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Statistical Applications in Genetics and Molecular Biology

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Volume 11, Issue 3 (Feb 2012)

Non-Iterative, Regression-Based Estimation of Haplotype Associations with Censored Survival Outcomes

Benjamin French
  • University of Pennsylvania
/ Thomas Lumley
  • University of Auckland
/ Thomas P. Cappola
  • University of Pennsylvania
/ Nandita Mitra
  • University of Pennsylvania
Published Online: 2012-02-15 | DOI: https://doi.org/10.1515/1544-6115.1764

The general availability of reliable and affordable genotyping technology has enabled genetic association studies to move beyond small case-control studies to large prospective studies. For prospective studies, genetic information can be integrated into the analysis via haplotypes, with focus on their association with a censored survival outcome. We develop non-iterative, regression-based methods to estimate associations between common haplotypes and a censored survival outcome in large cohort studies. Our non-iterative methods—weighted estimation and weighted haplotype combination—are both based on the Cox regression model, but differ in how the imputed haplotypes are integrated into the model. Our approaches enable haplotype imputation to be performed once as a simple data-processing step, and thus avoid implementation based on sophisticated algorithms that iterate between haplotype imputation and risk estimation. We show that non-iterative weighted estimation and weighted haplotype combination provide valid tests for genetic associations and reliable estimates of moderate associations between common haplotypes and a censored survival outcome, and are straightforward to implement in standard statistical software. We apply the methods to an analysis of HSPB7-CLCNKA haplotypes and risk of adverse outcomes in a prospective cohort study of outpatients with chronic heart failure.

Keywords: Cox regression; phase ambiguity; prospective study; unphased genotypes

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Published Online: 2012-02-15

Citation Information: Statistical Applications in Genetics and Molecular Biology, ISSN (Online) 1544-6115, DOI: https://doi.org/10.1515/1544-6115.1764. Export Citation

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