In this article, we compared various methods for selecting ancestry informative SNPs using simulations as well as SNP genotype data from samples of admixed populations and showed that the In measure estimates ancestry proportion (in an admixed population) with lower bias and mean square error.
Ethnic outliers were identified by multi-dimensional scaling, combining the iCOGS data with the three Hapmap2 populations, based on a subset of 37 000 uncorrelated markers that passed QC (including ∼1000 selected as ancestry informative markers).
Ethnic outliers were identified by multidimensional scaling, combining the iCOGS array data with the three Hapmap2 populations, based on a subset of 37,000 uncorrelated markers that passed quality control (including ~1,000 selected as ancestry informative markers).
For visualization of results in Figure 1, we selected the ancestry groups that most closely corresponded in the PC space to the Caucasian American women of our sample; these groups included the Italians, Tuscans, French, Orcadians, Russians, Adygei, Spanish, and Ashkenazi Jews.
In the second step, we selected key ancestry-predictive g-eQTL from the sets of g-eQTL identified in "CHB or JPT", "CHB and JPT", or "CHB-specific or JPT-specific" through a classification analysis, using BIASLESS software.
The choice of which of these measures to use should depend on the efficiency of each measure in selecting most ancestry informative markers.
We then ranked the participant list by "gh variants", "coding variants", and "total variants" to create an overall ranking beyond the participants already selected because of ancestry and actionable indications.
BF selected and verified ancestry of the animals used in this study, supervised all of the data analysis, designed and analyzed the SNP genotype assay and wrote the manuscript.
In our race- and ethnicity-matched study population, we have previously calculated genetic ancestry on the basis of a panel of 96 ancestry informative markers selected to distinguish continental origin among California Hispanics [ 19].
Several measures of marker informativeness for ancestry have been developed to select the most ancestry informative markers (reviewed in Rosenberg et al., 2003 [ 10]) from an ever-increasing wealth of genomic databases [ 15- 18].
