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BMC Bioinformatics. 2012;13 Suppl 14:S2. doi: 10.1186/1471-2105-13-S14-S2. Epub 2012 Sep 7.

Bag of Naïve Bayes: biomarker selection and classification from genome-wide SNP data.

Author information

1
Department of Information Engineering, University of Padova, 35131 Padova, Italy.

Abstract

BACKGROUND:

Multifactorial diseases arise from complex patterns of interaction between a set of genetic traits and the environment. To fully capture the genetic biomarkers that jointly explain the heritability component of a disease, thus, all SNPs from a genome-wide association study should be analyzed simultaneously.

RESULTS:

In this paper, we present Bag of Naïve Bayes (BoNB), an algorithm for genetic biomarker selection and subjects classification from the simultaneous analysis of genome-wide SNP data. BoNB is based on the Naïve Bayes classification framework, enriched by three main features: bootstrap aggregating of an ensemble of Naïve Bayes classifiers, a novel strategy for ranking and selecting the attributes used by each classifier in the ensemble and a permutation-based procedure for selecting significant biomarkers, based on their marginal utility in the classification process. BoNB is tested on the Wellcome Trust Case-Control study on Type 1 Diabetes and its performance is compared with the ones of both a standard Naïve Bayes algorithm and HyperLASSO, a penalized logistic regression algorithm from the state-of-the-art in simultaneous genome-wide data analysis.

CONCLUSIONS:

The significantly higher classification accuracy obtained by BoNB, together with the significance of the biomarkers identified from the Type 1 Diabetes dataset, prove the effectiveness of BoNB as an algorithm for both classification and biomarker selection from genome-wide SNP data.

AVAILABILITY:

Source code of the BoNB algorithm is released under the GNU General Public Licence and is available at http://www.dei.unipd.it/~sambofra/bonb.html.

PMID:
23095127
PMCID:
PMC3439675
DOI:
10.1186/1471-2105-13-S14-S2
[Indexed for MEDLINE]
Free PMC Article

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