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Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing

Author

Listed:
  • Igor Mandric

    (University of California, Los Angeles)

  • Jeremy Rotman

    (University of California, Los Angeles
    School of Pharmacy, University of Southern California)

  • Harry Taegyun Yang

    (University of California, Los Angeles
    University of California, Los Angeles)

  • Nicolas Strauli

    (University of California, San Francisco)

  • Dennis J. Montoya

    (University of California, Los Angeles)

  • William Van Der Wey

    (University of California, Los Angeles)

  • Jiem R. Ronas

    (University of California, Los Angeles)

  • Benjamin Statz

    (University of California, Los Angeles)

  • Douglas Yao

    (University of California, Los Angeles
    Harvard Medical School)

  • Velislava Petrova

    (Wellcome Trust Sanger Institute)

  • Alex Zelikovsky

    (Georgia State University
    I.M. Sechenov First Moscow State Medical University)

  • Roberto Spreafico

    (Institute for Quantitative and Computational Biosciences, University of California, Los Angeles)

  • Sagiv Shifman

    (The Institute of Life Sciences, The Hebrew University of Jerusalem)

  • Noah Zaitlen

    (University of California, San Francisco)

  • Maura Rossetti

    (David Geffen School of Medicine, University of California, Los Angeles)

  • K. Mark Ansel

    (University of California, San Francisco)

  • Eleazar Eskin

    (University of California, Los Angeles
    David Geffen School of Medicine at UCLA
    David Geffen School of Medicine at UCLA)

  • Serghei Mangul

    (University of California, Los Angeles
    School of Pharmacy, University of Southern California
    Institute for Quantitative and Computational Biosciences, University of California, Los Angeles)

Abstract

Profiling immunoglobulin (Ig) receptor repertoires with specialized assays can be cost-ineffective and time-consuming. Here we report ImReP, a computational method for rapid and accurate profiling of the Ig repertoire, including the complementary-determining region 3 (CDR3), using regular RNA sequencing data such as those from 8,555 samples across 53 tissues types from 544 individuals in the Genotype-Tissue Expression (GTEx v6) project. Using ImReP and GTEx v6 data, we generate a collection of 3.6 million Ig sequences, termed the atlas of immunoglobulin repertoires (TAIR), across a broad range of tissue types that often do not have reported Ig repertoires information. Moreover, the flow of Ig clonotypes and inter-tissue repertoire similarities across immune-related tissues are also evaluated. In summary, TAIR is one of the largest collections of CDR3 sequences and tissue types, and should serve as an important resource for studying immunological diseases.

Suggested Citation

  • Igor Mandric & Jeremy Rotman & Harry Taegyun Yang & Nicolas Strauli & Dennis J. Montoya & William Van Der Wey & Jiem R. Ronas & Benjamin Statz & Douglas Yao & Velislava Petrova & Alex Zelikovsky & Rob, 2020. "Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16857-7
    DOI: 10.1038/s41467-020-16857-7
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