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J Comput Biol. 2016 Jun;23(6):483-94. doi: 10.1089/cmb.2016.0010. Epub 2016 May 5.

Immunoglobulin Classification Using the Colored Antibody Graph.

Author information

1
1 Bioinformatics and Systems Biology Program, University of California San diego , La Jolla, California.
2
2 Department of Computer Science and Engineering, University of California San diego , La Jolla, California.

Abstract

The somatic recombination of V, D, and J gene segments in B-cells introduces a great deal of diversity, and divergence from reference segments. Many recent studies of antibodies focus on the population of antibody transcripts that show which V, D, and J gene segments have been favored for a particular antigen, a repertoire. To properly describe the antibody repertoire, each antibody must be labeled by its constituting V, D, and J gene segment, a task made difficult by somatic recombination and hypermutation events. While previous approaches to repertoire analysis were based on sequential alignments, we describe a new de Bruijn graph-based algorithm to perform VDJ labeling and benchmark its performance.

KEYWORDS:

antibody repertoire analysis; de Bruijn graph; immunoglobulin classification

PMID:
27149636
PMCID:
PMC4904161
DOI:
10.1089/cmb.2016.0010
[Indexed for MEDLINE]
Free PMC Article

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