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Open Access Research article

Identification of a small optimal subset of CpG sites as bio-markers from high-throughput DNA methylation profiles

Hailong Meng1, Edward L Murrelle2 and Guoya Li2*

Author Affiliations

1 Scientific Division, ClearPoint Resources Inc., Richmond, VA 23219, USA

2 Life Sciences Research, Altria Client Services, Richmond, VA 23219, USA

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BMC Bioinformatics 2008, 9:457  doi:10.1186/1471-2105-9-457

Published: 27 October 2008



DNA methylation patterns have been shown to significantly correlate with different tissue types and disease states. High-throughput methylation arrays enable large-scale DNA methylation analysis to identify informative DNA methylation biomarkers. The identification of disease-specific methylation signatures is of fundamental and practical interest for risk assessment, diagnosis, and prognosis of diseases.


Using published high-throughput DNA methylation data, a two-stage feature selection method was developed to select a small optimal subset of DNA methylation features to precisely classify two sample groups. With this approach, a small number of CpG sites were highly sensitive and specific in distinguishing lung cancer tissue samples from normal lung tissue samples.


This study shows that it is feasible to identify DNA methylation biomarkers from high-throughput DNA methylation profiles and that a small number of signature CpG sites can suffice to classify two groups of samples. The computational method we developed in the study is efficient to identify signature CpG sites from disease samples with complex methylation patterns.