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Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DenmarkDepartment of Mathematical Sciences, Aalborg University, Denmark
Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DenmarkDepartment of Mathematical Sciences, Aalborg University, Denmark
Individuals from Slovenia, Greece, Albania, and Eritrea were typed with the Precision ID Ancestry Panel and included among GenoGeographer’s nine reference populations (Sub-Saharan Africa, Horn of Africa, North Africa, Middle East, Europe, South/Central Asia, East Asia, and East and West Greenland). We tested the performance of GenoGeographer with the Admixture Module on AIM profiles of 3548 individuals assumed to belong to one of the reference populations. A total of 3387 (95.5 %) profiles were assigned to one or more of the reference populations, either a single population or an admixture of two or more populations, while 161 (4.5 %) profiles were not assigned to any reference population or admixtures thereof. For 1486 AIM profiles with no reference population of origin in GenoGeographer, the rejection rate was more than 70 % for AIM profiles from North and South America and less than 20 % for those from Central, North, and Northeast Asia.
The precision of the ancestry prediction using ancestry informative markers (AIMs) is dependent on well-defined reference populations with high-quality genotypes [
]. Previous studies showed that GenoGeographer rejected more than 20 % of AIM profiles, probably due to genetic admixture of the rejected AIM profiles [
Ancestry prediction efficiency of the software GenoGeographer using a z-score method and the ancestry informative markers in the Precision ID Ancestry Panel.
] to test if the admixture module decreased the rejection rate without increasing the population assignment error rate.
2. Materials and methods
Individuals from Albania (N = 94), Slovenia (N = 96), Greece (N = 79), and Eritrea (N = 88) were typed for 165 AIMs with the Precision ID Ancestry Panel (Thermo Fisher Scientific). AIM profiles of 5034 individuals from 123 countries were retrieved from publically accessible databases [
Ancestry prediction efficiency of the software GenoGeographer using a z-score method and the ancestry informative markers in the Precision ID Ancestry Panel.
Albania, Greece, and Slovenia were included in the European reference population, while Eritrea was included together with the Somalian reference population to constitute “Horn of Africa”.
3. Results and discussion
Of the 5034 test AIM profiles, 3548 profiles were assumed to have a population of origin among the reference populations present in GenoGeographer. The AIM profiles were from individuals from Sub-Saharan Africa, the Horn of Africa, North Africa, the Middle-East, Europe, South/Central Asia, East Asia, and East and West Greenland. A total of 161 (4.5 %) profiles were not assigned to any reference population or admixtures thereof, while 3387 (95.5 %) profiles were assigned to one or more of the reference populations either as single populations or admixtures of two or more populations. Of the AIM profiles with assigned reference populations, 3231 (95.4 %) were assigned to reference populations concordant with the reported populations of origin. In areas with no reference population like the Americas, GenoGeographer rejected the majority of the AIM profiles. However, many of the profiles from Central Asia and Siberia were predicted as genetic admixtures with a Greenlandic component. Fig. 1 shows a world map with the approximate geographic origin of the tested AIM profiles. The pie charts represent the ancestry prediction with the GenoGeographer Admixture Module. In geographic areas represented by the reference populations, the prediction error was low. In geographic areas with high levels of genetic admixture such as the Middle East and North Africa, the GenoGeographer Admixture Module also predicted the genetic admixtures. In areas with no reference population like the Americas, GenoGeographer rejected the majority of the AIM profiles. However, many of the profiles from Central Asia and Siberia were predicted as genetic admixtures with a Greenlandic component.
Fig. 1World map with pie charts showing the results of GenoGeographer analysis of 5034 AIM profiles.
Supplementing GenoGeographer with the Admixture Module decreased the rejection rate without increasing the assignment error rate for AIM profiles when the expected population of origin was included among the GenoGeographer reference populations. For AIM profiles with no reference population of origin in GenoGeographer, the rejection rate was high for AIM profiles from North and South America and lower for those from Central, North, and Northeast Asia.
Conflict of interest
The authors declare no conflict of interest.
References
Themudo G.E.
Mogensen H.S.
Børsting C.
Morling N.
Frequencies of HID-ion ampliseq ancestry panel markers among Greenlanders.
Ancestry prediction efficiency of the software GenoGeographer using a z-score method and the ancestry informative markers in the Precision ID Ancestry Panel.
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