes. Int J Lab Hematol 2016; 37 Suppl 1:115-21. [PMID: 25976969 DOI: 10.1111/ijlh.12361] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/13/2015] [Indexed: 11/28/2022]
Abstract
Myeloid malignancies including acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) are a heterogeneous group of disorders that share a common biology and are a major source of morbidity and mortality. In the last several years, studies using next-generation sequencing (NGS) have identified a core set of recurrently mutated myeloid malignancy genes in the majority of patients with AML and MDS, including those with normal cytogenetics. DNA-level mutations in several of these genes including NPM1, FLT3, and CEBPA in AML and ASXL1, ETV6, EZH2, RUNX1, and TP53 in MDS are associated with changes in patient outcomes and are now tested for in clinical laboratories. In addition to providing prognostic information, these gene mutations can be used to monitor patient disease burden through the use of ultrasensitive detection techniques. In this review, we will focus on the clinical utility of various NGS-based methods including whole-genome sequencing, exome sequencing, and targeted panel-based sequencing in the initial diagnosis and management of AML and MDS and cover recent methodological advances for the molecular monitoring of AML and MDS.
Collapse
Affiliation(s)
- E J Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - B Tandon
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| |
Collapse
|
70
|
Sun Y, Ren Q, Liu B, Qin Y, Zhao S. Enzyme-free and sensitive electrochemical determination of the FLT3 gene based on a dual signal amplified strategy: Controlled nanomaterial multilayers and a target-catalyzed hairpin assembly. Biosens Bioelectron 2016; 78:7-13. [DOI: 10.1016/j.bios.2015.11.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/03/2015] [Accepted: 11/05/2015] [Indexed: 01/27/2023]
|
71
|
Au CH, Wa A, Ho DN, Chan TL, Ma ESK. Clinical evaluation of panel testing by next-generation sequencing (NGS) for gene mutations in myeloid neoplasms. Diagn Pathol 2016; 11:11. [PMID: 26796102 PMCID: PMC4722624 DOI: 10.1186/s13000-016-0456-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 01/14/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genomic techniques in recent years have allowed the identification of many mutated genes important in the pathogenesis of acute myeloid leukemia (AML). Together with cytogenetic aberrations, these gene mutations are powerful prognostic markers in AML and can be used to guide patient management, for example selection of optimal post-remission therapy. The mutated genes also hold promise as therapeutic targets themselves. We evaluated the applicability of a gene panel for the detection of AML mutations in a diagnostic molecular pathology laboratory. METHODS Fifty patient samples comprising 46 AML and 4 other myeloid neoplasms were accrued for the study. They consisted of 19 males and 31 females at a median age of 60 years (range: 18-88 years). A total of 54 genes (full coding exons of 15 genes and exonic hotspots of 39 genes) were targeted by 568 amplicons that ranged from 225 to 275 bp. The combined coverage was 141 kb in sequence length. Amplicon libraries were prepared by TruSight myeloid sequencing panel (Illumina, CA) and paired-end sequencing runs were performed on a MiSeq (Illumina) genome sequencer. Sequences obtained were analyzed by in-house bioinformatics pipeline, namely BWA-MEM, Samtools, GATK, Pindel, Ensembl Variant Effect Predictor and a novel algorithm ITDseek. RESULTS The mean count of sequencing reads obtained per sample was 3.81 million and the mean sequencing depth was over 3000X. Seventy-seven mutations in 24 genes were detected in 37 of 50 samples (74 %). On average, 2 mutations (range 1-5) were detected per positive sample. TP53 gene mutations were found in 3 out of 4 patients with complex and unfavorable cytogenetics. Comparing NGS results with that of conventional molecular testing showed a concordance rate of 95.5 %. After further resolution and application of a novel bioinformatics algorithm ITDseek to aid the detection of FLT3 internal tandem duplication (ITD), the concordance rate was revised to 98.2 %. CONCLUSIONS Gene panel testing by NGS approach was applicable for sensitive and accurate detection of actionable AML gene mutations in the clinical laboratory to individualize patient management. A novel algorithm ITDseek was presented that improved the detection of FLT3-ITD of varying length, position and at low allelic burden.
Collapse
Affiliation(s)
- Chun Hang Au
- Division of Molecular Pathology, Department of Pathology, 1/F Li Shu Fan Block, Hong Kong Sanatorium & Hospital 2 Village Road, Happy Valley, Hong Kong, China.
| | - Anna Wa
- Division of Molecular Pathology, Department of Pathology, 1/F Li Shu Fan Block, Hong Kong Sanatorium & Hospital 2 Village Road, Happy Valley, Hong Kong, China.
| | - Dona N Ho
- Division of Molecular Pathology, Department of Pathology, 1/F Li Shu Fan Block, Hong Kong Sanatorium & Hospital 2 Village Road, Happy Valley, Hong Kong, China.
| | - Tsun Leung Chan
- Division of Molecular Pathology, Department of Pathology, 1/F Li Shu Fan Block, Hong Kong Sanatorium & Hospital 2 Village Road, Happy Valley, Hong Kong, China.
| | - Edmond S K Ma
- Division of Molecular Pathology, Department of Pathology, 1/F Li Shu Fan Block, Hong Kong Sanatorium & Hospital 2 Village Road, Happy Valley, Hong Kong, China.
| |
Collapse
|
72
|
Fisher KE, Zhang L, Wang J, Smith GH, Newman S, Schneider TM, Pillai RN, Kudchadkar RR, Owonikoko TK, Ramalingam SS, Lawson DH, Delman KA, El-Rayes BF, Wilson MM, Sullivan HC, Morrison AS, Balci S, Adsay NV, Gal AA, Sica GL, Saxe DF, Mann KP, Hill CE, Khuri FR, Rossi MR. Clinical Validation and Implementation of a Targeted Next-Generation Sequencing Assay to Detect Somatic Variants in Non-Small Cell Lung, Melanoma, and Gastrointestinal Malignancies. J Mol Diagn 2016; 18:299-315. [PMID: 26801070 DOI: 10.1016/j.jmoldx.2015.11.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/05/2015] [Accepted: 11/19/2015] [Indexed: 12/30/2022] Open
Abstract
We tested and clinically validated a targeted next-generation sequencing (NGS) mutation panel using 80 formalin-fixed, paraffin-embedded (FFPE) tumor samples. Forty non-small cell lung carcinoma (NSCLC), 30 melanoma, and 30 gastrointestinal (12 colonic, 10 gastric, and 8 pancreatic adenocarcinoma) FFPE samples were selected from laboratory archives. After appropriate specimen and nucleic acid quality control, 80 NGS libraries were prepared using the Illumina TruSight tumor (TST) kit and sequenced on the Illumina MiSeq. Sequence alignment, variant calling, and sequencing quality control were performed using vendor software and laboratory-developed analysis workflows. TST generated ≥500× coverage for 98.4% of the 13,952 targeted bases. Reproducible and accurate variant calling was achieved at ≥5% variant allele frequency with 8 to 12 multiplexed samples per MiSeq flow cell. TST detected 112 variants overall, and confirmed all known single-nucleotide variants (n = 27), deletions (n = 5), insertions (n = 3), and multinucleotide variants (n = 3). TST detected at least one variant in 85.0% (68/80), and two or more variants in 36.2% (29/80), of samples. TP53 was the most frequently mutated gene in NSCLC (13 variants; 13/32 samples), gastrointestinal malignancies (15 variants; 13/25 samples), and overall (30 variants; 28/80 samples). BRAF mutations were most common in melanoma (nine variants; 9/23 samples). Clinically relevant NGS data can be obtained from routine clinical FFPE solid tumor specimens using TST, benchtop instruments, and vendor-supplied bioinformatics pipelines.
Collapse
Affiliation(s)
- Kevin E Fisher
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia; Department of Pathology, Texas Children's Hospital, Houston, Texas; Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas.
| | - Linsheng Zhang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Jason Wang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia; Department of Pathology, University of Texas Southwestern and Children's Medical Center, Dallas, Texas
| | - Geoffrey H Smith
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Scott Newman
- Biostatistics and Bioinformatics Shared Resource, Emory University, Atlanta, Georgia
| | - Thomas M Schneider
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Rathi N Pillai
- Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, Georgia; Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Ragini R Kudchadkar
- Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, Georgia; Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Taofeek K Owonikoko
- Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, Georgia; Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Suresh S Ramalingam
- Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, Georgia; Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - David H Lawson
- Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, Georgia; Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Keith A Delman
- Winship Cancer Institute, Emory University, Atlanta, Georgia; Department of Surgery, Emory University School of Medicine, Atlanta, Georgia
| | - Bassel F El-Rayes
- Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, Georgia; Winship Cancer Institute, Emory University, Atlanta, Georgia
| | | | - H Clifford Sullivan
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Annie S Morrison
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Serdar Balci
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - N Volkan Adsay
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Anthony A Gal
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Gabriel L Sica
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Debra F Saxe
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Karen P Mann
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Charles E Hill
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Fadlo R Khuri
- Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, Georgia; Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Michael R Rossi
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia; Department of Radiation Oncology, Emory University School of Medicine, Atlanta, Georgia
| |
Collapse
|
73
|
Shen W, Szankasi P, Sederberg M, Schumacher J, Frizzell KA, Gee EP, Patel JL, South ST, Xu X, Kelley TW. Concurrent detection of targeted copy number variants and mutations using a myeloid malignancy next generation sequencing panel allows comprehensive genetic analysis using a single testing strategy. Br J Haematol 2016; 173:49-58. [PMID: 26728869 DOI: 10.1111/bjh.13921] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/19/2015] [Indexed: 02/06/2023]
Abstract
Currently, comprehensive genetic testing of myeloid malignancies requires multiple testing strategies with high costs. Somatic mutations can be detected by next generation sequencing (NGS) but copy number variants (CNVs) require cytogenetic methods including karyotyping, fluorescence in situ hybidization and microarray. Here, we evaluated a new method for CNV detection using read depth data derived from a targeted NGS mutation panel. In a cohort of 270 samples, we detected pathogenic mutations in 208 samples and targeted CNVs in 68 cases. The most frequent CNVs were 7q deletion including LUC7L2 and EZH2, TP53 deletion, ETV6 deletion, gain of RAD21 on 8q, and 5q deletion, including NSD1 and NPM1. We were also able to detect exon-level duplications, including so-called KMT2A (MLL) partial tandem duplication, in 9 cases. In the 63 cases that were negative for mutations, targeted CNVs were observed in 4 cases. Targeted CNV detection by NGS had very high concordance with single nucleotide polymorphism microarray, the current gold standard. We found that ETV6 deletion was strongly associated with TP53 alterations and 7q deletion was associated with mutations in TP53, KRAS and IDH1. This proof-of-concept study demonstrates the feasibility of using the same NGS data to simultaneously detect both somatic mutations and targeted CNVs.
Collapse
Affiliation(s)
- Wei Shen
- ARUP Laboratories, Salt Lake City, UT, USA
| | | | | | | | | | | | - Jay L Patel
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Sarah T South
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Xinjie Xu
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Todd W Kelley
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| |
Collapse
|
74
|
Yang R, Nelson AC, Henzler C, Thyagarajan B, Silverstein KAT. ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly. Genome Med 2015; 7:127. [PMID: 26643039 PMCID: PMC4671222 DOI: 10.1186/s13073-015-0251-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/18/2015] [Indexed: 12/30/2022] Open
Abstract
Comprehensive identification of insertions/deletions (indels) across the full size spectrum from second generation sequencing is challenging due to the relatively short read length inherent in the technology. Different indel calling methods exist but are limited in detection to specific sizes with varying accuracy and resolution. We present ScanIndel, an integrated framework for detecting indels with multiple heuristics including gapped alignment, split reads and de novo assembly. Using simulation data, we demonstrate ScanIndel’s superior sensitivity and specificity relative to several state-of-the-art indel callers across various coverage levels and indel sizes. ScanIndel yields higher predictive accuracy with lower computational cost compared with existing tools for both targeted resequencing data from tumor specimens and high coverage whole-genome sequencing data from the human NIST standard NA12878. Thus, we anticipate ScanIndel will improve indel analysis in both clinical and research settings. ScanIndel is implemented in Python, and is freely available for academic use at https://github.com/cauyrd/ScanIndel.
Collapse
Affiliation(s)
- Rendong Yang
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, 117 Pleasant St. SE, RM 541, Minneapolis, MN, 55455, USA.
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Christine Henzler
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, 117 Pleasant St. SE, RM 541, Minneapolis, MN, 55455, USA.
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Kevin A T Silverstein
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, 117 Pleasant St. SE, RM 541, Minneapolis, MN, 55455, USA.
| |
Collapse
|
75
|
Ziai JM, Siddon AJ. Pathology Consultation on Gene Mutations in Acute Myeloid Leukemia. Am J Clin Pathol 2015; 144:539-54. [PMID: 26386075 DOI: 10.1309/ajcp77zfpuqgygwy] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVES Acute myeloid leukemia (AML) is a rapidly fatal disease without the use of aggressive chemotherapy regimens. Cytogenetic and molecular studies are commonly used to classify types of AML based on prognosis, as well as to determine therapeutic regimens. METHODS Although there are several AML classifications determined by particular translocations, cytogenetically normal AML represents a molecularly, as well as clinically, heterogeneous group of diseases. Laboratory evaluation of AML will become increasingly important as new mutations with both prognostic and therapeutic implications are being recognized. Moreover, because many patients with AML are being treated more effectively, these mutations may become increasingly useful as markers of minimal residual disease, which can be interpreted in an individualized approach. RESULTS Current laboratory studies of gene mutations in AML include analysis of NPM1, FLT3, CEBPA, and KIT. In addition to these genes, many other genes are emerging as potentially useful in determining patients' prognosis, therapy, and disease course. CONCLUSIONS This article briefly reviews the current most clinically relevant gene mutations and their clinical and immunophenotypic features, prognostic information, and methods used for detection.
Collapse
Affiliation(s)
| | - Alexa J. Siddon
- Departments of Pathology, Yale School of Medicine, New Haven, CT
- Laboratory Medicine, Yale School of Medicine, New Haven, CT
- VA Connecticut Healthcare, West Haven, CT
| | | |
Collapse
|
76
|
Berenstein R. Class III Receptor Tyrosine Kinases in Acute Leukemia - Biological Functions and Modern Laboratory Analysis. Biomark Insights 2015; 10:1-14. [PMID: 26309392 PMCID: PMC4527365 DOI: 10.4137/bmi.s22433] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/02/2015] [Accepted: 07/04/2015] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is a complex disease caused by deregulation of multiple signaling pathways. Mutations in class III receptor tyrosine kinases (RTKs) have been implicated in alteration of cell signals concerning the growth and differentiation of leukemic cells. Point mutations, insertions, or deletions of RTKs as well as chromosomal translocations induce constitutive activation of the receptor, leading to uncontrolled proliferation of undifferentiated myeloid blasts. Aberrations can occur in all domains of RTKs causing either the ligand-independent activation or mimicking the activated conformation. The World Health Organization recommended including RTK mutations in the AML classification since their detection in routine laboratory diagnostics is a major factor for prognostic stratification of patients. Polymerase chain reaction (PCR)-based methods are well-validated for the detection of fms-related tyrosine kinase 3 (FLT3) mutations and can easily be applied for other RTKs. However, when methodological limitations are reached, accessory techniques can be applied. For a higher resolution and more quantitative approach compared to agarose gel electrophoresis, PCR fragments can be separated by capillary electrophoresis. Furthermore, high-resolution melting and denaturing high-pressure liquid chromatography are reliable presequencing screening methods that reduce the sample amount for Sanger sequencing. Because traditional DNA sequencing is time-consuming, next-generation sequencing (NGS) is an innovative modern possibility to analyze a high amount of samples simultaneously in a short period of time. At present, standardized procedures for NGS are not established, but when this barrier is resolved, it will provide a new platform for rapid and reliable laboratory diagnostic of RTK mutations in patients with AML. In this article, the biological and physiological role of RTK mutations in AML as well as possible laboratory methods for their detection will be reviewed.
Collapse
Affiliation(s)
- Rimma Berenstein
- Department of Hematology, Oncology and Tumourimmunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
77
|
Lee LA, Arvai KJ, Jones D. Annotation of Sequence Variants in Cancer Samples: Processes and Pitfalls for Routine Assays in the Clinical Laboratory. J Mol Diagn 2015; 17:339-51. [PMID: 25977238 DOI: 10.1016/j.jmoldx.2015.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/12/2015] [Accepted: 03/23/2015] [Indexed: 12/16/2022] Open
Abstract
As DNA sequencing of multigene panels becomes routine for cancer samples in the clinical laboratory, an efficient process for classifying variants has become more critical. Determining which germline variants are significant for cancer disposition and which somatic mutations are integral to cancer development or therapy response remains difficult, even for well-studied genes such as BRCA1 and TP53. We compare and contrast the general principles and lines of evidence commonly used to distinguish the significance of cancer-associated germline and somatic genetic variants. The factors important in each step of the analysis pipeline are reviewed, as are some of the publicly available annotation tools. Given the range of indications and uses of cancer sequencing assays, including diagnosis, staging, prognostication, theranostics, and residual disease detection, the need for flexible methods for scoring of variants is discussed. The usefulness of protein prediction tools and multimodal risk-based or Bayesian approaches are highlighted. Using TET2 variants encountered in hematologic neoplasms, several examples of this multifactorial approach to classifying sequence variants of unknown significance are presented. Although there are still significant gaps in the publicly available data for many cancer genes that limit the broad application of explicit algorithms for variant scoring, the elements of a more rigorous model are outlined.
Collapse
Affiliation(s)
- Lobin A Lee
- Department of Pathology, Quest Diagnostics Nichols Institute, Chantilly, Virginia.
| | - Kevin J Arvai
- Department of Pathology, Quest Diagnostics Nichols Institute, Chantilly, Virginia
| | - Dan Jones
- Department of Pathology, Quest Diagnostics Nichols Institute, Chantilly, Virginia
| |
Collapse
|
78
|
Ohgami RS, Ma L, Merker JD, Gotlib JR, Schrijver I, Zehnder JL, Arber DA. Next-generation sequencing of acute myeloid leukemia identifies the significance of TP53, U2AF1, ASXL1, and TET2 mutations. Mod Pathol 2015; 28:706-14. [PMID: 25412851 PMCID: PMC5436901 DOI: 10.1038/modpathol.2014.160] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/19/2014] [Accepted: 10/20/2014] [Indexed: 02/06/2023]
Abstract
We assessed the frequency and clinicopathologic significance of 19 genes currently identified as significantly mutated in myeloid neoplasms, RUNX1, ASXL1, TET2, CEBPA, IDH1, IDH2, DNMT3A, FLT3, NPM1, TP53, NRAS, EZH2, CBL, U2AF1, SF3B1, SRSF2, JAK2, CSF3R, and SETBP1, across 93 cases of acute myeloid leukemia (AML) using capture target enrichment and next-generation sequencing. Of these cases, 79% showed at least one nonsynonymous mutation, and cases of AML with recurrent genetic abnormalities showed a lower frequency of mutations versus AML with myelodysplasia-related changes (P<0.001). Mutational analysis further demonstrated that TP53 mutations are associated with complex karyotype AML, whereas ASXL1 and U2AF1 mutations are associated with AML with myelodysplasia-related changes. Furthermore, U2AF1 mutations were specifically associated with trilineage morphologic dysplasia. Univariate analysis demonstrated that U2AF1 and TP53 mutations are associated with absence of clinical remission, poor overall survival (OS), and poor disease-free survival (DFS; P<0.0001), whereas TET2 and ASXL1 mutations are associated with poor OS (P<0.03). In multivariate analysis, U2AF1 and TP53 mutations retained independent prognostic significance in OS and DFS, respectively. Our results demonstrate unique relationships between mutations in AML, clinicopathologic prognosis, subtype categorization, and morphologic dysplasia.
Collapse
Affiliation(s)
- Robert S Ohgami
- Department of Pathology, Stanford University Medical Center, Stanford, CA, USA
| | - Lisa Ma
- Department of Pathology, Stanford University Medical Center, Stanford, CA, USA
| | - Jason D Merker
- Department of Pathology, Stanford University Medical Center, Stanford, CA, USA
| | - Jason R Gotlib
- Division of Hematology, Department of Medicine, Stanford University Medical Center, Stanford, CA, USA
| | - Iris Schrijver
- Department of Pathology, Stanford University Medical Center, Stanford, CA, USA
| | - James L Zehnder
- 1] Department of Pathology, Stanford University Medical Center, Stanford, CA, USA [2] Division of Hematology, Department of Medicine, Stanford University Medical Center, Stanford, CA, USA
| | - Daniel A Arber
- Department of Pathology, Stanford University Medical Center, Stanford, CA, USA
| |
Collapse
|
79
|
|
80
|
Bolli N, Manes N, McKerrell T, Chi J, Park N, Gundem G, Quail MA, Sathiaseelan V, Herman B, Crawley C, Craig JIO, Conte N, Grove C, Papaemmanuil E, Campbell PJ, Varela I, Costeas P, Vassiliou GS. Characterization of gene mutations and copy number changes in acute myeloid leukemia using a rapid target enrichment protocol. Haematologica 2014; 100:214-22. [PMID: 25381129 DOI: 10.3324/haematol.2014.113381] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Prognostic stratification is critical for making therapeutic decisions and maximizing survival of patients with acute myeloid leukemia. Advances in the genomics of acute myeloid leukemia have identified several recurrent gene mutations whose prognostic impact is being deciphered. We used HaloPlex target enrichment and Illumina-based next generation sequencing to study 24 recurrently mutated genes in 42 samples of acute myeloid leukemia with a normal karyotype. Read depth varied between and within genes for the same sample, but was predictable and highly consistent across samples. Consequently, we were able to detect copy number changes, such as an interstitial deletion of BCOR, three MLL partial tandem duplications, and a novel KRAS amplification. With regards to coding mutations, we identified likely oncogenic variants in 41 of 42 samples. NPM1 mutations were the most frequent, followed by FLT3, DNMT3A and TET2. NPM1 and FLT3 indels were reported with good efficiency. We also showed that DNMT3A mutations can persist post-chemotherapy and in 2 cases studied at diagnosis and relapse, we were able to delineate the dynamics of tumor evolution and give insights into order of acquisition of variants. HaloPlex is a quick and reliable target enrichment method that can aid diagnosis and prognostic stratification of acute myeloid leukemia patients.
Collapse
Affiliation(s)
- Niccolò Bolli
- Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, UK Department of Haematology, University of Cambridge, UK Department of Haematology, Addenbrookes Hospital, Cambridge, UK
| | - Nicla Manes
- Department of Haematology, Addenbrookes Hospital, Cambridge, UK Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Thomas McKerrell
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Jianxiang Chi
- The Center for the Study of Haematological Malignancies, Nicosia, Cyprus
| | - Naomi Park
- Sequencing Research and Development, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Michael A Quail
- Sequencing Research and Development, Wellcome Trust Sanger Institute, Cambridge, UK
| | | | - Bram Herman
- Agilent Technologies, Agilent Technologies LDA UK Ltd., Cheadle, UK
| | - Charles Crawley
- Department of Haematology, Addenbrookes Hospital, Cambridge, UK
| | - Jenny I O Craig
- Department of Haematology, Addenbrookes Hospital, Cambridge, UK
| | - Natalie Conte
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK EMBL-European Bioinformatics Institute, Cambridge, UK
| | - Carolyn Grove
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Elli Papaemmanuil
- Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Paul Costeas
- The Center for the Study of Haematological Malignancies, Nicosia, Cyprus Molecular Haematology and Immunogenetics Center, The Karaiskakio Foundation, Nicosia, Cyprus
| | - George S Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
| |
Collapse
|
81
|
Hagemann IS, Devarakonda S, Lockwood CM, Spencer DH, Guebert K, Bredemeyer AJ, Al-Kateb H, Nguyen TT, Duncavage EJ, Cottrell CE, Kulkarni S, Nagarajan R, Seibert K, Baggstrom M, Waqar SN, Pfeifer JD, Morgensztern D, Govindan R. Clinical next-generation sequencing in patients with non-small cell lung cancer. Cancer 2014; 121:631-9. [DOI: 10.1002/cncr.29089] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/22/2014] [Accepted: 08/27/2014] [Indexed: 01/21/2023]
Affiliation(s)
- Ian S. Hagemann
- Division of Laboratory and Genomic Medicine; Department of Pathology and Immunology; Washington University; St. Louis Missouri
| | - Siddhartha Devarakonda
- Section of Medical Oncology, Division of Hematology and Oncology, Department of Medicine; Washington University; St. Louis Missouri
| | - Christina M. Lockwood
- Division of Laboratory and Genomic Medicine; Department of Pathology and Immunology; Washington University; St. Louis Missouri
| | - David H. Spencer
- Division of Laboratory and Genomic Medicine; Department of Pathology and Immunology; Washington University; St. Louis Missouri
| | - Kalin Guebert
- Section of Medical Oncology, Division of Hematology and Oncology, Department of Medicine; Washington University; St. Louis Missouri
| | - Andrew J. Bredemeyer
- Division of Laboratory and Genomic Medicine; Department of Pathology and Immunology; Washington University; St. Louis Missouri
| | - Hussam Al-Kateb
- Division of Laboratory and Genomic Medicine; Department of Pathology and Immunology; Washington University; St. Louis Missouri
| | - TuDung T. Nguyen
- Division of Laboratory and Genomic Medicine; Department of Pathology and Immunology; Washington University; St. Louis Missouri
| | - Eric J. Duncavage
- Division of Laboratory and Genomic Medicine; Department of Pathology and Immunology; Washington University; St. Louis Missouri
| | - Catherine E. Cottrell
- Division of Laboratory and Genomic Medicine; Department of Pathology and Immunology; Washington University; St. Louis Missouri
| | - Shashikant Kulkarni
- Division of Laboratory and Genomic Medicine; Department of Pathology and Immunology; Washington University; St. Louis Missouri
| | - Rakesh Nagarajan
- Division of Laboratory and Genomic Medicine; Department of Pathology and Immunology; Washington University; St. Louis Missouri
| | - Karen Seibert
- Division of Laboratory and Genomic Medicine; Department of Pathology and Immunology; Washington University; St. Louis Missouri
| | - Maria Baggstrom
- Section of Medical Oncology, Division of Hematology and Oncology, Department of Medicine; Washington University; St. Louis Missouri
| | - Saiama N. Waqar
- Section of Medical Oncology, Division of Hematology and Oncology, Department of Medicine; Washington University; St. Louis Missouri
| | - John D. Pfeifer
- Division of Laboratory and Genomic Medicine; Department of Pathology and Immunology; Washington University; St. Louis Missouri
| | - Daniel Morgensztern
- Section of Medical Oncology, Division of Hematology and Oncology, Department of Medicine; Washington University; St. Louis Missouri
| | - Ramaswamy Govindan
- Section of Medical Oncology, Division of Hematology and Oncology, Department of Medicine; Washington University; St. Louis Missouri
| |
Collapse
|
82
|
Cheng DT, Cheng J, Mitchell TN, Syed A, Zehir A, Mensah NYT, Oultache A, Nafa K, Levine RL, Arcila ME, Berger MF, Hedvat CV. Detection of mutations in myeloid malignancies through paired-sample analysis of microdroplet-PCR deep sequencing data. J Mol Diagn 2014; 16:504-518. [PMID: 25017477 DOI: 10.1016/j.jmoldx.2014.05.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 04/24/2014] [Accepted: 05/09/2014] [Indexed: 01/10/2023] Open
Abstract
Amplicon-based methods for targeted resequencing of cancer genes have gained traction in the clinic as a strategy for molecular diagnostic testing. An 847-amplicon panel was designed with the RainDance DeepSeq system, covering most exons of 28 genes relevant to acute myeloid leukemia and myeloproliferative neoplasms. We developed a paired-sample analysis pipeline for variant calling and sought to assess its sensitivity and specificity relative to a set of samples with previously identified mutations. Thirty samples with known mutations in JAK2, NPM1, DNMT3A, MPL, IDH1, IDH2, CEBPA, and FLT3, were profiled and sequenced to high depth. Variant calling using an unmatched Hapmap DNA control removed a substantial number of artifactual calls regardless of algorithm used or variant class. The removed calls were nonunique, had lower variant frequencies, and tended to recur in multiple unrelated samples. Analysis of sample replicates revealed that reproducible calls had distinctly higher variant allele depths and frequencies compared to nonreproducible calls. On the basis of these differences, filters on variant frequency were chosen to select for reproducible calls. The analysis pipeline successfully retrieved the associated known variant in all tested samples and uncovered additional mutations in some samples corresponding to well-characterized hotspot mutations in acute myeloid leukemia. We have developed a paired-sample analysis pipeline capable of robust identification of mutations from microdroplet-PCR sequencing data with high sensitivity and specificity.
Collapse
Affiliation(s)
- Donavan T Cheng
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York.
| | - Janice Cheng
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Talia N Mitchell
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Aijazuddin Syed
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Nana Yaa T Mensah
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Alifya Oultache
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York; Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Cyrus V Hedvat
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| |
Collapse
|
83
|
Abstract
High-throughput DNA sequencing has revolutionized the study of cancer genomics with numerous discoveries that are relevant to cancer diagnosis and treatment. The latest sequencing and analysis methods have successfully identified somatic alterations, including single-nucleotide variants, insertions and deletions, copy-number aberrations, structural variants and gene fusions. Additional computational techniques have proved useful for defining the mutations, genes and molecular networks that drive diverse cancer phenotypes and that determine clonal architectures in tumour samples. Collectively, these tools have advanced the study of genomic, transcriptomic and epigenomic alterations in cancer, and their association to clinical properties. Here, we review cancer genomics software and the insights that have been gained from their application.
Collapse
|
84
|
Kristensen T, Larsen M, Rewes A, Frederiksen H, Thomassen M, Møller MB. Clinical Relevance of Sensitive and Quantitative STAT3 Mutation Analysis Using Next-Generation Sequencing in T-Cell Large Granular Lymphocytic Leukemia. J Mol Diagn 2014; 16:382-92. [DOI: 10.1016/j.jmoldx.2014.02.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/07/2014] [Accepted: 02/19/2014] [Indexed: 10/25/2022] Open
|
85
|
Lin MT, Mosier SL, Thiess M, Beierl KF, Debeljak M, Tseng LH, Chen G, Yegnasubramanian S, Ho H, Cope L, Wheelan SJ, Gocke CD, Eshleman JR. Clinical validation of KRAS, BRAF, and EGFR mutation detection using next-generation sequencing. Am J Clin Pathol 2014; 141:856-66. [PMID: 24838331 DOI: 10.1309/ajcpmwgwgo34egod] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVES To validate next-generation sequencing (NGS) technology for clinical diagnosis and to determine appropriate read depth. METHODS We validated the KRAS, BRAF, and EGFR genes within the Ion AmpliSeq Cancer Hotspot Panel using the Ion Torrent Personal Genome Machine (Life Technologies, Carlsbad, CA). RESULTS We developed a statistical model to determine the read depth needed for a given percent tumor cellularity and number of functional genomes. Bottlenecking can result from too few input genomes. By using 16 formalin-fixed, paraffin-embedded (FFPE) cancer-free specimens and 118 cancer specimens with known mutation status, we validated the six traditional analytic performance characteristics recommended by the Next-Generation Sequencing: Standardization of Clinical Testing Working Group. Baseline noise is consistent with spontaneous and FFPE-induced C:G→T:A deamination mutations. CONCLUSIONS Redundant bioinformatic pipelines are essential, since a single analysis pipeline gave false-negative and false-positive results. NGS is sufficiently robust for the clinical detection of gene mutations, with attention to potential artifacts.
Collapse
Affiliation(s)
- Ming-Tseh Lin
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Stacy L. Mosier
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Michele Thiess
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Katie F. Beierl
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Marija Debeljak
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Li-Hui Tseng
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Guoli Chen
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | | | - Hao Ho
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Leslie Cope
- Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Sarah J. Wheelan
- Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christopher D. Gocke
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
- Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - James R. Eshleman
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
- Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD
| |
Collapse
|
86
|
Onsongo G, Erdmann J, Spears MD, Chilton J, Beckman KB, Hauge A, Yohe S, Schomaker M, Bower M, Silverstein KAT, Thyagarajan B. Implementation of Cloud based next generation sequencing data analysis in a clinical laboratory. BMC Res Notes 2014; 7:314. [PMID: 24885806 PMCID: PMC4036707 DOI: 10.1186/1756-0500-7-314] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 05/06/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The introduction of next generation sequencing (NGS) has revolutionized molecular diagnostics, though several challenges remain limiting the widespread adoption of NGS testing into clinical practice. One such difficulty includes the development of a robust bioinformatics pipeline that can handle the volume of data generated by high-throughput sequencing in a cost-effective manner. Analysis of sequencing data typically requires a substantial level of computing power that is often cost-prohibitive to most clinical diagnostics laboratories. FINDINGS To address this challenge, our institution has developed a Galaxy-based data analysis pipeline which relies on a web-based, cloud-computing infrastructure to process NGS data and identify genetic variants. It provides additional flexibility, needed to control storage costs, resulting in a pipeline that is cost-effective on a per-sample basis. It does not require the usage of EBS disk to run a sample. CONCLUSIONS We demonstrate the validation and feasibility of implementing this bioinformatics pipeline in a molecular diagnostics laboratory. Four samples were analyzed in duplicate pairs and showed 100% concordance in mutations identified. This pipeline is currently being used in the clinic and all identified pathogenic variants confirmed using Sanger sequencing further validating the software.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Kevin A T Silverstein
- Research Informatics Support Systems, Minnesota Supercomputing Institute, University of Minnesota, Room 599 Walter Library 117 Pleasant St SE, Minneapolis, MN 55455, USA.
| | | |
Collapse
|
87
|
Abel HJ, Al-Kateb H, Cottrell CE, Bredemeyer AJ, Pritchard CC, Grossmann AH, Wallander ML, Pfeifer JD, Lockwood CM, Duncavage EJ. Detection of gene rearrangements in targeted clinical next-generation sequencing. J Mol Diagn 2014; 16:405-17. [PMID: 24813172 DOI: 10.1016/j.jmoldx.2014.03.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 02/24/2014] [Accepted: 03/06/2014] [Indexed: 12/30/2022] Open
Abstract
The identification of recurrent gene rearrangements in the clinical laboratory is the cornerstone for risk stratification and treatment decisions in many malignant tumors. Studies have reported that targeted next-generation sequencing assays have the potential to identify such rearrangements; however, their utility in the clinical laboratory is unknown. We examine the sensitivity and specificity of ALK and KMT2A (MLL) rearrangement detection by next-generation sequencing in the clinical laboratory. We analyzed a series of seven ALK rearranged cancers, six KMT2A rearranged leukemias, and 77 ALK/KMT2A rearrangement-negative cancers, previously tested by fluorescence in situ hybridization (FISH). Rearrangement detection was tested using publicly available software tools, including Breakdancer, ClusterFAST, CREST, and Hydra. Using Breakdancer and ClusterFAST, we detected ALK rearrangements in seven of seven FISH-positive cases and KMT2A rearrangements in six of six FISH-positive cases. Among the 77 ALK/KMT2A FISH-negative cases, no false-positive identifications were made by Breakdancer or ClusterFAST. Further, we identified one ALK rearranged case with a noncanonical intron 16 breakpoint, which is likely to affect its response to targeted inhibitors. We report that clinically relevant chromosomal rearrangements can be detected from targeted gene panel-based next-generation sequencing with sensitivity and specificity equivalent to that of FISH while providing finer-scale information and increased efficiency for molecular oncology testing.
Collapse
Affiliation(s)
- Haley J Abel
- Department of Genetics, Washington University, St. Louis, Missouri
| | - Hussam Al-Kateb
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri
| | - Catherine E Cottrell
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri
| | - Andrew J Bredemeyer
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Allie H Grossmann
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, Utah
| | | | - John D Pfeifer
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri
| | - Christina M Lockwood
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri.
| |
Collapse
|
88
|
White BS, DiPersio JF. Genomic tools in acute myeloid leukemia: From the bench to the bedside. Cancer 2014; 120:1134-44. [PMID: 24474533 DOI: 10.1002/cncr.28552] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 11/14/2013] [Indexed: 12/28/2022]
Abstract
Since its use in the initial characterization of an acute myeloid leukemia (AML) genome, next-generation sequencing (NGS) has continued to molecularly refine the disease. Here, the authors review the spectrum of NGS applications that have subsequently delineated the prognostic significance and biologic consequences of these mutations. Furthermore, the role of this technology in providing a high-resolution glimpse of AML clonal heterogeneity, which may inform future choice of targeted therapy, is discussed. Although obstacles remain in applying these techniques clinically, they have already had an impact on patient care.
Collapse
Affiliation(s)
- Brian S White
- Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri; The Genome Institute, Washington University, St. Louis, Missouri
| | | |
Collapse
|
89
|
Ankala A, Hegde M. Genomic Technologies and the New Era of Genomic Medicine. J Mol Diagn 2014; 16:7-10. [DOI: 10.1016/j.jmoldx.2013.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 11/08/2013] [Accepted: 11/12/2013] [Indexed: 10/26/2022] Open
|
90
|
Abel HJ, Duncavage EJ. Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches. Cancer Genet 2013; 206:432-40. [PMID: 24405614 DOI: 10.1016/j.cancergen.2013.11.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 11/06/2013] [Accepted: 11/15/2013] [Indexed: 10/26/2022]
Abstract
Next generation sequencing (NGS), or massively paralleled sequencing, refers to a collective group of methods in which numerous sequencing reactions take place simultaneously, resulting in enormous amounts of sequencing data for a small fraction of the cost of Sanger sequencing. Typically short (50-250 bp), NGS reads are first mapped to a reference genome, and then variants are called from the mapped data. While most NGS applications focus on the detection of single nucleotide variants (SNVs) or small insertions/deletions (indels), structural variation, including translocations, larger indels, and copy number variation (CNV), can be identified from the same data. Structural variation detection can be performed from whole genome NGS data or "targeted" data including exomes or gene panels. However, while targeted sequencing greatly increases sequencing coverage or depth of particular genes, it may introduce biases in the data that require specialized informatic analyses. In the past several years, there have been considerable advances in methods used to detect structural variation, and a full range of variants from SNVs to balanced translocations to CNV can now be detected with reasonable sensitivity from either whole genome or targeted NGS data. Such methods are being rapidly applied to clinical testing where they can supplement or in some cases replace conventional fluorescence in situ hybridization or array-based testing. Here we review some of the informatics approaches used to detect structural variation from NGS data.
Collapse
Affiliation(s)
- Haley J Abel
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
91
|
Cottrell CE, Al-Kateb H, Bredemeyer AJ, Duncavage EJ, Spencer DH, Abel HJ, Lockwood CM, Hagemann IS, O'Guin SM, Burcea LC, Sawyer CS, Oschwald DM, Stratman JL, Sher DA, Johnson MR, Brown JT, Cliften PF, George B, McIntosh LD, Shrivastava S, Nguyen TT, Payton JE, Watson MA, Crosby SD, Head RD, Mitra RD, Nagarajan R, Kulkarni S, Seibert K, Virgin HW, Milbrandt J, Pfeifer JD. Validation of a next-generation sequencing assay for clinical molecular oncology. J Mol Diagn 2013; 16:89-105. [PMID: 24211365 DOI: 10.1016/j.jmoldx.2013.10.002] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 08/23/2013] [Accepted: 10/01/2013] [Indexed: 11/29/2022] Open
Abstract
Currently, oncology testing includes molecular studies and cytogenetic analysis to detect genetic aberrations of clinical significance. Next-generation sequencing (NGS) allows rapid analysis of multiple genes for clinically actionable somatic variants. The WUCaMP assay uses targeted capture for NGS analysis of 25 cancer-associated genes to detect mutations at actionable loci. We present clinical validation of the assay and a detailed framework for design and validation of similar clinical assays. Deep sequencing of 78 tumor specimens (≥ 1000× average unique coverage across the capture region) achieved high sensitivity for detecting somatic variants at low allele fraction (AF). Validation revealed sensitivities and specificities of 100% for detection of single-nucleotide variants (SNVs) within coding regions, compared with SNP array sequence data (95% CI = 83.4-100.0 for sensitivity and 94.2-100.0 for specificity) or whole-genome sequencing (95% CI = 89.1-100.0 for sensitivity and 99.9-100.0 for specificity) of HapMap samples. Sensitivity for detecting variants at an observed 10% AF was 100% (95% CI = 93.2-100.0) in HapMap mixes. Analysis of 15 masked specimens harboring clinically reported variants yielded concordant calls for 13/13 variants at AF of ≥ 15%. The WUCaMP assay is a robust and sensitive method to detect somatic variants of clinical significance in molecular oncology laboratories, with reduced time and cost of genetic analysis allowing for strategic patient management.
Collapse
Affiliation(s)
- Catherine E Cottrell
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Hussam Al-Kateb
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri.
| | - Andrew J Bredemeyer
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Eric J Duncavage
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - David H Spencer
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Haley J Abel
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Christina M Lockwood
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Ian S Hagemann
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Stephanie M O'Guin
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Lauren C Burcea
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Christopher S Sawyer
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Dayna M Oschwald
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Jennifer L Stratman
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Dorie A Sher
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Mark R Johnson
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Justin T Brown
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Paul F Cliften
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Bijoy George
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Leslie D McIntosh
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Savita Shrivastava
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Tudung T Nguyen
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Jacqueline E Payton
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Mark A Watson
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Seth D Crosby
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Richard D Head
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Robi D Mitra
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Rakesh Nagarajan
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Shashikant Kulkarni
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri; Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Karen Seibert
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Herbert W Virgin
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Jeffrey Milbrandt
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - John D Pfeifer
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| |
Collapse
|
92
|
Spencer DH, Tyagi M, Vallania F, Bredemeyer AJ, Pfeifer JD, Mitra RD, Duncavage EJ. Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data. J Mol Diagn 2013; 16:75-88. [PMID: 24211364 DOI: 10.1016/j.jmoldx.2013.09.003] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 08/16/2013] [Accepted: 09/04/2013] [Indexed: 12/31/2022] Open
Abstract
Next-generation sequencing (NGS) is becoming a common approach for clinical testing of oncology specimens for mutations in cancer genes. Unlike inherited variants, cancer mutations may occur at low frequencies because of contamination from normal cells or tumor heterogeneity and can therefore be challenging to detect using common NGS analysis tools, which are often designed for constitutional genomic studies. We generated high-coverage (>1000×) NGS data from synthetic DNA mixtures with variant allele fractions (VAFs) of 25% to 2.5% to assess the performance of four variant callers, SAMtools, Genome Analysis Toolkit, VarScan2, and SPLINTER, in detecting low-frequency variants. SAMtools had the lowest sensitivity and detected only 49% of variants with VAFs of approximately 25%; whereas the Genome Analysis Toolkit, VarScan2, and SPLINTER detected at least 94% of variants with VAFs of approximately 10%. VarScan2 and SPLINTER achieved sensitivities of 97% and 89%, respectively, for variants with observed VAFs of 1% to 8%, with >98% sensitivity and >99% positive predictive value in coding regions. Coverage analysis demonstrated that >500× coverage was required for optimal performance. The specificity of SPLINTER improved with higher coverage, whereas VarScan2 yielded more false positive results at high coverage levels, although this effect was abrogated by removing low-quality reads before variant identification. Finally, we demonstrate the utility of high-sensitivity variant callers with data from 15 clinical lung cancers.
Collapse
Affiliation(s)
- David H Spencer
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri
| | - Manoj Tyagi
- Department of Genetics, Washington University, St. Louis, Missouri
| | - Francesco Vallania
- Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | | | - John D Pfeifer
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri
| | - Rob D Mitra
- Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri.
| |
Collapse
|
93
|
Pritchard CC, Salipante SJ, Koehler K, Smith C, Scroggins S, Wood B, Wu D, Lee MK, Dintzis S, Adey A, Liu Y, Eaton KD, Martins R, Stricker K, Margolin KA, Hoffman N, Churpek JE, Tait JF, King MC, Walsh T. Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens. J Mol Diagn 2013; 16:56-67. [PMID: 24189654 DOI: 10.1016/j.jmoldx.2013.08.004] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/25/2013] [Accepted: 08/07/2013] [Indexed: 11/15/2022] Open
Abstract
Recent years have seen development and implementation of anticancer therapies targeted to particular gene mutations, but methods to assay clinical cancer specimens in a comprehensive way for the critical mutations remain underdeveloped. We have developed UW-OncoPlex, a clinical molecular diagnostic assay to provide simultaneous deep-sequencing information, based on >500× average coverage, for all classes of mutations in 194 clinically relevant genes. To validate UW-OncoPlex, we tested 98 previously characterized clinical tumor specimens from 10 different cancer types, including 41 formalin-fixed paraffin-embedded tissue samples. Mixing studies indicated reliable mutation detection in samples with ≥ 10% tumor cells. In clinical samples with ≥ 10% tumor cells, UW-OncoPlex correctly identified 129 of 130 known mutations [sensitivity 99.2%, (95% CI, 95.8%-99.9%)], including single nucleotide variants, small insertions and deletions, internal tandem duplications, gene copy number gains and amplifications, gene copy losses, chromosomal gains and losses, and actionable genomic rearrangements, including ALK-EML4, ROS1, PML-RARA, and BCR-ABL. In the same samples, the assay also identified actionable point mutations in genes not previously analyzed and novel gene rearrangements of MLL and GRIK4 in melanoma, and of ASXL1, PIK3R1, and SGCZ in acute myeloid leukemia. To best guide existing and emerging treatment regimens and facilitate integration of genomic testing with patient care, we developed a framework for data analysis, decision support, and reporting clinically actionable results.
Collapse
Affiliation(s)
- Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington.
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, Washington; Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Karen Koehler
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Christina Smith
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Sheena Scroggins
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Brent Wood
- Department of Laboratory Medicine, University of Washington, Seattle, Washington; Department of Pathology, University of Washington, Seattle, Washington
| | - David Wu
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Ming K Lee
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington
| | - Suzanne Dintzis
- Department of Pathology, University of Washington, Seattle, Washington
| | - Andrew Adey
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Yajuan Liu
- Department of Pathology, University of Washington, Seattle, Washington
| | - Keith D Eaton
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
| | - Renato Martins
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
| | - Kari Stricker
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
| | - Kim A Margolin
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
| | - Noah Hoffman
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Jane E Churpek
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Jonathan F Tait
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Mary-Claire King
- Department of Genome Sciences, University of Washington, Seattle, Washington; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington
| | - Tom Walsh
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington
| |
Collapse
|
94
|
Rao AV, Smith BD. Are results of targeted gene sequencing ready to be used for clinical decision making for patients with acute myelogenous leukemia? Curr Hematol Malig Rep 2013; 8:149-55. [PMID: 23595294 DOI: 10.1007/s11899-013-0161-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Acute myeloid leukemia (AML) is the most common acute leukemia in the USA, which despite recent advances, continues to have a high mortality rate. It is a biologically active disease characterized by numerous cytogenetic abnormalities and multiple genetic mutations. Next-generation sequencing (NGS) will perhaps not reveal all the factors that make AML a complex disease, but does have the potential to affect the diagnosis and risk stratification of AML patients and allow more personalized therapy. AML cells are easy to obtain from the patient and samples are only minimally contaminated with normal cells, which makes it an attractive cancer to study. Several studies have now demonstrated that the majority of AML patients are cytogenetically normal and the genome of these patients may contain fewer mutations than cancer genomes that are highly aneuploidy, suggesting that mutations in diploid genomes are more likely to be pathogenetically relevant. Whole-genome, exome, transcriptome, and targeted gene sequencing studies have been conducted successfully in AML and have provided with valuable information. The challenges for the future include: reducing the cost of sequencing, understanding epigenetic changes, managing data across various platforms, separating the driver mutations from the sea of passenger mutations, and finally, educating future generations to allow a better understanding and easy availability of these complex methodologies.
Collapse
Affiliation(s)
- Arati V Rao
- Division of Hematologic Malignancies and Cell Therapy, Duke University Medical Center, 2400 Pratt Street, Suite 9010, Durham, NC 27710, USA.
| | | |
Collapse
|
95
|
Mathews J, Duncavage EJ, Pfeifer JD. Characterization of translocations in mesenchymal hamartoma and undifferentiated embryonal sarcoma of the liver. Exp Mol Pathol 2013; 95:319-24. [PMID: 24120702 DOI: 10.1016/j.yexmp.2013.09.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 09/27/2013] [Indexed: 01/28/2023]
Abstract
BACKGROUND Mesenchymal hamartoma of the liver (MHL) is an uncommon benign primary liver tumor that typically occurs in the pediatric population, although cases have been described in adults. MHL is sometimes associated with the highly malignant undifferentiated embryonal sarcoma (UES), and the synchronous or metachronous occurrence of MHL and UES suggests they share a common genetic link. Although the exact mechanism of tumorigenesis has not been identified, MHL cases harbor recurring chromosomal rearrangements involving 19q13. DESIGN In order to provide more details on the genetic events of MHL tumorigenesis, capture-based next generation sequencing (NGS) targeted to loci recently shown to be involved in a translocation in a case of UES arising in MHL (specifically, the MALAT1 gene on chromosome 11 and a gene poor region termed MHLB1 on chromosome 19) was performed on formalin fixed paraffin embedded tissue from seven cases of MHL. RESULTS Chromosome rearrangements involving the MHLB1 locus were identified in three of the seven cases, including the translocation t(11,19)(q13.1;q13.42) involving the MALAT1 gene; the translocation t(2,19)(q31.1;q13.42) involving AK023515, an uncharacterized noncoding gene; and the inversion inv(19,19)(q13.42;q13.43) involving the PEG3 gene encoding a Kruppel-type zinc-finger protein. Rearrangements were exclusively identified in pediatric tumors. In each case, the presence of the rearrangement was confirmed by PCR and interphase FISH. Interphase FISH also demonstrated that the arrangements occur within the spindle cell component but not within the epithelial components of the tumor. CONCLUSIONS Since the MHLB1 locus contains a CpG-rich region whose methylation regulates C19MC miRNA genes, rearrangements that disrupt this region may contribute to MHL development through alteration of miRNA expression. The demonstration that the loose stromal cells harbor the rearrangements indicates that (some cases of) MHL are a neoplastic process due to a somatic genetic change and not a germline abnormality.
Collapse
Affiliation(s)
- James Mathews
- Lauren V. Ackerman Laboratory of Surgical Pathology, Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA.
| | | | | |
Collapse
|
96
|
Vollbrecht C, König K, Heukamp L, Büttner R, Odenthal M. [Molecular pathology of the lungs. New perspectives by next generation sequencing]. DER PATHOLOGE 2013; 34:16-24. [PMID: 23389825 DOI: 10.1007/s00292-012-1704-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Lung cancer is one of the most frequent malignancies in the western world. Its frequent association with a wide spectrum of mutations in genes encoding various signal transducers that are often linked to therapy response, emphasizes the obvious need for improved, fast and highly efficient approaches in molecular pathology. Comprehensive analyses of the mutation status of progression and therapy relevant genes can be performed by the novel sequencing forms named next generation sequencing (NGS) providing extremely high capacities for ultra-deep sequence analyses. The 454 pyrosequencing method, the sequencing by synthesis and the semiconductor sequencing platform are now available for parallel sequencing approaches of multitudinous target genes linked to multiple tumor DNA applications. The "one molecule, one clone, one read" principle by the NGS approaches supplies not only information on allele frequencies and mutation rates but also has the advantage of a very sensitive detection of low frequency variants.
Collapse
Affiliation(s)
- C Vollbrecht
- Institut für Pathologie, Universitätsklinik zu Köln, Kerpener Str. 62, 50924, Köln, Deutschland
| | | | | | | | | |
Collapse
|
97
|
Liu C, Yang X, Duffy B, Mohanakumar T, Mitra RD, Zody MC, Pfeifer JD. ATHLATES: accurate typing of human leukocyte antigen through exome sequencing. Nucleic Acids Res 2013; 41:e142. [PMID: 23748956 PMCID: PMC3737559 DOI: 10.1093/nar/gkt481] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Human leukocyte antigen (HLA) typing at the allelic level can in theory be achieved using whole exome sequencing (exome-seq) data with no added cost but has been hindered by its computational challenge. We developed ATHLATES, a program that applies assembly, allele identification and allelic pair inference to short read sequences, and applied it to data from Illumina platforms. In 15 data sets with adequate coverage for HLA-A, -B, -C, -DRB1 and -DQB1 genes, ATHLATES correctly reported 74 out of 75 allelic pairs with an overall concordance rate of 99% compared with conventional typing. This novel approach should be broadly applicable to research and clinical laboratories.
Collapse
Affiliation(s)
- Chang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | | | | | | | | | | |
Collapse
|
98
|
Wertheim GBW, Daber R, Bagg A. Molecular diagnostics of acute myeloid leukemia: it's a (next) generational thing. J Mol Diagn 2012; 15:27-30. [PMID: 23159532 DOI: 10.1016/j.jmoldx.2012.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 08/14/2012] [Indexed: 12/28/2022] Open
Abstract
This commentary highlights the article by Spencer et al that outlines a novel next-generation sequencing-based method for the detection of FLT3 mutations.
Collapse
Affiliation(s)
- Gerald B W Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19014, USA.
| | | | | |
Collapse
|