SNPs Dotaz Zobrazit nápovědu
PURPOSE OF THE STUDY The aim of the present study was to determine the potential effects of single nucleotide polymorphisms (SNPs) of TGFB1 and IL-6 on the development and severity of the disease in patients with DDH and investigate the relationship of these two gene polymorphisms. MATERIAL AND METHODS This case control study was conducted on 105 patients diagnosed with DDH and 119 healthy control subjects of any age. The DDH patients were classified according to the Hartofilakidis and IHDI classifications for adult and pediatric patients, respectively. Genomic DNA was isolated from peripheral blood samples using the Salting-out method. TGFB1 gene p.Pro10Leu (c.29C>T) (rs1800470) and IL-6 572G>C (rs1800796) polymorphisms were analyzed using Sanger DNA sequencing. RESULTS There was no statistically significant relationship of TGFB1 and IL-6 SNPs for DDH. When the rs1800470 and rs1800796 polymorphisms were compared according to family history, the homozygous mutation rate of TGFB1 gene was found to be significantly higher in patients with a positive family history than in patients with a negative family history. No significant relationship was found between rs1800796 polymorphisms and family history. TGFB1 homozygous mutation rate was determined to be statistically higher in the positive family history group than control group. No similar relationship was found between the negative family history group and the control group. No statistically significant relationship was determined between rs1800470 and rs1800796 and the severity of DDH. CONCLUSIONS rs1800796 and rs1800470 polymorphisms do not appear to be major responsible genetic factors for DDH. However, the determination of a correlation between a positive family history and homozygous mutation rate of the TGFB1 gene indicates that this gene may have a greater effect on DDH development. Key words: developmental dysplasia of the hip, interleukin-6, transforming growth factor beta 1, case control study.
- MeSH
- dítě MeSH
- dospělí MeSH
- frekvence genu MeSH
- interleukin-6 * genetika MeSH
- jednonukleotidový polymorfismus MeSH
- lidé MeSH
- studie případů a kontrol MeSH
- transformující růstový faktor beta1 genetika MeSH
- vývojová dysplazie kyčelního kloubu * MeSH
- Check Tag
- dítě MeSH
- dospělí MeSH
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Tench (Tinca tinca L.) has great economic potential due to its high rate of fecundity and long-life span. Population genetic studies based on allozymes, microsatellites, PCR-RFLP and sequence analysis of genes and DNA fragments have revealed the presence of Eastern and Western phylogroups. However, the lack of genomic resources for this species has complicated the development of genetic markers. In this study, the tench transcriptome and genome were sequenced by high-throughput sequencing. A total of 60,414 putative SNPs were identified in the tench transcriptome using a computational pipeline. A set of 96 SNPs was selected for validation and a total of 92 SNPs was validated, resulting in the highest conversion and validation rate for a non-model species obtained to date (95.83%). The validated SNPs were used to genotype 140 individuals belonging to two tench breeds (Tabor and Hungarian), showing low (FST = 0.0450) but significant (<0.0001) genetic differentiation between the two tench breeds. This implies that set of validated SNPs array can be used to distinguish the tench breeds and that it might be useful for studying a range of associations between DNA sequence and traits of importance. These genomic resources created for the tench will provide insight into population genetics, conservation fish stock management, and aquaculture.
- MeSH
- chov MeSH
- Cyprinidae klasifikace genetika MeSH
- druhová specificita MeSH
- fylogeneze MeSH
- genetické markery MeSH
- genom MeSH
- genová ontologie MeSH
- jednonukleotidový polymorfismus MeSH
- populační genetika MeSH
- rybářství MeSH
- transkriptom MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
Infrequent and rare genetic variants in the human population vastly outnumber common ones. Although they may contribute significantly to the genetic basis of a disease, these seldom-encountered variants may also be miss-identified as pathogenic if no correct references are available. Somatic and germline TP53 variants are associated with multiple neoplastic diseases, and thus have come to serve as a paradigm for genetic analyses in this setting. We searched 14 independent, globally distributed datasets and recovered TP53 SNPs from 202,767 cancer-free individuals. In our analyses, 19 new missense TP53 SNPs, including five novel variants specific to the Asian population, were recurrently identified in multiple datasets. Using a combination of in silico, functional, structural, and genetic approaches, we showed that none of these variants displayed loss of function compared to the normal TP53 gene. In addition, classification using ACMG criteria suggested that they are all benign. Considered together, our data reveal that the TP53 coding region shows far more polymorphism than previously thought and present high ethnic diversity. They furthermore underline the importance of correctly assessing novel variants in all variant-calling pipelines associated with genetic diagnoses for cancer.
Genetic susceptibility for sarcoidosis and Löfgren's syndrome (LS) has been associated with prognosis. Human leukocyte antigen (HLA)-DRB1*03 is over-represented in LS, and is associated with a good prognosis, whereas HLA-DRB1*15-positive patients have a more chronic course of sarcoidosis. These HLA-DRB1 types can be easily tagged by single nucleotide polymorphisms (SNPs). Our aim was to evaluate the association between these tag SNPs and bronchoalveolar lavage (BAL) characteristics. In 29 patients, both complete HLA-DRB1* locus genotyping and SNP tagging was performed in parallel. HLA-DRB1 type was inferred from the presence of *03 tag rs2040410 allele A and referred to as *03. HLA-DRB1*15 was inferred from the presence of tag SNP rs3135388 allele A and referred to as *15. For BAL analysis, 122 patients with LS and 165 patients with non-LS sarcoidosis were included. BAL lymphocyte subsets were analyzed by flow cytometry. The presence of tag SNPs completely corresponded with HLA-DRB1*03/*15 genotypes in all 29 patients in whom both HLA-DRB1* genotyping and SNP tagging was performed. In all patients together, *03+ /*15- patients showed a higher CD4+ /CD8+ ratio than *03- /*15+ (P = 0·004) and *03- /*15- (P = 0·001). LS patients with *03+ /*15- had a lower BAL lymphocyte count compared to *03- /*15+ patients (P = 0·011). Non-LS sarcoidosis patients with *03+ /*15- patients showed a decreased CD103+ CD4+ /CD4+ ratio compared to *03- /*15+ patients (P = 0·045) and *03- /*15- patients (P = 0·018). We found that HLA-DRB1*03 and HLA-DRB1*15 can be approximated by genotyping of tag SNPs and corresponds with the degree of lymphocytosis and cell phenotypes in BAL in both LS and non-LS sarcoidosis patients.
- MeSH
- alely * MeSH
- bronchoalveolární laváž MeSH
- CD4-pozitivní T-lymfocyty * imunologie patologie MeSH
- CD8-pozitivní T-lymfocyty * imunologie patologie MeSH
- dospělí MeSH
- genotypizační techniky MeSH
- HLA-DRB1 řetězec * genetika imunologie MeSH
- jednonukleotidový polymorfismus * MeSH
- lidé středního věku MeSH
- lidé MeSH
- plicní sarkoidóza * genetika imunologie patologie MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- klinické zkoušky MeSH
- multicentrická studie MeSH
- práce podpořená grantem MeSH
INTRODUCTION: Using genome-wide screening, a polymorphism within the second intron of the FTO gene (rs2302673) was found to be associated with smoking habits in females. In a population-based, cross-sectional study, we analyzed three tagging FTO single-nucleotide polymorphisms (SNPs) for their association with smoking behavior. METHODS: Subjects from the Czech post-MONICA study, including 1,191 adult males (32.1% smokers) and 1,368 adult females (22.5% smokers) were included in this study. Smoking habits were obtained through questionnaire data analysis, and three FTO tagging SNPs were genotyped (rs17817449: intron 1, rs2302673: intron 2, and rs17818902: intron 3). RESULTS: We detected slightly lower frequencies (p = .043) of the GG genotype of the rs17818902 SNP in males who quit smoking compared with others. However, the significance disappeared after adjusting for multiple testing. Within the entire population, or in either males or females alone, we failed to detect a significant difference between other FTO genotypes and smoking status. Also, the number of cigarettes smoked per day was independent of individual FTO genotypes in both genders. CONCLUSIONS: We did not find an association between the FTO gene tagging variants and smoking status. FTO is unlikely to be a major genetic determinant of smoking status.
- MeSH
- dospělí MeSH
- genetická predispozice k nemoci MeSH
- genotyp MeSH
- jednonukleotidový polymorfismus genetika MeSH
- kouření genetika MeSH
- lidé středního věku MeSH
- lidé MeSH
- proteiny genetika MeSH
- průřezové studie MeSH
- průzkumy a dotazníky MeSH
- tabákové výrobky MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
The occurrence of boar taint in meat from uncastrated males may significantly affect the economics of pork production. The aim of this study was to analyse associations of four single nucleotide polymorphisms (SNPs) in the porcine CYP2E1 gene with skatole, indole, and androstenone levels in the Czech Large White-Czech Landrace commercial crossbreds. The SNPs were: g.2412C>T, c.1422C>T, c.1423G>A and c.*14G>T. Skatole, indole and androstenone levels were estimated by HPLC, and genotypes at the SNPs were determined by PCR-RFLP. SNPs c.1423G>A and c.*14G>T were in complete linkage disequilibrium. In boars, all SNPs were associated with the indole levels (P<0.05; P<0.01). There also were differences in the skatole levels in different genotypes, but these were not significant. No associations with androstenone levels were found. The associations of the SNPs with indole compounds should be studied in other commercial populations of boars to verify the favourable alleles and genotypes, with the prospect for their application in marker-assisted selection.
- MeSH
- androsteny analýza MeSH
- červené maso MeSH
- cytochrom P-450 CYP2E1 genetika MeSH
- genetické asociační studie MeSH
- indoly analýza MeSH
- jednonukleotidový polymorfismus * MeSH
- křížení genetické MeSH
- mapování chromozomů MeSH
- skatol analýza MeSH
- Sus scrofa genetika MeSH
- tuková tkáň chemie MeSH
- vazebná nerovnováha MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
INTRODUCTION: Chronic thromboembolic pulmonary hypertension (CTEPH) and venous thromboembolism (VTE) are thought to share many common risk factors. Our study aimed to determine the frequencies of 5 thrombosis-related gene single nucleotide polymorphisms (SNPs) associated with VTE in patients with CTEPH (n 129) compared with a control group of healthy individuals without a history of VTE (n 2637). METHODS: The SNPs of the following genes were investigated: F5 (F V Leiden, rs6025), F2 prothrombin (rs1799963), fibrinogen gamma (FGG, rs2066865), F11 (rs2289252) and ABO (non-O, rs8176719) in both groups. RESULTS: The study found that the rs1799963 variant was more common in patients with chronic thromboembolic pulmonary hypertension (CTEPH) compared to the control group (p < .0001). The GA heterozygous variant showed a significant increase with an odds ratio (OR) of 4.480 (95% CI: 2.344-8.562) or a finding by maximum likelihood analysis (MLA) with p < .0001. Additionally, there was a notable increase in the rs8176719 variant with p < .0001 in CTEPH patients. Both the homozygous G/G variant and the heterozygous -/G variant also showed an increase, with OR of 4.2317 (95% CI: 2.45571-7.2919) and 2.4324 (95% CI: 1.46435-4.0403) respectively, or MLA (p < .0001 and p .0006). The study also revealed a higher prevalence of the heterozygous C/T variant of rs2289252 in CTEPH patients, with an OR of 1.5543 (95% CI: 1.02503-2.3568) or MLA (p .0379). CONCLUSION: The study suggests that the observed gene polymorphisms F2 (rs1799963), ABO (rs8176719), and F11 (rs2289252) may play a role as independent heritable risk factors in the development of CTEPH.
- MeSH
- ABO systém krevních skupin genetika MeSH
- chronická nemoc MeSH
- dospělí MeSH
- faktor V genetika MeSH
- fibrinogen genetika MeSH
- incidence MeSH
- jednonukleotidový polymorfismus * MeSH
- lidé středního věku MeSH
- lidé MeSH
- plicní embolie genetika MeSH
- plicní hypertenze * genetika MeSH
- protrombin genetika MeSH
- senioři MeSH
- trombofilie genetika MeSH
- žilní tromboembolie genetika MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
AIM: To investigate whether selected single nucleotide polymorphisms (SNPs) in miR-196a2, miR-27a and miR-146a genes are associated with sporadic colorectal cancer (CRC). METHODS: In order to investigate the effect of these SNPs in CRC, we performed a case-control study of 197 cases of sporadic CRC and 212 cancer-free controls originating from the Central-European Caucasian population using TaqMan Real-Time polymerase chain reaction and allelic discrimination analysis. RESULTS: The genotype and allele frequencies of SNPs were compared between the cases and the controls. None of the performed analysis showed any statistically significant results. CONCLUSION: Our data suggest a lack of association between rs11614913, rs895819 and rs2910164 and colorectal cancer risk in the Central-European Caucasian population, a population with an extremely high incidence of sporadic colorectal cancer.
- MeSH
- adenokarcinom etnologie genetika patologie MeSH
- běloši genetika MeSH
- frekvence genu MeSH
- genetická predispozice k nemoci MeSH
- hodnocení rizik MeSH
- incidence MeSH
- jednonukleotidový polymorfismus MeSH
- kolorektální nádory etnologie genetika patologie MeSH
- kvantitativní polymerázová řetězová reakce MeSH
- lidé středního věku MeSH
- lidé MeSH
- logistické modely MeSH
- mikro RNA genetika MeSH
- odds ratio MeSH
- rizikové faktory MeSH
- rozdělení chí kvadrát MeSH
- senioři MeSH
- studie případů a kontrol MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
Theory predicts that naturally occurring hybrid zones between genetically distinct taxa can move over space and time as a result of selection and/or demographic processes, with certain types of hybrid zones being more or less likely to move. Determining whether a hybrid zone is stationary or moving has important implications for understanding evolutionary processes affecting interactions in hybrid populations. However, direct observations of hybrid zone movement are difficult to make unless the zone is moving rapidly. Here, evidence for movement in the house mouse Mus musculus domesticus × Mus musculus musculus hybrid zone is provided using measures of LD and haplotype structure among neighbouring SNP markers from across the genome. Local populations of mice across two transects in Germany and the Czech Republic were sampled, and a total of 1301 mice were genotyped at 1401 markers from the nuclear genome. Empirical measures of LD provide evidence for extinction and (re)colonization in single populations and, together with simulations, suggest hybrid zone movement because of either geography-dependent asymmetrical dispersal or selection favouring one subspecies over the other.
- MeSH
- genotypizační techniky MeSH
- haplotypy MeSH
- hybridizace genetická * MeSH
- jednonukleotidový polymorfismus * MeSH
- myši genetika MeSH
- populační genetika * MeSH
- sekvenční analýza DNA MeSH
- vazebná nerovnováha * MeSH
- zeměpis MeSH
- zvířata MeSH
- Check Tag
- myši genetika MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
- Geografické názvy
- Česká republika MeSH
- Německo MeSH
Homocystinuria is most frequently due to deficiency of cystathionine beta-synthase (CBS). We identified IVS12 as a polymorphism hot spot of the human CBS gene and report five novel single nucleotide polymorphisms (SNPs): g.13514G>A, g.13617A>G, g.13715C>T, g.13800G>A, and g.13904C>T. Analyzing 50 control DNA samples of unaffected and unrelated subjects of German origin the observed frequencies of heterozygosity were 0.02, 0.36, 0.18, 0.36, and 0.36, respectively. These polymorphic markers were combined into four distinct IVS12-haplotypes A1, A2, B1, and B2, revealing frequencies of 0.75, 0.01, 0.15, and 0.09, respectively, with an observed overall frequency of heterozygosity at 0.38. This haplotype system and the SNP c.699 were employed in the analysis of ten alleles affected by the most prevalent CBS mutation, c.833T>C (exon 8; I278T). We found that the I278T alleles segregate with at least two distinct haplotypes characterized by upstream and downstream polymorphic sites instead of sharing a common ancestral haplotype. This was a remarkable finding even in patients with very similar ethnic background. The novel haplotype system may facilitate future studies on the evolution of the CBS gene and might be suited for genotyping of families affected by homocystinuria. Copyright 2001 Wiley-Liss, Inc.
- MeSH
- alely * MeSH
- běloši genetika MeSH
- cystathionin-beta-synthasa * genetika MeSH
- etnicita genetika MeSH
- frekvence genu genetika MeSH
- haplotypy * genetika MeSH
- heterozygot MeSH
- homocystinurie * enzymologie genetika MeSH
- jednonukleotidový polymorfismus * genetika MeSH
- lidé MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, P.H.S. MeSH
- Geografické názvy
- Německo MeSH
