ImSpectR - R package to quantify immune repertoire diversity in spectratype and repertoire sequencing data.

Autor:	Cordes M; Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands.; Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands., Pike-Overzet K; Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands., van Eggermond M; Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands., Vloemans S; Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands., Baert MR; Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands., Garcia-Perez L; Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands., Staal FJT; Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands., Reinders MJT; Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands.; The Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands., van den Akker E; Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands.; The Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.; Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2019 Oct 30. Date of Electronic Publication: 2019 Oct 30.
DOI:	10.1093/bioinformatics/btz804
Abstrakt:	Summary: An effective immune system is characterized by a diverse immune repertoire. There is a strong demand for accurate and quantitative methods to assess the diversity of the immune repertoire for various (pre-)clinical applications, including the diagnosis and prognosis of primary immune deficiencies, or to assess the response to therapy. Current strategies for immune diversity assessment generally comprise the visual inspection of the length distribution of rearranged T- and B-cell receptors. Visual inspections, however, are prone to subjective assessments and thus lead to biases. Here, we introduce ImSpectR, a unified approach to quantify immunodiversity using either spectratype, repertoire sequencing or single cell RNA sequencing data. ImSpectR scores various types of deviations from the expected length distribution and integrates these into one measure, allowing for robust quantitative comparisons of immune diversity across individuals or conditions. Availability: R-package is available for download on GitHub at https://github.com/martijn-cordes/ImSpectR. Supplementary Information: Supplementary data are available at Bioinformatics online. (© The Author(s) 2019. Published by Oxford University Press.)
Databáze:	MEDLINE
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