Cordes M, Pike-Overzet K, van Eggermond M, Vloemans S, Baert MR, Garcia-Perez L, Staal FJT, Reinders MJT, van den Akker EB. ImSpectR - R package to quantify immune repertoire diversity in spectratype and repertoire sequencing data.
Bioinformatics 2019;
36:btz804. [PMID:
31665245 PMCID:
PMC7703782 DOI:
10.1093/bioinformatics/btz804]
[Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/29/2019] [Accepted: 10/24/2019] [Indexed: 11/29/2022] Open
Abstract
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.
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