Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing

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; Roberto Spreafico; Sagiv Shifman; Noah Zaitlen; Maura Rossetti; K. Mark Ansel; Eleazar Eskin; Serghei Mangul

doi:10.1038/s41467-020-16857-7

Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing

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, Roberto Spreafico, Sagiv Shifman, Noah Zaitlen, Maura Rossetti, K. Mark Ansel, Eleazar Eskin, Serghei Mangul^*

^*Corresponding author for this work

Department of Genetics

Research output: Contribution to journal › Article › peer-review

44 Scopus citations

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.

Original language	English
Article number	3126
Journal	Nature Communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-16857-7
State	Published - 1 Dec 2020

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Publisher Copyright:
© 2020, The Author(s).

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Mandric, I., Rotman, J., Yang, H. T., Strauli, N., Montoya, D. J., Van Der Wey, W., Ronas, J. R., Statz, B., Yao, D., Petrova, V., Zelikovsky, A., Spreafico, R., Shifman, S., Zaitlen, N., Rossetti, M., Ansel, K. M., Eskin, E., & Mangul, S. (2020). Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing. Nature Communications, 11(1), Article 3126. https://doi.org/10.1038/s41467-020-16857-7

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title = "Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing",

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.",

author = "Igor Mandric and Jeremy Rotman and Yang, {Harry Taegyun} and Nicolas Strauli and Montoya, {Dennis J.} and {Van Der Wey}, William and Ronas, {Jiem R.} and Benjamin Statz and Douglas Yao and Velislava Petrova and Alex Zelikovsky and Roberto Spreafico and Sagiv Shifman and Noah Zaitlen and Maura Rossetti and Ansel, {K. Mark} and Eleazar Eskin and Serghei Mangul",

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Mandric, I, Rotman, J, Yang, HT, Strauli, N, Montoya, DJ, Van Der Wey, W, Ronas, JR, Statz, B, Yao, D, Petrova, V, Zelikovsky, A, Spreafico, R, Shifman, S, Zaitlen, N, Rossetti, M, Ansel, KM, Eskin, E & Mangul, S 2020, 'Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing', Nature Communications, vol. 11, no. 1, 3126. https://doi.org/10.1038/s41467-020-16857-7

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AU - Mandric, Igor

AU - Rotman, Jeremy

AU - Yang, Harry Taegyun

AU - Strauli, Nicolas

AU - Montoya, Dennis J.

AU - Van Der Wey, William

AU - Ronas, Jiem R.

AU - Statz, Benjamin

AU - Yao, Douglas

AU - Petrova, Velislava

AU - Zelikovsky, Alex

AU - Spreafico, Roberto

AU - Shifman, Sagiv

AU - Zaitlen, Noah

AU - Rossetti, Maura

AU - Ansel, K. Mark

AU - Eskin, Eleazar

AU - Mangul, Serghei

PY - 2020/12/1

Y1 - 2020/12/1

N2 - 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.

AB - 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.

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Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing

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