Comparison of the ABC and ACMG systems for variant classification.

The ABC and ACMG variant classification systems were compared by asking mainly European clinical laboratories to classify variants in 10 challenging cases using both systems, and to state if the variant in question would be reported as a relevant result or not as a measure of clinical utility. In contrast to the ABC system, the ACMG system was not made to guide variant reporting but to determine the likelihood of pathogenicity. Nevertheless, this comparison is justified since the ACMG class determines variant reporting in many laboratories. Forty-three laboratories participated in the survey. In seven cases, the classification system used did not influence the reporting likelihood when variants labeled as "maybe report" after ACMG-based classification were included. In three cases of population frequent but disease-associated variants, there was a difference in favor of reporting after ABC classification. A possible reason is that ABC step C (standard variant comments) allows a variant to be reported in one clinical setting but not another, e.g., based on Bayesian-based likelihood calculation of clinical relevance. Finally, the selection of ACMG criteria was compared between 36 laboratories. When excluding criteria used by less than four laboratories (<10%), the average concordance rate was 46%. Taken together, ABC-based classification is more clear-cut than ACMG-based classification since molecular and clinical information is handled separately, and variant reporting can be adapted to the clinical question and phenotype. Furthermore, variants do not get a clinically inappropriate label, like pathogenic when not pathogenic in a clinical context, or variant of unknown significance when the significance is known.

Mitochondrial DNA variability and Covid-19 in the Slovak population.

Recent studies have shown that mitochondria are involved in the pathogenesis of Covid-19. Mitochondria play a role in production of reactive oxygen species and induction of an innate immune response, both important during infections. Common variability of mitochondrial DNA (mtDNA) can affect oxidative phosphorylation and the risk or lethality of cardiovascular, neurodegenerative diseases and sepsis. However, it is unclear whether susceptibility of severe Covid-19 might be affected by mtDNA variation. Thus, we have analyzed mtDNA in a sample of 446 Slovak patients hospitalized due to Covid-19 and a control population group consisting of 1874 individuals. MtDNA variants in the HVRI region have been analyzed and classified into haplogroups at various phylogenetic levels. Binary logistic regression was used to assess the risk of Covid-19. Haplogroups T1, H11, K and variants 16256C > T, 16265A > C, 16293A > G, 16311 T > C and 16399A > G were associated with an increased Covid-19 risk. On contrary, Haplogroup J1, haplogroup clusters H + U5b and T2b + U5b, and the mtDNA variant 16189 T > C were associated with decreased risk of Covid-19. Following the application of the Bonferroni correction, statistical significance was observed exclusively for the cluster of haplogroups H + U5b. Unsurprisingly, the most significant factor contributing to the mortality of patients with Covid-19 is the age of patients. Our findings suggest that mtDNA haplogroups can play a role in Covid-19 pathogenesis, thus potentially useful in identifying susceptibility to its severe form. To confirm these associations, further studies taking into account the nuclear genome or other non-biological influences are needed.

Return to the New Normal: Empirical Analysis of Changes in E-Consumer Behavior during the COVID-19 Pandemic.

The global pandemic caused by the new coronavirus has largely changed established business practices. The aim of this study is to present the results of eighteen months of intensive research into the effects of the pandemic on e-consumer behavior. In one of the most active e-commerce markets in Europe, the Czech Republic, we analyzed a sample of more than one and a half million Facebook users in terms of their C2B interactions on the B2C activities of the five major e-commerce market players. The measurements were carried out in three periods, which corresponded to the onset of the first wave, the peak, and the fading of the second wave of the pandemic. This enabled us to monitor the effect of seasonality and the stabilization of patterns of consumer behavior during the coronavirus crisis. The results suggest that a specific panic pattern of e-consumer behavior was developed at the time of the onset of the pandemic. However, as the pandemic progressed, the market adapted to a new normal, which, as evidenced by the change in trends, appears to be a combination of the pre-pandemic and pandemic behavioral patterns. Using a statistical analysis, it was possible to identify the delta of changes within the patterns of consumer behavior, thus fulfilling the final condition for creating an empirical model of the impacts of the COVID-19 pandemic on e-consumer behavior presented in this study.

The results of multigene panel sequencing in Slovak HBOC families.

Hereditary breast and ovarian cancer (HBOC) is primarily associated with mutations in the BRCA1/2 genes. However, causal variants in other high, moderate, and low penetrance genes proportionally increase the risk of breast/ovarian cancer. This study aims to provide data about the mutation spectrum of HBOC-associated genes in Slovak HBOC families and estimate the ratio of BRCA versus non-BRCA causal variants. We used panel sequencing containing 22 high/moderate-risk susceptibility genes and parallel MLPA analysis of BRCA1/2, CHEK2 genes, to analyze 94 individuals with a strong family/personal history of breast and/or ovarian cancer. The analyzed group consisted of 80 patients diagnosed with cancer (85.1%) and 14 healthy individuals (14.9%) with a positive family history of HBOC syndrome. In total, we have identified 22 causal DNA variants (23.4%) showing 15 primary findings in BRCA1/2 genes (68.2%) and 7 positive secondary findings in CHEK2, PALB2, CDH1, and MUTYH genes (31.8%). The most frequent pathogenic alterations were BRCA1 mutations c.181T>G and CNV variant (c.5573-?_c.5701+?)del, known as deletion of exons 21-22. Besides known mutations, the BRCA1 variant c.2794del (p.Val932Leufs*68) and variant c.2480dup (p.Tyr827*) in the CDH1 gene represent the novel, previously unpublished variants that might be population-specific. In conclusion, we provide the first report of multigene panel testing in Slovak HBOC families demonstrating that almost one-third of pathogenic mutations are situated in susceptibility genes other than BRCA1/2. Although multigene panel testing requires precise data filtration and interpretation, it might bring the relevant data for clinical management of the patients.

[Epicardial fat and osteoprotegerin - does a mutual relation exist? Pilot study]. / Epikardiální tuk a osteoprotegerin - existují vzájemné souvislosti? Pilotní studie.

INTRODUCTION: Epicardial fat (EPI) plays important role in development of metabolic and cardiovascular diseases. According to population studies EPI represents independent risk factor of cardiovascular diseases (CVD) and also for neoplasms. Osteoprotegerin (OPG) is a glycoprotein which have role in regulation of immune and cardiovascular systems. High serum levels of OPG are connected with high cardiovascular risk. The aim of our study was to evaluate possible correlation between EPI and OPG level in asymptomatic relatives of patients with CVD. MATERIAL AND METHODS: 53 asymptomatic relatives (37 male) (median age 53 years) of patients with CVD (ischemic heart disease, cerebrovascular disease) were included. Physical examination and biochemistry analysis were performed. GE Vivid 7 (GE Medical) was used for echocardiography. EPI was measured according to guidelines using parasternal long axis in diastole as a space in front of right ventricle. RESULTS: EPI was present in 46 subjects (86.8 %) with mean value of 2.91 mm. In 10 subjects was the amount of EPI > 5 mm. Spearmann correlation analysis found statistically significant correlation between EPI and OPG (r = 0.271; p = 0.05) and age (r = 0.500; p < 0.0001). We have not found correlation between EPI, glycaemia and level of insulin, glycated Hb, total, LDL, HDL cholesterol and triglycerides. CONCLUSION: We have found positive correlation between EPI and OPG. More studies are needed to confirm applicability of this correlation in risk stratification.Key words: cardiovascular risk - epicardial fat - osteoprotegerin.

[Treatment of liver cirrhosis - actually possibility of ambulant internist]. / Aktuální moznosti lécby jaterní cirhózy v ambulanci internisty.

UNLABELLED: There are 40 000-60 000 patients with cirrhosis in the Czech Republic. 2 000 die of this disease yearly. This group of patients needs a complex treatment and it is mostly an internist cooperating with other specialists. The most important for an ambulant internist is to diagnose the disease as soon as possible and start with treatment of chronic liver disease that could lead to a cirrhosis. It means especially chronic viral hepatitis, alcoholic or non-alcoholic steatosis/steatohepatitis, auto-immune liver damage and metabolic disease. The next step is to diagnose the cirrhosis in time when it is in no manifest stage. The third step is to diagnose and treat the liver decompensation. It means consequences of the portal hypertension, it is ascit, esophageal or gastric varices, hepatorenal syndrome. Next there are consequences of the metabolic insufficiency, it is icterus, coagulopathy and hepatic encephalopathy. It is necessary to diagnose and cure cholestasis from the very first extrahepatic causes. For a successful treatment of the hepatocellular carcinoma originated almost exclusively in the grounds of the cirrhosis must be early diagnosed. The ambulant internist respective hepatologist must diagnose the stage of the cirrhosis and decide when a hospitalization is necessary. Also a close cooperation with other specialists is urgent if it is about a liver transplantation. The treatment of successive stages of the cirrhosis is a topic of the showed educational article. KEY WORDS: compensated/decompensated liver cirrhosis - diet/nutrition in liver cirrhosis - etiology and diagnose of liver cirrhosis - treatment of liver insufficiency/failure - treatment of portal hypertension and its complications.

Long-term follow-up of children and adolescents with primary sclerosing cholangitis and autoimmune sclerosing cholangitis.

BACKGROUND: Sclerosing cholangitis (SC) is a chronic cholestatic hepatobiliary disease with uncertain long-term prognosis in pediatric patients. This study aimed to evaluate long-term results in children with SC according to the types of SC. METHODS: We retrospectively followed up 25 children with SC over a period of 4-17 years (median 12). The diagnosis of SC was based on biochemical, histological and cholangiographic findings. Patients fulfilling diagnostic criteria for probable or definite autoimmune hepatitis at the time of diagnosis were defined as having autoimmune sclerosing cholangitis (ASC); other patients were included in a group of primary sclerosing cholangitis (PSC). The incidence of the following complications was studied: obstructive cholangitis, portal hypertension, advanced liver disease and death associated with the primary disease. RESULTS: Fourteen (56%) patients had PSC and 11 (44%) had ASC. Patients with ASC were significantly younger at the time of diagnosis (12.3 vs 15.4 years, P=0.032) and had higher IgG levels (22.7 vs 17.2 g/L, P=0.003). The mentioned complications occurred in 4 (16%) patients with SC, exclusively in the PSC group: one patient died from colorectal cancer, one patient underwent liver transplantation and two patients, in whom severe bile duct stenosis was present at diagnosis, were endoscopically treated for acute cholangitis. Furthermore, two other children with ASC and 2 children with PSC had elevated aminotransferase levels. The 10-year overall survival was 95.8% in all patients, 100% in patients without complicated liver disease, and 75.0% in patients with complications. CONCLUSION: In children, ASC is a frequent type of SC, whose prognosis may be better than that in patients with PSC.

Clinical monitoring: infliximab biosimilar CT-P13 in the treatment of Crohn's disease and ulcerative colitis.

OBJECTIVE: The infliximab biosimilar CT-P13 (Remsima(®), Inflectra(®)) was approved in Europe for the treatment of inflammatory bowel disease (IBD) based on extrapolation of data from patients with rheumatic disease. Because there are limited published reports on clinical outcomes for IBD patients treated with CT-P13, we monitored responses to induction treatment with this biosimilar in patients with Crohn's disease (CD) or ulcerative colitis (UC) in centres across the Czech Republic. MATERIAL AND METHODS: Fifty-two patients with CD (n = 30) or UC (n = 22) were treated with 5 mg/kg CT-P13 for up to 14 weeks. Effectiveness of therapy was evaluated with the Crohn's Disease Activity Index (CDAI) or the Mayo Scoring System (MSS) in patients with CD or UC, respectively, before and after 14 weeks. Additional goals were to evaluate weight changes, serum C-reactive protein (CRP) levels, and complications/adverse events. RESULTS: In patients with CD, remission (CDAI <150) was achieved in 50.0% of cases, and partial response (≥70-point decrease in CDAI score from baseline) in the remaining 50.0%. In patients with UC, remission (total score on partial Mayo index ≤2 points) was achieved in 40.9% of cases, partial response (≥2-point decrease in partial Mayo score from baseline) in 54.5%, and no response in 4.5%. There were statistically significant improvements in CDAI, MSS and CRP serum levels after 14 weeks of therapy, and body weight increased. Four adverse events were identified (n = 1 each): lower-extremity phlebothrombosis, herpes labialis, pneumonia and allergic reaction. CONCLUSIONS: This prospective observational study provides evidence of the effectiveness of CT-P13 in IBD.

Acute pancreatitis as the first manifestation of duodenal MALT lymphoma.

BACKGROUND: Possibly any tumor that can cause mechanical obstruction of the distal bile duct can induce acute pancreatitis. However, acute pancreatitis as the first clinical manifestation of duodenal lymphoma is extremely rare. OBJECTIVE: To report the case of a patient with acute pancreatitis as an extremely rare first manifestation of duodenal MALT lymphoma and possible association with erythema nodosum. METHODS: Case report of a 66-year-old woman who was diagnosed with acute pancreatitis caused by infiltration with duodenal lymphoma. RESULTS: Acute pancreatitis was confirmed by CT imaging. Detailed investigation revealed a duodenal mass causing pancreatic injury. Histological analysis established the diagnosis of MALT lymphoma. The patient's medical history also included erythema nodosum. Complete remission of the malignancy was achieved with chemotherapy. CONCLUSION: This is the first published case report of acute pancreatitis caused by the growth of duodenal MALT lymphoma. An association with erythema nodosum is possible.

[Advances in diagnosis and therapy of inflammatory bowel diseases]. / Pokroky v diagnostice a lécbe nespecifických strevních zánetu

The inflammatory bowel diseases have been an interesting topic not only for gastroenterologists, but also for other medical professionals, since the beginning of the last century, when this group of inflammatory autoimmune diseases was revealed. Logically, the doyen of Czech gastroenterology, Professor MUDr. Zdenek Maratka, DrSc., who dedicated a substantial part of his life to research into inflammatory bowel disease, particularly ulcerative colitis, was no exception. The current century is characterized by a very rapid development of scientific research and almost immediate introduction of scientific knowledge into clinical practice. In the area of inflammatory bowel diseases, the biggest advances have been made in diagnosis and therapy. The examination of the small bowel and large bowel by magnetic resonance belongs at the very pinnacle in the non-invasive diagnosis of the lower part of the gastrointestinal tract. The administration of biological therapy to patients with the most severe forms of inflammatory bowel diseases should be considered a breakthrough since the introduction of corticosteroids into the therapy of inflammatory bowel diseases in the 1950s.

Chronic pancreatitis associated with the p.G208A variant of PRSS1 gene in a European patient.

CONTEXT: The major etiologic factor of chronic pancreatitis in adults is excessive alcohol consumption, whereas among children structural anomalies, systemic and metabolic disorders, and genetic factors are prevalent. Mutations in the cationic trypsinogen gene (PRSS1) cause hereditary pancreatitis, while mutations in serine protease inhibitor Kazal type 1 (SPINK1), cystic fibrosis transmembrane conductance regulator (CFTR) and chymotrypsin C (CTRC) genes have been shown to associate with chronic pancreatitis as independent risk factors. CASE REPORT: We present a case of 13-year-old boy with idiopathic chronic pancreatitis. Given the unexplained attacks of pancreatitis since early childhood and despite the negative family history, molecular-genetic analysis of four pancreatitis susceptibility genes (PRSS1, SPINK1, CTRC and CFTR) was performed. The boy was found to carry the c.623G>C (p.G208A) mutation of the PRSS1 gene and the c.180C>T (p.G60G) mutation of the CTRC gene, both in heterozygous state. These mutations are considered as contributing risk factors for chronic pancreatitis. CONCLUSIONS: In children with idiopathic chronic pancreatitis genetic causes should be considered, even in absence of positive family history. To the best of our knowledge, this is the first description of a European patient with chronic pancreatitis associated with the p.G208A mutation of PRSS1 gene. This mutation was previously reported only in Asian subjects and is thought to be a unique genetic cause of pancreatitis in Asia.

Acute upper gastrointestinal bleeding in liver cirrhosis patients.

OBJECTIVES: This study focuses on the etiology of acute upper gastrointestinal (GIT) bleeding in liver cirrhosis patients. METHODS: A prospective examination of 137 liver cirrhosis patients with acute upper GIT bleeding. All patients underwent endoscopic examination and in the case of multiple findings, definition of the source of bleeding was based on the endoscopic report. RESULTS: The most frequent causes of acute bleeding were: oesophageal varices (57.7%), peptic gastric and duodenal ulcers (18.2%), portal hypertension gastropathy (9.5%), gastric varices (5.1%), reflux oesophagitis (2.9%), Mallory-Weiss syndrome (2.9%) and erosive gastropathy (1.5%). A negative diagnosis was made in not more than 2.2% of patients. The majority of cases showed multiple findings in the upper digestive tract, each of which was a potential cause of bleeding. The mortality in all bleeding cirrhotic patients was 14.6%, 18.6% of which occurred in the varicose type of bleeding and 7.8% in the non-varicose type. CONCLUSIONS: Portal hypertension led to bleeding caused by varices and portal hypertension gastropathy in 72.3% of patients, 62.8% of patients suffered from purely varicose bleeding and 37.2% from non-varicose bleeding. Early, detailed endoscopic examination leading to appropriate diagnosis and treatment is of paramount importance.

Comprehensive genetic characterization of hereditary breast/ovarian cancer families from Slovakia.

Germline mutations in the BRCA1/2 genes account for the majority of hereditary breast ovarian cancer (HBOC). Identification of causal mutations may have significant impact on clinical management of such families. Despite high mutation detection rate, many HBOC cases remain without identified cause. These cases warrant use of several analysis methods, such as those for large genomic rearrangements and DNA copy number changes, or analysis other genes, shown to be associated with increased HBOC risk. We assessed 585 Slovak HBOC for the presence of mutations in BRCA genes. Sequencing revealed mutations in 100 families, representing 17.1% (88 and 12% of mutations were located in BRCA1 and BRCA2, respectively). Four of the mutations, c.80+4del4, c.1938_1947del10 and c.1166delG in BRCA1 and c.6589delA in BRCA2 gene have been described only in Slovak population. Using MLPA analysis, we detected two large genomic rearrangements in three families, a deletion of exons 21 and 22, and a rare deletion of a whole BRCA1 gene. Twenty-seven different variants of uncertain clinical effect (four novel) and 14 distinct SNP BRCA1 haplotypes were detected. Their potential effect was considered using the prediction software packages Align-GVGD, Pmut and Polyphen. We observed that the best clinical criterion for the initiation of BRCA1 analysis is the presence of breast cancer at 40 years of age in the association with the presence of ovarian cancer diagnosed around the age of 50. Conversely, the best clinical criterion for starting with BRCA2 analysis is the presence of breast cancer diagnosed in older age (above 50), or the presence of breast cancer in conjunction with carcinomas at different sites e.g., prostate, colorectum, ovary and uterus. Finally we have seen that the analyses of other HBOC risk gene TP53 and specific mutation in CHEK2*c.1100delC in Slovak HBOC families were not efficient since no mutations were found in these genes.

Exogenous alkaline phosphatase for the treatment of patients with moderate to severe ulcerative colitis.

BACKGROUND: Increased activity of intestinal alkaline phosphatase (AP) occurs locally in patients with ulcerative colitis (UC), aimed at repairing inflammatory tissue damage. We evaluated the safety and preliminary efficacy of exogenous AP administered to patients with UC in an open-label, first-in-patient exploratory trial, conducted in the Internal Medicine and Gastroenterology hospital departments in the Czech Republic and Italy. METHODS: Twenty-one patients were enrolled (13 females), age 23-54 years, with steroid- and/or immunosuppressant-refractory, moderate/severe UC (Mayo score 6-11). Oral AP enzyme 30,000 U was administered daily for 7 days, intraduodenally. Efficacy outcomes were changes in Mayo score at Day 21 posttreatment; changes in Modified Truelove-Witts Severity index (MTWSI) at Days 21, 63; C-reactive protein and stool calprotectin levels at Days 7, 21, 63. Safety evaluations were adverse events and laboratory abnormalities reported up to Day 63 posttreatment. RESULTS: No clinically relevant adverse events causing withdrawal or considered serious, or laboratory abnormalities or antibody formation against AP were observed. Mayo scores were significantly decreased at Day 21, and MTWSI at Days 21 and 63. C-reactive protein and stool calprotectin levels were decreased at Days 21 and 63. Clinical response on the Mayo score after a single 7-day AP course was 48% at Day 21. CONCLUSIONS: In this uncontrolled trial, administration of exogenous AP enzyme daily over a 7-day course to patients with UC was associated with short-term improvement in disease activity scores, with clinical effects being observed within 21 days and associated with reductions in C-reactive protein and stool calprotectin. AP enzyme treatment was well tolerated and nonimmunogenic.

Identification of a novel mutations BRCA1*c.80 + 3del4 and BRCA2*c.6589delA in Slovak HBOC families.

Mutations in the BRCA1 and BRCA2 genes account for the majority of hereditary breast ovarian cancer (HBOC) cases. However, after BRCA1 and BRCA2 screening still the most HBOC cases remain negative for any mutational event. Accordingly, in these cases raises the relevance to analyze the unusual BRCA1/2 variants of uncertain clinical significance. Complex RNA/cDNA analysis may constitute the solution and help to interpret the HBOC syndrome in the family. In our study we analyzed the novel, to our knowledge, not yet published mutations identified in Slovak HBOC families, c.80 + 3del4 (IVS2 + 3delAGTC) in BRCA1 gene and mutation c.6589delA (6817delA) in BRCA2 gene. To determine the effect of the BRCA1 mutation, we applied different approaches: segregation analysis of mutation with disease, presence in the set of unaffected controls and finally RNA/cDNA BRCA1 analysis. Novel BRCA2 mutation was determined performing direct sequencing analysis. In conclusion, considering the results from all used techniques we approved the mentioned mutations as seriously pathogenic and disease causing with clear effect on the onset of HBOC syndrome.