publication . Article . 2005

Cluster analysis and association study of structured multilocus genotype data

Akira Shoji; Takahiro Nakamura; Naoyuki Kamatani; Hironori Fujisawa;
Open Access
  • Published: 04 Feb 2005 Journal: Journal of Human Genetics, volume 50, pages 53-61 (issn: 1434-5161, eissn: 1435-232X, Copyright policy)
  • Publisher: Springer Science and Business Media LLC
Abstract
We propose an algorithm for testing association using structured multilocus genotype data. The algorithm implements the clustering of the data by a hierarchical clustering technique and a k-means algorithm. After clustering, the program analyzes all the clusters together using the Mantel–Haenszel (MH) test, by which common associations in the clusters are examined. To use the MH test, the number of subpopulations has to be determined. A method of cross-validation (CV) and the k-means algorithm are applied for estimating the number of subpopulations. The algorithm described was implemented in the computer program POPSTRUCT. In the simulation study, we found that ...
Subjects
free text keywords: Genetics(clinical), Genetics, Bioinformatics, Genotype, k-means clustering, Population, education.field_of_study, education, Locus (genetics), Allele frequency, Minor allele frequency, Cluster analysis, Mathematics, Statistics, Hierarchical clustering
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