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Does replication groups scoring reduce false positive rate in SNP interaction discovery?

Marko Toplak and Tomaz Curk and Janez Demsar and Blaz Zupan (2010) Does replication groups scoring reduce false positive rate in SNP interaction discovery?. BMC Genomics, 11 . p. 58.

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    BACKGROUNG. Computational methods that infer single nucleotide polymorphism (SNP) interactions from phenotype data may uncover new biological mechanisms in non-Mendelian diseases. However, practical aspects of such analysis face many problems. Present experimental studies typically use SNP arrays with hundreds of thousands of SNPs but record only hundreds of samples. Candidate SNP pairs inferred by interaction analysis may include a high proportion of false positives. Recently, Gayan et al. (2008) proposed to reduce the number of false positives by combining results of interaction analysis performed on subsets of data (replication groups), rather than analyzing the entire data set directly. If performing as hypothesized, replication groups scoring could improve interaction analysis and also any type of feature ranking and selection procedure in systems biology. Because Gayan et al. do not compare their approach to the standard interaction analysis techniques, we here investigate if replication groups indeed reduce the number of reported false positive interactions. RESULTS. A set of simulated and false interaction-imputed experimental SNP data sets were used to compare the inference of SNP-SNP interactions by means of replication groups to the standard approach where the entire data set was directly used to score all candidate SNP pairs. In all our experiments, the inference of interactions from the entire data set (e.g. without using the replication groups) reported fewer false positives. CONCLUSIONS. With respect to the direct scoring approach the utility of replication groups does not reduce false positive rates, and may, depending on the data set, often perform worse.

    Item Type: Article
    Keywords: SNP interactions, epistasis, feature selection, replication groups scoring, interaction discovery, data mining, genomics
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    Institution: University of Ljubljana
    Department: Faculty of Computer and Information Science
    Divisions: Faculty of Computer and Information Science > Artificial Intelligence Laboratory
    Item ID: 1016
    Date Deposited: 19 Feb 2010 09:42
    Last Modified: 05 Dec 2013 14:26
    URI: http://eprints.fri.uni-lj.si/id/eprint/1016

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