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Other well-known mutational hotspots, T152C, T195C, T16189C, and T16311C, occupy different positions in the ranking (which in part mirrors the stochastic nature of the simulation approach used in the present study), but all are listed among the top 15 top mtSNPs in the three main continental groups when looking at the HD values (Table 2 and S1).
The estimates above were obtained considering the three main continental groups: Europe, Asia, and Africa.
This database contains 1,440,616 SNPs genotyped in a total of 1,218 individual samples belonging to the following main continental groups: 472 Africans, 58 Americans, 101 Central-South Asians, 364 East Asians and 223 Europeans.
The majority of the panels are designed with the aim of distinguishing main continental groups (e.g. Africans, Asians, Europeans, Americans) owing to the known difficulties of using small SNP panels to classify individuals when they belong to closely related populations.
The results of the present study indicate that the best way to ensure the good performance of a panel is to incorporate the largest possible number of AIMs (at least >400 when considering main continental groups).
All of these panels were originally designed to differentiate the three main continental groups (Europe, East Asia and Sub-Saharan Africa), some of them also including other ancestral groups (see Table 1).
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More than 2,000 complete genomes representing three main continental human population groups (Africa, Europe, and Asia) and two admixed populations ("African-Americans" and "Hispanics") were collected from GenBank and the literature, and were used as training sets.
PCA plot based on the 46 AIMs analyzed in the present study (Additional file 5) shows the relationship of the Guatemalan individuals with the three main CEPH panel continental groups, namely, Africans, Europeans and Native Americans, in the Euclidean space.
We have used a simulation-based approach to evaluate the discrimination power of mtSNPs in different population contexts, including samples representing the main continental regions and admixed population groups.
Pairwise FST values were calculated between continental groups, and between the individual populations based on the continental groupings identified by Rosenberg et al. [10].
Disappointed by the performances of the six African teams, of whom only Ghana progressed beyond the group stage, Jordaan believes they suffered from having their main continental cup competition staged five months before the World Cup.
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