Feature selection using a one dimensional naïve Bayes' classifier increases the accuracy of support vector machine classification of CDR3 repertoires

Mattia Cinelli, Yuxin Sun, Katharine Best, James M. Heather, Shlomit Reich-Zeliger, Eric Shifrut, Nir Friedman, John Shawe-Taylor, Benny Chain*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

49 Scopus citations


Motivation: Somatic DNA recombination, the hallmark of vertebrate adaptive immunity, has the potential to generate a vast diversity of antigen receptor sequences. How this diversity captures antigen specificity remains incompletely understood. In this study we use high throughput sequencing to compare the global changes in T cell receptor β chain complementarity determining region 3 (CDR3β) sequences following immunization with ovalbumin administered with complete Freund's adjuvant (CFA) or CFA alone. Results: The CDR3b sequences were deconstructed into short stretches of overlapping contiguous amino acids. The motifs were ranked according to a one-dimensional Bayesian classifier score comparing their frequency in the repertoires of the two immunization classes. The top ranking motifs were selected and used to create feature vectors which were used to train a support vector machine. The support vector machine achieved high classification scores in a leave-one-out validation test reaching >90% in some cases. Summary: The study describes a novel two-stage classification strategy combining a onedimensional Bayesian classifier with a support vector machine. Using this approach we demonstrate that the frequency of a small number of linear motifs three amino acids in length can accurately identify a CD4 T cell response to ovalbumin against a background response to the complex mixture of antigens which characterize Complete Freund's Adjuvant. Availability and implementation: The sequence data is available at www.ncbi.nlm.nih.gov/sra/? term1/4SRP075893. The Decombinator package is available at github.com/innate2adaptive/ Decombinator. The R package e1071 is available at the CRAN repository https://cran.r-project.org/ web/packages/e1071/index.html.

Original languageAmerican English
Pages (from-to)951-955
Number of pages5
Issue number7
StatePublished - 1 Apr 2017
Externally publishedYes

Bibliographical note

Funding Information:
Mattia Cinelli is supported by a studentship from Microsoft Research. This research was funded by studentships from the UK MRC and the EPSRC and supported by the National Institute for Health Research UCL Hospitals Biomedical Research Centre. This research was supported by grants from the Minerva Foundation with funding from the Federal German Ministry for Education and Research, the I-CORE Program of the Planning and Budgeting Committee and the Israel Science Foundation.

Publisher Copyright:
© The Author 2016. Published by Oxford University Press.


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