SWIGH-SCORE: A translational light-weight approach in computational detection of rearranged immunoglobulin heavy chain to be used in monoclonal lymphoproliferative disorders.

Autor:	Hansen MH; 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., Maagaard M; 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., Cédile O; 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., Nyvold CG; 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.
Jazyk:	angličtina
Zdroj:	MethodsX [MethodsX] 2024 May 10; Vol. 12, pp. 102741. Date of Electronic Publication: 2024 May 10 (Print Publication: 2024).
DOI:	10.1016/j.mex.2024.102741
Abstrakt:	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. Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. (© 2024 The Authors.)
Databáze:	MEDLINE
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