Genetic relationships of European, Mediterranean, and SW Asian populations using a panel of 55 AISNPs

Andrew J Pakstis,Nina Mjølsnes Salvo,Amel Ben Ammar Elgaaïed ,Serkan Doğan ,Pavlos Neophytou ,Kirstin Janssen,Eida Khalaf Almohammed,Özlem Bülbül ,Hasan Emin Balkaya,Ditte Truelsen ,Gunn-Hege Olsen,Lotfi Cherni,Usha Soundararajan,Cemal Gürkan ,Mustafa Doğan ,Judith R Kidd,Houssein Khodjet‐El‐Khil ,Sami Boussetta,Haseena Rajeevan,Vânia Pereira ,Sibte Hadi,Kenneth K Kídd

doi:10.1038/s41431-019-0466-6

Abstract

The set of 55 ancestry informative SNPs (AISNPs) originally developed by the Kidd Lab has been studied on a large number of populations and continues to be applied to new population samples. The existing reference database of population samples allows the relationships of new population samples to be inferred on a global level. Analyses show that these autosomal markers constitute one of the better panels of AISNPs. Continuing to build this reference database enhances its value. Because more than half of the 25 ethnic groups recently studied with these AISNPs are from Southwest Asia and the Mediterranean region, we present here various analyses focused on populations from these regions along with selected reference populations from nearby regions where genotype data are available. Many of these ethnic groups have not been previously studied for forensic markers. Data on populations from other world regions have also been added to the database but are not included in these focused analyses. The new population samples added to ALFRED and FROG-kb increase the total to 164 population samples that have been studied for all 55 AISNPs.

Highlights

In previous publications [1, 2] we reported on the increasing number of population samples from major continental regions that had been studied for the panel of 55 ancestry informative single nucleotide polymorphisms (AISNPs) [3]
Some of the 55 SNPs have frequency data in ALlele FREquency Database (ALFRED) for >164 populations; those populations could not be included as reference populations in Forensic Reference-Resource on Genetics knowledge base (FROG-kb) because they do not have frequencies for all 55 of the SNPs
The graphical presentations based on analyses of the 55 AISNP panel show very strong geographical clustering of the 76 reference populations analyzed from Southwest Asia–Europe and the immediately adjacent areas

Summary

Introduction

Med.yale.edu) and the Forensic Reference-Resource on Genetics knowledge base Given this global resource, studies of additional populations, especially for geographic regions poorly represented in the current dataset, are likely to be informative on the newly studied regions as well as the global pattern of variation. We describe the newest reference populations that have become available for this set of AISNPs. As more than half of these populations represent ethnic groups from Southwest Asia and the Mediterranean, a number of which have either not been studied before or else not in an integrated manner, we take this opportunity to present analyses focused on groups from this region of the world and selected populations from immediately surrounding geographical region

Methods

Results

Conclusion