Admixture Aberration Analysis: Application to Mapping in Admixed Population Using Pooled DNA

作者：Bercovici Sivan^*; Geiger Dan

来源：Journal of Computational Biology, 2011, 18(3): 237-249.

DOI：10.1089/cmb.2010.0250

• computational molecular biology
• genetic mapping
• genetic variation
• machine learning
• Markov chains

Admixture mapping is a gene mapping approach used for the identification of genomic regions harboring disease susceptibility genes in the case of recently admixed populations such as African Americans. We present a novel method for admixture mapping, called admixture aberration analysis (AAA) that uses a DNA pool of affected admixed individuals. We demonstrate through simulations that AAA is a powerful and economical mapping method under a range of scenarios, capturing complex human diseases such as hypertension and end-stage kidney disease. The method has a low false-positive rate and is robust to deviation from model assumptions. Finally, we apply AAA on 600 prostate cancer-affected African Americans, replicating a known risk locus. Simulation results indicate that the method can yield over 96% reduction in genotyping. Our method is implemented as a Java program called AAAmap and is freely available at http://bioinfo.cs.technion.ac.il/AAAmap.

• 出版日期2011-3