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Khvorykh G.V.

National Research Center «Kurchatov Institute»

Ageeva E.S.

V.I. Vernadsky Crimean Federal University

Kubyshkin A.V.

V.I. Vernadsky Crimean Federal University

Bioinformatics selection of tagging polymorphisms for studying the functions of the VAV3 gene

Authors:

Khvorykh G.V., Ageeva E.S., Kubyshkin A.V.

More about the authors

Journal: Molecular Genetics, Microbiology and Virology. 2025;43(4‑2): 91‑96

DOI: 10.17116/molgen20254304291

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Table of contents

BIOINFORMATICS SELECTION OF TAGGING POLYMORPHISMS FOR STUDYING THE FUNCTIONS OF THE VAV3 GENE
BIOINFORMATICS SELECTION OF TAGGING POLYMORPHISMS FOR STUDYING THE FUNCTIONS OF THE VAV3 GENE

To cite this article:

Khvorykh GV, Ageeva ES, Kubyshkin AV. Bioinformatics selection of tagging polymorphisms for studying the functions of the VAV3 gene. Molecular Genetics, Microbiology and Virology. 2025;43(4‑2):91‑96. (In Russ.)
https://doi.org/10.17116/molgen20254304291

Подписка 2026 Молекулярная генетика, микробиология и вирусология (Molecular Genetics, Microbiology and Virology)
МСФ на ЯМ
Использование инфографики авторами научных работ
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Abstract:

INTRODUCTION

The VAV3 gene is promising for studying its role in the development of molecular mechanisms of pathology. The GWAS Catalog database contains 53 studies of 44 phenotypes, in which single nucleotide polymorphism variants of the VAV3 gene were identified with a statistical significance level of p-value<1 × 10-05.

THE PURPOSE OF THE STUDY

Is to form a sample of marker SNPs to test the hypotheses of the participation of VAV3 in the formation of phenotypic traits in representatives of the Russian ethnic group.

MATERIAL AND METHODS

To achieve this goal, we used bioinformatics methods, applying them to genotypic data from 1000 Genomes Project.

RESULTS

Number of 1000 Genomes Project (phase III) SNPs located within the boundaries of the VAV3 gene with a 5000 bp offset. from the 5´ and 3´ ends, and the MAF of at least 10% was 688.

Grouping polymorphisms based on the distance between them takes into account the interaction between SNPs in a block. The number of polymorphisms marked by these tagSNPs did not exceed 4. The intersection of tagSNP lists obtained by two methods showed tagSNPs that were more effective. Tagger and TAGster identified a common marker SNP, rs345292, marking 16 highly linked SNPs. Tagger and Clustag identified rs12733154, which marked blocks of 39 polymorphisms. TAGster and Clustag pointed to rs71655926, which marks 10 polymorphisms. These tagSNPs are located in the introns of the gene of interest and can be considered candidates for association studies.

CONCLUSION

Comparative analysis allowed us to identify three tagSNPs with at least 10 marked polymorphisms confirmed by two methods: rs345292, rs12733154, rs71655926. These polymorphisms may be candidates for studying the role of the VAV3 gene in the mechanisms of pathology development.

Keywords:

single-nucleotide polymorphism
tagging SNP
VAV3

Authors:

Khvorykh G.V.

National Research Center «Kurchatov Institute»

Ageeva E.S.

V.I. Vernadsky Crimean Federal University

Kubyshkin A.V.

V.I. Vernadsky Crimean Federal University

Received:

06.07.2025

Accepted:

05.10.2025

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References:

  1. Cherfils J, Zeghouf M. Regulation of small GTPases by GEFs, GAPs, and GDIs. Physiol Rev. 2013;93(1):269-309.  https://doi.org/10.1152/physrev.00003.2012
  2. Movilla N, Bustelo XR. Biological and regulatory properties of Vav-3, a new member of the Vav family of oncoproteins. Mol Cell Biol. 1999;19(11):7870-85.  https://doi.org/10.1128/mcb.19.11.7870
  3. Bustelo XR. Vav family exchange factors: an integrated regulatory and functional view. Small GTPases. 2014;5(2):e973757. https://doi.org/10.4161/21541248.2014.973757
  4. Abdellaoui A, Yengo L, Verweij KJH, Visscher PM. 15 years of GWAS discovery: Realizing the promise. The American Journal of Human Genetics. 2023;110(2):179-194.  https://doi.org/10.1016/j.ajhg.2022.12.011
  5. Kichaev G, Bhatia G, Loh PR, Gazal S, Burch K, Freund, MK et al. Leveraging polygenic functional enrichment to improve GWAS power. The American Journal of Human Genetics. 2018;104(1):65-75.  https://doi.org/10.1016/j.ajhg.2018.11.008
  6. Mathieu S, Briend M, Abner E, Couture C, Li Z, Bossé Y, et al. Genetic association and Mendelian randomization for hypothyroidism highlight immune molecular mechanisms. iScience. 2022;25(9):104992. https://doi.org/10.1016/j.isci.2022.104992
  7. Fujikawa K, Iwata T, Inoue K, Akahori M, Kadotani H, Fukaya M, et al. VAV2 and VAV3 as candidate disease genes for spontaneous glaucoma in mice and humans. PLoS ONE. 2010;5(2):e9050. https://doi.org/10.1371/journal.pone.0009050
  8. Liang YJ, Wang YY, Rong SS, Chen ZJ, Chen SY, Tham JA, et al. Genetic associations of primary Angle-Closure disease. JAMA Ophthalmology. 2024;142(5):437.  https://doi.org/10.1001/jamaophthalmol.2024.0363
  9. Chen Y, André M, Adhikari K, Blin M, Bonfante B, Mendoza‐Revilla J, et al. A genome‐wide association study identifies novel gene associations with facial skin wrinkling and mole count in Latin Americans. British Journal of Dermatology. 2021;185(5):988-998.  https://doi.org/10.1111/bjd.20436
  10. Wu J, Lin C, Yang C, Pan L, Liu H, Zhu S, et al. Identification and validation of key biomarkers and potential therapeutic targets for primary open-angle glaucoma. Science China Life Sciences. 2023;66(12):2837-2850. https://doi.org/10.1007/s11427-022-2344-5
  11. Batista-Liz JC, Calvo-Río V, Sebastián Mora-Gil M, Sevilla-Pérez B, Márquez A, Leonardo MT, et al. Mucosal immune defence gene polymorphisms as relevant players in the pathogenesis of IGA vasculitis? International Journal of Molecular Sciences. 2023;24(17):13063. https://doi.org/10.3390/ijms241713063
  12. Aleksic B, Kushima I, Hashimoto R, Ohi K, Ikeda M, Yoshimi A, et al. Analysis of the VAV3 as candidate gene for schizophrenia: Evidences from Voxel-Based Morphometry and Mutation Screening. Schizophrenia Bulletin. 2012;39(3):720-728.  https://doi.org/10.1093/schbul/sbs038
  13. Han X, Shen Q, Hou C, Yang H, Chen W, Zeng Y, et al. Disease clusters subsequent to anxiety and stress-related disorders and their genetic determinants. Nature Communications. 2024;15(1). https://doi.org/10.1038/s41467-024-45445-2
  14. Chen J, Zhang C, Peng J, Tang C, Zhang C, Zhang M, et al. Gender-specific lncRNA-miRNA-mRNA regulatory network to reveal potential genes for primary open-angle glaucoma. Experimental Eye Research. 2023;236:109668. https://doi.org/10.1016/j.exer.2023.109668
  15. Xia C, Zhu K, Zhang Y, Chen J, Yu C, Gao T, et al. Serum exosome-derived miR-146a-3p promotes macrophage M2 polarization in allergic rhinitis by targeting VAV3 via PI3K/AKT/mTOR pathway. International Immunopharmacology. 2023;124:110997. https://doi.org/10.1016/j.intimp.2023.110997
  16. Hill WG, Robertson A. Linkage disequilibrium in finite populations. Theoretical and Applied Genetics. 1968;38(6):226-231.  https://doi.org/10.1007/BF01245622
  17. Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA. Selecting a maximally informative set of Single-Nucleotide polymorphisms for association analyses using linkage disequilibrium. The American Journal of Human Genetics. 2004;74(1):106-120.  https://doi.org/10.1086/381000
  18. Khvorykh G, Khrunin A, Filippenkov I, Stavchansky V, Dergunova L, Limborska S. A workflow for selection of single nucleotide polymorphic markers for studying of genetics of ischemic stroke outcomes. Genes. 2021;12(3):328.  https://doi.org/10.3390/genes12030328
  19. Auton A, Abecasis GR, Altshuler DM (Co-Chair), et al. A global reference for human genetic variation. Nature. 2015;526(7571):68-74.  https://doi.org/10.1038/nature15393
  20. Nelis M, Esko T, Mägi R, Zimprich F, Zimprich A, Toncheva D, et al. Genetic Structure of Europeans: A View from the North–East. PLoS ONE. 2009;4(5):e5472. https://doi.org/10.1371/journal.pone.0005472
  21. Khrunin AV, Khokhrin DV, Filippova IN, Esko T, Nelis M, Bebyakova NA, et al. A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe. PLoS ONE. 2013;8(3):e58552. https://doi.org/10.1371/journal.pone.0058552
  22. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156-2158. https://doi.org/10.1093/bioinformatics/btr330
  23. Koranne S. Hierarchical Data Format 5: HDF5. In: Handbook of Open Source Tools. Springer, Boston, MA. 2011. https://doi.org/10.1007/978-1-4419-7719-9_10
  24. Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2004;21(2):263-265.  https://doi.org/10.1093/bioinformatics/bth457
  25. Xu Z, Kaplan NL, Taylor JA. TAGster: efficient selection of LD tag SNPs in single or multiple populations. Bioinformatics. 2007;23(23):3254-3255. https://doi.org/10.1093/bioinformatics/btm426
  26. Ao SI, Yip K, Ng M, Cheung D, Fong PY, Melhado I, et al. CLUSTAG: hierarchical clustering and graph methods for selecting tag SNPs. Bioinformatics. 2004;21(8):1735-1736. https://doi.org/10.1093/bioinformatics/bti201
  27. de Bakker P. I. W. Selection and Evaluation of Tag-SNPs Using Tagger and HapMap. In Cold Spring Harbor Protocols. 2009;6:ip67. https://doi.org/10.1101/pdb.ip67
  28. Wickham H. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. 2016. https://doi.org/10.1007/978-3-319-24277-4
  29. Hunter JD. MatPlotLib: a 2D Graphics environment. Computing in Science & Engineering. 2007;9(3):90-95.  https://doi.org/10.1109/mcse.2007.55
  30. GNU P. Free Software Foundation. Bash (5.1)[Unix shell program]. 2020. https://www.gnu.org/software/bash
  31. Wall L, Christiansen T, Orwant J. Programming Perl, 3rd ed.; O’Reilly Media, Inc.: Sebastopol, CA, USA, 2000; ISBN 978-0-596-00027-1. 
  32. R Core Team. R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing, Vienna, Austria, 2021.
  33. Rossum G, Drake FL. Python 3 Reference Manual; CreateSpace: Scotts Valley, CA, USA, 2009.
  34. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature. 2001;409(6822):928-933.  https://doi.org/10.1038/35057149
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