Hansen Marcus Høy, Maagaard Markus, Cédile Oriane, Nyvold Charlotte Guldborg
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.
MethodsX. 2024 May 10;12:102741. doi: 10.1016/j.mex.2024.102741. eCollection 2024 Jun.
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 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 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.
我们展示了一种用于单克隆淋巴细胞增殖性疾病克隆分型和可测量残留疾病（MRD）评估的轻量级工具。这是一种转化方法，能够通过计算检测重排的免疫球蛋白重链基因序列。•该克隆分型工具强调跨测序平台的并行化和适用性。•该算法基于对Smith-Waterman算法的改编，用于对第二代和第三代测序仪生成的 reads 进行局部比对。为了进行方法验证，我们使用来自一名多发性骨髓瘤患者的CD138+浆细胞的系列稀释液，展示了诊断性骨髓中免疫球蛋白重链基因的靶向序列。使用LymphoTrack检测法为三个测序平台Ion S5（赛默飞世尔科技公司）、MiSeq（Illumina）和MinION（牛津纳米孔公司）制备了诊断样本的测序文库。进行了基本的质量过滤，并在 shell 和 C 语言中开发了一种基于 Smith-Waterman 的算法，用于使用FASTQ数据文件进行克隆分型和MRD评估。在三种不同的测序平台上展示了其性能。
