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Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing.
Mandric, Igor; Rotman, Jeremy; Yang, Harry Taegyun; Strauli, Nicolas; Montoya, Dennis J; Van Der Wey, William; Ronas, Jiem R; Statz, Benjamin; Yao, Douglas; Petrova, Velislava; Zelikovsky, Alex; Spreafico, Roberto; Shifman, Sagiv; Zaitlen, Noah; Rossetti, Maura; Ansel, K Mark; Eskin, Eleazar; Mangul, Serghei.
Affiliation
  • Mandric I; Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.
  • Rotman J; Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.
  • Yang HT; Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1540 Alcazar Street, Los Angeles, CA, 90033, USA.
  • Strauli N; Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.
  • Montoya DJ; Bioinformatics Interdepartmental Ph.D. Program, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA, 90095-1570, USA.
  • Van Der Wey W; Biomedical Sciences Graduate Program, University of California, San Francisco, 1675 Owens Street, Suite 310, San Francisco, CA, 94143-0523, USA.
  • Ronas JR; Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.
  • Statz B; Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.
  • Yao D; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, 609 Charles E. Young Drive East, Los Angeles, CA, 90095, USA.
  • Petrova V; Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.
  • Zelikovsky A; Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.
  • Spreafico R; Program in Bioinformatics and Integrative Genomics, Harvard Medical School, 10 Shattuck Street, Suite 514, Boston, MA, 02115, USA.
  • Shifman S; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
  • Zaitlen N; Department of Computer Science, Georgia State University, 33 Gilmer Street SE, Atlanta, GA, 30303, USA.
  • Rossetti M; The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
  • Ansel KM; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA, 90095, USA.
  • Eskin E; Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
  • Mangul S; Department of Medicine, University of California, San Francisco, 533 Parnassus Avenue, San Francisco, CA, 94143, USA.
Nat Commun ; 11(1): 3126, 2020 06 19.
Article in En | MEDLINE | ID: mdl-32561710
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Computational Biology / Complementarity Determining Regions / RNA-Seq Limits: Humans Language: En Journal: Nat Commun Journal subject: BIOLOGIA / CIENCIA Year: 2020 Document type: Article Affiliation country: United States
Fulltext
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Computational Biology / Complementarity Determining Regions / RNA-Seq Limits: Humans Language: En Journal: Nat Commun Journal subject: BIOLOGIA / CIENCIA Year: 2020 Document type: Article Affiliation country: United States