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.

Now published in GigaScience doi: 10.1093/gigascience/giaa159

Taras K. Oleksyk 1Department of Biological Sciences, Uzhhorod National University, Uzhhorod 88000, Ukraine2Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA3Departamento de Biología, Universidad de Puerto Rico, Mayagüez, 00682, Puerto RicoFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Taras K. OleksykFor correspondence: oleksyk@oakland.edu remills@umich.eduWalter W. Wolfsberger 1Department of Biological Sciences, Uzhhorod National University, Uzhhorod 88000, Ukraine2Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA3Departamento de Biología, Universidad de Puerto Rico, Mayagüez, 00682, Puerto RicoFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlexandra Weber 4Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKhrystyna Shchubelka 2Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA3Departamento de Biología, Universidad de Puerto Rico, Mayagüez, 00682, Puerto Rico5Department of Medicine, Uzhhorod National University, Uzhhorod 88000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteOlga T. Oleksyk 6A. Novak Transcarpathian Regional Clinical Hospital, Uzhhorod 88000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteOlga Levchuk 7Astra Dia Inc., Uzhhorod 88000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlla Patrus 7Astra Dia Inc., Uzhhorod 88000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNelya Lazar 7Astra Dia Inc., Uzhhorod 88000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteStephanie O. Castro-Marquez 2Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA3Departamento de Biología, Universidad de Puerto Rico, Mayagüez, 00682, Puerto RicoFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePatricia Boldyzhar 5Department of Medicine, Uzhhorod National University, Uzhhorod 88000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlina Urbanovych 8Lviv National Medical University, Lviv 79010, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKateryna Malyar 10I.I.Mechnikov Dnipro Regional Clinical Hospital, Dnipro 49000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSvitlana Chervyakova 11Chernihiv Regional Hospital, Chernihiv 14039, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteOlena Podoroha 12Sumy Diagnostic Center, Sumy 40000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNatalia Kovalchuk 13Rivne Regional Specialized Hospital of Radiation Protection, Rivne 33028, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYaroslava Hasynets 1Department of Biological Sciences, Uzhhorod National University, Uzhhorod 88000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJuan L. Rodriguez-Flores 14Department of Genetic Medicine, Weill Cornell Medical College, New York, NY 10065, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSarah Medley 2Department of Biological Sciences, Oakland University, Rochester, MI 48309, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFabia Battistuzzi 2Department of Biological Sciences, Oakland University, Rochester, MI 48309, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRyan Liu 15BGI, Shenzhen CHINAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYong Hou 15BGI, Shenzhen CHINAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSiru Chen 15BGI, Shenzhen CHINAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHuanming Yang 15BGI, Shenzhen CHINAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMeredith Yeager 16Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMichael Dean 16Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael DeanRyan E. Mills 17Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: oleksyk@oakland.edu remills@umich.eduVolodymyr Smolanka 5Department of Medicine, Uzhhorod National University, Uzhhorod 88000, UkraineFind this author on Google ScholarFind this author on PubMedSearch for this author on this site

A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa159 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

These peer reviews were as follows:

Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102600 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102601

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Genome diversity in Ukraine

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Abstract

Background

Results

Conclusions

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