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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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Boyle EM, Deshpande S, Tytarenko R, Ashby C, Wang Y, Bauer MA, Johnson SK, Wardell CP, Thanendrarajan S, Zangari M, Facon T, Dumontet C, Barlogie B, Arbini A, Rustad EH, Maura F, Landgren O, Zhan F, van Rhee F, Schinke C, Davies FE, Morgan GJ, Walker BA. The molecular make up of smoldering myeloma highlights the evolutionary pathways leading to multiple myeloma. Nat Commun 2021; 12:293. [PMID: 33436579 PMCID: PMC7804406 DOI: 10.1038/s41467-020-20524-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/08/2020] [Indexed: 12/28/2022] Open
Abstract
Smoldering myeloma (SMM) is associated with a high-risk of progression to myeloma (MM). We report the results of a study of 82 patients with both targeted sequencing that included a capture of the immunoglobulin and MYC regions. By comparing these results to newly diagnosed myeloma (MM) we show fewer NRAS and FAM46C mutations together with fewer adverse translocations, del(1p), del(14q), del(16q), and del(17p) in SMM consistent with their role as drivers of the transition to MM. KRAS mutations are associated with a shorter time to progression (HR 3.5 (1.5–8.1), p = 0.001). In an analysis of change in clonal structure over time we studied 53 samples from nine patients at multiple time points. Branching evolutionary patterns, novel mutations, biallelic hits in crucial tumour suppressor genes, and segmental copy number changes are key mechanisms underlying the transition to MM, which can precede progression and be used to guide early intervention strategies. Progression from asymptomatic smoldering multiple myeloma (SMM) to symptomatic Multiple Myeloma occurs at different rates in different patients. Here, the authors report fewer NRAS and FAM46C mutations and adverse translocations in SMM compared to MM, while KRAS mutations are associated with a shorter time to progression.
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Affiliation(s)
- Eileen M Boyle
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,INSERM 1052/CNRS 5286 Cancer Research Center of Lyon, Lyon, France.,Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Shayu Deshpande
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ruslana Tytarenko
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Cody Ashby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yan Wang
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Michael A Bauer
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Sarah K Johnson
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Christopher P Wardell
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Maurizio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Thierry Facon
- Service des maladies du sang. Hôpital Claude Huriez, Lille University Hospital, Lille, France
| | - Charles Dumontet
- INSERM 1052/CNRS 5286 Cancer Research Center of Lyon, Lyon, France
| | - Bart Barlogie
- Division of Hematology, The Mount Sinai Hospital, New York, NY, USA
| | - Arnaldo Arbini
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Even H Rustad
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Francesco Maura
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ola Landgren
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fenghuang Zhan
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Carolina Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Faith E Davies
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Gareth J Morgan
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
| | - Brian A Walker
- Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA.
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