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This article is part of the supplement: Selected articles from the Second Annual Translational Bioinformatics Conference (TBC 2012)

Open Access Research

Diplotyper: diplotype-based association analysis

Sunshin Kim1, KyungChae Park2, Chol Shin3, Nam H Cho4, Jeong-Jae Ko1, InSong Koh5* and KyuBum Kwack1*

Author Affiliations

1 Department of Biomedical Science, College of Life Science, CHA University, Seongnam, Korea

2 Department of Family Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Korea

3 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Ansan, Korea

4 Department of Preventive Medicine, Ajou University School of Medicine, Suwon, Korea

5 Department of Physiology, College of Medicine, Hanyang University, Seoul, Korea

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BMC Medical Genomics 2013, 6(Suppl 2):S5  doi:10.1186/1755-8794-6-S2-S5

Published: 7 May 2013



It was previously reported that an association analysis based on haplotype clusters increased power over single-locus tests, and that another association test based on diplotype trend regression analysis outperformed other, more common association approaches. We suggest a novel algorithm to combine haplotype cluster- and diplotype-based analyses.


Diplotyper combines a novel algorithm designed to cluster haplotypes of interest from a given set of haplotypes with two existing tools: Haploview, for analyses of linkage disequilibrium blocks and haplotypes, and PLINK, to generate all possible diplotypes from given genotypes of samples and calculate linear or logistic regression. In addition, procedures for generating all possible diplotypes from the haplotype clusters and transforming these diplotypes into PLINK formats were implemented.


Diplotyper is a fully automated tool for performing association analysis based on diplotypes in a population. Diplotyper was tested through association analysis of hepatic lipase (LIPC) gene polymorphisms or diplotypes and levels of high-density lipoprotein (HDL) cholesterol.


Diplotyper is useful for identifying more precise and distinct signals over single-locus tests.