Genome diversity in Ukraine

Abstract

Background The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for public data release. BGISEQ-500 sequence data and genotypes by an Illumina GWAS chip were cross-validated on multiple samples and additionally referenced to 1 sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. Results The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide polymorphisms, and microsatellites. To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied population. Conclusions Our results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces and cannot be ignored in future genetic and biomedical studies. These data will contribute a wealth of new information bringing forth a wealth of novel, endemic and medically related alleles.

In silico Analysis of Publicly Available Transcriptomics Data Identifies Putative Prognostic and Therapeutic Molecular Targets for Papillary Thyroid Carcinoma

“… 23 Ukrainian population show more prevalence to a different DNA repair gene; RAD51. 24 However, the South Korean population seem to have prevalence of deletion mutations in Sialic Acid Binding Ig Like Lectin 14 (SIGLEC14) 25 which is linked to inflammasome activation in macrophage. 26 Thus, the different mutations in the different populations may have role in shaping the transcriptomics profile in those populations.…”

The Pioneer Advantage: Filling the blank spots on the map of genome diversity in Europe

“…In the second stage of mapping worldwide genome diversity, national projects replaced the global surveys to serve as a major reference resource for human genetic variation and to provide locally based annotation of disease variants. National genome projects were supported by country governments [ 5 , 6 ], international collaborations [ 7 ], and/or groups of enthusiasts [ 8 ]. These efforts continued to contribute, without the unified systematic global strategy.…”

“…Recently, analysis of the data from whole-genome studies, one in Ukraine [ 8 ] and one in Russia [ 24 ], clearly demonstrated that intrinsic genomic diversity from Eastern Europe had been poorly represented. The SNP allele frequency differences are large enough to provide previously unknown dimensions of population structure.…”

“…The principal component analysis of Russian subpopulations from Pskov and Novgorod in the European part of Russia compared with other populations of Europe and Asia (264 study participants) demonstrated genetic distinctiveness as great or greater than differences between populations of neighboring Finns, Swedes, and Estonians [ 24 ]. A subsequent analysis of Ukrainian genomes showed that the Ukrainian cluster was distinct from publicly available European populations or publicly available genomes from subpopulations of ethnic Russians in the European part of Russia [ 3 , 8 ].…”

“…These 2 studies discovered millions of mutations, many of which were previously not described (478,000 in Ukraine [ 8 ] and approximately 300,000 in 2 populations from the European Russia [ 24 ]) and reported major differences in frequencies of medically related alleles between Eastern Europe and the rest of the continent. This wealth of genomic variation uncovered in Ukraine and, to the lesser extent, in Russia was not due to the particularly high variation within the Ukrainian population but to the absence of sampling variation from the countries around Ukraine.…”