Identification of 400 Ancestry-Informative Markers (AIMs) for DNA Forensics
We have assembled a set of
400 single nucleotide polymorphisms (SNPs)
that are highly informative on the continental origin of a human DNA sample.
All of these ancestry-informative markers (AIMs) have off-the-shelf ABI TaqMan assays for genotyping on a real-time PCR machine found in
most forensics laboratories.
Evaluating AIMs with the Perlegen genotype data set
To demonstrate the effectiveness of these AIMs for identifying probable continent of origin, we simulated a forensic
experiment using freely available genotype data from Perlegen Sciences. In a 2005 study, Perlegen genotyped 1,586,383 SNPs across the human genome in
71 Americans of European, African, and Asian ancestry. 178 of their SNPs were in our AIM set. We predicted the probable continent of origin for each of the
Perlegen samples using their AIM genotypes. Just 10 of our AIMs were sufficient to predict continental origins of Perlegen samples with 100% accuracy (Figure 1).
Figure 1. Accuracy of continent-of-origin predictions for Perlegen samples based on AIM genotypes. Correct predictions
were "African" for the African-American samples, "European" for the European-American samples, and "Chinese" for the Chinese-American samples.
Methods for AIM identification and selection
We began with the 5,287 "Most Informative" AIMs identified by Tian et al., filtering out SNPs with ambiguous alleles (G/C or A/T) or those lacking frequency
data from the International HapMap Project. Next, we selected the 100 most divergent SNPs for each HapMap panel comparison
(CEU-CHB, CEU-JPT, CEU-YRI, CHB-JPT, YRI-CHB, YRI-JPT), yielding 600 SNPs. Of these, some 549 had existing ABI TaqMan assays. We sorted assayable AIMs by their
ability to distinguish among all four panels; the 400 best assayable AIMs were selected for our set.
|
