Abstract
The benefits of ancestry informative SNP (AISNP) panels can best accrue and be properly evaluated only as sufficient reference population data become readily accessible. Ideally the set of reference populations should approximate the genetic diversity of human populations worldwide. The Kidd and Seldin AISNP sets are two panels that have separately accumulated thus far the largest and most diverse collections of data on human reference populations from the major continental regions. A recent tally in the ALFRED allele frequency database finds 164 reference populations available for all the 55 Kidd AISNPs and 132 reference populations for all the 128 Seldin AISNPs. Although much more of the genetic diversity in human populations around the world still needs to be documented, 81 populations have genotype data available for all 170 AISNPs in the union of the Kidd and Seldin panels. In this report we examine admixture and principal component analyses on these 81 worldwide populations and some regional subsets of these reference populations to determine how well the combined panel illuminates population relationships. Analyses of this dataset that focused on Native American populations revealed very strong cluster patterns associated with many of the individual populations studied.
Highlights
The benefits of ancestry informative SNP (AISNP) panels can best accrue and be properly evaluated only as sufficient reference population data become readily accessible
The potential utility of ancestry informative markers (AIMs), especially ancestry informative SNPs (AISNPS), for forensic, anthropological, and medical applications has been reflected in part by a large number of research reports
A recent tally from the ALlele FREquency Database (ALFRED: https//alfred.med.yale.edu) and the Forensic Reference-Resource on Genetics knowledge base (FROG-kb: https//frog.med.yale.edu) shows that complete frequency data have accumulated on 132 reference populations for the 128 Seldin AISNPs and on 164 reference populations for the 55 Kidd AISNPs
Summary
The benefits of ancestry informative SNP (AISNP) panels can best accrue and be properly evaluated only as sufficient reference population data become readily accessible. The benefits of particular AISNP and other AIM panels can only accrue and be properly evaluated as the data for them accumulate and become readily accessible on a large number of reference populations approximating the genetic diversity of human populations worldwide. We report selected analyses not previously presented on 81 population samples that have genotypes and allele frequencies available for 170 markers This represents the union of SNPs in two of the AISNP panels that are among the few AIM panels that have been studied on a large number of diverse human populations. We note that a commercial kit, the ThermoFisher Precision ID Ancestry panel, is based on the union of these two panels and includes 165 of the full 170 AISNPs. In recent years an increasing number of studies have appeared reporting SNP frequencies and/or genotypes for this panel (see e.g. our recent paper[14] citing six of these studies). Populations with data for all 170 SNPs are included here
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