HPlus Help

1. What is HPlus?

HPlus is a user-friendly software application for estimating haplotype frequencies, inferring individual haplotypes, and most significantly assessing haplotypic associations with various types of phenotypes. HPlus handles bi-allelic genetic markers such as SNPs, and multi-allelic genetic markers such as microsatellites. HPlus can perform association analysis using

binary phenotypes such as disease status from case-control studies or cohort studies,
continuous outcome(s) such as adulthood heights or biomarkers from clinical follow-up studies, cohort studies, or intervention studies, and
survival outcomes from clinic trials, cohort studies or clinical follow-up studies.

Finally, HPlus allows you to incorporate covariates such as demographic or clinical variables into haplotypic association analyses. These covariates can be treated as confounding variables to be adjusted for during the haplotypic association analysis. In addition you can assess gene-environment interactions between covariates and haplotypes. HPlus also allow users to perform stratified analysis by grouping variables chosen by users.

When working with a large number of markers, which may cover a large region in the genome, over several candidate genes or even whole chromosome, you may define 'marker groupings' to perform group-specific associations. Such marker groupings could be clusters of markers within genes, or per-specific region, or 'haplotype-block' structures defined by other methodologies. In a future version, HPlus will be extended to include haplotype block identification.

Statistical methodologies implemented in HPlus are developed by Lue Ping Zhao and Shuying Sue Li with their collaborators at the Fred Hutchinson Cancer Research Center. See the references for technical papers.

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