Towards Personalized Medicine: Using Bayesian Methods in Genome-enabled Prediction of Complex Human Diseases — ASN Events

Towards Personalized Medicine: Using Bayesian Methods in Genome-enabled Prediction of Complex Human Diseases (#140)

Sylvia Young 1 , Daniel Gianola 2 , Grant Morahan 1
  1. Centre for Medical Research, The University of Western Australia, Nedlands, WA, Australia
  2. Departments of Animal Sciences and Biostatistics & Medical Informatics, The University of Wisconsin-Madison, Madison, WI, the United States of America

Genome-wide genotyping data have opened the prospect of precision medicine and disease prevention by developing tests specific for individual subjects' specific set of genetic variants. Conventional GWAS [1] [2] have been hugely successful over the past decade in detecting specific single nucleotide polymorphisms (SNPs)  in association with many diseases [3] [4] and traits of interest [5]. The challenge in the post-GWAS era is to develop new methods to implement precision medicine and prediction of disease risk.

We have used novel methods of prediction using whole genome-enabled Bayesian and other models. In contrast to univariate approaches (as implemented in GWAS),  genomic prediction models have multivariate characteristics enabling them to avoid colinearity between SNPs, which was known as a drawback of GWAS.  As is well known, prior probability density functions of biomarker effects [6] have been playing a key role in Bayesian methods. In this work we assigned a mixture of linear and Gaussian distribution on the marker effects. We illustrate the model setup and the performance of genome-enabled models in predicting human disease outcomes by using later-onset Alzheimer's disease dataset as an example. Proposed Bayesian models have shown superb predictive capability than ordinary linear models, and have identified novel mutations that could not have been found by traditional analysis methods.

  1. Pearson TA, Manolio TA (March 2008). "How to interpret a genome-wide association study". JAMA. 299 (11): 1335–44
  2. "Genome-Wide Association Studies". National Human Genome Research Institute
  3. Wellcome Trust Case Control Consortium, Burton PR; Clayton DG; Cardon LR; et al. (June 2007). "Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls". Nature. 447 (7145): 661–78
  4. Manolio TA, Guttmacher, AE, Manolio TA. (July 2010). "Genomewide association studies and assessment of the risk of disease". N. Engl. J. Med. 363 (2): 166–76
  5. Strawbridge RJ, Dupuis J, Prokopenko I, Barker A, et al. (October 2011). "Genome-Wide Association Identifies Nine Common Variants Associated With Fasting Proinsulin Levels and Provides New Insights Into the Pathophysiology of Type 2 Diabetes". Diabetes. 60 (10)
  6. Gianola D (July 2013). "Priors in whole-genome regression: the Bayesian alphabet returns", Genetics, v149(3) : 573-96
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