BASIC: BCR assembly from single cells

Stefan Canzar, Karlynn E. Neu, Qingming Tang, Patrick C. Wilson, Aly A. Khan

Research output: Contribution to journalArticlepeer-review

63 Scopus citations

Abstract

Motivation: The B-cell receptor enables individual B cells to identify diverse antigens, including bacterial and viral proteins. While advances in RNA-sequencing (RNA-seq) have enabled high throughput profiling of transcript expression in single cells, the unique task of assembling the full-length heavy and light chain sequences from single cell RNA-seq (scRNA-seq) in B cells has been largely unstudied. Results: We developed a new software tool, BASIC, which allows investigators to use scRNA-seq for assembling BCR sequences at single-cell resolution. To demonstrate the utility of our software, we subjected nearly 200 single human B cells to scRNA-seq, assembled the full-length heavy and the light chains, and experimentally confirmed these results by using single-cell primer-based nested PCRs and Sanger sequencing. Availability and Implementation: http://ttic.uchicago.edu/∼aakhan/BASIC Contact: Aakhan@ttic.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Original languageEnglish (US)
Pages (from-to)425-427
Number of pages3
JournalBioinformatics
Volume33
Issue number3
DOIs
StatePublished - Feb 1 2017

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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