Ancestry analysis of BAC clones that are the source of the human genome reference sequence across the chromosome 1 locus.

<p>The human genome reference sequence across the admixture peak is pieced together from 5 BAC clones, which turn out to be a mosaic of European and African ancestry. To determine ancestry, we examined the haplotype of the human genome reference sequence for 284 SNPs for which data are available from the International Haplotype Map Project, and then output the ratio of the number of perfect matches to the reference sequence haplotype in 120 European American to the number of perfect matches in 120 West African chromosomes (conservatively adding 1 to the counts). Values above 10 indicate strong (>10∶1) evidence for a European haplotype, and values below 0.1 indicate strong (<1∶10) evidence for an African haplotype. RPCI-11, the individual who is the source of ∼74% of the human genome reference sequence, has two clones of entirely African and two clones of entirely European ancestry at this locus, strongly indicating that the human genome reference sequence is primarily that of an African American. We included these BAC clones in our search for polymorphisms across the admixture peak that were consistent with being fixed in frequency between European and African populations.