Admixture analysis using complete genomes

A paper presented last month at the Genetics 2010 conference:
Complete genome sequencing and analysis of diploid African-American and Mexican-American genomes: implications for personal ancestry reconstruction and multi-ethnic medical genomics. Carlos D. Bustamante. Genetics, Stanford University School of Medicine, Stanford, CA.
Understanding the contribution of rare and common genetic genetic variants to disease susceptibility will likely require multi- and trans-ethnic sequencing studies that compare the genomes of many individuals with and without a particular disease. Of particular importance will be accounting for the role of population stratification at fine scales both in terms of genomic and geographic location. Here, we present results from sequencing, assembly, and genomic analysis of two diploid genomes from Phase 3 HapMap sequenced to ~20X coverage using SoLiD technology. The donor individuals are of Mexican-American and African-American ancestry and represent the first "admixed" genomes to be sequenced to high coverage. We demonstrate that genomic sequencing provides finer resolution of "admixture breakpoints" based on allele frequency estimates from HapMap and TGP. For each admixed genome, we use the distribution of admixture breakpoints to infer the personal admixture history of the sample and patterns of genomic diversity to reconstruct the demographic history of European, African, and Native American continental populations.
Someone involved in the research comments:
the added value of our research is that we can show the approximate number of generations at which the genetic mixing occurred, estimate the rate at which admixture occurred, and understand better the genetic diversity in the ancestral populations.

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