An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings.

Published

Journal Article

As computational power improves, the application of more advanced machine learning techniques to the analysis of large genome-wide association (GWA) datasets becomes possible. While most traditional statistical methods can only elucidate main effects of genetic variants on risk for disease, certain machine learning approaches are particularly suited to discover higher order and non-linear effects. One such approach is the Random Forests (RF) algorithm. The use of RF for SNP discovery related to human disease has grown in recent years; however, most work has focused on small datasets or simulation studies which are limited.Using a multiple sclerosis (MS) case-control dataset comprised of 300 K SNP genotypes across the genome, we outline an approach and some considerations for optimally tuning the RF algorithm based on the empirical dataset. Importantly, results show that typical default parameter values are not appropriate for large GWA datasets. Furthermore, gains can be made by sub-sampling the data, pruning based on linkage disequilibrium (LD), and removing strong effects from RF analyses. The new RF results are compared to findings from the original MS GWA study and demonstrate overlap. In addition, four new interesting candidate MS genes are identified, MPHOSPH9, CTNNA3, PHACTR2 and IL7, by RF analysis and warrant further follow-up in independent studies.This study presents one of the first illustrations of successfully analyzing GWA data with a machine learning algorithm. It is shown that RF is computationally feasible for GWA data and the results obtained make biologic sense based on previous studies. More importantly, new genes were identified as potentially being associated with MS, suggesting new avenues of investigation for this complex disease.

Full Text

Duke Authors

Cited Authors

  • Goldstein, BA; Hubbard, AE; Cutler, A; Barcellos, LF

Published Date

  • June 14, 2010

Published In

Volume / Issue

  • 11 /

Start / End Page

  • 49 -

PubMed ID

  • 20546594

Pubmed Central ID

  • 20546594

Electronic International Standard Serial Number (EISSN)

  • 1471-2156

International Standard Serial Number (ISSN)

  • 1471-2156

Digital Object Identifier (DOI)

  • 10.1186/1471-2156-11-49

Language

  • eng