Panel of X-linked single-nucleotide polymorphic markers for DNA identification (XSNPid) based on multiplex genotyping by multilocus PCR and MALDI-TOF mass spectrometry

Human genetic markers linked with the X chromosome (X-linked) are used in the field of population and medical genetics, as well as for DNA identification of individuals in forensic science and forensic medicine. We proposed an XSNPid panel that consists of 66 unlinked single nucleotide X chromosome markers and developed a protocol for their multiplex genotyping using multilocus PCR and MALDI-TOF mass spectrometry. The XSNPid panel is genotyped within two multiplexes (36 and 30 markers). The developed protocol provides an efficient genotype reading; the fraction of determined genotypes is 98.29%. The high level of gene diversity (0.461) for the X-linked SNPs included in the panel is characteristic of the Russian population. A total of 63 out of 66 markers that provide a high efficiency of genotyping and independent inheritance are suitable for DNA identification purposes. The XSNPid panel is characterized by a very high discriminating ability when studying the Russian population. The probability of genotype coincidence in two unrelated individuals is 9 × 10^–27 for women and 2 × 10^–18 for men. Also, the XSNPid panel has a greater multiplex capacity in addition to a higher discriminating ability compared to the other closest analogues of the X chromosome SNP sets, which makes it more cost effective and less time consuming. The XSNPid panel is a convenient tool, not only for individual DNA identification, but also for population genetic studies.     

Search for genetic markers of climatic adaptation in populations of North Eurasia

Genetic diversity of native populations of North Eurasia is investigated using a panel of genetic markers of candidate genes for cold climate adaptation. A high level of within- and between-population variability is detected. Comparative analysis of data on North Eurasian populations combined with data on worldwide populations from the 1000 Genomes and HDGP projects reveals correlations of genetic diversity in candidate genes for cold climate adaptation with key climate parameters, as well as the increase of genetic diversity in markers of this group of genes with the increase of latitude, that is, as modern humans migrated out of Africa. Using the method of searching for extreme empirical values of the coefficient of genetic diversity, signals of directional selection for markers of six genes adaptive to cold (MYOF, LONP2, IFNL4, MKL1, SLC2A12, and CPT1A) are found. The data are discussed in framework of the hypothesis of decanalization of genome–phenome relationships under the pressure of natural selection during human settlement throughout the world.     

Association of the genenetic polymorphism of cytokines and their receptors with climate and geographic factors in human populations

The variability of eight polymorphic variants of the IL4, IL4R, IL10, IL13, IL12A, and IL12RB2 genes encoding key cytokines and their receptors in 57 world populations has been assessed. A correlation between the allele frequency distribution of the examined genes and climatic and geographic factors was observed.     

The Multiplex Genotyping Method for Single-Nucleotide Polymorphisms of Genes Associated with Obesity and Body Mass Index

Russian Journal of Genetics - Obesity is one of the global health problems resulting in significant economic and social damage in both developed and developing countries. Overweight and obesity are...     

Development of Multiplex Genotyping Method of Polymorphic Markers of Genes Associated with Cognitive Abilities

A developed method of multiplex genotyping of polymorphic markers of genes associated with cognitive abilities and neuropsychiatric diseases is based on multilocus PCR and MALDI-TOF mass spectrometry of DNA molecules. The frequencies of 32 single-nucleotide markers localized in 24 genes are analyzed in a sample of elderly people from the Russian population of Tomsk. The data obtained are compared with data for populations from the 1000 Genomes Project.     

The Role of Natural Selection in the Formation of the Genetic Structure of Populations by SNP Markers in Association with Body Mass Index and Obesity

Molecular Biology - Abstract—Obesity is one of the major challenges in modern society. More than a third of the world’s population suffers froms overweight. This phenotype affects the...     

Association study of genetic markers of schizophrenia and its cognitive endophenotypes

A replicative analysis of associations of 15 SNPs located in the regions of 11 genes (TCF4, VRK2, NOTCH4, ZNF804A, AGBL1, RELN, ZFP64P1, KCNB2, CSMD1, CPVL, NRIP1) and three intergenic regions (SLCO6A1/LINCOO491, LOC105376248/LOC105376249, SPA17/NRGN) with schizophrenia was conducted in the Russian population of the Siberian region. These SNPs were previously identified in genome-wide association studies (GWAS) of schizophrenia and cognitive abnormalities. The present study confirmed associations of KCNB2 rs2247572, CSMD1 rs2616984, and intergenic rs12807809 located in SPA17/NRGN with schizophrenia. It was established that the frequency of the CSMD1 rs2616984 G/G genotype was higher in patients compared to the control group (OR = 1.73; CI: 1.14–2.62; р = 0.0337). The frequencies of the KCNB2 rs2247572 TT genotype (OR = 0.41; CI: 0.20–0.87; р = 0.0485) and intergenic rs12807809 CT genotype located in SPA17/NRGN (OR = 0.70; CI: 0.53–0.94; р = 0.0464) were significantly decreased in patients compared to the control group.     

Variability and identification power of 60 X-chromosome in two native Siberian populations

Genetic diversity of 60 X-chromosome single nucleotide polymorphisms (XSNPid panel) in populations of Siberian Tatars and Tuvinians is described. A close spectrum of allele frequencies and a low level of their genetic differentiation (G_st = 0.021) is revealed. High discriminating power of the XSNPid panel in populations under study is demonstrated. The random matching probability (MP) of multilocus genotypes in males is 1.12 × 10^–18 in Siberian Tatars and 7.77 × 10^–16 in Tuvans. In females, MP is several orders of magnitude lower: 1.51 × 10^–25 in Siberian Tatars and 1.83 × 10^–23 in Tuvinians.     

Signals of Positive Selection in Human Populations of Siberia and European Russia

Russian Journal of Genetics - Human adaptation to extreme climatic and geographic conditions mediated by natural selection may be one of the major factors for formation of genetic structure in...