publication . Article . 2009

Predictive modeling in case-control single-nucleotide polymorphism studies in the presence of population stratification: a case study using Genetic Analysis Workshop 16 Problem 1 dataset.

Arshadi, Niloofar; Chang, Billy; Kustra, Rafal;
Open Access
  • Published: 01 Dec 2009 Journal: BMC Proceedings, volume 3, page S60 (issn: 1753-6561, Copyright policy)
  • Publisher: Springer Nature
In this paper, we apply the gradient-boosting machine predictive model to the rheumatoid arthritis data for predicting the case-control status. QQ-plot suggests severe population stratification. In univariate genome-wide association studies, a correction factor for ethnicity confounding can be derived. Here we propose a novel strategy to deal with population stratification in the context of multivariate predictive modeling. We address the problem by clustering the subjects on the axes of genetic variations, and building a predictive model separately in each cluster. This allows us to control ethnicity without explicitly including it in the model, which could mar...
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Medicine, Medicine, business.industry, business, Population stratification, Statistics, Genetic variation, Cluster analysis, Genetic association, Univariate, Multivariate statistics, Bioinformatics, Single-nucleotide polymorphism, Confounding, Proceedings
Related Organizations
Funded by
  • Funder: Wellcome Trust (WT)
NIH| Genetic Analysis of Common Diseases: An Evaluation
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM031575-22

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