SUMMARY: The SNPman program calls the genotypes of single nucleotide polymorphisms (SNP) from TaqMan allelic discrimination assays. It utilizes the fluorescence data collected over the whole PCR run, rather than relying on the end point fluorescence measurements that is the basis of the genotype calling process in most software solutions sold with the real-time instruments. This inspection of run data facilitates genotype calls in difficult sample sets, especially in those containing various concentrations of DNA or inhibitors, as indicated by results of a reanalysis of 3738 genotyping samples. The program works with data from three different widely used PCR instruments. AVAILABILITY: The compiled program is available online at http://sourceforge.net/projects/snpman/files/, along with its user documentation and demonstration data files. It is free of charge for non-commercial users. CONTACT: Ondrej.Cinek@Lfmotol.cuni.cz SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• MeSH
• alely * MeSH
• genotypizační techniky * MeSH
• jednonukleotidový polymorfismus * MeSH
• polymerázová řetězová reakce metody   MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Bardet-Biedl syndrome (BBS) is a recessive genetic disease causing multiple organ anomalies. Most patients carry mutations in genes encoding for the subunits of the BBSome, an octameric ciliary transport complex, or accessory proteins involved in the BBSome assembly or function. BBS proteins have been extensively studied using in vitro, cellular, and animal models. However, the molecular functions of particular BBS proteins and the etiology of the BBS symptoms are still largely elusive. In this study, we applied a meta-analysis approach to study the genotype-phenotype association in humans using our database of all reported BBS patients. The analysis revealed that the identity of the causative gene and the character of the mutation partially predict the clinical outcome of the disease. Besides their potential use for clinical prognosis, our analysis revealed functional differences of particular BBS genes in humans. Core BBSome subunits BBS2, BBS7, and BBS9 manifest as more critical for the function and development of kidneys than peripheral subunits BBS1, BBS4, and BBS8/TTC8, suggesting that incomplete BBSome retains residual function at least in the kidney.

• Klíčová slova
• BBS, BBSome, Bardet-Biedl syndrome, ciliopathy, genotype-phenotype, kidney disease, meta-analysis, rare disease,
• MeSH
• ADP-ribosylační faktory genetika   MeSH
• Bardetův-Biedlův syndrom diagnóza   genetika   MeSH
• fenotyp * MeSH
• genetická predispozice k nemoci * MeSH
• genetické asociační studie * metody   MeSH
• genotyp * MeSH
• kognitivní dysfunkce genetika   MeSH
• ledviny abnormality   MeSH
• lidé MeSH
• mutace MeSH
• nemoci ledvin vrozené   genetika   MeSH
• penetrance MeSH
• proteiny genetika   MeSH
• vrozené vady genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• metaanalýza MeSH
• práce podpořená grantem MeSH
• Názvy látek
• ADP-ribosylační faktory MeSH
• ARL6 protein, human MeSH Prohlížeč
• Bbs2 protein, human MeSH Prohlížeč
• proteiny MeSH

Genotyping of hepatitis C virus (HCV) is of relevance to scheduling the treatment of patients with chronic hepatitis C (VHC), making their prognosis and monitoring the treatment efficacy. A set of 62 sera testing HCV RNA positive in Cobas Amplicor HCV 2.0 test (CA) were genotyped using Versant HCV Genotype Assay (LiPA) Bayer, i.e. the reverse hybridization method, with the CA amplified product being directly used in the assay. Fifty-six out of 57 samples reactive in reverse hybridization (92%) were genotyped. One sample showed a profile differing from any genotype, five samples were not reactive and one sample was not tested within this study design. Two out of five non-reactive sera and one non-tested serum could be genotyped by nested PCR based reverse hybridization. It can be concluded that the CA product resulting from one-step HCV RNA amplification is suitable for use in genotyping by reverse hybridization. The CA product based genotyping procedure is easier to perform, less time-consuming and less costly. The nested PCR based procedure could be used for typing of sera with lower HCV concentrations nontypeable with the combination of CA and Versant HCV Genotype Assay. Forty-eight selected samples were typed not only by reverse hybridization but also by a serological kit Murex HCV Serotyping 1-6 Assay (Abbot Murex). Thirty-seven (77%) of these sera, including all of three sera negative in reverse hybridization, appeared typeable by this kit. Although less sensitive, serotyping may be of relevance to typing of sera with low HCV levels or not containing detectable viral NA which are nontypeable by reverse hybridization. Thirty-three sera appeared genotypeable by both of the methods tested with the results being in good agreement. In two cases only the serotyping method revealed one more type of virus (mixed genotype) compared to the reverse hybridization.

• MeSH
• chronická hepatitida C virologie   MeSH
• genotyp MeSH
• Hepacivirus klasifikace   genetika   MeSH
• hybridizace nukleových kyselin MeSH
• lidé MeSH
• polymerázová řetězová reakce MeSH
• RNA virová analýza   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• anglický abstrakt MeSH
• časopisecké články MeSH
• Názvy látek
• RNA virová MeSH

PURPOSE: Noonan syndrome (NS) is an autosomal-dominant disorder characterized by craniofacial dysmorphism, growth retardation, cardiac abnormalities, and learning difficulties. It belongs to the RASopathies, which are caused by germ-line mutations in genes encoding components of the RAS mitogen-activated protein kinase (MAPK) pathway. RIT1 was recently reported as a disease gene for NS, but the number of published cases is still limited. METHODS: We sequenced RIT1 in 310 mutation-negative individuals with a suspected RASopathy and prospectively in individuals who underwent genetic testing for NS. Using a standardized form, we recorded clinical features of all RIT1 mutation-positive patients. Clinical and genotype data from 36 individuals with RIT1 mutation reported previously were reviewed. RESULTS: Eleven different RIT1 missense mutations, three of which were novel, were identified in 33 subjects from 28 families; codons 57, 82, and 95 represent mutation hotspots. In relation to NS of other genetic etiologies, prenatal abnormalities, cardiovascular disease, and lymphatic abnormalities were common in individuals with RIT1 mutation, whereas short stature, intellectual problems, pectus anomalies, and ectodermal findings were less frequent. CONCLUSION: RIT1 is one of the major genes for NS. The RIT1-associated phenotype differs gradually from other NS subtypes, with a high prevalence of cardiovascular manifestations, especially hypertrophic cardiomyopathy, and lymphatic problems.Genet Med 18 12, 1226-1234.

• MeSH
• fenotyp MeSH
• genetické asociační studie MeSH
• genotyp MeSH
• hypertrofická kardiomyopatie genetika   patologie   MeSH
• lidé MeSH
• Noonanové syndrom genetika   patologie   MeSH
• Ras proteiny genetika   MeSH
• rodokmen MeSH
• vrozené srdeční vady genetika   patologie   MeSH
• zárodečné mutace MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• Ras proteiny MeSH
• RIT1 protein, human MeSH Prohlížeč

WT1 mutations cause a wide spectrum of renal and extrarenal manifestations. Here we evaluated disease prevalence, phenotype spectrum, and genotype-phenotype correlations of 61 patients with WT1-related steroid-resistant nephrotic syndrome relative to 700 WT1-negative patients, all with steroid-resistant nephrotic syndrome. WT1 patients more frequently presented with chronic kidney disease and hypertension at diagnosis and exhibited more rapid disease progression. Focal segmental glomerulosclerosis was equally prevalent in both cohorts, but diffuse mesangial sclerosis was largely specific for WT1 disease and was present in 34% of cases. Sex reversal and/or urogenital abnormalities (52%), Wilms tumor (38%), and gonadoblastoma (5%) were almost exclusive to WT1 disease. Missense substitutions affecting DNA-binding residues were associated with diffuse mesangial sclerosis (74%), early steroid-resistant nephrotic syndrome onset, and rapid progression to ESRD. Truncating mutations conferred the highest Wilms tumor risk (78%) but typically late-onset steroid-resistant nephrotic syndrome. Intronic (KTS) mutations were most likely to present as isolated steroid-resistant nephrotic syndrome (37%) with a median onset at an age of 4.5 years, focal segmental glomerulosclerosis on biopsy, and slow progression (median ESRD age 13.6 years). Thus, there is a wide range of expressivity, solid genotype-phenotype associations, and a high risk and significance of extrarenal complications in WT1-associated nephropathy. We suggest that all children with steroid-resistant nephrotic syndrome undergo WT1 gene screening.

• MeSH
• časové faktory MeSH
• chronická renální insuficience diagnóza   epidemiologie   genetika   terapie   MeSH
• dítě MeSH
• fenotyp MeSH
• fokálně segmentální glomeruloskleróza diagnóza   epidemiologie   genetika   terapie   MeSH
• genetická predispozice k nemoci MeSH
• genetické asociační studie MeSH
• genetické testování metody   MeSH
• incidence MeSH
• kojenec MeSH
• lidé MeSH
• mutace * MeSH
• mutační analýza DNA MeSH
• nefrotický syndrom vrozené   diagnóza   epidemiologie   genetika   terapie   MeSH
• předškolní dítě MeSH
• prevalence MeSH
• prognóza MeSH
• progrese nemoci MeSH
• proteiny WT1 genetika   MeSH
• registrace MeSH
• rizikové faktory MeSH
• věk při počátku nemoci MeSH
• Check Tag
• dítě MeSH
• kojenec MeSH
• lidé MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• multicentrická studie MeSH
• práce podpořená grantem MeSH
• Názvy látek
• proteiny WT1 MeSH
• WT1 protein, human MeSH Prohlížeč

In order to find new informative predictors of myocardial infarction, we performed an analysis of genotype frequencies of polymorphic markers of SELE (rs2076059, 3832T > C), SELP (rs6131, S290 N), SELL (rs1131498, F206L), ICAM1 (rs5498, K469E), VCAM1 (rs3917010, c.928 + 420A > C), PECAM1 (rs668, V125L), VEGFA (rs35569394, -2549(18)I/D), CCL2 (rs1024611, -2518A > G), NOS3 (rs1799983, E298D), and DDAH1 (rs669173, c.303 + 30998A > G) genes in the group of Russian men with myocardial infarction (N = 315) and the control group of corresponding ethnicity, gender, and age (N = 286). Using Markov chain Monte-Carlo method (APSampler), we found genotype combinations associated with increased and decreased risk of myocardial infarction. The most significant associations were detected for PECAM1*V/V + DDAH1*C (OR = 4.17 CI 1.56-11.15 Pperm = 0.005) SELE*C + VEGFA*I + CCL2*G + VCAM1*A + NOS3*D (OR = 2.74 CI 1.66-4.52 Pperm = 2.09 × 10(-5)), and VEGFA*D/D + CCL2*A + DDAH1*C (OR = 0.44 CI 0.28-0.7 Pperm = 7.89 × 10(-5)) genotype combinations.

• Klíčová slova
• Genetic testing, Myocardial infarction, Risk prediction,
• MeSH
• amidohydrolasy genetika   MeSH
• antigeny CD31 genetika   MeSH
• dospělí MeSH
• frekvence genu MeSH
• genetická predispozice k nemoci MeSH
• genetické asociační studie MeSH
• genetické testování MeSH
• infarkt myokardu etnologie   genetika   MeSH
• jednonukleotidový polymorfismus MeSH
• lidé středního věku MeSH
• lidé MeSH
• studie případů a kontrol MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Rusko MeSH
• Názvy látek
• amidohydrolasy MeSH
• antigeny CD31 MeSH
• dimethylargininase MeSH Prohlížeč

Mucopolysaccharidosis type II (Hunter syndrome, MPS II, OMIM 309900) is an X-linked lysosomal storage disorder caused by deficiency of iduronate-2-sulfatase (IDS). We analyzed clinical and laboratory data from 44 Slavic patients with this disease. In total, 21 Czech, 7 Slovak, 9 Croatian and 7 Serbian patients (43 M/1 F) were included in the study (median age 11.0 years, range 1.2-43 years). Birth prevalence ranged from 1:69,223 (Serbia) to 1:192,626 (Czech Rep.). In the majority of patients (71%), the disease manifested in infancy. Cognitive functions were normal in 10 patients. Four, six and 24 patients had mild, moderate, and severe developmental delay, respectively, typically subsequent to developmental regression (59%). Residual enzyme activity showed no predictive value, and estimation of glycosaminoglycans (GAGs) had only limited importance for prognosis. Mutation analysis performed in 36 families led to the identification of 12 novel mutations, eight of which were small deletions/insertions. Large deletions/rearrangements and all but one small deletion/insertion led to a severe phenotype. This genotype-phenotype correlation was also identified in six cases with recurrent missense mutations. Based on patient genotype, the severity of the disease may be predicted with high probability in approximately half of MPS II patients.

• Klíčová slova
• Hunter syndrome, MPS II, Slavic origin, genotype-phenotype correlation, mucopolysaccharidosis type II,
• MeSH
• dítě MeSH
• dospělí MeSH
• genetické asociační studie MeSH
• glykoproteiny genetika   MeSH
• glykosaminoglykany moč   MeSH
• kojenec MeSH
• lidé MeSH
• mladiství MeSH
• mladý dospělý MeSH
• mukopolysacharidóza II etiologie   genetika   MeSH
• mutace * MeSH
• předškolní dítě MeSH
• Check Tag
• dítě MeSH
• dospělí MeSH
• kojenec MeSH
• lidé MeSH
• mladiství MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH
• Chorvatsko MeSH
• Slovenská republika MeSH
• Srbsko MeSH
• Názvy látek
• glykoproteiny MeSH
• glykosaminoglykany MeSH
• IDS protein, human MeSH Prohlížeč

BACKGROUND: The genetic basis of hypertrophic cardiomyopathy (HCM) is complex, and the relationship between genotype status and clinical outcome is incompletely resolved. METHODS AND RESULTS: We assessed a large international HCM cohort to define in contemporary terms natural history and clinical consequences of genotype. Consecutive patients (n=1468) with established HCM diagnosis underwent genetic testing. Patients with pathogenic (or likely pathogenic) variants were considered genotype positive (G+; n=312; 21%); those without definite disease-causing mutations (n=651; 44%) or variants of uncertain significance (n=505; 35%) were considered genotype negative (G-). Patients were followed up for a median of 7.8 years (interquartile range, 3.5-13.4 years); HCM end points were examined by cumulative event incidence. Over follow-up, 135 (9%) patients died, 33 from a variety of HCM-related causes. After adjusting for age, all-cause and HCM-related mortality did not differ between G- versus G+ patients (hazard ratio [HR], 0.78 [95% CI, 0.46-1.31]; P=0.37; HR, 0.93 [95% CI, 0.38-2.30]; P=0.87, respectively). Adverse event rates, including heart failure progression to class III/IV, heart transplant, or heart failure death, did not differ (G- versus G+) when adjusted for age (HR, 1.20 [95% CI, 0.63-2.26]; P=0.58), nor was genotype independently associated with sudden death event risk (HR, 1.39 [95% CI, 0.88-2.21]; P=0.16). In multivariable analysis, age was the only independent predictor of all-cause and HCM-related mortality, heart failure progression, and sudden death events. CONCLUSIONS: In this large consecutive cohort of patients with HCM, genotype (G+ or G-) was not a predictor of clinical course, including all-cause and HCM-related mortality and risk for heart failure progression or sudden death. G+ status should not be used to dictate clinical management or predict outcome in HCM.

• Klíčová slova
• genotype, hypertrophic cardiomyopathy, mortality, outcomes, sudden death,
• MeSH
• časové faktory MeSH
• dospělí MeSH
• fenotyp MeSH
• genetická predispozice k nemoci MeSH
• genetické testování metody   MeSH
• genotyp * MeSH
• hypertrofická kardiomyopatie * genetika   mortalita   diagnóza   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mutace MeSH
• náhlá srdeční smrt etiologie   epidemiologie   MeSH
• prognóza MeSH
• progrese nemoci MeSH
• rizikové faktory MeSH
• senioři MeSH
• srdeční selhání genetika   mortalita   MeSH
• transplantace srdce MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• multicentrická studie MeSH

OBJECTIVE: To evaluate the effectiveness of the fetal KEL and RHCE genotype assessment in alloimmunized pregnant women by minisequencing. DESIGN: Prospective cohort study. SETTING: Obstetrics and Gynecology Clinic of the Faculty of Medicine UP and the University Hospital Olomouc; Institute of Medical Genetics of the Faculty of Medicine UP and the University Hospital Olomouc; Transfusion Department of the University Hospital Olomouc; Institute of Biophysics of the Faculty of Medicine UP Olomouc. SUBJECT AND METHOD: In the years 2001-2019, 366 samples of pregnant women in the first and second trimester were assessed KEL (n = 327) or RHCE (n = 39) genotype from the free fetal DNA circulating in the peripheral blood by minisequencing. The genotype of the fetus was verified from the buccal smear of the newborn. RESULTS: The KEL genotype was assessed in 327 women (the presence of a variant of the KEL1 alele, which corresponds to the presence of the erythrocyte antigen “K“. The analysis failed in 2 cases (2/327), 16 heterozygote women (KEL1/KEL2) were excluded and in the case of 309 homozygote women (KEL2/KEL2) the fetal KEL genotype was assessed. In the case of 95.8% of the fetuses (296/309) and 95.5% of the newborns (295/309), the KEL2/KEL2 genotype was assessed. In the case of 4.2 % of the fetuses (13/309) and 4.5% of the newborns (14/309), the KEL1/KEL2 genotype was assessed. The sensitivity was 92.86%. The specificity was 100%. The RHCE genotype was assessed in 39 women. In the case of 22 women, the presence of a variant of the RHCE gene, which corresponds to the presence of the erythrocyte antigen “C“/“c“, was assessed. 5 heterozygote women (C/c) were excluded. In the case of 11 homozygote women (C/C), the RHCE genotype was assessed. In the case of 64% (7/11) of the fetuses and newborns, the C/c genotype was assessed, in the case of 36% (4/11) the C/C genotype was assessed. In the case of 6 homozygote women (c/c), the RHCE genotype was assessed. In the case of 67% (4/6) of the fetuses and newborns, the C/c genotype was assessed, in the case of 33% (2/6) the c/c genotype was assessed. The sensitivity and specificity were 100%. In the case of 17 women, the presence of the variant of the RHCE gene, which corresponds to the presence of the erythrocyte antigen “E“/“e“, was assessed. 1 heterozygote woman (E/e) was excluded. In the case of 16 homozygote women (e/e), the RHCE genotype was assessed. In the case of 75% (12/16) of the fetuses and newborns, the e/e genotype was assessed, in the case of 25% (4/16) the E/e genotype was assessed. The sensitivity and specificity were 100%. CONCLUSION: The minisequencing method using the capillary electrophoresis enabled a reliable detection of the fetal KEL and RHCE genotype from the peripheral blood of pregnant women.

• Klíčová slova
• KEL and RHCE genotype, alloimmunization, cell free DNA, pregnancy,
• MeSH
• DNA * MeSH
• genotyp MeSH
• krevní skupiny - systém Rh-Hr genetika   MeSH
• lidé MeSH
• membránové glykoproteiny MeSH
• metaloendopeptidasy MeSH
• novorozenec MeSH
• plod * MeSH
• prospektivní studie MeSH
• těhotenství MeSH
• Check Tag
• lidé MeSH
• novorozenec MeSH
• těhotenství MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA * MeSH
• KEL protein, human MeSH Prohlížeč
• krevní skupiny - systém Rh-Hr MeSH
• membránové glykoproteiny MeSH
• metaloendopeptidasy MeSH
• RHCE protein, human MeSH Prohlížeč

OBJECTIVE: In the Czech Republic in all women within a first trimester screening a laboratory testing for RhD blood group from the peripheral blood should be performed. The aim of the screening is to diagnose RhD negative pregnant women, who may be at risk of developing RhD alloimmunization if the fetus is RhD positive. Currently, the prevention of RhD alloimmunization is carried out regardless of the knowledge of RHD fetal status. Already at the beginning of pregnancy it is possible to determine the RHD genotype of the fetus non-invasively due to cell free fetal DNA circulating in maternal peripheral blood detection. The issue of screening examination of fetal RHD genotype is solved worldwide. In some European countries, the examination is routinely established and thus contributes to the optimization of prenatal care for RhD negative pregnant women, immunoglobulin administration is targeted only in pregnancies with RhD positive fetus. The aim of our study is to evaluate clinical and laboratory effectiveness of fetal RHD genotype screening in RhD negative women by TaqMan Real-time PCR method. Designe: Prospective cohort study. SETTING: Obstetrics and Gynecology Clinic of the Faculty of Medicine University Palacky and the University Hospital Olomouc; Institute of Medical Genetics of the Faculty of Medicine UP and the University Hospital Olomouc; Transfusion Department of the University Hospital Olomouc; Institute of Biophysics of the Faculty of Medicine UP Olomouc. MATERIAL AND METHODS: In 2011-2015 at the University Hospital Olomouc 337 examinations of RHD fetal genotype were performed in pregnant women in first and second trimester and evaluated by TaqMan Real-time PCR, followed by verification of the newborn RHD genotype. RESULTS: Methodology of fetal RHD genotype examination is accurate, reliable and useful in clinical practice. The sensitivity was 97.8%. The specificity was 98.7%. When assessing the effectiveness of the introduction of non- -invasive fetal RHD genotype screening in RhD negative women, it is necessary to assess the medical, organizational and economic aspects. More consistent prevention of RhD alloimmunization in the cases actually indicated may reduce the incidence of RhD alloimmunization. CONCLUSION: From the medical point of view the RHD genotype determination in all RhD negative women at the beginning of pregnancy seems effective. It allows to diagnose about 40% of pregnancies with RhD negative fetuses that do not require administration of IgG anti-D. IgG anti-D should be administered only in indicated cases. Determination of fetal RHD genotype by using TaqMan Real-time PCR is useful in clinical practice.

• Klíčová slova
• RhD negative women, TaqMan Real-time polymerase chain reaction, cell free fetal DNA, fetal RHD genotype, immunglobulin (Ig) G anti-D, pregnancy, prevention of RhD alloimmunization,
• MeSH
• genotyp MeSH
• krevní skupiny - systém Rh-Hr * genetika   MeSH
• lidé MeSH
• novorozenec MeSH
• plod MeSH
• prenatální diagnóza MeSH
• prenatální péče * MeSH
• prospektivní studie MeSH
• těhotenství MeSH
• Check Tag
• lidé MeSH
• novorozenec MeSH
• těhotenství MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH
• Evropa MeSH
• Názvy látek
• krevní skupiny - systém Rh-Hr * MeSH