Analysis Of Genotype Combinations Research Articles

Bacillus ginsengisoli sp. nov., isolated from soil of a ginseng field

A novel bacterial strain DCY53(T) was isolated from a soil sample from a ginseng field and was characterized using a polyphasic approach. Cells were Gram-reaction-positive, rod-shaped, endospore-forming and motile with flagella. The strain was aerobic, catalase- and oxidase-positive, optimum growth temperature and pH were 30-37 °C and 6.0-7.5, respectively. On the basis of 16S rRNA gene sequence analysis, strain DCY53(T) was shown to belong to the genus Bacillus and the closest phylogenetic relatives were Bacillus pocheonensis KCTC 13943(T) (98.3 %), Bacillus bataviensis LMG 21833(T) (98.0 %), Bacillus soli LMG 21838(T) (97.9 %), Bacillus drentensis LMG 21831(T) (97.8 %), Bacillus niacini DSM 2923(T) (97.8 %), Bacillus novalis LMG 21837(T) (97.7 %), Bacillus vireti LMG 21834(T) (97.6 %) and Bacillus fumarioli LMG 17489(T) (97.3 %). The DNA G+C content was 43.6 mol% and the predominant respiratory quinone was MK-7. The major fatty acids were iso-C14 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0. The DNA-DNA relatedness with closest relatives was below 55 %. The results of the genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that DCY53(T) represented a novel species within the genus Bacillus, for which we propose the name Bacillus ginsengisoli. The type strain is DCY53(T) ( = KCTC 13945(T) = JCM 17335(T)).

Effect of common polymorphisms in folate uptake and metabolism genes on frequency of micronucleated lymphocytes in a South Australian cohort

Single nucleotide polymorphisms (SNPs) in genes that control folate uptake and metabolism may have an important effect on chromosomal stability. The present study investigated the effect of common SNPs in some of these critical genes on frequency of lymphocytes with micronuclei, a biomarker of chromosome breakage or loss. 164 individuals (94 males and 70 females) of different age ranging from 18 to 73 years participated in this study. Polymorphisms in GCPII (C1561T), RFC (G80A), MTR (A2756G), MTRR (A66G and C524T), TS (tandem repeats, 6 bp deletion in 3′-UTR region) and MTHFR (C677T and A1298C) were detected using PCR-based methods. Frequency of binucleated (BN) lymphocytes containing one or more micronuclei (BN-MN) was determined using the cytokinesis-block micronucleus (CBMN) assay and adjusted for the effects of age and gender. We did not find any significant association between BN-MN frequency and the common SNPs in GCPII, MTRR, TS and MTHFR genes. BN-MN frequency in individuals who carried at least one copy of the rarer G allele for MTR (A2756G) or were homozygotes for the more common G allele for RFC (G80A) had a 14% or 19% lower BN-MN frequency compared to the alternative genotypes for that SNP respectively. It was evident from genotype combination analyses that BN-MN frequency per 1000 BN cells was highest in those with the combined MTR (2756) AA and RFC (80) GA or AA genotype (13.6‰) and lowest in those with the combined MTR (2756) AG or GG and RFC (80) GG genotypes (9.5‰) ( P trend = 0.015). The RFC G80A and MTR A2756G polymorphisms and their combinations may be important variables that substantially affect lymphocyte BN-MN frequency in this South Australian cohort.

Impact of alcohol consumption with polymorphisms in alcohol‐metabolizing enzymes on pancreatic cancer risk in Japanese

The putative impact of alcohol on pancreatic cancer (PC) risk remains controversial. Here, we conducted a case-control study in Japanese to assess the impact of alcohol in conjunction with polymorphisms in alcohol-metabolizing enzymes. Cases were 160 patients with pancreatic cancer at Aichi Cancer Center, Nagoya, Japan. Two control groups of 800 age- and sex-matched non-cancer subjects each were independently selected. The impact of alcohol and polymorphisms in aldehyde dehydrogenase 2 (ALDH2) Glu504Lys, alcohol dehydrogenase (ADH) 1B His48Arg, and ADH1C Arg272Gln on PC risk was examined with multivariate analysis adjusted for potential confounders to estimate odds ratios (ORs) and 95% confidence intervals (CIs). Results showed no independent impact of alcohol or genotype on PC risk except former drinking. To avoid reverse causation, former drinkers were excluded in further analyses. In the analysis of the combined effects of alcohol consumption and genotype, significant impact of alcohol was seen for those subjects with ALDH2 Lys+ allele, ADH1B His/His, or ADH1C Arg/Arg (trend P = 0.077, 0.003, or 0.020, respectively), each of which is associated with a high concentration or rapid production of acetaldehyde. Analysis of genotype combinations showed that ‘ever drinking’ with both ADH1B His/His and ALDH2 Lys + was the most potent risk factor for PC relative to ‘never drinkers’ with both ADH1B His/His and ALDH2 Glu/Glu [OR (95% CI); 4.09 (1.30–12.85)]. These results indicate that alcohol has an impact on PC risk when the effects of alcohol consumption and metabolism are combined. Acetaldehyde may be involved in the mechanisms underlying PC development.

Distinct alleles of mannose-binding lectin (MBL) and surfactant proteins A (SP-A) in patients with chronic cavitary pulmonary aspergillosis and allergic bronchopulmonary aspergillosis

Distinct host immune status predisposes to different forms of pulmonary aspergillosis. Patients with chronic cavitary pulmonary aspergillosis (CCPA; n=15) or allergic bronchopulmonary aspergillosis (ABPA; n=7) of Caucasian origin were screened for single nucleotide polymorphisms (SNPs) in the collagen region of surfactant proteins A1 (SP-A1) and A2 (SP-A2) and mannose binding lectin (MBL). The T allele at T1492C and G allele at G1649C of SP-A2 were observed at slightly higher frequencies in ABPA patients (86% and 93%) than in controls (63% and 83%), and the C alleles at position 1492 and 1649 were found in higher frequencies in CCPA patients (33% and 25%) than in ABPA patients (14% and 7%) (all p>0.05). However, the CC genotype at position 1649 of SP-A2 was significantly associated with CCPA (chi(2)=7.94; p(corr)< or =0.05). Similarly, ABPA patients showed a higher frequency of the TT genotype (71%) at 1492 of SP-A2 than controls (43%) and CCPA patients (41%) (p>0.05). In the case of MBL, the T allele (OR=3.1, range 1.2-8.9; p< or =0.02) and CT genotype (chi(2)=6.54; p(corr)< or =0.05) at position 868 (codon 52) were significantly associated with CCPA, but not with ABPA. Further analysis of genotype combinations at position 1649 of SP-A2 and at 868 of MBL between patient groups showed that both CC/CC and CC/CT SP-A2/MBL were found only in CCPA patients, while GG/CT SP-A2/MBL was significantly higher in CCPA patients in comparison to ABPA patients (p< or =0.05). SNPs analysed in SP-A1 did not differ between cases and controls. Distinct alleles, genotypes and genotype combinations of SP-A2 and MBL may contribute to differential susceptibility of the host to CCPA or ABPA.

Folate metabolic gene polymorphisms and childhood acute lymphoblastic leukemia: a case–control study

We genotyped six folate metabolic pathway genes for 11 polymorphisms in 460 cases of childhood acute lymphoblastic leukemia (ALL) and 552 ethnically matched controls. None of the polymorphisms except the 66A>G (I22M) in the 5-methyltetrahydrofolate-homocysteine methyltransferase reductase (MTRR) gene showed any effect on disease risk. The carriers of the G-allele were associated with a marginal decreased risk of ALL (gender-adjusted global P=0.03; multiple-testing corrected P=0.25). Analysis of four polymorphisms in the MTRR gene showed statistically significant differences in haplotype distribution between cases and controls (global P<0.0001). The haplotypes GCAC (odds ratio (OR) 0.5, 95% confidence interval (CI) 0.4-0.6) and ATAC (OR 0.5, 95% CI 0.3-0.6) were associated with a reduced risk and the haplotypes ACAC (OR 2.3, 95% CI 1.8-2.9) and GTAC (OR 1.8, 95% CI 1.4-2.3) with an increased risk. The genotype-combination analyses indicated that the best model stratifies cases and controls based on the 66A>G and the 524C>T polymorphisms in the MTRR gene (global P=0.03). Our results suggest that, besides a weak association of childhood ALL with the 66A>G polymorphism, haplotypes within the MTRR gene may, in part, account for population-based differences in risk.

Polymorphisms in the KDR and POSTN Genes: Association with Breast Cancer Susceptibility and Prognosis

Angiogenesis is an important step in the development of cancer. Vascular endothelial growth factor is a major regulator of breast cancer angiogenesis, the effects of which are transmitted through the kinase domain receptor (KDR). Up-regulation of KDR by periostin (POSTN) induces angiogenesis. We screened the KDR and the POSTN genes for published single nucleotide polymorphisms (SNPs) and chose two SNPs in each gene for further analyses. We carried out a case-control study consisting of 412 familial and 912 unselected breast cancer cases together with ethnically and geographically selected controls. Genotype, haplotype and genotype combination analyses were carried out to evaluate their effect on susceptibility to and prognosis of breast cancer. A haplotype in the POSTN gene was associated with an increased risk even after correction for multiple comparisons. Nominal associations between the SNPs and prognostic indicators were also observed. Tumors of the KDR 472His allele carriers were less often progesterone receptor negative according to both genotype and haplotype analyses (OR 0.61, 95%CI 0.40-0.92 and OR 0.60, 95%CI 0.40-0.91, respectively). The POSTN -33G allele carriers had more often high grade and estrogen receptor negative tumors (OR 1.75, 95%CI 1.02-3.01 and OR 1.70, 95%CI 1.04-2.78, respectively). The overall and cancer specific survival after 15 years of follow-up was more than 75%, and it did not depend on the genotype. Although a major effect of the SNPs in the KDR and the POSTN genes on breast cancer susceptibility and prognosis was excluded, the effect of the POSTN C-33G SNP on prognosis needs further characterization.

PRKCA and Multiple Sclerosis: Association in Two Independent Populations

Multiple sclerosis (MS) is a chronic disease of the central nervous system responsible for a large portion of neurological disabilities in young adults. Similar to what occurs in numerous complex diseases, both unknown environmental factors and genetic predisposition are required to generate MS. We ascertained a set of 63 Finnish MS families, originating from a high-risk region of the country, to identify a susceptibility gene within the previously established 3.4-Mb region on 17q24. Initial single nucleotide polymorphism (SNP)-based association implicated PRKCA (protein kinase C alpha) gene, and this association was replicated in an independent set of 148 Finnish MS families (p = 0.0004; remaining significant after correction for multiple testing). Further, a dense set of 211 SNPs evenly covering the PRKCA gene and the flanking regions was selected from the dbSNP database and analyzed in two large, independent MS cohorts: in 211 Finnish and 554 Canadian MS families. A multipoint SNP analysis indicated linkage to PRKCA and its telomeric flanking region in both populations, and SNP haplotype and genotype combination analyses revealed an allelic variant of PRKCA, which covers the region between introns 3 and 8, to be over-represented in Finnish MS cases (odds ratio = 1.34, 95% confidence interval 1.07–1.68). A second allelic variant, covering the same region of the PRKCA gene, showed somewhat stronger evidence for association in the Canadian families (odds ratio = 1.64, 95% confidence interval 1.39–1.94). Initial functional relevance for disease predisposition was suggested by the expression analysis: The transcript levels of PRKCA showed correlation with the copy number of the Finnish and Canadian “risk” haplotypes in CD4-negative mononuclear cells of five Finnish multiplex families and in lymphoblast cell lines of 11 Centre d'Etude du Polymorphisme Humain (CEPH) individuals of European origin.

Common paraoxonase gene variants, mortality risk and fatal cardiovascular events in elderly subjects

Recent studies indicate that the enzyme paraoxonase may be an important modulator of cardiovascular disease risk because of its ability to protect LDL from oxidation. We tested for association between two functional variants of the paraoxonase gene (Met-55/Leu and Gln-192/Arg) and both all-cause mortality and fatal cardiovascular disease. This was done within a population-based study among subjects aged 85 years and over in a cross-sectional and a prospective design. In the cross-sectional analysis, the distribution of both paraoxonase genotypes was found to be similar in the subset of 364 elderly subjects who were born in Leiden, The Netherlands, as compared with 250 young subjects whose families originated from the same geographical region. The polymorphisms were in strong linkage disequilibrium ( P<0.00001) and the frequency of the haplotype carrying both risk alleles was not lower in the elderly than in the young (0.313 vs. 0.284). The complete cohort of 666 elderly subjects was followed over 10 years. The risk of all-cause and cardiovascular mortality was not increased in elderly subjects with the paraoxonase Leu/Leu (RR, 1.1 [95% CI, 0.9–1.5] and 1.3 [95% CI, 0.8–2.0], respectively) or the Arg/Arg genotype (RR, 0.9 [95% CI, 0.7–1.2] and 0.7 [95% CI, 0.4–1.3], respectively). In a subset of patients with diabetes, the all-cause mortality risk was elevated in Arg/Arg carriers (RR, 2.1 [95% CI, 0.8–5.8]) but this did not reach statistical significance. Analysis of genotype combinations did not yield significant associations with mortality. The paraoxonase gene variants, previously associated with coronary artery disease, are thus not likely to have a major effect on the risk of fatal cardiovascular disease in the population at large. Adverse effects of the gene variants might be observed in subjects exposed to factors that enhance oxidative stress such as diabetes.