Decoding a highly mixed Kazakh genome

Madina Seidualy, Asta Blazyte, Sungwon Jeon, Youngjune Bhak, Yeonsu Jeon, Jungeun Kim, Jon Anders Eriksson, Dan Bolser, Changhan Yoon, Andrea Manica, Semin Lee, Jong Bhak

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)


We provide a Kazakh whole genome sequence (MJS) and analyses with the largest comparative Kazakh genomic data available to date. We found 102,240 novel SNVs and a high level of heterozygosity. ADMIXTURE analysis confirmed a significant proportion of variations in this individual coming from all continents except Africa and Oceania. A principal component analysis showed neighboring Kalmyk, Uzbek, and Kyrgyz populations to have the strongest resemblance to the MJS genome which reflects fairly recent Kazakh history. MJS’s mitochondrial haplogroup, J1c2, probably represents an early European and Near Eastern influence to Central Asia. This was also supported by the heterozygous SNPs associated with European phenotypic features and strikingly similar Kazakh ancestral composition inferred by ADMIXTURE. Admixture (f3) analysis showed that MJS’s genomic signature is best described as a cross between the Neolithic East Asian (Devil’s Gate1) and the Bronze Age European (Halberstadt_LBA1) components rather than a contemporary admixture.

Original languageEnglish
Pages (from-to)557-568
Number of pages12
JournalHuman Genetics
Issue number5
Early online date2 Feb 2020
Publication statusPublished - 1 May 2020


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