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Open Access Methodology article

Construction of gene clusters resembling genetic causal mechanisms for common complex disease with an application to young-onset hypertension

Ke-Shiuan Lynn1, Chen-Hua Lu1, Han-Ying Yang1, Wen-Lian Hsu1 and Wen-Harn Pan23*

Author Affiliations

1 Institute of Information Science, Academia Sinica, Taipei, Taiwan

2 Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan

3 National Health Research Institutes, Mialoli, Taiwan

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BMC Genomics 2013, 14:497  doi:10.1186/1471-2164-14-497

Published: 23 July 2013

Abstract

Background

Lack of power and reproducibility are caveats of genetic association studies of common complex diseases. Indeed, the heterogeneity of disease etiology demands that causal models consider the simultaneous involvement of multiple genes. Rothman’s sufficient-cause model, which is well known in epidemiology, provides a framework for such a concept. In the present work, we developed a three-stage algorithm to construct gene clusters resembling Rothman’s causal model for a complex disease, starting from finding influential gene pairs followed by grouping homogeneous pairs.

Results

The algorithm was trained and tested on 2,772 hypertensives and 6,515 normotensives extracted from four large Caucasian and Taiwanese databases. The constructed clusters, each featured by a major gene interacting with many other genes and identified a distinct group of patients, reproduced in both ethnic populations and across three genotyping platforms. We present the 14 largest gene clusters which were capable of identifying 19.3% of hypertensives in all the datasets and 41.8% if one dataset was excluded for lack of phenotype information. Although a few normotensives were also identified by the gene clusters, they usually carried less risky combinatory genotypes (insufficient causes) than the hypertensive counterparts. After establishing a cut-off percentage for risky combinatory genotypes in each gene cluster, the 14 gene clusters achieved a classification accuracy of 82.8% for all datasets and 98.9% if the information-short dataset was excluded. Furthermore, not only 10 of the 14 major genes but also many other contributing genes in the clusters are associated with either hypertension or hypertension-related diseases or functions.

Conclusions

We have shown with the constructed gene clusters that a multi-causal pie-multi-component approach can indeed improve the reproducibility of genetic markers for complex disease. In addition, our novel findings including a major gene in each cluster and sufficient risky genotypes in a cluster for disease onset (which coincides with Rothman’s sufficient cause theory) may not only provide a new research direction for complex diseases but also help to reveal the disease etiology.

Keywords:
Genetic causal mechanism; Sufficient cause; Data-mining; Young-onset hypertension; Complex disease