Population biobanks: Organizational models and prospects of application in gene geography and personalized medicine

Balanovska, Elena; Zhabagin, Maxat; Agdzhoyan, A. T.; Chukhryaeva, Marina; Nv, Markina; Balaganskaya, Olga; Skhalyakho, R. A.; Yusupov, Yusup M.; Utevska, Olga; Bogunov, Yu. V.; Asilguzhin, R. R.; Dolinina, D. O.; Кагазежева, Ж. А.; Damba, Larissa; Zaporozhchenko, Valery; Romanov, A. G.; Dibirova, Kh. D.; Кузнецова, М. А.; Lavryashina, M. B.; Pocheshkhova, Elvira; Balanovsky, Oleg

doi:10.1134/s1022795416120024

Cited by 29 publications

(11 citation statements)

References 27 publications

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“…Blood samples were collected in 2009–2012 by the expeditions of the Laboratory of Human Population Genetics of the Research Centre for Medical Genetics, Genome Geography Laboratory of the Vavilov Institute of General Genetics, The National Laboratory Astana of Nazarbayev University, Forensic science centre of the Ministry of Justice of the Republic of Kazakhstan (Astana), Center of High Technologies and Institute of Bioorganic Chemistry (Tashkent), partially under the auspices of the Genographic Project. All expeditions were supervised by Elena Balanovska and followed the same sampling rules 44 .…”

Section: Methodsmentioning

confidence: 99%

The Connection of the Genetic, Cultural and Geographic Landscapes of Transoxiana

Zhabagin

Balanovska

Sabitov

et al. 2017

Sci Rep

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We have analyzed Y-chromosomal variation in populations from Transoxiana, a historical region covering the southwestern part of Central Asia. We studied 780 samples from 10 regional populations of Kazakhs, Uzbeks, Turkmens, Dungans, and Karakalpaks using 35 SNP and 17 STR markers. Analysis of haplogroup frequencies using multidimensional scaling and principal component plots, supported by an analysis of molecular variance, showed that the geographic landscape of Transoxiana, despite its distinctiveness and diversity (deserts, fertile river basins, foothills and plains) had no strong influence on the genetic landscape. The main factor structuring the gene pool was the mode of subsistence: settled agriculture or nomadic pastoralism. Investigation of STR-based clusters of haplotypes and their ages revealed that cultural and demic expansions of Transoxiana were not closely connected with each other. The Arab cultural expansion introduced Islam to the region but did not leave a significant mark on the pool of paternal lineages. The Mongol expansion, in contrast, had enormous demic success, but did not impact cultural elements like language and religion. The genealogy of Muslim missionaries within the settled agricultural communities of Transoxiana was based on spiritual succession passed from teacher to disciple. However, among Transoxianan nomads, spiritual and biological succession became merged.

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Section: Methodsmentioning

confidence: 99%

The Connection of the Genetic, Cultural and Geographic Landscapes of Transoxiana

Zhabagin

Balanovska

Sabitov

et al. 2017

Sci Rep

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“…The high-quality photos of members of indigenous North Eurasian communities were obtained during the field trips coordinated by the Biobank of North Eurasia [16]. The eye and hair color phenotypes were called based on these photos by three experts: two were physical anthropologists with deep experience in phenotyping, and the third was the specially trained geneticist.…”

Section: Phenotypingmentioning

confidence: 99%

Optimizing the genetic prediction of the eye and hair color for North Eurasian populations

et al. 2020

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Background Predicting the eye and hair color from genotype became an established and widely used tool in forensic genetics, as well as in studies of ancient human populations. However, the accuracy of this tool has been verified on the West and Central Europeans only, while populations from border regions between Europe and Asia (like Caucasus and Ural) also carry the light pigmentation phenotypes. Results We phenotyped 286 samples collected across North Eurasia, genotyped them by the standard HIrisPlex-S markers and found that predictive power in Caucasus/Ural/West Siberian populations is reasonable but lower than that in West Europeans. As these populations have genetic ancestries different from that of West Europeans, we hypothesized they may carry a somewhat different allele spectrum. Thus, for all samples we performed the exome sequencing additionally enriched with the 53 genes and intergenic regions known to be associated with the eye/hair color. Our association analysis replicated the importance of the key previously known SNPs but also identified five new markers whose eye color prediction power for the studied populations is compatible with the two major previously well-known SNPs. Four out of these five SNPs lie within the HERС2 gene and the fifth in the intergenic region. These SNPs are found at high frequencies in most studied populations. The released dataset of exomes from Russian populations can be further used for population genetic and medical genetic studies. Conclusions This study demonstrated that precision of the established systems for eye/hair color prediction from a genotype is slightly lower for the populations from the border regions between Europe and Asia that for the West Europeans. However, this precision can be improved if some newly revealed predictive SNPs are added into the panel. We discuss that the replication of these pigmentation-associated SNPs on the independent North Eurasian sample is needed in the future studies.

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“…Samples representing the populations of Russia and its closest neighbors in North Eurasia (post-Soviet states and Mongolia) were provided by the Biobank of North Eurasia. 8 The study was approved by the Ethics Committee of the Research Centre for Medical Genetics; informed consent was obtained from every donor. The analyzed samples represented a vast territory encompassing much of Russia, its neighbor states and most ethnic groups inhabiting this area ( Figure 1 ).…”

Section: Methodsmentioning

confidence: 99%

Variation of Genomic Sites Associated with Severe Covid-19 Across Populations: Global and National Patterns

Balanovsky¹,

Петрушенко²,

Мирзаев³

et al. 2021

PGPM

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Population biobanks: Organizational models and prospects of application in gene geography and personalized medicine

Cited by 29 publications

References 27 publications

The Connection of the Genetic, Cultural and Geographic Landscapes of Transoxiana

The Connection of the Genetic, Cultural and Geographic Landscapes of Transoxiana

Optimizing the genetic prediction of the eye and hair color for North Eurasian populations

Variation of Genomic Sites Associated with Severe Covid-19 Across Populations: Global and National Patterns

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