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Godley LA. Prioritization of patients for germline testing based on tumor profiling of hematopoietic malignancies. Front Oncol 2023; 13:1084736. [PMID: 36793609 PMCID: PMC9923095 DOI: 10.3389/fonc.2023.1084736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 01/17/2023] [Indexed: 01/31/2023] Open
Abstract
Germline predisposition to hematopoietic malignancies is more common than previously appreciated, with several clinical guidelines advocating for cancer risk testing in an expanding pool of patients. As molecular profiling of tumor cells becomes a standard practice for prognostication and defining options for targeted therapies, recognition that germline variants are present in all cells and can be identified by such testing becomes paramount. Although not to be substituted for proper germline cancer risk testing, tumor-based profiling can help prioritize DNA variants likely to be of germline origin, especially when they are present on sequential samples and persist into remission. Performing germline genetic testing as early during patient work-up as possible allows time to plan allogeneic stem cell transplantation using appropriate donors and optimize post-transplant prophylaxis. Health care providers need to be attentive to the differences between molecular profiling of tumor cells and germline genetic testing regarding ideal sample types, platform designs, capabilities, and limitations, to allow testing data to be interpreted as comprehensively as possible. The myriad of mutation types and growing number of genes involved in germline predisposition to hematopoietic malignancies makes reliance on detection of deleterious alleles using tumor-based testing alone very difficult and makes understanding how to ensure adequate testing of appropriate patients paramount.
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Affiliation(s)
- Lucy A Godley
- Section of Hematology/Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, United States
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Zelinova K, Jagelkova M, Laucekova Z, Bobrovska M, Dankova Z, Grendar M, Dokus K. Molecular analysis of circulating tumor DNA from breast cancer patients before and after surgery and following adjuvant chemotherapy. Mol Clin Oncol 2020; 13:26. [PMID: 32765873 PMCID: PMC7403808 DOI: 10.3892/mco.2020.2096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 06/11/2020] [Indexed: 12/24/2022] Open
Abstract
The primary aim of the present study is to provide a complex molecular profile of tumors using liquid biopsy and to monitor profile changes over time in association with surgery and administered adjuvant therapy. Our secondary aim was to compare the liquid biopsy profile with the tissue biopsy and assess concordance. A total of 27 samples of circulating tumor DNA (ctDNA) collected from 9 breast cancer patients at three different time points and their matched formalin-fixed and paraffin-embedded (FFPE) samples of primary tumor were analyzed with targeted next-generation sequencing. Somatic pathogenic variants were detected before surgery in samples from 5 patients (55.6%). The most frequently mutated genes were phosphatase and tensin homolog (4/9, 44.4%) and tumor protein 53 (4/9, 44.4%). Serial sampling of ctDNA enabled the detection of more variants compared with single-time tissue primary tumor biopsy. There were 17 ctDNA variants across all samples, but only 6 FFPE variants across all patients. In addition, the concordance between ctDNA and FFPE DNA was determined in only 1 patient, and this was connected with higher variant allele frequency. The findings of the present study suggest that liquid biopsy and tissue biopsy may be used as complementary analyses to adequately capture all tumor variants.
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Affiliation(s)
- Katarina Zelinova
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, SK-036 01 Martin, Slovakia.,Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, SK-036 01 Martin, Slovakia
| | - Marianna Jagelkova
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, SK-036 01 Martin, Slovakia.,Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, SK-036 01 Martin, Slovakia
| | - Zuzana Laucekova
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, SK-036 01 Martin, Slovakia
| | - Martina Bobrovska
- Department of Pathological Anatomy, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, SK-036 01 Martin, Slovakia
| | - Zuzana Dankova
- Division of Oncology, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, SK-036 01 Martin, Slovakia
| | - Marian Grendar
- Department of Bioinformatics, Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, SK-036 01 Martin, Slovakia
| | - Karol Dokus
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin University Hospital, SK-036 01 Martin, Slovakia.,Second Department of Obstetrics and Gynecology, Slovak Medical University, Faculty Hospital with Polyclinic of F.D. Roosevelt, 975 17 Banska Bystrica, Slovakia
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Zehnbauer BA. The Journal of Molecular Diagnostics: 20 Years Defining Professional Practice. J Mol Diagn 2019; 21:938-942. [PMID: 31635797 DOI: 10.1016/j.jmoldx.2019.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 01/09/2023] Open
Abstract
This editorial highlights 20 years of JMD defining professional practice.
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Affiliation(s)
- Barbara A Zehnbauer
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia (Editor-in-Chief).
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Abstract
Advances in nucleic acid sequencing and genotyping technologies have facilitated the discovery of an increasing number of single-nucleotide variations (SNVs) associated with disease onset, progression, and response to therapy. The reliable detection of such disease-specific SNVs can ensure timely and effective therapeutic action, enabling precision medicine. This has driven extensive efforts in recent years to develop novel methods for the fast and cost-effective analysis of targeted SNVs. In this Review, we highlight the most recent and significant advances made toward the development of such methodologies.
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Affiliation(s)
- Alireza Abi
- Department of Chemistry, Faculty of Sciences, Shiraz University, Shiraz 7194684795, Iran
| | - Afsaneh Safavi
- Department of Chemistry, Faculty of Sciences, Shiraz University, Shiraz 7194684795, Iran
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Hoskinson DC, Dubuc AM, Mason-Suares H. The current state of clinical interpretation of sequence variants. Curr Opin Genet Dev 2017; 42:33-39. [PMID: 28157586 DOI: 10.1016/j.gde.2017.01.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/20/2016] [Accepted: 01/09/2017] [Indexed: 01/19/2023]
Abstract
Accurate and consistent variant classification is required for Precision Medicine. But clinical variant classification remains in its infancy. While recent guidelines put forth jointly by the American College of Medical Genetics and Genomics (ACMG) and Association of Molecular Pathology (AMP) for the classification of Mendelian variants has advanced the field, the degree of subjectivity allowed by these guidelines can still lead to inconsistent classification across clinical molecular genetic laboratories. In addition, there are currently no such guidelines for somatic cancer variants, only published institutional practices. Additional variant classification guidelines, including disease- or gene-specific criteria, along with inter-laboratory data sharing is critical for accurate and consistent variant interpretation.
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Affiliation(s)
- Derick C Hoskinson
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, 65 Landsdowne Str., Cambridge, MA 02115 USA
| | - Adrian M Dubuc
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, 75 Francis Str., Boston, MA 02115 USA
| | - Heather Mason-Suares
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, 65 Landsdowne Str., Cambridge, MA 02115 USA; Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, 75 Francis Str., Boston, MA 02115 USA.
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Abstract
Next-generation sequencing (NGS) has been rapidly integrated into molecular pathology, dramatically increasing the breadth genomic of information available to oncologists and their patients. This review will explore the ways in which this new technology is currently applied to bolster care for patients with solid tumors and hematological malignancies, focusing on practices and guidelines for assessing the technical validity and clinical utility of DNA variants identified during clinical NGS oncology testing.
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Affiliation(s)
- Samuel P Strom
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
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Froyen G, Broekmans A, Hillen F, Pat K, Achten R, Mebis J, Rummens JL, Willemse J, Maes B. Validation and Application of a Custom-Designed Targeted Next-Generation Sequencing Panel for the Diagnostic Mutational Profiling of Solid Tumors. PLoS One 2016; 11:e0154038. [PMID: 27101000 PMCID: PMC4839685 DOI: 10.1371/journal.pone.0154038] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/07/2016] [Indexed: 01/15/2023] Open
Abstract
The inevitable switch from standard molecular methods to next-generation sequencing for the molecular profiling of tumors is challenging for most diagnostic laboratories. However, fixed validation criteria for diagnostic accreditation are not in place because of the great variability in methods and aims. Here, we describe the validation of a custom panel of hotspots in 24 genes for the detection of somatic mutations in non-small cell lung carcinoma, colorectal carcinoma and malignant melanoma starting from FFPE sections, using 14, 36 and 5 cases, respectively. The targeted hotspots were selected for their present or future clinical relevance in solid tumor types. The target regions were enriched with the TruSeq approach starting from limited amounts of DNA. Cost effective sequencing of 12 pooled libraries was done using a micro flow cell on the MiSeq and subsequent data analysis with MiSeqReporter and VariantStudio. The entire workflow was diagnostically validated showing a robust performance with maximal sensitivity and specificity using as thresholds a variant allele frequency >5% and a minimal amplicon coverage of 300. We implemented this method through the analysis of 150 routine diagnostic samples and identified clinically relevant mutations in 16 genes including KRAS (32%), TP53 (32%), BRAF (12%), APC (11%), EGFR (8%) and NRAS (5%). Importantly, the highest success rate was obtained when using also the low quality DNA samples. In conclusion, we provide a workflow for the validation of targeted NGS by a custom-designed pan-solid tumor panel in a molecular diagnostic lab and demonstrate its robustness in a clinical setting.
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Affiliation(s)
- Guy Froyen
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
- * E-mail:
| | - An Broekmans
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - Femke Hillen
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - Karin Pat
- Department of Pneumology, Jessa Hospital, Hasselt, Belgium
| | - Ruth Achten
- Department of Pathology, Jessa Hospital, Hasselt, Belgium
| | - Jeroen Mebis
- Department of Medical Oncology, Jessa Hospital, Hasselt, Belgium
| | - Jean-Luc Rummens
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - Johan Willemse
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
- Department of Clinical Biology, AZ Turnhout, Turnhout, Belgium
| | - Brigitte Maes
- Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
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Kanagal-Shamanna R, Singh RR, Routbort MJ, Patel KP, Medeiros LJ, Luthra R. Principles of analytical validation of next-generation sequencing based mutational analysis for hematologic neoplasms in a CLIA-certified laboratory. Expert Rev Mol Diagn 2016; 16:461-72. [PMID: 26765348 DOI: 10.1586/14737159.2016.1142374] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Targeted therapy based on mutational profiles is the current standard of practice for the management of patients with hematologic malignancies. Next-generation sequencing (NGS)- based analysis has been adopted by clinical laboratories for high-throughput mutational profiling of myeloid and lymphoid neoplasms. The technology is fairly novel and complex, hence both validation and test implementation in a CLIA-certified laboratory differ substantially from traditional sequencing platforms. Recently, organizations such as the American College of Medical Genetics, Centers for Disease Control and Prevention and College of American Pathologists have published principles and guidelines for NGS test development to ensure standardization of testing across institutions. Summarized here are the recommendations from these organizations as they pertain to targeted NGS-based testing of hematologic malignancies ('liquid tumors'), with particular emphasis on myeloid neoplasms.
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Affiliation(s)
- Rashmi Kanagal-Shamanna
- a Department of Hematopathology , The University of Texas at M.D. Anderson Cancer Center , Houston , TX , USA
| | - Rajesh R Singh
- a Department of Hematopathology , The University of Texas at M.D. Anderson Cancer Center , Houston , TX , USA
| | - Mark J Routbort
- a Department of Hematopathology , The University of Texas at M.D. Anderson Cancer Center , Houston , TX , USA
| | - Keyur P Patel
- a Department of Hematopathology , The University of Texas at M.D. Anderson Cancer Center , Houston , TX , USA
| | - L Jeffrey Medeiros
- a Department of Hematopathology , The University of Texas at M.D. Anderson Cancer Center , Houston , TX , USA
| | - Rajyalakshmi Luthra
- a Department of Hematopathology , The University of Texas at M.D. Anderson Cancer Center , Houston , TX , USA
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Big Data and Cancer Research. BIG DATA ANALYTICS 2016. [DOI: 10.1007/978-81-322-3628-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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