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, 27 (12), 1885-1893

Genetic Relationships of European, Mediterranean, and SW Asian Populations Using a Panel of 55 AISNPs

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Genetic Relationships of European, Mediterranean, and SW Asian Populations Using a Panel of 55 AISNPs

Andrew J Pakstis et al. Eur J Hum Genet.

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.

Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1
PCA results based on the 55 AISNP allele frequencies for 76 reference populations consisting of 43 groups from SW Asia–Europe and 33 selected populations in adjacent world regions. The 16 out of 25 new reference populations listed alphabetically in the inset box are from SW Asia, Europe, North Africa, East Africa
Fig. 2
Fig. 2
Estimated cluster membership bar plot via STRUCTURE for 43 reference populations in Southwest Asia—Europe and 33 selected populations in adjacent world regions—Africa, South Central Asia, Central Asia, Siberia. Displaying the highest likelihood run out of 20 runs at K = 6
Fig. 3
Fig. 3
The 30 highest likelihoods calculated by FROG-kb for two Kurdish individuals based on the 55 AISNP panel and 164 current reference populations. The dot next to the value for the probability of genotype in each population identify results within one order of magnitude of the highest likelihood and therefore not significantly different
Fig. 4
Fig. 4
Random match probability and most common genotype frequency for each of 76 populations based on the 55 AISNP panel

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References

    1. Pakstis AJ, Haigh E, Cherni L, Ben Ammar ElGaaied A, Barton A, Evsanaa B, et al. 52 additional reference population samples for the 55 AISNP panel. Forensic Sci Int Genet. 2015;19:269–71. doi: 10.1016/j.fsigen.2015.08.003. - DOI - PubMed
    1. Pakstis AJ, Kang L, Liu L, Zhang Z, Jin T, Grigorenko EL, et al. Increasing the reference populations for the 55 AISNP panel: the need and benefits. Int J Leg Med. 2017;131:913–7. doi: 10.1007/s00414-016-1524-z. - DOI - PMC - PubMed
    1. Kidd KK, Speed WC, Pakstis AJ, Furtado MR, Fang R, Madbouly A, et al. Progress toward an efficient panel of SNPs for ancestry inference. Forensic Sci Int Genet. 2014;10:23–32. doi: 10.1016/j.fsigen.2014.01.002. - DOI - PubMed
    1. Cann HM, deToma C, Cazes L, Legrand M-F, Morel V, Piouffre L, et al. A human genome diversity cell line panel. Science. 2002;296:261–2. doi: 10.1126/science.296.5566.261b. - DOI - PubMed
    1. The 1000 Genomes Project Consortium. Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, et al. A global reference for human genetic variation. Nature. 2015;526:68–74. doi: 10.1038/nature15393. - DOI - PMC - PubMed
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