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Minimal SNP Overlap Among Multiple Panels of Ancestry informative Markers Argues for More International Collaboration

NCJ Number
Date Published
July 2016
8 pages
U. Soundararajan, L. B. Yun, M. S. Shi, Kenneth K. Kidd
This article reports on a project that identified 21 largely independent published panels of ancestry informative SNPs (AISNPs) and examined their union of 1,397 SNPs.
The century-old use of genetic markers to determine population relationships has morphed in modern forensics into use of markers to determine the ancestry of an individual from a DNA sample. Researchers have identified sets of SNPs that have frequency differences among populations and many sets of SNPs have been published for the purpose of inferring ancestry. Such inference also requires reference datasets for the particular set of SNPs selected. The current study found that no SNP occurred in more than 6 panels. The 1,397 SNPs in 21 panels yielded a largely empty matrix that is inhibiting progress on more refined ability to infer ancestry for a forensic sample. The most common set of reference populations is the HGDP set of 52 small population samples totaling a thousand individuals. Only 46 (3 percent) of the 1,397 SNPs occur in three or more panels. The project assembled a new dataset for 44 of those SNPs involving 4,559 individuals from 73 populations. Analyses of this dataset provided clear differentiation of only five biogeographic regions: sub-Saharan Africa, Europe and Southwest Asia, South Asia, East Asia, and the Americas. This is an inadequate level of biogeographic resolution already exceeded by other panels. The project concluded that more such AISNP panels are not needed and that the forensic community must collaborate to develop a common set of highly differentiating AISNPs typed on a very large number of population samples. How that can be accomplished will be the subject of future discussion. (Publisher abstract modified)
Date Created: December 26, 2017