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Akkari Y, Baughn LB, Kim A, Karaca E, Raca G, Shao L, Mikhail FM. Section E6.1-6.6 of the American College of Medical Genetics and Genomics (ACMG) Technical Laboratory Standards: Cytogenomic studies of acquired chromosomal abnormalities in neoplastic blood, bone marrow, and lymph nodes. Genet Med 2024; 26:101054. [PMID: 38349293 DOI: 10.1016/j.gim.2023.101054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 04/09/2024] Open
Abstract
Cytogenomic analyses of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes are instrumental in the clinical management of patients with hematologic neoplasms. Cytogenetic analyses assist in the diagnosis of such disorders and can provide important prognostic information. Furthermore, cytogenetic studies can provide crucial information regarding specific genetically defined subtypes of these neoplasms that may have targeted therapies. At time of relapse, cytogenetic analysis can confirm recurrence of the original neoplasm, detect clonal disease evolution, or uncover a new unrelated neoplastic process. This section deals specifically with the technical standards applicable to cytogenomic studies of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes. This updated Section E6.1-6.6 supersedes the previous Section E6 in Section E: Clinical Cytogenetics of the American College of Medical Genetics and Genomics Technical Standards for Clinical Genetics Laboratories.
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Affiliation(s)
- Yassmine Akkari
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Annette Kim
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Ender Karaca
- Department of Pathology, Baylor University Medical Center, Dallas, TX; Texas A&M School of Medicine, Texas A&M University, Dallas, TX
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA; Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Lina Shao
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
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2
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Clarke SE, Fuller KA, Erber WN. Chromosomal defects in multiple myeloma. Blood Rev 2024; 64:101168. [PMID: 38212176 DOI: 10.1016/j.blre.2024.101168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/01/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024]
Abstract
Multiple myeloma is a plasma cell neoplasm driven by primary (e.g. hyperdiploidy; IGH translocations) and secondary (e.g. 1q21 gains/amplifications; del(17p); MYC translocations) chromosomal events. These are important to detect as they influence prognosis, therapeutic response and disease survival. Currently, cytogenetic testing is most commonly performed by interphase fluorescence in situ hybridisation (FISH) on aspirated bone marrow samples. A number of variations to FISH methodology are available, including prior plasma cell enrichment and incorporation of immunophenotypic plasma cell identification. Other molecular methods are increasingly being utilised to provide a genome-wide view at high resolution (e.g. single nucleotide polymorphism (SNP) microarray analysis) and these can detect abnormalities in most cases. Despite their wide application at diagnostic assessment, both FISH and SNP-array have relatively low sensitivity, limiting their use for identification of prognostically significant low-level sub-clones or for disease monitoring. Next-generation sequencing is increasingly being used to detect mutations and new FISH techniques such as by flow cytometry are in development and may address some of the current test limitations. Here we review the primary and secondary cytogenetic aberrations in myeloma and discuss the range of techniques available for their assessment.
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Affiliation(s)
- Sarah E Clarke
- School of Biomedical Sciences, The University of Western Australia (M504), Crawley, WA 6009, Australia; Department of Haematology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Murdoch, WA 6150, Australia.
| | - Kathryn A Fuller
- School of Biomedical Sciences, The University of Western Australia (M504), Crawley, WA 6009, Australia.
| | - Wendy N Erber
- School of Biomedical Sciences, The University of Western Australia (M504), Crawley, WA 6009, Australia; PathWest Laboratory Medicine WA, Royal Perth Hospital, Perth, WA 6000, Australia.
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3
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Cárdenas MC, García-Sanz R, Puig N, Pérez-Surribas D, Flores-Montero J, Ortiz-Espejo M, de la Rubia J, Cruz-Iglesias E. Recommendations for the study of monoclonal gammopathies in the clinical laboratory. A consensus of the Spanish Society of Laboratory Medicine and the Spanish Society of Hematology and Hemotherapy. Part I: Update on laboratory tests for the study of monoclonal gammopathies. Clin Chem Lab Med 2023; 61:2115-2130. [PMID: 37477188 DOI: 10.1515/cclm-2023-0326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/29/2023] [Indexed: 07/22/2023]
Abstract
Monoclonal gammopathies (MG) are characterized by the proliferation of plasma cells that produce identical abnormal immunoglobulins (intact or some of their subunits). This abnormal immunoglobulin component is called monoclonal protein (M-protein), and is considered a biomarker of proliferative activity. The identification, characterization and measurement of M-protein is essential for the management of MG. We conducted a systematic review of the different tests and measurement methods used in the clinical laboratory for the study of M-protein in serum and urine, the biochemistry and hematology tests necessary for clinical evaluation, and studies in bone marrow, peripheral blood and other tissues. This review included literature published between 2009 and 2022. The paper discusses the main methodological characteristics and limitations, as well as the purpose and clinical value of the different tests used in the diagnosis, prognosis, monitoring and assessment of treatment response in MG. Included are methods for the study of M-protein, namely electrophoresis, measurement of immunoglobulin levels, serum free light chains, immunoglobulin heavy chain/light chain pairs, and mass spectrometry, and for the bone marrow examination, morphological analysis, cytogenetics, molecular techniques, and multiparameter flow cytometry.
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Affiliation(s)
- María C Cárdenas
- Department of Clinical Analysis, Hospital Clinico San Carlos, Madrid, Spain
- Protein Commission, Spanish Society of Laboratory Medicine (SEQCML), Barcelona, Spain
| | - Ramón García-Sanz
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), CIBERONC and Center for Cancer Research-IBMCC (University of Salamanca-CSIC), Salamanca, Spain
- Spanish Society of Hematology and Hemotherapy (SEHH), Madrid, Spain
| | - Noemí Puig
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), CIBERONC and Center for Cancer Research-IBMCC (University of Salamanca-CSIC), Salamanca, Spain
- Spanish Society of Hematology and Hemotherapy (SEHH), Madrid, Spain
| | - David Pérez-Surribas
- Laboratori Pasteur, Andorra La Vella, Andorra
- Protein Commission, Spanish Society of Laboratory Medicine (SEQCML), Barcelona, Spain
| | - Juan Flores-Montero
- Hematology Department, University Hospital of Salamanca, Research Biomedical Institute of Salamanca (IBSAL), CIBERONC and Center for Cancer Research-IBMCC (University of Salamanca-CSIC), Salamanca, Spain
- Spanish Society of Hematology and Hemotherapy (SEHH), Madrid, Spain
| | - María Ortiz-Espejo
- Department of Clinical Analysis, Hospital Universitario Marqués de Valdecilla, Santander, Spain
- Protein Commission, Spanish Society of Laboratory Medicine (SEQCML), Barcelona, Spain
| | - Javier de la Rubia
- Hematology Department, Hospital Universitario y Politécnico La Fe & Universidad Católica de Valencia, Instituto de Investigación Sanitaria La Fe Centro de Investigación Biomédica en Red de Cáncer, CIBERONC CB16/12/00284, Instituto de Salud Carlos III, Valencia, Spain
- Spanish Society of Hematology and Hemotherapy (SEHH), Madrid, Spain
| | - Elena Cruz-Iglesias
- Department of Laboratory Medicine, Osakidetza Basque Health Service, Basurto University Hospital, Bilbao, Spain
- Protein Commission, Spanish Society of Laboratory Medicine (SEQCML), Barcelona, Spain
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4
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Kadam Amare P, Nikalje Khasnis S, Hande P, Lele H, Wable N, Kaskar S, Nikam Gujar N, Gardi N, Prabhudesai A, Todi K, Waghole R, Roy P. Cytogenetic Abnormalities in Multiple Myeloma: Incidence, Prognostic Significance, and Geographic Heterogeneity in Indian and Western Populations. Cytogenet Genome Res 2023; 162:529-540. [PMID: 36780889 PMCID: PMC10534967 DOI: 10.1159/000529191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/11/2023] [Indexed: 02/15/2023] Open
Abstract
Multiple myeloma (MM) is a genetically complex and heterogeneous neoplasm in which cytogenetics is a major factor playing an important role in the risk stratification of disease. High-risk MM based upon cytogenetic classification includes primary IGH translocations t(4;14), t(14;16), t(14;20), and secondary progressive aberrations such as gain/amp(1q), 1p deletion, del(17p), and hypodiploidy. Several studies have proved that interphase FISH can detect primary as well as secondary cryptic aberrations very efficiently in lowest 5-10% abnormal plasma cell population. The present large-scale study was undertaken to evaluate the incidence of cytogenetic abnormalities, to analyse the correlation of conventional karyotyping with FISH, and to seek the geographic heterogeneity in the incidence of primary as well as secondary aberrations in our Indian versus Western populations. We conducted prospective studies of 1,104 patients consecutively referred from the primary, secondary, and tertiary oncology centres from all over India. Interphase FISH was performed on isolated plasma cells. Karyotype analysis was done as per ISCN 2016 and 2020. FISH could detect cytogenetic abnormalities in 67.6% of the cases with an incidence of 59% non-hyperdiploidy. The incidence of IGH translocation was 26% versus literature frequency of 40-50% which was mainly due to a low incidence (6%) of t(11;14) in contrast to 15-20% in other series. Additionally, the association of secondary progressive aberrations in the hyperdiploid group rather than the non-hyperdiploid group in our patients is not a common finding. A biallelic inactivation of TP53 as an ultra-high risk factor was detected in old-aged patients. These observations disclose the novel findings and strongly indicate the racial disparity which leads to geographic heterogeneity. In contrast to FISH, conventional karyotyping could detect MM-related aberrations in 50% of cases, of which 44% revealed highly complex karyotypes with common aberrations of chromosome 1q. Overall, FISH was found to be a novel, easy approach with high success rate and capability of detection of all cytogenetic abnormalities that add valid information for the risk stratification of disease. This, in future, in combination with mutation profile and gene expression profile will help in further refinement of disease and identification of actionable targets.
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Affiliation(s)
- Pratibha Kadam Amare
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | | | - Pranita Hande
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | - Hrushikesh Lele
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | - Nishigandha Wable
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | - Snehal Kaskar
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | - Nikita Nikam Gujar
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | - Nilesh Gardi
- ACTREC, Tata Memorial Center, Navi Mumbai, India
| | - Aniket Prabhudesai
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | - Karishma Todi
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | - Rohit Waghole
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
| | - Pritha Roy
- Oncocytogenetics and Oncomolecular Department, Lilac Insights Pvt. Ltd, Navi Mumbai, India
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5
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Sudha P, Ahsan A, Ashby C, Kausar T, Khera A, Kazeroun MH, Hsu CC, Wang L, Fitzsimons E, Salminen O, Blaney P, Czader M, Williams J, Abu Zaid MI, Ansari-Pour N, Yong KL, van Rhee F, Pierceall WE, Morgan GJ, Flynt E, Gooding S, Abonour R, Ramasamy K, Thakurta A, Walker BA. Myeloma Genome Project Panel is a Comprehensive Targeted Genomics Panel for Molecular Profiling of Patients with Multiple Myeloma. Clin Cancer Res 2022; 28:2854-2864. [PMID: 35522533 PMCID: PMC9250632 DOI: 10.1158/1078-0432.ccr-21-3695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/11/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE We designed a comprehensive multiple myeloma targeted sequencing panel to identify common genomic abnormalities in a single assay and validated it against known standards. EXPERIMENTAL DESIGN The panel comprised 228 genes/exons for mutations, 6 regions for translocations, and 56 regions for copy number abnormalities (CNA). Toward panel validation, targeted sequencing was conducted on 233 patient samples and further validated using clinical FISH (translocations), multiplex ligation probe analysis (MLPA; CNAs), whole-genome sequencing (WGS; CNAs, mutations, translocations), or droplet digital PCR (ddPCR) of known standards (mutations). RESULTS Canonical immunoglobulin heavy chain translocations were detected in 43.2% of patients by sequencing, and aligned with FISH except for 1 patient. CNAs determined by sequencing and MLPA for 22 regions were comparable in 103 samples and concordance between platforms was R2 = 0.969. Variant allele frequency (VAF) for 74 mutations were compared between sequencing and ddPCR with concordance of R2 = 0.9849. CONCLUSIONS In summary, we have developed a targeted sequencing panel that is as robust or superior to FISH and WGS. This molecular panel is cost-effective, comprehensive, clinically actionable, and can be routinely deployed to assist risk stratification at diagnosis or posttreatment to guide sequencing of therapies.
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Affiliation(s)
- Parvathi Sudha
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Aarif Ahsan
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Cody Ashby
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Tasneem Kausar
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Akhil Khera
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Mohammad H. Kazeroun
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Chih-Chao Hsu
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Lin Wang
- Department of Pathology and Laboratory Research, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | | | - Outi Salminen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Patrick Blaney
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Magdalena Czader
- Department of Pathology and Laboratory Research, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Jonathan Williams
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Mohammad I. Abu Zaid
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Naser Ansari-Pour
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Kwee L. Yong
- Cancer Institute, University College London, London, United Kingdom
| | - Frits van Rhee
- Myeloma Center, Winthrop P. Rockefeller Cancer institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Gareth J. Morgan
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Erin Flynt
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Sarah Gooding
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Oxford Center for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
| | - Rafat Abonour
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Karthik Ramasamy
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Oxford Center for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Anjan Thakurta
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
- Oxford Center for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Brian A. Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
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6
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Hagen P, Sellin M, Berg S, Zhang J. Increasing genomic discovery in newly diagnosed multiple myeloma: defining disease biology and its correlation to risk. Ann Hematol 2022; 101:1407-1420. [PMID: 35585246 PMCID: PMC9756633 DOI: 10.1007/s00277-022-04856-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/25/2022] [Indexed: 01/03/2023]
Abstract
Our understanding of MM genomics has expanded rapidly in the past 5-10 years as a consequence of cytogenetic analyses obtained in routine clinical practice as well as the ability to perform whole-exome/genome sequencing and gene expression profiling on large patient data sets. This knowledge has offered new insights into disease biology and is increasingly defining high-risk genomic patterns. In this manuscript, we present a thorough review of our current knowledge of MM genomics. The epidemiology and biology of chromosomal abnormalities including both copy number abnormalities and chromosomal translocation are described in full with a focus on those most clinically impactful such as 1q amplification and del(17p) as well as certain chromosome 14 translocations. A review of our ever-expanding knowledge of genetic mutations derived from recent whole-genome/exome data sets is then reviewed including those that drive disease pathogenesis from precursor states as well as those that may impact clinical outcomes. We then transition and attempt to elucidate how both chromosomal abnormalities and gene mutations are evolving our understanding of disease risk. We conclude by offering our perspectives moving forward as to how we might apply whole-genome/exome-level data in addition to routine cytogenetic analyses to improve patient outcomes as well as further knowledge gaps that must be addressed.
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Affiliation(s)
- Patrick Hagen
- Department of Hematology/Oncology, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Mark Sellin
- Department of Hematology/Oncology, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Stephanie Berg
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Jiwang Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA,Department of Pathology and Department of Radiation Oncology, Loyola University Medical Center, Maywood, IL, 60153, USA
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7
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How I Treat High-risk Multiple Myeloma. Blood 2021; 139:2889-2903. [PMID: 34727187 DOI: 10.1182/blood.2020008733] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/26/2021] [Indexed: 11/20/2022] Open
Abstract
Survival of multiple myeloma (MM) has significantly improved over the last decade; however, a composed group of patients (15-20%), named high-risk (HR) MM, still experience reduced survival. Both tumor biology and suboptimal/absent responses to therapy may underlie HR definition and a clear uniform identification of risk factors is crucial for a proper management of these patients. In biologic-HRMM, MRD negativity attainment and sustain, inside and outside BM, should be the primary goal and therapy should be adapted in patients with frailty to reduce toxicity and improve quality of life. MM treatment has traditionally been tailored on age and more recently frailty or comorbidities, but very rarely on the biology of the disease, mainly because of the lack of a clear benefit derived from a specific drug/combination, inhomogeneity in HR definition and lack of data coming from prospective, properly designed clinical trials. Some attempts have been successfully made recently in this direction. In this review, we are discussing the current different definitions of HR and the need for a consensus, the results of available trials in HR patients and the way through risk-adapted treatment strategies. For this purpose, we are proposing several clinical cases of difficult-to-treat patients throughout different treatment phases.
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8
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Hassan H, Szalat R. Genetic Predictors of Mortality in Patients with Multiple Myeloma. APPLICATION OF CLINICAL GENETICS 2021; 14:241-254. [PMID: 33953598 PMCID: PMC8092627 DOI: 10.2147/tacg.s262866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/31/2021] [Indexed: 12/19/2022]
Abstract
Multiple myeloma (MM) is a heterogeneous disease featured by clonal plasma cell proliferation and genomic instability. The advent of next-generation sequencing allowed unraveling the complex genomic landscape of the disease. Several recurrent genomic aberrations including immunoglobulin genes translocations, copy number abnormalities, complex chromosomal events, transcriptomic and epigenomic deregulation, and mutations define various molecular subgroups with distinct outcomes. In this review, we describe the recurrent genomic events identified in MM impacting patients’ outcome and survival. These genomic aberrations constitute new markers that could be incorporated into a prognostication model to eventually guide therapy at every stage of the disease.
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Affiliation(s)
- Hamza Hassan
- Department of Hematology and Medical Oncology, Boston University Medical Center, Boston, MA, USA
| | - Raphael Szalat
- Department of Hematology and Medical Oncology, Boston University Medical Center, Boston, MA, USA.,Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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9
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Theodorakakou F, Dimopoulos MA, Kastritis E. Mutation-dependent treatment approaches for patients with complex multiple myeloma. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2021. [DOI: 10.1080/23808993.2021.1893605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Foteini Theodorakakou
- Plasma Cell Dyscrasia Unit, Department of Clinical Therapeutics, National and Kapodistrian University of Athens, Athens, Greece
| | - Meletios A. Dimopoulos
- Plasma Cell Dyscrasia Unit, Department of Clinical Therapeutics, National and Kapodistrian University of Athens, Athens, Greece
| | - Efstathios Kastritis
- Plasma Cell Dyscrasia Unit, Department of Clinical Therapeutics, National and Kapodistrian University of Athens, Athens, Greece
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10
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Ashby C, Rutherford M, Bauer MA, Peterson EA, Wang Y, Boyle EM, Wardell CP, Walker BA. TarPan: an easily adaptable targeted sequencing panel viewer for research and clinical use. BMC Bioinformatics 2020; 21:144. [PMID: 32293247 PMCID: PMC7158102 DOI: 10.1186/s12859-020-3477-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/31/2020] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The study of cancer genomics continually matures as the number of patient samples sequenced increases. As more data is generated, oncogenic drivers for specific cancer types are discovered along with their associated risks. This in turn leads to potential treatment strategies that pave the way to precision medicine. However, significant financial and analytical barriers make it infeasible to sequence the entire genome of every patient. In contrast, targeted sequencing panels give reliable information on relevant portions of the genome at a fiscally responsible cost. Therefore, we have created the Targeted Panel (TarPan) Viewer, a software tool, to investigate this type of data. RESULTS TarPan Viewer helps investigators understand data from targeted sequencing data by displaying the information through a web browser interface. Through this interface, investigators can easily observe copy number changes, mutations, and structural events in cancer samples. The viewer runs in R Shiny with a robust SQLite backend and its input is generated from bioinformatic algorithms reliably described in the literature. Here we show the results from using TarPan Viewer on publicly available follicular lymphoma, breast cancer, and multiple myeloma data. In addition, we have tested and utilized the viewer internally, and this data has been used in high-impact peer-reviewed publications. CONCLUSIONS We have designed a flexible, simple to setup viewer that is easily adaptable to any type of cancer targeted sequencing, and has already proven its use in a research laboratory environment. Further, we believe with deeper sequencing and/or more targeted application it could be of use in the clinic in conjunction with an appropriate targeted sequencing panel as a cost-effective diagnostic test, especially in cancers such as acute leukemia or diffuse large B-cell lymphoma that require rapid interventions.
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Affiliation(s)
- Cody Ashby
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA. .,Cancer Institute: Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - Michael Rutherford
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Cancer Institute: Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Michael A Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Cancer Institute: Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Erich A Peterson
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yan Wang
- Cancer Institute: Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Eileen M Boyle
- Cancer Institute: Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Christopher P Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Cancer Institute: Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Brian A Walker
- Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA
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11
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Maura F, Rustad EH, Boyle EM, Morgan GJ. Reconstructing the evolutionary history of multiple myeloma. Best Pract Res Clin Haematol 2020; 33:101145. [PMID: 32139011 PMCID: PMC7389821 DOI: 10.1016/j.beha.2020.101145] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/09/2020] [Indexed: 02/08/2023]
Abstract
Multiple myeloma is the second most common lymphoproliferative disorder, characterized by aberrant expansion of monoclonal plasma cells. In the last years, thanks to novel next generation sequencing technologies, multiple myeloma has emerged as one of the most complex hematological cancers, shaped over time by the activity of multiple mutational processes and by the acquisition of key driver events. In this review, we describe how whole genome sequencing is emerging as a key technology to decipher this complexity at every stage of myeloma development: precursors, diagnosis and relapsed/refractory. Defining the time windows when driver events are acquired improves our understanding of cancer etiology and paves the way for early diagnosis and ultimately prevention.
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Affiliation(s)
- Francesco Maura
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Even H Rustad
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eileen M Boyle
- NYU Langone, Perlmutter Cancer Center, New York, NY, USA
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Janz S, Zhan F, Sun F, Cheng Y, Pisano M, Yang Y, Goldschmidt H, Hari P. Germline Risk Contribution to Genomic Instability in Multiple Myeloma. Front Genet 2019; 10:424. [PMID: 31139207 PMCID: PMC6518313 DOI: 10.3389/fgene.2019.00424] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 04/17/2019] [Indexed: 12/14/2022] Open
Abstract
Genomic instability, a well-established hallmark of human cancer, is also a driving force in the natural history of multiple myeloma (MM) - a difficult to treat and in most cases fatal neoplasm of immunoglobulin producing plasma cells that reside in the hematopoietic bone marrow. Long recognized manifestations of genomic instability in myeloma at the cytogenetic level include abnormal chromosome numbers (aneuploidy) caused by trisomy of odd-numbered chromosomes; recurrent oncogene-activating chromosomal translocations that involve immunoglobulin loci; and large-scale amplifications, inversions, and insertions/deletions (indels) of genetic material. Catastrophic genetic rearrangements that either shatter and illegitimately reassemble a single chromosome (chromotripsis) or lead to disordered segmental rearrangements of multiple chromosomes (chromoplexy) also occur. Genomic instability at the nucleotide level results in base substitution mutations and small indels that affect both the coding and non-coding genome. Sometimes this generates a distinctive signature of somatic mutations that can be attributed to defects in DNA repair pathways, the DNA damage response (DDR) or aberrant activity of mutator genes including members of the APOBEC family. In addition to myeloma development and progression, genomic instability promotes acquisition of drug resistance in patients with myeloma. Here we review recent findings on the genetic predisposition to myeloma, including newly identified candidate genes suggesting linkage of germline risk and compromised genomic stability control. The role of ethnic and familial risk factors for myeloma is highlighted. We address current research gaps that concern the lack of studies on the mechanism by which germline risk alleles promote genomic instability in myeloma, including the open question whether genetic modifiers of myeloma development act in tumor cells, the tumor microenvironment (TME), or in both. We conclude with a brief proposition for future research directions, which concentrate on the biological function of myeloma risk and genetic instability alleles, the potential links between the germline genome and somatic changes in myeloma, and the need to elucidate genetic modifiers in the TME.
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Affiliation(s)
- Siegfried Janz
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Fenghuang Zhan
- Department of Internal Medicine, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA, United States.,Holden Comprehensive Cancer Center, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA, United States
| | - Fumou Sun
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Yan Cheng
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Michael Pisano
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States.,Interdisciplinary Graduate Program in Immunology, The University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA, United States
| | - Ye Yang
- The Third Affiliated Hospital, Nanjing University of Chinese Medicine, Nanjing, China.,Ministry of Education's Key Laboratory of Acupuncture and Medicine Research, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hartmut Goldschmidt
- Medizinische Klinik V, Universitätsklinikum Heidelberg, Heidelberg, Germany.,Nationales Centrum für Tumorerkrankungen, Heidelberg, Germany
| | - Parameswaran Hari
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
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