Article

Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays

Department of Biochemistry, Stanford Genome Technology Center, Stanford University, Stanford, California, USA.
Journal of the American Medical Informatics Association (Impact Factor: 3.93). 06/2012; 19(e1):e21-e27. DOI: 10.1136/amiajnl-2011-000737
Source: PubMed

ABSTRACT Objective
We investigated the common-disease relevant information obtained from sequencing compared with that reported from genotyping arrays.

Materials and methods
Using 187 publicly available individual human genomes, we constructed genomic disease risk summaries based on 55 common diseases with reported gene–disease associations in the research literature using two different risk models, one based on the product of likelihood ratios and the other on the allelic variant with the maximum associated disease risk. We also constructed risk profiles based on the single nucleotide polymorphisms (SNPs) of these individuals that could be measured or imputed from two common genotyping array platforms.

Results
We show that the model risk predictions derived from sequencing differ substantially from those obtained from the SNPs measured on commercially available genotyping arrays for several different non-monogenic diseases, although high density genotyping arrays give identical results for many diseases.

Conclusions
Our approach may be used to compare the ability of different platforms to probe known genetic risks disease by disease.

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Available from: Alexander A Morgan, Jun 04, 2015
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