International Multiconference “Bioinformatics of Genome Regulation and Structure\Systems Biology”

Tag

SNP

4 RESULTS
Systems computational biology: analysis, mathematical modeling and information technologies symposiumGene Network of Type 2 Diabetes: Reconstruction and Analysis

Gene Network of Type 2 Diabetes: Reconstruction and Analysis

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Zamyatin Vladimir Igorevich1, Mustafin Zakhar Sergeevich2, Matushkin Yury Georgievich3, Afonnikov Dmitry Arkadievich4, Klimontov Vadim Valerievich5, Lashin Sergey Aleksandrovich6
1Institute of Cytology and Genetics, Novosibirsk State University, zamyatin@bionet.nsc.ru
2Institute of Cytology and Genetics, Novosibirsk State University, mustafin@bionet.nsc.ru
3Institute of Cytology and Genetics, Novosibirsk State University, mat@bionet.nsc.ru
4Institute of Cytology and Genetics, Novosibirsk State University, ada@bionet.nsc.ru
5Institute of Cytology and Genetics, Novosibirsk State University, klimontov@mail.ru
6Institute of Cytology and Genetics, Novosibirsk State University, lashin@bionet.nsc.ru

Currently, due to the appearance of an increasing number of genomic, molecular, histological data, there is an intensive detailing of individual molecular genetic systems of the human body and phenotypic deviations caused by violations in one or more elements of these systems. At the same time, there is no, as such, a holistic understanding of the nature of the formation and course of type II diabetes, which includes a sufficient amount of available experimental data. In this study, we reconstructed gene networks of transcriptional regulation, functional connectivity, and protein-protein interactions for type 2 diabetes. Information on the evolutionary age of genes was superimposed on the network; it was shown that the genes in question are predominantly “evolutionarily old”. New genes have been found that were not previously associated with type 2 diabetes, such as PER1, PER3, ARHGEF4, genes whose homologues are associated with the onset of diabetes in mice – CLOCK, ARNTL (encoding transcription factors) – the goals for subsequent experimental confirmation. Validation of gene networks by analysis of tissue-specific expression has shown that most genes included in putative signal transduction pathways are expressed in the same tissues.

Genomics, transcriptomics, bioinformatics symposiumGenome-wide association study of Parkinson’s disease using MAX3 test

Genome-wide association study of Parkinson’s disease using MAX3 test

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Georgii Ozhegov1, Dmitry Poverin2, Sergey Medvedev3, Suren Zakian4, Yuri Vyatkin5, Sergey Postovalov6
1Kazan Federal University, Kazan, Russia; Novel Software Systems, Ltd., Novosibirsk, Russia, georgii_provisor@mail.ru
2Novosibirsk State Technical University, Novosibirsk, Russia, foxlandg@gmail.com
3Federal Research Center Institute of Cytology and Genetics, Novosibirsk, Russia, medvedev@bionet.nsc.ru
4Federal Research Center Institute of Cytology and Genetics, Novosibirsk, Russia, zakian@bionet.nsc.ru
5Novosibirsk State University, Novosibirsk, Russia; Novel Software Systems, Ltd., Novosibirsk, Russia, yuri@nprog.ru
6Novosibirsk State Technical University, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia, postovalovsn@gmail.com

Whole exomes for a set of patients with Parkinson’s disease (PD) were sequenced to conduct a genome-wide association study (GWAS) using MAX3 test to find novel genomic variants associated with the disease. As a result, several new variants were identified.

Systems Biology and Biomedicine symposiumAssociations of methylation level of promoter region of MLH1 gene and genotypes of the exonic rs1799977

Associations of methylation level of promoter region of MLH1 gene and genotypes of the exonic rs1799977

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Nadezhda Babushkina1, Anton Markov2, Irina Goncharova3, Ramil Salakhov4, Iuliia Koroleva5, Anna Postrigan6, Aleksei Zarubin7, Aleksei Sleptcov8, Aksana Kucher9, Maria Nazarenko10
1Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, nad.babushkina@medgenetics.ru
2Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, anton.markov@medgenetics.ru
3Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, irina.goncharova@medgenetics.ru
4Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, ramil.salakhov@medgenetics.ru
5Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, yuliya.koroleva@medgenetics.ru
6Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, postrigan.anna@medgenetics.ru
7Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, aleksei.zarubin@medgenetics.ru
8Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, alexei.sleptcov@medgenetics.ru
9Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, aksana.kucher@medgenetics.ru
10Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, maria.nazarenko@medgenetics.ru

The eQTL SNP in exon 8 of the MLH1 gene rs1799977, may affect the methylation level of the promoter region of the same gene. When studying both the effects of methylation level and individual SNPs on the formation of phenotypic variability in humans and the risk of developing pathological conditions, it is necessary to use a integrated data analysis approach.

Systems Biology and Biomedicine symposiumWhole-exome Sequencing Association Studies On Impaired Spermatogenesis In Different Ethnic Groups In Russia

Whole-exome Sequencing Association Studies On Impaired Spermatogenesis In Different Ethnic Groups In Russia

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Semyon K. Kolmykov1, Gennadiy V.Vasiliev2, Mikhail P. Ponomarenko3, Maxim A. Kleshev4, Aleksandr V. Osadchuk5, Ludmila V. Osadchuk6
1Institute of Cytology and Genetics SB RAS, kolmykovsk@gmail.com
2Institute of Cytology and Genetics SB RAS, genn@bionet.nsc.ru
3FRC Institute of Cytology and Genetics SB RAS, pon@bionet.nsc.ru
4Institute of Cytology and Genetics SB RAS, max82cll@bionet.nsc.ru
5Institute of Cytology and Genetics SB RAS, osadchuk@bionet.nsc.ru
6Institute of Cytology and Genetics SB RAS, losadch@bionet.nsc.ru

In this study we identified single nucleotide polymorphisms in whole-exome sequencing data for different ethnic groups in Russia: Slavs, Yakuts and Buryats, and investigated its associations with impaired spermatogenesis.