Chien-Hsun Huang

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Interest is increasing in epistasis as a possible source of the unexplained variance missed by genome-wide association studies. The Genetic Analysis Workshop 16 Group 9 participants evaluated a wide variety of classical and novel analytical methods for detecting epistasis, in both the statistical and machine learning paradigms, applied to both real and(More)
Rheumatoid arthritis (RA, MIM 180300) is a chronic and complex autoimmune disease. Using the North American Rheumatoid Arthritis Consortium (NARAC) data set provided in Genetic Analysis Workshop 16 (GAW16), we used the genotype-trait distortion (GTD) scores and proposed analysis procedures to capture the gene-gene interaction effects of multiple(More)
The genes PTPN22 and HLA-DRB1 have been found by a number of studies to confer an increased risk for rheumatoid arthritis (RA), which indicates that both genes play an important role in RA etiology. It is believed that they not only have strong association with RA individually, but also interact with other related genes that have not been found to have(More)
Both common variants and rare variants are involved in the etiology of most complex diseases in humans. Developments in sequencing technology have led to the identification of a high density of rare variant single-nucleotide polymorphisms (SNPs) on the genome, each of which affects only at most 1% of the population. Genotypes derived from these SNPs allow(More)
Current sequencing technology enables generation of whole genome sequencing data sets that contain a high density of rare variants, each of which is carried by, at most, 5% of the sampled subjects. Such variants are involved in the etiology of most common diseases in humans. These diseases can be studied by relevant longitudinal phenotype traits. Tests for(More)
Many institutionalized patients and their healthcare providers are dissatisfied with current laxative therapy. This study compared therapeutic efficacy, safety, and laxative cost of an herbal formula (CCH1) and lactulose for long stay patients with constipation. In this double-blind, double-dummy, and placebo-controlled trial, we randomized 93 residents(More)
In this study, we analyze the Genetic Analysis Workshop 17 data to identify regions of single-nucleotide polymorphisms (SNPs) that exhibit a significant influence on response rate (proportion of subjects with an affirmative affected status), called the affected ratio, among rare variants. Under the null hypothesis, the distribution of rare variants is(More)
Genome-wide association studies have been successful at identifying common disease variants associated with complex diseases, but the common variants identified have small effect sizes and account for only a small fraction of the estimated heritability for common diseases. Theoretical and empirical studies suggest that rare variants, which are much less(More)
Biodiversity results from multiple evolutionary mechanisms, including genetic variation and natural selection. Whole-genome duplications (WGDs), or polyploidizations, provide opportunities for large-scale genetic modifications. Many evolutionarily successful lineages, including angiosperms and vertebrates, are ancient polyploids, suggesting that WGDs are a(More)
Environment has long been known to play an important part in disease etiology. However, not many genome-wide association studies take environmental factors into consideration. There is also a need for new methods to identify the gene-environment interactions. In this study, we propose a 2-step approach incorporating an influence measure that capturespure(More)