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Clique-Based Clustering of Correlated SNPs in a Gene Can Improve Performance of Gene-Based Multi-Bin Linear Combination Test
Joint Authors
Yoo, Yun Joo
Kim, Sun Ah
Bull, Shelley B.
Source
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-08-04
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Abstract EN
Gene-based analysis of multiple single nucleotide polymorphisms (SNPs) in a gene region is an alternative to single SNP analysis.
The multi-bin linear combination test (MLC) proposed in previous studies utilizes the correlation among SNPs within a gene to construct a gene-based global test.
SNPs are partitioned into clusters of highly correlated SNPs, and the MLC test statistic quadratically combines linear combination statistics constructed for each cluster.
The test has degrees of freedom equal to the number of clusters and can be more powerful than a fully quadratic or fully linear test statistic.
In this study, we develop a new SNP clustering algorithm designed to find cliques, which are complete subnetworks of SNPs with all pairwise correlations above a threshold.
We evaluate the performance of the MLC test using the clique-based CLQ algorithm versus using the tag-SNP-based LDSelect algorithm.
In our numerical power calculations we observed that the two clustering algorithms produce identical clusters about 40~60% of the time, yielding similar power on average.
However, because the CLQ algorithm tends to produce smaller clusters with stronger positive correlation, the MLC test is less likely to be affected by the occurrence of opposing signs in the individual SNP effect coefficients.
American Psychological Association (APA)
Yoo, Yun Joo& Kim, Sun Ah& Bull, Shelley B.. 2015. Clique-Based Clustering of Correlated SNPs in a Gene Can Improve Performance of Gene-Based Multi-Bin Linear Combination Test. BioMed Research International،Vol. 2015, no. 2015, pp.1-11.
https://search.emarefa.net/detail/BIM-1057002
Modern Language Association (MLA)
Yoo, Yun Joo…[et al.]. Clique-Based Clustering of Correlated SNPs in a Gene Can Improve Performance of Gene-Based Multi-Bin Linear Combination Test. BioMed Research International No. 2015 (2015), pp.1-11.
https://search.emarefa.net/detail/BIM-1057002
American Medical Association (AMA)
Yoo, Yun Joo& Kim, Sun Ah& Bull, Shelley B.. Clique-Based Clustering of Correlated SNPs in a Gene Can Improve Performance of Gene-Based Multi-Bin Linear Combination Test. BioMed Research International. 2015. Vol. 2015, no. 2015, pp.1-11.
https://search.emarefa.net/detail/BIM-1057002
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1057002