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
• Názvy látek
• genetické markery MeSH

We investigated the genetic structure of three phenotypically distinct ecotypic groups of Norway spruce (Picea abies) belonging to three elevational classes; namely, low- (acuminata), medium- (europaea), and high-elevation (obovata) form, each represented by 150 trees. After rigorous filtering, we used 1916 Genotyping-by-Sequencing generated SNPs for analysis. Outputs from three multivariate analysis methods (Bayesian clustering algorithm implemented in STRUCTURE, Principal Component Analysis, and the Discriminant Analysis of Principal Components) indicated the presence of a distinct genetic cluster representing the high-elevation ecotypic group. Our findings bring a vital message to forestry practice affirming that artificial transfer of forest reproductive material, especially for stands under harsh climate conditions, should be considered with caution.

• MeSH
• algoritmy MeSH
• analýza hlavních komponent MeSH
• Bayesova věta MeSH
• diskriminační analýza MeSH
• ekotyp MeSH
• genetická variace MeSH
• genotyp MeSH
• jednonukleotidový polymorfismus * MeSH
• lesnictví MeSH
• mapování chromozomů MeSH
• multivariační analýza MeSH
• podnebí MeSH
• pyl MeSH
• sekvenční analýza DNA MeSH
• smrk genetika   MeSH
• zeměpis MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem 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.

• MeSH
• geny p53 genetika   MeSH
• jednonukleotidový polymorfismus genetika   MeSH
• lidé MeSH
• missense mutace genetika   MeSH
• nádorový supresorový protein p53 genetika   MeSH
• nádory genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• nádorový supresorový protein p53 MeSH

Fluoride is one of the abundant elements found in the Earth's crust and is a global environmental issue. The present work aimed to find the impact of chronic consumption of fluoride contained groundwater on human subjects. Five hundred and twelve volunteers from different areas of Pakistan were recruited. Cholinergic status, acetylcholinesterase and butyrylcholinesterase gene SNPs and pro-inflammatory cytokines were examined. Association analysis, regression and other standard statistical analyses were performed. Physical examination of the fluoride endemic areas' participants revealed the symptoms of dental and skeletal fluorosis. Cholinergic enzymes (AChE and BChE) were significantly increased among different exposure groups. ACHE gene 3'-UTR variant and BCHE K-variant showed a significant association with risk of fluorosis. Pro-inflammatory cytokines (TNF-α, IL-1β and IL-6) were found to be increased and have a significant correlation in response to fluoride exposure and cholinergic enzymes. The study concludes that chronic consumption of high fluoride-contained water is a risk factor for developing low-grade systemic inflammation through the cholinergic pathway and the studied cholinergic gene SNPs were identified to be associated with the risk of flurosis.

• Klíčová slova
• ACHE gene SNPs and BCHE K- variant, Cholinergic, Drinking water, Fluoride, Pro-inflammatory cytokines,
• MeSH
• acetylcholinesterasa * metabolismus   MeSH
• butyrylcholinesterasa genetika   metabolismus   MeSH
• cholinergní látky MeSH
• cytokiny genetika   MeSH
• fluoridy škodlivé účinky   MeSH
• jednonukleotidový polymorfismus MeSH
• lidé MeSH
• podzemní voda * MeSH
• populační skupiny MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Pákistán MeSH
• Názvy látek
• acetylcholinesterasa * MeSH
• butyrylcholinesterasa MeSH
• cholinergní látky MeSH
• cytokiny MeSH
• fluoridy MeSH

BACKGROUND: Fast, cheap and reliable methods are needed to identify large populations, which may be at risk in relation to environmental exposure. Polymorphisms in NAT1 (N-acetyl transferase) may be suitable markers to identify individuals at risk. RESULTS: A strategy allowing to address simultaneously 24 various genetic variants in the NAT1 gene using the single sequencing reaction method on the same PCR product is described. A modified automated DNA sequencing using only one of the sequence terminators was used to genotype PCR products in single-track sequencing reactions of NAT1 and was shown to be universal for both DNA sequencing using labeled primers and labeled nucleotides. By this method we detected known SNPs at site T640G, which confers the NAT1*11 allele with frequency of 0.036, further T1088A and C1095A with frequency of 0.172 and 0.188, respectively and a deletion of TAATAATAA in the poly A signal area with a frequency 0.031. All observed frequencies were in Hardy Weinberg equilibrium and comparable to those in Caucasian population. The single-track signatures of the variant genotypes were verified on samples previously genotyped by RLFP. CONCLUSIONS: The method could be of great help to scientists in the field of molecular epidemiology of screening of large populations for known informative biomarkers of susceptibility, such as NAT1.

• MeSH
• arylamin-N-acetyltransferasa genetika   MeSH
• genetická predispozice k nemoci genetika   MeSH
• genetické testování metody   MeSH
• genotyp MeSH
• izoenzymy genetika   MeSH
• jednonukleotidový polymorfismus genetika   MeSH
• lidé MeSH
• mutační analýza DNA metody   MeSH
• polymerázová řetězová reakce MeSH
• vystavení vlivu životního prostředí MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• arylamin-N-acetyltransferasa MeSH
• izoenzymy MeSH
• N-acetyltransferase 1 MeSH Prohlížeč

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.

• Klíčová slova
• MHC, T cells, lung,
• 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
• Názvy látek
• HLA-DRB1 řetězec * MeSH
• HLA-DRB1*15 antigen MeSH Prohlížeč

IGF2-in3-G3072A is a causative mutation for paternally expressed quantitative trait loci on the p arm of porcine chromosome 2 with substantial effect on muscle growth and backfat thickness. The linkage disequilibrium between IGF2-in3-G3072A and IGF2-in7-G162C (IGF2-NciI) in four breeds and associations between these polymorphisms and growth and meat performance in pigs of the Large White breed were analysed. A significant effect of these polymorphisms on backfat thickness and lean meat content was found. In addition, we identified two new single nucleotide polymorphisms (SNPs) in intron 7 of the gene. The existence of complete linkage disequilibrium between IGF2-in3-G3072A locus in the population under study where the locus segregated and SNPs in intron 7 of the IGF2 gene detectable with simple and reliable polymerase chain reaction-restriction fragment length polymorphism techniques (G162C, C179G and G186T) offer possibilities to use these SNPs for genotyping of quantitative trait nucleotide in Large White and Landrace breeds.

• MeSH
• DNA primery chemie   MeSH
• frekvence genu genetika   MeSH
• insulinu podobný růstový faktor II MeSH
• jednonukleotidový polymorfismus genetika   MeSH
• lokus kvantitativního znaku genetika   fyziologie   MeSH
• maso normy   MeSH
• mutace genetika   fyziologie   MeSH
• polymerázová řetězová reakce veterinární   MeSH
• polymorfismus délky restrikčních fragmentů MeSH
• prasata genetika   růst a vývoj   fyziologie   MeSH
• proteiny genetika   fyziologie   MeSH
• vazebná nerovnováha MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Názvy látek
• DNA primery MeSH
• IGF2 protein, human MeSH Prohlížeč
• insulinu podobný růstový faktor II MeSH
• proteiny 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
• gen pro FTO 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 epidemiologie   MeSH
• Názvy látek
• FTO protein, human MeSH Prohlížeč
• gen pro FTO MeSH
• proteiny 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.

• Klíčová slova
• Association study, Colorectal cancer, MicroRNA, Single nucleotide polymorphism,
• 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 epidemiologie   MeSH
• Názvy látek
• mikro RNA MeSH
• MIRN146 microRNA, human MeSH Prohlížeč
• MIRN196 microRNA, human MeSH Prohlížeč
• MIRN27 microRNA, human MeSH Prohlížeč

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.

• Klíčová slova
• Allele frequencies, Boar taint, Genotyping, HPLC, PCR–RFLP, Polymorphism,
• 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
• Názvy látek
• androst-16-en-3-one MeSH Prohlížeč
• androsteny MeSH
• cytochrom P-450 CYP2E1 MeSH
• indole MeSH Prohlížeč
• indoly MeSH
• skatol MeSH