[Genetic risk assessment of the joint effect of several genes: Critical appraisal].

When assessing the combined action of genes on the quantitative or qualitative phenotype we encounter a phenomenon that could be named the "paradox of the risk score summation." It arises when the search of risk allele and assessment of their combined action are performed with the same single dataset. Too often such methodological error occurs when calculating the so called genetic risk score (GRS), which refers to the total number of alleles associated with the disease. Examples from numerous published genetic association studies are considered in which the claimed statistically significant effects can be attributed to the "risk score summation paradox." In the second section of the review we discuss the current modifications of multiple regression analysis addressed to the so called "n ≪ p problem" (the number of points is much smaller than the number of possible predictors). Various algorithms for the model selection (searching the significant predictor combinations) are considered, beginning from the common marginal screening of the "top" predictors to LASSO and other modern algorithms of compressed sensing.

[The study of aberrant methylation in blood leukocytes of liquidators of the Chernobyl accident].

The study of aberrant methylation of CpG islands in the promoter regions of genes (P16/CDKN2A, P14/ARF, RASSF1A, GSTP1) in blood leukocytes of liquidators of the Chernobyl accident (n = 83, 38-76 years of age) and control subjects of two groups (n = 48, age ≤ 35 and n = 65, age > 35) was carried out using methylation-sensitive restriction endonuclease analysis followed by PCR. The total number of AciI sites in the analyzed fragments ranged from 2 to 7 for different genes. Only 1 subject (2.1%) from the control group (healthy young individuals, age ≤ 35) has methylation of the studied CpG--dinucleotides of RASSF1A gene. Promoter methylation of at least one of the genes analyzed was observed in 28.92% liquidators and significantly exceeded (p = 0.016) such rate in a one-age (> 35 years of age) control group (12.31%). A significantly elevated frequency (p = 0.023) of individuals with abnormal methylation of GSTP1 gene in the group of liquidators as compared to the control group was revealed. The occurrence of promoter methylation of RASSF1A gene significantly correlated with aging both in the control group (r = 0.214; p = 0.023) and in the liquidators of the Chernobyl accident (r = 0.230; p = 0.036). No similar trend was found for other genes. Multiple regression analysis showed that the growth in the number of methylated loci of a set of genes p16, p14 and GSTP1 is exclusively due to the fact of exposure (OR = 7.32, 95% CI = 2.49-25.83, p-value = 2.7 x 10(-5)). The results obtained demonstrate for the first time the reality of the radiation-induced aberrant methylation of CpG islands in promoters of genes involved in the basic protective, functions of cells in the human body in remote periods after radiation exposure.

The Impact of ADH1B Alleles and Educational Status on Levels and Modes of Alcohol Consumption in Russian Male Individuals.

Alcohol abuse is one of the main reasons behind the low life span in Russia. Both social and genetic factors affect the alcohol consumption level. The genetic factors are alleles of the alcohol dehydrogenase ADH1B and aldehyde dehydrogenaseALDH2 genes. We have typed and found frequencies for the alleles in a cohort of 642 men, ethnic Russians. The individuals of the cohort were asked to complete a questionnaire in the framework of the Izhevsk Family Study (Leon et al., 2007, 2009) regarding the amount of alcohol consumed and on the type of hazardous alcohol consumption (nonbeverage alcohol consumption and the so-called "zapoï" which is a Russian term for a heavy drinking bout lasting for at least 2 days, when an individual is withdrawn from the normal social life). The ADH1B*48His allele was found among heterozygous individuals only (N=68, 10.6% of the cohort). The ALDH2*504Lys allele was also found among heterozygous individuals only (N=2, 0.3%) The effect of ADH1B alleles and the influence of the education level on the amount and type of alcohol consumed had not previously been studied in Russians. We have found that the amount of consumed alcohol is 21.6% lower (1733 g of ethanol per year) for ADH1B*48His allele carriers in the cohort of Russian men. The amount of consumed alcohol was found to be 9.8% lower (793 g of ethanol per year) in the case when individuals had a higher education as compared to those who had a secondary- or elementary school education level in the same cohort. Hence, the protective effect of the genetic factor (ADH1B*48His allele carriage) has proven to be more pronounced than the influence of the social factor (education level) at the individual level in the cohort of Russian men. Both factors have also proven to have a protective effect against hazardous types of alcohol consumption. Zapoï was not scored among individuals of the cohort with ADH1B*48His allele carriage (OR=12.6, P=0.006), as compared to 8.4% of "zapoï" individuals who did not carry the ADH1B*48His allele (genotype Arg/Arg).The percentage of individuals who consume non-beverage alcohol is lower (0.6%) in the subcohort of people with a higher education degree. This percentage is higher (6.0%, OR=10.0, P=0.004) in the subcohort of people without a higher education degree.

[Genetic and cytogenetic predictors of human chromosomal radiosensitivity].

We studied association between the frequencies of gamma-induced (1 Gy in vitro) chromosome aberrations in blood lymphocytes and polymorphism of 45 repair candidate genes, detoxification and oxidative stress genes (53 sites) for 99 healthy volunteers. The levels of chromosome-type aberrations correlated with carriage of the minor alleles of the genes OGG1 Ser326Cys, ABCB1 Ile1145 = and NQO1 Pro187Ser (p = 0.0002). We have shown that all the revealed genetic associations were less effective in predicting chromosomal radiosensitivity as compared to the correlations between spontaneous and gamma-induced aberrations (p = 1.0 x 10(-6)). The addition of genetic markers to cytogenetic predictors improved the predictive accuracy for chromosomal radiosensitivity with the multiple correlation coefficient reaching R = 0.58 (p = 3.1 x 10(-8)). Thereby we were able to explain more than 30% of the population variability in chromosomal radiosensitivity.

Risk of HIV Infection and Lethality Are Decreased in CCR5del32 Heterozygotes: Focus Nosocomial Infection Study and Meta-analysis.

CCR5del32 Homozygous deletion in the chemokine receptor R5 gene provides almost complete protection to individuals against HIV infection. However, data relating to the protective effect forCCR5del32 heterozygous individuals have been contradictory. The frequency of theCCR5del32allele in population control cohorts was compared with that of a group of children (27 Kalmyks and 50 Russians) infected by G-subtype HIV-1 in a nosocomial outbreak. The frequency of theCCR5del32allele was shown to be lower among the infected children in comparison with that of the control group; however, the difference was small and statistically insignificant. Similar results were obtained in a number of earlier studies. The insignificance of the small differences could be a result of one of two reasons. (i) The fact that there is no protective effect of the heterozygous state, and that the phenomenon depends only on the fluctuation of allele frequencies. In this case, there would be no differences even if the infected cohort is enlarged. (ii)The protective effect of the heterozygous state is real; however, the size of the studied cohort is insufficient to demonstrate it. In order to discern between these two reasons, a meta-analysis of data from 25 published articles (a total of 5,963 HIV-infected individuals and 5,048 individuals in the control group, including the authors' own data) was undertaken. A conclusion was drawn from the meta-analysis that theCCR5del32 allele protects individuals against the HIV infection even in a heterozygous state (OR=1.22, 95%CI=1.10-1.36). The risk of HIV infection forCCR5 wt/del32 heterozygotes was lower by at least 13% as compared to that for wild typeCCR5 wt/wthomozygotes. Prior to this study, no data of the type or any conclusions had been published for Caucasians. The mortality rate in the 15 years following the infection was found to be approximately 40% lower forCCR5del32 heterozygotes in comparison with that for the wild type homozygotes in the studied group. The size of the studied group was insufficient to claim difference validity (OR=2.0;p= 0.705), even though the effect quantitatively matched the published data. The features of the meta-analysis influencing the threshold level and the statistical validity of the effects are being discussed. The level of theCCR5del32 protective effect on the chances to be infected with HIV and on the outcome of the HIV infection was assessed for various ethnic groups.

[Morphological abnormalities among the offspring of irradiated pines (pinus sylvestris L.) from chernobyl populations].

The significant changes of the quantitative signs and the increase in the frequency of morphological abnormalities were found among the offspring of pines (Pinus sylvestris L.) exposed as a result of the Chernobyl accident. We have detected that the typical effects of radiation exposure (stimulation, inhibition, abnormalities of morphogenesis) are transmitted to the offspring of irradiated pine trees. The mechanisms of their occurrence are discussed.

[Candidate gene association study of the radiosensitivity of human chromosomes with candidate gene polymorphisms upon exposure to gamma-irradiation in vitro and in vitro].

The genotypic associations of the frequencies of spontaneous and radiation-induced chromosome aberrations in human lymphocytes were studied to develop genetic tests for elevated and reduced radiosensitivity. Cytogenetic analysis and genotyping (19 sites of detoxification and DNA repair genes) were carried out for a sample of Chernobyl cleanup workers (n = 83) and for a homogenous control sample of volunteers (n = 99). In both groups, the frequency of chromosome-type aberrations proved to be elevated in carriers of minor alleles in the XPD gene (sites T2251G (Lys751Gln) and G862A (Asp312Asn)) and a combination of GSTM1-GSTT1-positive genotypes. The polymorphism of these gene did not affect the frequency of gamma-radiation-induced aberrations in the controls (1 Gy in vitro), which was associated with the alleles of the OGG1, XRCC1, and CYP1A1 genes. Thus, the frequencies of spontaneous and in vitro induced chromosome-type aberrations are associated with the alleles of different xenobiotic detoxification and DNA repair genes. At the same time, among the cleanup workers (irradiated in vivo), the elevated frequency of aberrations was observed in the carriers of the genotypes associated with the higher rate of spontaneous (but not induced in vitro) cytogenetic damages in the controls.

[Variability in the frequency of TCR-mutant lymphocytes associated with gene polymorphisms in women living in radiation-polluted areas].

The paper presents the results of an association study of a predisposition to increased somatic mutagenesis detected by the test for TCR-mutant lymphocytes (CD3-CD4+ phenotype). A study group consisted of 251 women who lived in the towns polluted by radionuclides after the Chernobyl accident and had estrogen-dependent reproductive system diseases (uterine myoma, fibrocystic mastopathy). The carriage of minor alleles in the genes (CYP1A1, GSTM1, and ABCB1) of all three stages of detoxification of xenobiotics was associated with the rise in the spontaneous frequency of TCR-mutant cells. Overweight modified the genotype (at CYP1A1 and GSTT1 loci) - environment interaction. When background radiation became higher, the contribution of minor alleles in the CYP1A1 genes to the instability recorded as the elevated frequency of TCR-mutant cells increased.

[Complex study of the mutagenic effect of soil pollutions with petrochemical products in the Chechen Republic].

A study to evaluate congenital morphogenetic variants (CMGVs) and the association of the polymorphism of the xenobiotic detoxification and repair genes with cytogenetic parameters was conducted for the first time in children living in different climatic zones and areas polluted with primary petroleum refining products. Analysis of CMGVs and cytogenetic parameters in children points to the total genotoxic impact of oil pollutions. The children's higher sensitivity to environmental pollution is associated with the polymorphism of the detoxification gene, with the base excision repair gene XRCC1 in particular.

Association of cytokine gene alleles with the inflammation of human periodontal tissue.

Gingivitis and periodontitis are chronic inflammatory diseases of the periodontal tissue in humans caused by both environmental and genetic factors. The human cytokine genes that regulate the immune response may play an important role in the development of these chronic inflammatory diseases. The aim of this study is to analyze the allele status of eight human cytokine genes and to associate it with the inflammation of periodontal tissue in humans. A total of 296 unrelated males of Russian origin were studied. A significant association of theIL1BandIL6 minor alleles and gingivitis was found. In addition, we found a significant association of the OHI-S index with theIL18gene alleles. The influence of genetic factors on gingivitis may contribute to the understanding of the mechanisms of interaction between genetic and environmental factors in periodontal conditions, and to the identification of risk groups for effective prevention and treatment.

[Genetic study of predisposition to community-acquired pneumonia].

The study included 243 patients with acute community-acquired pneumonia and 173 healthy subjects. The following candidate loci were used to investigate genetic variability: 3 sites of CYP1A1, GSTM1, GSTT1, GSTP1, ACE gene of the rennin-angiotensin system, chemokine receptor gene CCR5. Enhanced predisposition to pneumonia was shown to be characteristic of homozygotes in deletion at the ACE locus (OR = 1.8; p = 0.013), carriers of normal alleles of the GSTM1 locus (OR = 1.7; p = 0.010), and homozygotes in allele 606T of the CYP1A1 gene (OR = 1.6; p = 0.020).

[Allelic variants of polymorphic genes associated with a higher frequency of chromosome aberrations].

Genotypic associations were studied for the frequency of chromosome aberrations in human peripheral blood lymphocytes. Cytogenetic analysis (1000 metaphase plate per individual) and genotyping at 19 sites of genes involved in detoxification and DNA repair were performed in a sample of 83 Chernobyl liquidators and a matched control sample of 96 volunteers. In either sample, the frequency of chromosome aberrations was higher in carriers of the minor alleles of the XPD gene (sites 2251T > G and 862G > A) and the positive genotypes of the GSTM1-GSTT1 genes. The highest frequency of chromosome aberrations was observed in carriers of a combined genotype including at least one minor allele of the XPD sites + at least one insertion in the GSTM1-GSTT1 genes. The high-risk genotype, which had a prevalence of 64%, was strongly associated with a higher frequency of chromosome aberrations in both volunteers (OR = 6.9, P = 0.008) and Chernobyl liquidators (OR = 5.6, P = 0.002).

[The relationship between genotypes and frequencies of chromosome aberrations in human lymphocytes under irradiation in vivo and in vitro].

The data on the variability of an elevated level of the frequencies of chromosome aberrations for a group of liquidators of the Chernobyl Nuclear Station accident depending on genotypes by candidate loci are presented. The genotyping was carried out by sites, which previously showed the associations with the cytogenetic variability in control experiments. It was shown that, for a group of liquidators heterozygote by site SOD2 C47T, the control level of the frequency of chromosome aberrations is not exceeded significantly. At the tendency level, the frequency of aberrations for liquidators was reduced for double homozygotes by deletions of genes GSTM1-GSTT1 and for homozygotes by the minor allele of site CYP1A1 T606G that is in an accordance with the results of experiments with the control sampling. The elevated level of chromosome aberrations for liquidators, as a whole, is observed for genotypes, which are characteristic of an elevated level of spontaneous aberrations, and it does not completely correspond to genotypes with the elevated radiosensitivity of chromosomes.

[Remote consequences of a chronic radiation for the population of Hypochoeris maculata L growing on the territory of East-Ural radioactive trace].

The caryological study has been carried out on Hypochoeris maculata L. plants growing on the East-Urals radioactive trace. Two Hypochoeris maculata L. populations have been observed. The experimental population grows in contaminated area. 90Sr contamination density is 55 MBq/m2, 137Cs contamination density is 2.5 M Bq/m2. The control population grows in radionuclide-free area. Both in the experimental and in the control populations the plants have been detected bearing extra B-chromosomes in their karyotype. But their frequency was higher in the experimental population than in the control one. In the experimental population the plants with main A-chromosome set karyotype changes have been met in 9 families out of 30 families observed. In the control population one such family has been detected out of 27 families observed. Two plants with karyotype changes in both chromosome sets have been detected in one family of the experimental population, which indicates a possibility of sibling species appearance in the experimental population.

[Polymorphism of repair genes and cytogenetic radiation effects].

For 99 healthy volunteers, the frequencies of spontaneous and y-induced (1 Gy in vitro) chromosome aberrations in blood lymphocytes were compared with the results of PCR-genotyping by 8 repair genes: XRCC1, XPD, ERCC1, APEXI, RAD23B, OGG1, ATM, Tp53 (in all, 10 polymorphic sites). The frequency of spontaneous aberrations of chromosome type increased additively with the number of copies of minor allele of excision repair gene XPD variant *2251G and *862A D (p = 0.025). The frequency of gamma-induced chromosome aberrations proved to be elevated for the carriers of a minor allele OGG1*977G (p = 0.011). The significantly elevated number of gamma-induced chromosome aberrations was also observed for the carriers of major alleles XRCC1*G1996 and XRCC1*C589 (p = 0.002).

[Somatic mutagenesis in human lymphocytes depending on genotypes for detoxification and oxidative response loci].

Associations of polymorphism of seven detoxification genes and three genes of oxidative response with the frequency of chromosome aberrations in human peripheral blood lymphocytes were studied. The genotyping data were correlated with the frequencies of spontaneous and gamma-induced (1 Gy in vitro) chromosome aberrations estimated for a group of healthy donors (97 males under 25 years of age) by analyzing 500-1000 metaphase cells per individual. The spontaneous level of aberrations of the chromosomal type was reduced in homozygotes for the GSTM1 locus deletion, and especially in double homozygotes for deletions of the GSTM1 and GSTT1 genes. The frequency of gamma-induced chromosome aberrations was reduced in G/G homozygotes for the minor allele of the poorly studied CYP1A1 T606G site: 0.094 +/- 0.006 against 0.112 +/- 0.002 for T allele carriers (P = 0.004). Linkage of the T606G site with well known and functionally important sites of the CYP1A1 gene (A4889G, T3801C) was analyzed.

Association study of xenobiotic detoxication and repair genes with malignant brain tumors in children.

This study presents the results of research on DNA polymorphism in children with malignant brain tumors (172 patients, 183 in the control group). Genotyping was performed using an allele-specific tetraprimer reaction for the genes of the first (CYP1A1 (2 sites)) and second phases of xenobiotic detoxication (GSTM1, GSTT1, GSTP1, GSTM3), DNA repair genesXRCC1, XPD(2 sites),OGG1, as well asNOS1andMTHFR.The increased risk of disease is associated with a minor variant ofCYP1A1(606G) (p = 0.009; OR = 1.50) and a deletion variant ofGSTT1, (p = 0.013, OR = 1.96). Maximum disease risk was observed in carriers of double deletions inGSTT1-GSTM1(p = 0.017, OR = 2.42). The obtained results are discussed in reference to literary data on the risk of malignant brain tumor formation in children and adults.

[The effect of polymorphism of genes of xenobiotics detoxication on the frequencies of spontaneous and induced chromosome aberrations in human lymphocytes].

Here presented the data on the frequencies of chromosome aberrations in lymphocytes of peripheral blood of 97 volunteers depending on genotypes by genes of xenobiotics detoxication before and after gamma-irradiation with dose of 1 Gy in vitro. The frequencies of aberrations were estimated by analyzing not less than 500-1000 metaphases per person. The data of cytogenetic analysis were compared with the results of PCR-genotyping of loci GSTM1, GSTT1, GSTP1, CYP1A1, CYP2D6, NAT2, and MTHFR. The significant differences by the frequencies of aberrations between "single-locus" genotypes were not found except for GSTM1 locus, for which the enhanced frequency of spontaneous aberrations of chromosome type in "positive" genotypes compared to "zero" ones, i.e., homozygotes by deletion (p = 0.04) was observed. The minimum frequency of spontaneous aberrations of chromosome type was recorded for carriers of double homozygotes by deletion of GSTM1-GSTT1: 0.0006 +/- 0.0003 against 0.0027 +/- 0.0003 for the rest of genotypes (p = 0.016 by the Mann-Witney test). The frequency of gamma-induced chromosome aberrations was correlated with the total amount of minor alleles in loci GSTP1, NAT2, and MTHFR (r = 0.25 at p = 0.0065).

[The association of TCR-mutant cells with DNA polymorphism in women residing in radiation polluted regions of the Russian Federation].

Using flow-cytometric method the frequency of lymphocytes beaming mutations at T-cell receptor (TCR) locus was assessed in women residing in radiation polluted regions of Bryansk and Tula Districts. Simultaneously genotyping of the 8 polymorph loci for genes involved in detoxication of xenobiotics and oestrogen metabolism was carried out. The increased TCR-mutant cell frequency was found to be characteristic of homozygotes of the low activity appropriated enzymes for 3 loci (HFE187, GSTM1 and MTHFR) at least. This tendency was statistically significant in case of deletion polymorphism of the GSTM1 gene: TCR-mutant cell frequency of the homozygous carriers of a deletion at the GSTM1 locus was (4.63 +/- 0.18) x 10(-4) while it was (4.05 +/- 0.15) x 10(-4) in other groups of persons. The greatest mutant cell frequency was observed in carriers of the minor allele 4889G of the locus CYP1A. More often the increased values of the TCR-mutant cells (outside range "3sigma") were determined in women with genotypes A/G or G/G of the locus CYP1A1 (25%) than in carries of the normal genotype A/A (1.6%) (OR = 20.6; p = 0.0002). The comparison of the groups of women with reproductive system diseases reveals significant elevation in the mean TCR-mutant cell frequency in inhabitants of the most radiation polluted region among others.

[Gene polymorphisms in patients with Down's syndrome].

Polymorphisms of glutation-S-transferase (GSTM1, GSTT1 GSTP1) and methylentetrahydrofolate reductase (MTHFR) genes have been studied in DNA from blood lymphocytes of 18 patients with Down's syndrome and 61 controls. Frequencies of normal alleles of GST genotypes were lower in patients as compared to the controls. A DNA analysis of 11 patients and 17 controls revealed the presence of mutations in region 246-250 of exon 7 of the p53 gene in 4 patients. Mutations were not found in the control group. Due to the small sample size, the results of this study should be interpreted with caution and need replication in larger studies.