Genetic ancestry inference using support vector machines, and the active emergence of a unique American population.

ABSTRACT: We use genotype data from the Marshfield Clinical Research Foundation Personalized Medicine Research Project to investigate genetic similarity and divergence between Europeans and the sampled population of European Americans in Central Wisconsin, USA. To infer recent genetic ancestry of the sampled Wisconsinites, we train support vector machines (SVMs) on the positions of Europeans along top principal components (PCs). Our SVM models partition continent-wide European genetic variance into eight regional classes, which is an improvement over the geographically broader categories of recent ancestry reported by personal genomics companies. After correcting for misclassification error associated with the SVMs (<10%, in all cases), we observe a >14% discrepancy between insular ancestries report

SUBMITTER: Haasl RJ 

PROVIDER: S-EPMC3641388 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature