Research

A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data

Lung-Cheng Huang^1,2* , Sen-Yen Hsu^3* and Eugene Lin⁴

¹  Department of Psychiatry, National Taiwan University Hospital Yun-Lin Branch, Taiwan

²  Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan

³  Department of Psychiatry, Chi Mei Medical Center, Liouying, Tainan, Taiwan

⁴  Vita Genomics, Inc, 7 Fl, No 6, Sec 1, Jung-Shing Road, Wugu Shiang, Taipei, Taiwan

author email corresponding author email* Contributed equally

Journal of Translational Medicine 2009, 7:81doi:10.1186/1479-5876-7-81

Published:	22 September 2009

Abstract

Background

In the studies of genomics, it is essential to select a small number of genes that are more significant than the others for the association studies of disease susceptibility. In this work, our goal was to compare computational tools with and without feature selection for predicting chronic fatigue syndrome (CFS) using genetic factors such as single nucleotide polymorphisms (SNPs).

Methods

We employed the dataset that was original to the previous study by the CDC Chronic Fatigue Syndrome Research Group. To uncover relationships between CFS and SNPs, we applied three classification algorithms including naive Bayes, the support vector machine algorithm, and the C4.5 decision tree algorithm. Furthermore, we utilized feature selection methods to identify a subset of influential SNPs. One was the hybrid feature selection approach combining the chi-squared and information-gain methods. The other was the wrapper-based feature selection method.

Results

The naive Bayes model with the wrapper-based approach performed maximally among predictive models to infer the disease susceptibility dealing with the complex relationship between CFS and SNPs.

Conclusion

We demonstrated that our approach is a promising method to assess the associations between CFS and SNPs.