Barretts esophagus books 2

Publications

Eitan Halper-Stromberg, M.D., Ph.D.
Eitan Halper-Stromberg, M.D., Ph.D.

Looking for Clonality: Novel Sequencing Technology Helps Identify Clonal Rearrangements in Lymphoid Malignancies

CloneRetriever: Streamlining the diagnosis of lymphoid malignancies by next-generation sequencing

Clonal immunoglobulin and T-cell receptor rearrangements serve as tumor-specific markers that have become mainstays in the diagnosis and monitoring of lymphoid malignancies. Minimal residual disease detection of tumor clonotypes in lymphoblastic leukemia and multiple myeloma by next-generation sequencing (NGS) has become powerful disease endpoints that guide patient management. However, adoption of NGS for primary diagnosis remains limited partly due to the complexity of the sequencing data and lack of user-friendly software for data analysis and clone detection. In this study, we addressed these bioinformatics challenges by designing a novel web tool, CloneRetriever (CR), which uses machine-learning principles to generate clone classification schemes that are customizable, and can be applied to large datasets. CR has 2 applications: a "validation" mode to derive a clonality classifier, and a "live" mode to screen for clones. Using two separate datasets, we show that CR-generated classifiers yielded sensitivities of 81%-90% and specificities of 97%-100% to detect lymphoma clones, which was prospectively validated in a third dataset. CR is an out-of-the-box ready and user-friendly software designed to identify clonal rearrangements in large NGS datasets for the diagnosis of lymphoid malignancies. Go here to read more and try out CR.

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