Performance of a self-developed panel for biogeographic ancestry inference and dissection of the genetic background of three Tibetan groups

Abstract Background In this study, we used a panel consisting of 56 autosomal ancestry-informative insertion/deletions (AIM-InDels) for biogeographic ancestry inference, three Y-InDels, and one Amelogenin gene, and verified its performance in Gannan Tibetan, Qinghai Tibetan, and Tibet Tibetan groups. Meanwhile, we analyzed the genetic structures of these three Tibetan groups. Results The results showed that 56 AIM-InDels performed better at classifying African and East Asian individuals without noisy labels compared with other intercontinental populations. By the addition of noisy labels, the SVM model was robust when the proportion of noisy labels was small. Furthermore, the African and East Asian populations showed better performance than the other three intercontinental populations. And the 56 AIM-InDels could be used for individual identification and full sibling identification of three Tibetan groups. Population genetic analysis of three Tibetan groups showed that their genetic structures were similar to East Asian populations. Conclusions This panel can not only be effectively used for biogeographic ancestry inference in African and East Asian populations but also provide insights into the genetic structures of three Tibetan groups.