Gene Network of Type 2 Diabetes: Reconstruction and Analysis

Zamyatin Vladimir Igorevich1, Mustafin Zakhar Sergeevich2, Matushkin Yury Georgievich3, Afonnikov Dmitry Arkadievich4, Klimontov Vadim Valerievich5, Lashin Sergey Aleksandrovich61Institute of Cytology and Genetics, Novosibirsk State University, zamyatin@bionet.nsc.ru2Institute of Cytology and Genetics, Novosibirsk State University, mustafin@bionet.nsc.ru3Institute of Cytology and Genetics, Novosibirsk State University, mat@bionet.nsc.ru4Institute of Cytology and Genetics, Novosibirsk State University, ada@bionet.nsc.ru5Institute of Cytology and Genetics, Novosibirsk State University, klimontov@mail.ru6Institute 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.

Read More

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

Poster (download) 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.

Read More

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

Video (download) Nadezhda Babushkina1, Anton Markov2, Irina Goncharova3, Ramil Salakhov4, Iuliia Koroleva5, Anna Postrigan6, Aleksei Zarubin7, Aleksei Sleptcov8, Aksana Kucher9, Maria Nazarenko101Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, nad.babushkina@medgenetics.ru2Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, anton.markov@medgenetics.ru3Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, irina.goncharova@medgenetics.ru4Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, ramil.salakhov@medgenetics.ru5Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, yuliya.koroleva@medgenetics.ru6Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, postrigan.anna@medgenetics.ru7Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, aleksei.zarubin@medgenetics.ru8Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, alexei.sleptcov@medgenetics.ru9Research Institute of Medical Genetics, TNRMC RAS, Tomsk, Russia, aksana.kucher@medgenetics.ru10Research 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.

Read More

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

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.

Read More