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Yanus GA, Suspitsin EN, Imyanitov EN. The Spectrum of Disease-Associated Alleles in Countries with a Predominantly Slavic Population. Int J Mol Sci 2024; 25:9335. [PMID: 39273284 PMCID: PMC11394759 DOI: 10.3390/ijms25179335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/21/2024] [Accepted: 08/25/2024] [Indexed: 09/15/2024] Open
Abstract
There are more than 260 million people of Slavic descent worldwide, who reside mainly in Eastern Europe but also represent a noticeable share of the population in the USA and Canada. Slavic populations, particularly Eastern Slavs and some Western Slavs, demonstrate a surprisingly high degree of genetic homogeneity, and, consequently, remarkable contribution of recurrent alleles associated with hereditary diseases. Along with pan-European pathogenic variants with clearly elevated occurrence in Slavic people (e.g., ATP7B c.3207C>A and PAH c.1222C>T), there are at least 52 pan-Slavic germ-line mutations (e.g., NBN c.657_661del and BRCA1 c.5266dupC) as well as several disease-predisposing alleles characteristic of the particular Slavic communities (e.g., Polish SDHD c.33C>A and Russian ARSB c.1562G>A variants). From a clinical standpoint, Slavs have some features of a huge founder population, thus providing a unique opportunity for efficient genetic studies.
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Affiliation(s)
- Grigoriy A Yanus
- Laboratory of Molecular Diagnostics, St. Petersburg State Pediatric Medical University, 194100 St. Petersburg, Russia
| | - Evgeny N Suspitsin
- Department of Medical Genetics, St. Petersburg State Pediatric Medical University, 194100 St. Petersburg, Russia
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia
| | - Evgeny N Imyanitov
- Department of Medical Genetics, St. Petersburg State Pediatric Medical University, 194100 St. Petersburg, Russia
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia
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2
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Usoltsev D, Kolosov N, Rotar O, Loboda A, Boyarinova M, Moguchaya E, Kolesova E, Erina A, Tolkunova K, Rezapova V, Molotkov I, Melnik O, Freylikhman O, Paskar N, Alieva A, Baranova E, Bazhenova E, Beliaeva O, Vasilyeva E, Kibkalo S, Skitchenko R, Babenko A, Sergushichev A, Dushina A, Lopina E, Basyrova I, Libis R, Duplyakov D, Cherepanova N, Donner K, Laiho P, Kostareva A, Konradi A, Shlyakhto E, Palotie A, Daly MJ, Artomov M. Complex trait susceptibilities and population diversity in a sample of 4,145 Russians. Nat Commun 2024; 15:6212. [PMID: 39043636 PMCID: PMC11266540 DOI: 10.1038/s41467-024-50304-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/02/2024] [Indexed: 07/25/2024] Open
Abstract
The population of Russia consists of more than 150 local ethnicities. The ethnic diversity and geographic origins, which extend from eastern Europe to Asia, make the population uniquely positioned to investigate the shared properties of inherited disease risks between European and Asian ancestries. We present the analysis of genetic and phenotypic data from a cohort of 4,145 individuals collected in three metro areas in western Russia. We show the presence of multiple admixed genetic ancestry clusters spanning from primarily European to Asian and high identity-by-descent sharing with the Finnish population. As a result, there was notable enrichment of Finnish-specific variants in Russia. We illustrate the utility of Russian-descent cohorts for discovery of novel population-specific genetic associations, as well as replication of previously identified associations that were thought to be population-specific in other cohorts. Finally, we provide access to a database of allele frequencies and GWAS results for 464 phenotypes.
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Affiliation(s)
- Dmitrii Usoltsev
- Almazov National Medical Research Centre, St Petersburg, Russia
- ITMO University, St Petersburg, Russia
- Broad Institute, Cambridge, MA, USA
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Nikita Kolosov
- Almazov National Medical Research Centre, St Petersburg, Russia
- ITMO University, St Petersburg, Russia
- Broad Institute, Cambridge, MA, USA
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Oxana Rotar
- Almazov National Medical Research Centre, St Petersburg, Russia
| | - Alexander Loboda
- Almazov National Medical Research Centre, St Petersburg, Russia
- ITMO University, St Petersburg, Russia
- Broad Institute, Cambridge, MA, USA
| | | | | | | | - Anastasia Erina
- Almazov National Medical Research Centre, St Petersburg, Russia
| | | | - Valeriia Rezapova
- Almazov National Medical Research Centre, St Petersburg, Russia
- ITMO University, St Petersburg, Russia
- Broad Institute, Cambridge, MA, USA
| | - Ivan Molotkov
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Olesya Melnik
- Almazov National Medical Research Centre, St Petersburg, Russia
| | | | - Nadezhda Paskar
- Almazov National Medical Research Centre, St Petersburg, Russia
| | - Asiiat Alieva
- Almazov National Medical Research Centre, St Petersburg, Russia
| | - Elena Baranova
- Almazov National Medical Research Centre, St Petersburg, Russia
| | - Elena Bazhenova
- Almazov National Medical Research Centre, St Petersburg, Russia
| | - Olga Beliaeva
- Almazov National Medical Research Centre, St Petersburg, Russia
| | - Elena Vasilyeva
- Almazov National Medical Research Centre, St Petersburg, Russia
| | - Sofia Kibkalo
- Almazov National Medical Research Centre, St Petersburg, Russia
| | | | - Alina Babenko
- Almazov National Medical Research Centre, St Petersburg, Russia
| | | | | | | | | | - Roman Libis
- Orenburg State Medical University, Orenburg, Russia
| | - Dmitrii Duplyakov
- Samara State Medical University, Samara, Russia
- Samara Regional Cardiology Dispensary, Samara, Russia
| | | | - Kati Donner
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
| | - Paivi Laiho
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Anna Kostareva
- Almazov National Medical Research Centre, St Petersburg, Russia
- ITMO University, St Petersburg, Russia
| | - Alexandra Konradi
- Almazov National Medical Research Centre, St Petersburg, Russia
- ITMO University, St Petersburg, Russia
| | | | - Aarno Palotie
- Broad Institute, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Mark J Daly
- Broad Institute, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Mykyta Artomov
- Almazov National Medical Research Centre, St Petersburg, Russia.
- ITMO University, St Petersburg, Russia.
- Broad Institute, Cambridge, MA, USA.
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
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3
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Hemstrom W, Grummer JA, Luikart G, Christie MR. Next-generation data filtering in the genomics era. Nat Rev Genet 2024:10.1038/s41576-024-00738-6. [PMID: 38877133 DOI: 10.1038/s41576-024-00738-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2024] [Indexed: 06/16/2024]
Abstract
Genomic data are ubiquitous across disciplines, from agriculture to biodiversity, ecology, evolution and human health. However, these datasets often contain noise or errors and are missing information that can affect the accuracy and reliability of subsequent computational analyses and conclusions. A key step in genomic data analysis is filtering - removing sequencing bases, reads, genetic variants and/or individuals from a dataset - to improve data quality for downstream analyses. Researchers are confronted with a multitude of choices when filtering genomic data; they must choose which filters to apply and select appropriate thresholds. To help usher in the next generation of genomic data filtering, we review and suggest best practices to improve the implementation, reproducibility and reporting standards for filter types and thresholds commonly applied to genomic datasets. We focus mainly on filters for minor allele frequency, missing data per individual or per locus, linkage disequilibrium and Hardy-Weinberg deviations. Using simulated and empirical datasets, we illustrate the large effects of different filtering thresholds on common population genetics statistics, such as Tajima's D value, population differentiation (FST), nucleotide diversity (π) and effective population size (Ne).
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Affiliation(s)
- William Hemstrom
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
| | - Jared A Grummer
- Flathead Lake Biological Station, Wildlife Biology Program and Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Gordon Luikart
- Flathead Lake Biological Station, Wildlife Biology Program and Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Mark R Christie
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA.
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4
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Samoylov AN, Tumanova P, Pankratova SA, Ashryatova LS, Plotnikov D. Association of GNB3, ACE polymorphisms with POAG and NTG. Ophthalmic Genet 2024; 45:23-27. [PMID: 37997634 DOI: 10.1080/13816810.2023.2283415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
PURPOSE Primary open-angle glaucoma (POAG) represents the most prevalent form of glaucoma and stands as a foremost contributor to irreversible vision impairment on a global scale. Despite notable strides made in comprehending the genetic underpinnings of POAG, investigations within the context of Russia remain constrained. METHODS The study cohort comprised a total of 235 individuals, with 135 of them exhibiting various forms of glaucoma encompassing both POAG and (NTG, while the remaining 100 individuals served as control subjects. Each participant underwent a comprehensive ocular examination to ascertain their ocular health status. Genotyping of the relevant single nucleotide polymorphisms (SNPs) was carried out using the Taq Man genotyping assay. Specifically, the two SNPs under scrutiny were GNB3 rs5443 gene and ACE rs4646994. Statistical analysis was performed to evaluate the association of these SNPs with glaucoma risk. RESULTS The presence of the T allele of rs5443 was found to be associated with NTG (p = .004). However, no statistically significant correlation was identified between this SNP and POAG (p = .88). CONCLUSION This study provides evidence of an association between the T allele of rs5443 and a reduced susceptibility NTG within the Russian population. These observations augment the comprehension of the genetic underpinnings of glaucoma and hold potential implications for the prospective development of targeted therapeutic interventions.
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Affiliation(s)
- Alexander N Samoylov
- Kazan State Medical University, Kazan, Russian Federation
- Republican Clinical Ophthalmologic Hospital, Kazan, Russian Federation
| | - Polina Tumanova
- Republican Clinical Ophthalmologic Hospital, Kazan, Russian Federation
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5
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Chumakova OS, Baklanova TN, Milovanova NV, Zateyshchikov DA. Hypertrophic Cardiomyopathy in Underrepresented Populations: Clinical and Genetic Landscape Based on a Russian Single-Center Cohort Study. Genes (Basel) 2023; 14:2042. [PMID: 38002985 PMCID: PMC10671745 DOI: 10.3390/genes14112042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a common inherited cardiac disorder characterized by marked clinical and genetic heterogeneity. Ethnic groups underrepresented in studies may have distinctive characteristics. We sought to evaluate the clinical and genetic landscape of Russian HCM patients. A total of 193 patients (52% male; 95% Eastern Slavic origin; median age 56 years) were clinically evaluated, including genetic testing, and prospectively followed to document outcomes. As a result, 48% had obstructive HCM, 25% had HCM in family, 21% were asymptomatic, and 68% had comorbidities. During 2.8 years of follow-up, the all-cause mortality rate was 2.86%/year. A total of 5.7% received an implantable cardioverter-defibrillator (ICD), and 21% had septal reduction therapy. A sequencing analysis of 176 probands identified 64 causative variants in 66 patients (38%); recurrent variants were MYBPC3 p.Q1233* (8), MYBPC3 p.R346H (2), MYH7 p.A729P (2), TPM1 p.Q210R (3), and FLNC p.H1834Y (2); 10 were multiple variant carriers (5.7%); 5 had non-sarcomeric HCM, ALPK3, TRIM63, and FLNC. Thin filament variant carriers had a worse prognosis for heart failure (HR = 7.9, p = 0.007). In conclusion, in the Russian HCM population, the low use of ICD and relatively high mortality should be noted by clinicians; some distinct recurrent variants are suspected to have a founder effect; and family studies on some rare variants enriched worldwide knowledge in HCM.
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Affiliation(s)
- Olga S. Chumakova
- Moscow Healthcare Department, City Clinical Hospital 17, 119620 Moscow, Russia; (T.N.B.); (D.A.Z.)
- E.I. Chazov National Medical Research Center for Cardiology, 121552 Moscow, Russia
| | - Tatiana N. Baklanova
- Moscow Healthcare Department, City Clinical Hospital 17, 119620 Moscow, Russia; (T.N.B.); (D.A.Z.)
| | | | - Dmitry A. Zateyshchikov
- Moscow Healthcare Department, City Clinical Hospital 17, 119620 Moscow, Russia; (T.N.B.); (D.A.Z.)
- E.I. Chazov National Medical Research Center for Cardiology, 121552 Moscow, Russia
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6
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Albert EA, Kondratieva OA, Baranova EE, Sagaydak OV, Belenikin MS, Zobkova GY, Kuznetsova ES, Deviatkin AA, Zhurov AA, Karpulevich EA, Volchkov PY, Vorontsova MV. Transferability of the PRS estimates for height and BMI obtained from the European ethnic groups to the Western Russian populations. Front Genet 2023; 14:1086709. [PMID: 36726807 PMCID: PMC9885218 DOI: 10.3389/fgene.2023.1086709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023] Open
Abstract
Genetic data plays an increasingly important role in modern medicine. Decrease in the cost of sequencing with subsequent increase in imputation accuracy, and the accumulation of large amounts of high-quality genetic data enable the creation of polygenic risk scores (PRSs) to perform genotype-phenotype associations. The accuracy of phenotype prediction primarily depends on the overall trait heritability, Genome-wide association studies cohort size, and the similarity of genetic background between the base and the target cohort. Here we utilized 8,664 high coverage genomic samples collected across Russia by "Evogen", a Russian biomedical company, to evaluate the predictive power of PRSs based on summary statistics established on cohorts of European ancestry for basic phenotypic traits, namely height and BMI. We have demonstrated that the PRSs calculated for selected traits in three distinct Russian populations, recapitulate the predictive power from the original studies. This is evidence that GWAS summary statistics calculated on cohorts of European ancestry are transferable onto at least some ethnic groups in Russia.
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Affiliation(s)
- E. A. Albert
- National Medical Research Center for Endocrinology, Moscow, Russia,Life Sciences Research Center, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia,*Correspondence: E. A. Albert,
| | - O. A. Kondratieva
- Department of Information Systems, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia
| | | | | | | | | | | | - A. A. Deviatkin
- National Medical Research Center for Endocrinology, Moscow, Russia,Life Sciences Research Center, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - A. A. Zhurov
- National Medical Research Center for Endocrinology, Moscow, Russia
| | - E. A. Karpulevich
- Department of Information Systems, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia
| | - P. Y. Volchkov
- National Medical Research Center for Endocrinology, Moscow, Russia,Life Sciences Research Center, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - M. V. Vorontsova
- National Medical Research Center for Endocrinology, Moscow, Russia
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7
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Fedorova SA, Khusnutdinova EK. Genetic Structure and Genetic History of the Sakha (Yakuts) Population. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422120031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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8
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Oleksyk TK, Wolfsberger WW, Schubelka K, Mangul S, O'Brien SJ. The Pioneer Advantage: Filling the blank spots on the map of genome diversity in Europe. Gigascience 2022; 11:giac081. [PMID: 36085557 PMCID: PMC9463063 DOI: 10.1093/gigascience/giac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Documenting genome diversity is important for the local biomedical communities and instrumental in developing precision and personalized medicine. Currently, tens of thousands of whole-genome sequences from Europe are publicly available, but most of these represent populations of developed countries of Europe. The uneven distribution of the available data is further impaired by the lack of data sharing. Recent whole-genome studies in Eastern Europe, one in Ukraine and one in Russia, demonstrated that local genome diversity and population structure from Eastern Europe historically had not been fully represented. An unexpected wealth of genomic variation uncovered in these studies was not so much a consequence of high variation within their population, but rather due to the "pioneer advantage." We discovered more variants because we were the first to prospect in the Eastern European genome pool. This simple comparison underscores the importance of removing the remaining geographic genome deserts from the rest of the world map of the human genome diversity.
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Affiliation(s)
- Taras K Oleksyk
- Uzhhorod National University, Uzhhorod, 88000, Ukraine
- Oakland University, Department of Biological Sciences, Rochester, 48309 MI 48309-4479, USA
| | - Walter W Wolfsberger
- Oakland University, Department of Biological Sciences, Rochester, 48309 MI 48309-4479, USA
| | - Khrystyna Schubelka
- Oakland University, Department of Biological Sciences, Rochester, 48309 MI 48309-4479, USA
| | - Serghei Mangul
- University of Southern California, USC School of Pharmacy, Los Angeles, CA 90089, USA
| | - Stephen J O'Brien
- Nova Southeastern University, Halmos College of Natural Sciences and Oceanography, Fort Lauderdale, FL 33314, USA
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9
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Okovantsev VS, Ponomarev GY, Agdzhoyan AT, Agdzhoyan AT, Pylev VY, Balanovska EV. Peculiarity of Pomors of Onega Peninsula and Winter Coast in the genetic context of Northern Europe. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2022. [DOI: 10.24075/brsmu.2022.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The peculiarity of the Russian North gene pool has long become scientific fact, but has yet to receive informative explanation. Genetic drift cannot be the only contributing factor in the striking genetic differences between not only northern Russian populations and the southern ones, but among individual northern populations as well. Studying Russian North gene pools previously underrepresented in scientific literature may help understand this phenomenon. The work aimed to perform a subtotal study of the gene pool of the Arkhangelsk Oblast Pomors (Onega Coast, Summer Coast, the western fragment of the Winter Coast; n = 130) using a panel of 60 Y-chromosome SNP markers through multidimensional scaling and mapping of genetic distances. The frequencies of 14 identified haplogroups differ drastically in Pomor populations: haplogroups I1, R1a, and N3 each comprise a quarter of the total Pomor gene pool, I2-P37.2, and R1b each comprise about 8%, and the rest of the haplogroups are rare. The Onega Coast Pomors showed genetic similarity to a wide range of North-Eastern Europe Finnic-speaking populations, as well as to Russian populations with a strong pre-Slavic substratum. The Summer Coast Pomors are close to the Scandinavian gene pools, and the Winter Coast Pomors are similar only to specific Finn and Swede populations. None of the Pomor populations demonstrate genetic similarity with the Novgorod Oblast Russian populations, with which the origin of the Pomors is traditionally associated. The genetic distances between Pomor populations are so great, they are comparable to the general range of variability between the Eastern Slavic, Baltic, and Finno-Ugric peoples of the region. The reasons for such pronounced originality of Pomor populations presumably include, along with genetic drift, the gene pool of each population being underlied by a different pre-Slavic substrate, with later gene flows as an additional factor.
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Affiliation(s)
- VS Okovantsev
- Research Centre for Medical Genetics, Moscow, Russia
| | - GYu Ponomarev
- Research Centre for Medical Genetics, Moscow, Russia
| | | | | | - VYu Pylev
- Research Centre for Medical Genetics, Moscow, Russia
| | - EV Balanovska
- Research Centre for Medical Genetics, Moscow, Russia
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10
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Sotnikova EA, Kiseleva AV, Kutsenko VA, Zharikova AA, Ramensky VE, Divashuk MG, Vyatkin YV, Klimushina MV, Ershova AI, Revazyan KZ, Skirko OP, Zaicenoka M, Efimova IA, Pokrovskaya MS, Kopylova OV, Glechan AM, Shalnova SA, Meshkov AN, Drapkina OM. Identification of Pathogenic Variant Burden and Selection of Optimal Diagnostic Method Is a Way to Improve Carrier Screening for Autosomal Recessive Diseases. J Pers Med 2022; 12:jpm12071132. [PMID: 35887629 PMCID: PMC9322704 DOI: 10.3390/jpm12071132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022] Open
Abstract
Cystic fibrosis, phenylketonuria, alpha-1 antitrypsin deficiency, and sensorineural hearing loss are among the most common autosomal recessive diseases, which require carrier screening. The evaluation of population allele frequencies (AF) of pathogenic variants in genes associated with these conditions and the choice of the best genotyping method are the necessary steps toward development and practical implementation of carrier-screening programs. We performed custom panel genotyping of 3821 unrelated participants from two Russian population representative samples and three patient groups using real-time polymerase chain reaction (PCR) and next generation sequencing (NGS). The custom panel included 115 known pathogenic variants in the CFTR, PAH, SERPINA1, and GJB2 genes. Overall, 38 variants were detected. The comparison of genotyping platforms revealed the following advantages of real-time PCR: relatively low cost, simple genotyping data analysis, and easier detection of large indels, while NGS showed better accuracy of variants identification and capability for detection of additional pathogenic variants in adjacent regions. A total of 23 variants had significant differences in estimated AF comparing with non-Finnish Europeans from gnomAD. This study provides new AF data for variants associated with the studied disorders and the comparison of genotyping methods for carrier screening.
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Affiliation(s)
- Evgeniia A. Sotnikova
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Anna V. Kiseleva
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
- Correspondence:
| | - Vladimir A. Kutsenko
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, 1-73, Leninskie Gory, 119991 Moscow, Russia
| | - Anastasia A. Zharikova
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 1-73, Leninskie Gory, 119991 Moscow, Russia
| | - Vasily E. Ramensky
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 1-73, Leninskie Gory, 119991 Moscow, Russia
| | - Mikhail G. Divashuk
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia
| | - Yuri V. Vyatkin
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
- Novosibirsk State University, 1, Pirogova Str., 630090 Novosibirsk, Russia
| | - Marina V. Klimushina
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Alexandra I. Ershova
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Karina Z. Revazyan
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Olga P. Skirko
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Marija Zaicenoka
- Moscow Institute of Physics and Technology, Dolgoprudny, Institutskiy per.9, 141701 Dolgoprudny, Russia;
| | - Irina A. Efimova
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Maria S. Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Oksana V. Kopylova
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Anush M. Glechan
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Svetlana A. Shalnova
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Alexey N. Meshkov
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Oxana M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per.10, Bld. 3, 101000 Moscow, Russia; (E.A.S.); (V.A.K.); (A.A.Z.); (V.E.R.); (M.G.D.); (Y.V.V.); (M.V.K.); (A.I.E.); (K.Z.R.); (O.P.S.); (I.A.E.); (M.S.P.); (O.V.K.); (A.M.G.); (S.A.S.); (A.N.M.); (O.M.D.)
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11
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Genotype imputation and polygenic score estimation in northwestern Russian population. PLoS One 2022; 17:e0269434. [PMID: 35763490 PMCID: PMC9239469 DOI: 10.1371/journal.pone.0269434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 05/21/2022] [Indexed: 11/19/2022] Open
Abstract
Numerous studies demonstrated the lack of transferability of polygenic score (PGS) models across populations and the problem arising from unequal presentation of ancestries across genetic studies. However, even within European ancestry there are ethnic groups that are rarely presented in genetic studies. For instance, Russians, being one of the largest, diverse, and yet understudied group in Europe. In this study, we evaluated the reliability of genotype imputation for the Russian cohort by testing several commonly used imputation reference panels (e.g. HRC, 1000G, HGDP). HRC, in comparison with two other panels, showed the most accurate results based on both imputation accuracy and allele frequency concordance between masked and imputed genotypes. We built polygenic score models based on GWAS results from the UK biobank, measured the explained phenotypic variance in the Russian cohort attributed to polygenic scores for 11 phenotypes, collected in the clinic for each participant, and finally explored the role of allele frequency discordance between the UK biobank and the study cohort in the resulting PGS performance.
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12
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Jain M, Kamalov D, Tivtikyan A, Balatsky A, Samokhodskaya L, Okhobotov D, Kozlova P, Pisarev E, Zvereva M, Kamalov A. Urine TERT promoter mutations-based tumor DNA detection in patients with bladder cancer: A pilot study. Mol Clin Oncol 2021; 15:253. [PMID: 34712485 PMCID: PMC8548999 DOI: 10.3892/mco.2021.2415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
Telomerase reverse transcriptase (TERT) promoter mutations are the most frequent genetic events in bladder cancer (BC). The aim of the present pilot study was to evaluate the diagnostic potential of urine TERT promoter mutations-based liquid biopsy in patients with an ongoing oncological process, as well as in post-resection patients at risk of BC recurrence. A total of 60 patients were enrolled, of whom 27 patients had histologically proven BC; 23 had no signs of BC (control group); and 10 patients underwent transurethral malignancy resection 3-6 months prior to urine donation ('second look' group). Urine TERT promoter mutations were detected using Droplet Digital PCR. Receiver operating characteristic curve analysis revealed significant diagnostic power of the present approach (area under the curve: -0.768). At the cut-off value of tumor DNA fraction 0.34%, the sensitivity and specificity were 55.56 and 100%, respectively. In the positive samples, tumor DNA fraction varied significantly from 0.59 to 48.77%. In the 'second look' group, tumor DNA was detected in 4/10 patients, highlighting the possibility of BC recurrence with its fraction ranging only from 0.90 to 6.61%. Therefore, urine TERT promoter mutations-based liquid biopsy appears to be a promising tool for BC diagnosis and surveillance. The main study will include recruitment of additional patients, extension of the mutation panel, prolonged follow-up of the post-resection patients, as well as screening of industrial workers exposed to specific carcinogens.
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Affiliation(s)
- Mark Jain
- Medical Research and Educational Center, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - David Kamalov
- Medical Research and Educational Center, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Alexander Tivtikyan
- Medical Research and Educational Center, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Alexander Balatsky
- Medical Research and Educational Center, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Larisa Samokhodskaya
- Medical Research and Educational Center, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Dmitry Okhobotov
- Medical Research and Educational Center, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Polina Kozlova
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Eduard Pisarev
- Department of Bioinformatics and Bioengineering, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Maria Zvereva
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Armais Kamalov
- Medical Research and Educational Center, Lomonosov Moscow State University, 119992 Moscow, Russia
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13
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Ramensky VE, Ershova AI, Zaicenoka M, Kiseleva AV, Zharikova AA, Vyatkin YV, Sotnikova EA, Efimova IA, Divashuk MG, Kurilova OV, Skirko OP, Muromtseva GA, Belova OA, Rachkova SA, Pokrovskaya MS, Shalnova SA, Meshkov AN, Drapkina OM. Targeted Sequencing of 242 Clinically Important Genes in the Russian Population From the Ivanovo Region. Front Genet 2021; 12:709419. [PMID: 34691145 PMCID: PMC8529250 DOI: 10.3389/fgene.2021.709419] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/31/2021] [Indexed: 12/16/2022] Open
Abstract
We performed a targeted sequencing of 242 clinically important genes mostly associated with cardiovascular diseases in a representative population sample of 1,658 individuals from the Ivanovo region northeast of Moscow. Approximately 11% of 11,876 detected variants were not found in the Single Nucleotide Polymorphism Database (dbSNP) or reported earlier in the Russian population. Most novel variants were singletons and doubletons in our sample, and virtually no novel alleles presumably specific for the Russian population were able to reach the frequencies above 0.1-0.2%. The overwhelming majority (99.3%) of variants detected in this study in three or more copies were shared with other populations. We found two dominant and seven recessive known pathogenic variants with allele frequencies significantly increased compared to those in the gnomAD non-Finnish Europeans. Of the 242 targeted genes, 28 were in the list of 59 genes for which the American College of Medical Genetics and Genomics (ACMG) recommended the reporting of incidental findings. Based on the number of variants detected in the sequenced subset of ACMG59 genes, we approximated the prevalence of known pathogenic and novel or rare protein-truncating variants in the complete set of ACMG59 genes in the Ivanovo population at 1.4 and 2.8%, respectively. We analyzed the available clinical data and observed the incomplete penetrance of known pathogenic variants in the 28 ACMG59 genes: only 1 individual out of 12 with such variants had the phenotype most likely related to the variant. When known pathogenic and novel or rare protein-truncating variants were considered together, the overall rate of confirmed phenotypes was about 19%, with maximum in the subset of novel protein-truncating variants. We report three novel protein truncating variants in APOB and one in MYH7 observed in individuals with hypobetalipoproteinemia and hypertrophic cardiomyopathy, respectively. Our results provide a valuable reference for the clinical interpretation of gene sequencing in Russian and other populations.
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Affiliation(s)
- Vasily E Ramensky
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Alexandra I Ershova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Marija Zaicenoka
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia
| | - Anna V Kiseleva
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Anastasia A Zharikova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Yuri V Vyatkin
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Evgeniia A Sotnikova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Irina A Efimova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Mikhail G Divashuk
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia.,All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Olga V Kurilova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Olga P Skirko
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Galina A Muromtseva
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | | | | | - Maria S Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Svetlana A Shalnova
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Alexey N Meshkov
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
| | - Oxana M Drapkina
- National Medical Research Center for Therapy and Preventive Medicine, Moscow, Russia
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14
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SLC6A3 ( DAT1) as a Novel Candidate Biomarker Gene for Suicidal Behavior. Genes (Basel) 2021; 12:genes12060861. [PMID: 34199792 PMCID: PMC8227035 DOI: 10.3390/genes12060861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 12/02/2022] Open
Abstract
It has been previously shown that the serotonin and dopamine neurotransmitter systems might influence the predisposition to suicidal behavior. This study aims to estimate the contribution of 11 polymorphisms in the genes SLC6A4 (5HTT), HTR1A, HTR2A, HTR1B, SLC6A3 (DAT1), DRD4, DRD2, COMT, and BDNF to suicidal behavior and severity of symptoms of depression and anxiety in the Russian population. The study was performed on 100 patients with repeated suicide attempts and 154 controls. We first found an association between SLC6A3 (DAT1) 40 bp VNTR locus and suicidal behavior. This association was significant; when using the codominant (p = 0.006), dominant (p = 0.001), overdominant (p = 0.004), and log-additive (p = 0.004) models, LL genotype played a protective role (OR = 0.48, 0.29–0.82, p = 0.005). Difference in the distribution of COMT rs4680 genotypes was significant in the codominant (p = 0.04), dominant (p = 0.013), and log-additive (p = 0.02) models, and AA genotype might protect against suicide (OR = 0.49, 0.26–0.91, p = 0.025). SLC6A4 5-HTTLPR + rs25531 locus was significant in the recessive model (p = 0.024), and also affected the severity of symptoms of depression (p = 0.044) and personal anxiety (p = 0.029). Our results suggest that allelic variants of SLC6A3, COMT, and SLC6A4 genes might be considered as risk factors for suicidal attempts.
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15
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Oleksyk TK, Wolfsberger WW, Weber AM, Shchubelka K, Oleksyk OT, Levchuk O, Patrus A, Lazar N, Castro-Marquez SO, Hasynets Y, Boldyzhar P, Neymet M, Urbanovych A, Stakhovska V, Malyar K, Chervyakova S, Podoroha O, Kovalchuk N, Rodriguez-Flores JL, Zhou W, Medley S, Battistuzzi F, Liu R, Hou Y, Chen S, Yang H, Yeager M, Dean M, Mills RE, Smolanka V. Genome diversity in Ukraine. Gigascience 2021; 10:6079618. [PMID: 33438729 PMCID: PMC7804371 DOI: 10.1093/gigascience/giaa159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/21/2020] [Accepted: 12/15/2020] [Indexed: 01/21/2023] Open
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.
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Affiliation(s)
- Taras K Oleksyk
- Department of Biological Sciences, Uzhhorod National University, 32 Voloshyna Str., Uzhhorod 88000, Ukraine.,Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA
| | - Walter W Wolfsberger
- Department of Biological Sciences, Uzhhorod National University, 32 Voloshyna Str., Uzhhorod 88000, Ukraine.,Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA
| | - Alexandra M Weber
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Khrystyna Shchubelka
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA.,Department of Medicine, Uzhhorod National University, Uzhhorod 88000, Ukraine
| | - Olga T Oleksyk
- A. Novak Transcarpathian Regional Clinical Hospital, Uzhhorod 88000, Ukraine
| | | | | | | | - Stephanie O Castro-Marquez
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA.,Departamento de Biología, Universidad de Puerto Rico, Mayagüez, PR 00682, USA
| | - Yaroslava Hasynets
- Department of Biological Sciences, Uzhhorod National University, 32 Voloshyna Str., Uzhhorod 88000, Ukraine
| | - Patricia Boldyzhar
- Department of Medicine, Uzhhorod National University, Uzhhorod 88000, Ukraine
| | - Mikhailo Neymet
- Velyka Kopanya Family Hospital, Transcarpatia 90330, Ukraine
| | | | | | - Kateryna Malyar
- I.I.Mechnikov Dnipro Regional Clinical Hospital, Dnipro 49000, Ukraine
| | | | | | - Natalia Kovalchuk
- Rivne Regional Specialized Hospital of Radiation Protection, Rivne 33028, Ukraine
| | | | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah Medley
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA
| | - Fabia Battistuzzi
- Department of Biological Sciences,Oakland University, Dodge Hall, 118 Library Dr., Rochester, MI 48309, USA
| | - Ryan Liu
- BGI Shenzhen, Shenzhen, 518083, China
| | - Yong Hou
- BGI Shenzhen, Shenzhen, 518083, China
| | - Siru Chen
- BGI Shenzhen, Shenzhen, 518083, China
| | | | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Volodymyr Smolanka
- Department of Medicine, Uzhhorod National University, Uzhhorod 88000, Ukraine
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16
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Barbitoff YA, Skitchenko RK, Poleshchuk OI, Shikov AE, Serebryakova EA, Nasykhova YA, Polev DE, Shuvalova AR, Shcherbakova IV, Fedyakov MA, Glotov OS, Glotov AS, Predeus AV. Whole-exome sequencing provides insights into monogenic disease prevalence in Northwest Russia. Mol Genet Genomic Med 2019; 7:e964. [PMID: 31482689 PMCID: PMC6825859 DOI: 10.1002/mgg3.964] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/07/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Allele frequency data from large exome and genome aggregation projects such as the Genome Aggregation Database (gnomAD) are of ultimate importance to the interpretation of medical resequencing data. However, allele frequencies might significantly differ in poorly studied populations that are underrepresented in large-scale projects, such as the Russian population. METHODS In this work, we leveraged our access to a large dataset of 694 exome samples to analyze genetic variation in the Northwest Russia. We compared the spectrum of genetic variants to the dbSNP build 151, and made estimates of ClinVar-based autosomal recessive (AR) disease allele prevalence as compared to gnomAD r. 2.1. RESULTS An estimated 9.3% of discovered variants were not present in dbSNP. We report statistically significant overrepresentation of pathogenic variants for several Mendelian disorders, including phenylketonuria (PAH, rs5030858), Wilson's disease (ATP7B, rs76151636), factor VII deficiency (F7, rs36209567), kyphoscoliosis type of Ehlers-Danlos syndrome (FKBP14, rs542489955), and several other recessive pathologies. We also make primary estimates of monogenic disease incidence in the population, with retinal dystrophy, cystic fibrosis, and phenylketonuria being the most frequent AR pathologies. CONCLUSION Our observations demonstrate the utility of population-specific allele frequency data to the diagnosis of monogenic disorders using high-throughput technologies.
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Affiliation(s)
- Yury A. Barbitoff
- Bioinformatics InstituteSt. PetersburgRussia
- Department of Genetics and BiotechnologySt. Petersburg State UniversitySt. PetersburgRussia
| | | | | | - Anton E. Shikov
- Bioinformatics InstituteSt. PetersburgRussia
- City Hospital No. 40St. PetersburgRussia
| | - Elena A. Serebryakova
- Department of Genomic MedicineD.O. Ott Research Institute of Obstetrics, Gynaecology and ReproductionSt. PetersburgRussia
| | - Yulia A. Nasykhova
- Department of Genomic MedicineD.O. Ott Research Institute of Obstetrics, Gynaecology and ReproductionSt. PetersburgRussia
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation BiomedicineSt. Petersburg State UniversitySt. PetersburgRussia
| | | | | | - Irina V. Shcherbakova
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation BiomedicineSt. Petersburg State UniversitySt. PetersburgRussia
| | | | - Oleg S. Glotov
- City Hospital No. 40St. PetersburgRussia
- Department of Genomic MedicineD.O. Ott Research Institute of Obstetrics, Gynaecology and ReproductionSt. PetersburgRussia
| | - Andrey S. Glotov
- City Hospital No. 40St. PetersburgRussia
- Department of Genomic MedicineD.O. Ott Research Institute of Obstetrics, Gynaecology and ReproductionSt. PetersburgRussia
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation BiomedicineSt. Petersburg State UniversitySt. PetersburgRussia
- Institute of Living SystemsImmanuel Kant Baltic Federal UniversityKaliningradRussia
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