A ground truth based comparative study on detecting epistatic SNPs

Li Chen, Guoqiang Yu, David J. Miller, Lei Song, Carl Langefeld, David Herrington, Yongmei Liu, Yue Wang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Genome-wide association studies (GWAS) have been widely applied to identify informative SNPs associated with common and complex diseases. Besides single-SNP analysis, the interaction between SNPs is believed to play an important role in disease risk due to the complex networking of genetic regulations. While many approaches have been proposed for detecting SNP interactions, the relative performance and merits of these methods in practice are largely unclear. In this paper, a ground-truth based comparative study is reported involving 9 popular SNP detection methods using realistic simulation datasets. The results provide general characteristics and guidelines on these methods that may be informative to the biological investigators.

Original languageEnglish (US)
Title of host publicationProceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009
Pages26-31
Number of pages6
DOIs
StatePublished - 2009
Externally publishedYes
Event2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009 - Washington, DC, United States
Duration: Nov 1 2009Nov 4 2009

Other

Other2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009
CountryUnited States
CityWashington, DC
Period11/1/0911/4/09

Fingerprint

Single Nucleotide Polymorphism
Genes
Genome-Wide Association Study
Research Personnel
Guidelines

Keywords

  • Genome-wide association study
  • Single-nucleotide polymorphism
  • SNP interaction

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

Cite this

Chen, L., Yu, G., Miller, D. J., Song, L., Langefeld, C., Herrington, D., ... Wang, Y. (2009). A ground truth based comparative study on detecting epistatic SNPs. In Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009 (pp. 26-31). [5332132] https://doi.org/10.1109/BIBMW.2009.5332132

A ground truth based comparative study on detecting epistatic SNPs. / Chen, Li; Yu, Guoqiang; Miller, David J.; Song, Lei; Langefeld, Carl; Herrington, David; Liu, Yongmei; Wang, Yue.

Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009. 2009. p. 26-31 5332132.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Chen, L, Yu, G, Miller, DJ, Song, L, Langefeld, C, Herrington, D, Liu, Y & Wang, Y 2009, A ground truth based comparative study on detecting epistatic SNPs. in Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009., 5332132, pp. 26-31, 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009, Washington, DC, United States, 11/1/09. https://doi.org/10.1109/BIBMW.2009.5332132
Chen L, Yu G, Miller DJ, Song L, Langefeld C, Herrington D et al. A ground truth based comparative study on detecting epistatic SNPs. In Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009. 2009. p. 26-31. 5332132 https://doi.org/10.1109/BIBMW.2009.5332132
Chen, Li ; Yu, Guoqiang ; Miller, David J. ; Song, Lei ; Langefeld, Carl ; Herrington, David ; Liu, Yongmei ; Wang, Yue. / A ground truth based comparative study on detecting epistatic SNPs. Proceedings - 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2009. 2009. pp. 26-31
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