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Hansen MH, Maagaard M, Cédile O, Nyvold CG. SWIGH-SCORE: A translational light-weight approach in computational detection of rearranged immunoglobulin heavy chain to be used in monoclonal lymphoproliferative disorders. MethodsX 2024; 12:102741. [PMID: 38846434 PMCID: PMC11154698 DOI: 10.1016/j.mex.2024.102741] [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: 02/22/2024] [Revised: 04/23/2024] [Accepted: 05/02/2024] [Indexed: 06/09/2024] Open
Abstract
We present a lightweight tool for clonotyping and measurable residual disease (MRD) assessment in monoclonal lymphoproliferative disorders. It is a translational method that enables computational detection of rearranged immunoglobulin heavy chain gene sequences.•The swigh-score clonotyping tool emphasizes parallelization and applicability across sequencing platforms.•The algorithm is based on an adaptation of the Smith-Waterman algorithm for local alignment of reads generated by 2nd and 3rd generation of sequencers.For method validation, we demonstrate the targeted sequences of immunoglobulin heavy chain genes from diagnostic bone marrow using serial dilutions of CD138+ plasma cells from a patient with multiple myeloma. Sequencing libraries from diagnostic samples were prepared for the three sequencing platforms, Ion S5 (Thermo Fisher Scientific), MiSeq (Illumina), and MinION (Oxford Nanopore), using the LymphoTrack assay. Basic quality filtering was performed, and a Smith-Waterman-based swigh-score algorithm was developed in shell and C for clonotyping and MRD assessment using FASTQ data files. Performance is demonstrated across the three different sequencing platforms.
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Affiliation(s)
- Marcus Høy Hansen
- Haematology-Pathology Research Laboratory, Research Unit of Haematology, Department of Hematology, and Research Unit of Pathology, Department of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Markus Maagaard
- Haematology-Pathology Research Laboratory, Research Unit of Haematology, Department of Hematology, and Research Unit of Pathology, Department of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Oriane Cédile
- Haematology-Pathology Research Laboratory, Research Unit of Haematology, Department of Hematology, and Research Unit of Pathology, Department of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
- OPEN, Odense Patient data Explorative Network, Haematology-Pathology Research Laboratory, Odense University Hospital, Odense, Denmark
| | - Charlotte Guldborg Nyvold
- Haematology-Pathology Research Laboratory, Research Unit of Haematology, Department of Hematology, and Research Unit of Pathology, Department of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
- OPEN, Odense Patient data Explorative Network, Haematology-Pathology Research Laboratory, Odense University Hospital, Odense, Denmark
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Hansen MH, Cédile O, Abildgaard N, Nyvold CG. The potential of 3rd-generation nanopore sequencing for B-cell clonotyping in lymphoproliferative disorders. EJHAEM 2024; 5:290-293. [PMID: 38406528 PMCID: PMC10887334 DOI: 10.1002/jha2.815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 09/29/2023] [Accepted: 10/24/2023] [Indexed: 02/27/2024]
Abstract
Lymphoid malignancies are characterized by clonal cell expansion, often identifiable by unique immunoglobulin rearrangements. Heavy (IGH) and light-chain gene usage offers diagnostic insights and enables sensitive residual disease detection via next-generation sequencing. With its adaptable throughput and variable read lengths, Oxford Nanopore thirdgeneration sequencing now holds promise for clonotyping. This study analyzed CD138+ plasma-cell DNA from eight multiple myeloma patients, comparing clonotyping performance between Nanopore sequencing, Illumina MiSeq, and Ion Torrent S5. We demonstrated clonotype consistency across platforms through Smith-Waterman local alignment of nanopore reads. The mean clonal percentage of IGH V and J gene usage in the CD138+ cells was 69% for Nanopore, 67% for S5, and 76% for MiSeq. When aligned with known clonotypes, clonal cells averaged a 91% similarity, exceeding 85%. In summary, Nanopore sequencing, with its capacity for generating millions of high-quality reads, proves effective for detecting clonal IGH rearrangements. This versatile platform offers the potential for measuring residual disease down to a sensitivity level of 10-6 at a lower cost, marking a significant advancement in clonotyping techniques.
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Affiliation(s)
- Marcus H. Hansen
- Haematology‐Pathology Research Laboratory, Research Unit of HaematologyDepartment of Haematology, and Research Unit of PathologyDepartment of PathologyUniversity of Southern Denmark and Odense University HospitalOdenseDenmark
| | - Oriane Cédile
- Haematology‐Pathology Research Laboratory, Research Unit of HaematologyDepartment of Haematology, and Research Unit of PathologyDepartment of PathologyUniversity of Southern Denmark and Odense University HospitalOdenseDenmark
- OPEN, Odense Patient data Explorative Network, Odense University HospitalOdenseDenmark
| | - Niels Abildgaard
- Haematology‐Pathology Research Laboratory, Research Unit of HaematologyDepartment of Haematology, and Research Unit of PathologyDepartment of PathologyUniversity of Southern Denmark and Odense University HospitalOdenseDenmark
| | - Charlotte G. Nyvold
- Haematology‐Pathology Research Laboratory, Research Unit of HaematologyDepartment of Haematology, and Research Unit of PathologyDepartment of PathologyUniversity of Southern Denmark and Odense University HospitalOdenseDenmark
- OPEN, Odense Patient data Explorative Network, Odense University HospitalOdenseDenmark
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Guo J, Zhang Z, Wang H, Li Q, Fan M, Zhang W, Tao Q, Wang Z, Ling C, Xiao H, Gao Z, Zhai Z. SRRM2 may be a potential biomarker and immunotherapy target for multiple myeloma: a real-world study based on flow cytometry detection. Clin Exp Med 2024; 24:28. [PMID: 38289482 PMCID: PMC10827842 DOI: 10.1007/s10238-023-01272-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/29/2023] [Indexed: 02/01/2024]
Abstract
Serine/arginine repetitive matrix 2 (SRRM2) has been implicated in tumorigenesis, cancer development, and drug resistance through aberrant splicing; however, its correlation with multiple myeloma (MM) has not been reported. We investigated the potential of SRRM2 as a biomarker and immunotherapeutic target in MM by examining its expression in MM cells using flow cytometry. Our study included 95 patients with plasma cell disease, including 80 MM cases, and we detected SRRM2 expression on plasma cells and normal blood cells to analyze its relationship with clinical profiles. We found widespread positive expression of SRRM2 on plasma cells with little expression on normal blood cells, and its expression on abnormal plasma cells was higher than that on normal plasma cells. Comparative analysis with clinical data suggests that SRRM2 expression on plasma cells correlates with MM treatment response. MM patients with high SRRM2 expression had higher levels of serum β2-mg and LDH, ISS staging, and plasma cell infiltration, as well as high-risk mSMART 3.0 stratification and cytogenetic abnormalities, particularly 1q21 amplification. In patients with previous MM, high SRRM2 expression on plasma cells was associated with higher plasma cell infiltration, high-risk mSMART 3.0 risk stratification, cytogenetic abnormalities, more relapses, and fewer autologous stem cell transplant treatments. In summary, SRRM2 may serve as a novel biomarker and immunotherapeutic target for MM. Its expression level on plasma cells can help in risk stratification of MM and monitoring of treatment response.
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Affiliation(s)
- Jinjing Guo
- Department of Hematology, Hematological Research Center, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Department of Laboratory, Fuyang People's Hospital, Fuyang, China
| | - Zhiye Zhang
- Department of Hematology, Hematological Research Center, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Department of Hematology, Fuyang Hospital Affiliated to Anhui Medical University, Fuyang, China
| | - Huiping Wang
- Department of Hematology, Hematological Research Center, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Qian Li
- Department of Hematology, Hematological Research Center, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Mengmeng Fan
- Department of Hematology, Hematological Research Center, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Wanqiu Zhang
- Department of Hematology, Hematological Research Center, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Qianshan Tao
- Department of Hematology, Hematological Research Center, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zhitao Wang
- Department of Hematology, Hematological Research Center, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Chun Ling
- Department of Hematology, Hematological Research Center, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Department of Hematology, Affiliated Chuzhou Hospital of Anhui Medical University, Chuzhou, Anhui, China
| | - Hao Xiao
- Department of Hematology, Hematological Research Center, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zhimai Gao
- ZENO Biotechnology (Shenzhen) Co, Shenzhen, Guangzhou, China
| | - Zhimin Zhai
- Department of Hematology, Hematological Research Center, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.
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