A near full-length open reading frame next generation sequencing assay for genotyping and identification of resistance-associated variants in hepatitis C virus.

BACKGROUND: The current treatment options for hepatitis C virus (HCV), based on direct acting antivirals (DAA), are dependent on virus genotype and previous treatment experience. Treatment failures have been associated with detection of resistance-associated substitutions (RASs) in the DAA targets of HCV, the NS3, NS5A and NS5 B proteins. OBJECTIVE: To develop a next generation sequencing based method that provides genotype and detection of HCV NS3, NS5A, and NS5 B RASs without prior knowledge of sample genotype. STUDY DESIGN: In total, 101 residual plasma samples from patients with HCV covering 10 different viral subtypes across 4 genotypes with viral loads of 3.84-7.61 Log IU/mL were included. All samples were de-identified and consequently prior treatment status for patients was unknown. Almost full open reading frame amplicons (∼ 9 kb) were generated using RT-PCR with a single primer set. The resulting amplicons were sequenced with high throughput sequencing and analysed using an in-house developed script for detecting RASs. RESULTS: The method successfully amplified and sequenced 94% (95/101) of samples with an average coverage of 14,035; four of six failed samples were genotype 4a. Samples analysed twice yielded reproducible nucleotide frequencies across all sites. RASs were detected in 21/95 (22%) samples at a 15% threshold. The method identified one patient infected with two genotype 2b variants, and the presence of subgenomic deletion variants in 8 (8.4%) of 95 successfully sequenced samples. CONCLUSIONS: The presented method may provide identification of HCV genotype, RASs detection, and detect multiple HCV infection without prior knowledge of sample genotype.

The prevalence of umbilical and epigastric hernia repair: a nationwide epidemiologic study.

PURPOSE: Umbilical and epigastric hernia repair are common surgical procedures; however, the nationwide gender and age-specific prevalence of these repairs is unknown, and this knowledge could form the basis for new studies. METHODS: A nationwide register-based study covering all people living in Denmark on December 31st, 2010 was performed. Within this population all umbilical and epigastric hernia repairs from January 1st, 2006 to December 31st, 2010 were identified using data from the Danish National Hospital Register, and 5-year prevalence estimates were calculated. RESULTS: The study population covered 5,639,885 persons (49 % males). A total of 10,107 patients (68 % males) were operated for an umbilical hernia and 2412 patients (55 % males) were operated for an epigastric hernia. The age-specific 5-year prevalence differed for both hernia types. The highest 5-year prevalence of umbilical hernia repairs was seen in males aged 60-70 years with a 5-year prevalence of 0.53 % (95 % CI 0.51-0.56 %) and the highest age-specific 5-year prevalence of epigastric hernia repair was seen in 40-50 year females with a 5-year prevalence of 0.086 % (95 % CI 0.077-0.095 %). CONCLUSION: The gender and age-specific 5-year prevalence of umbilical and epigastric hernia repair differed in a nationwide population.

Risk of schizophrenia in relation to parental origin and genome-wide divergence.

BACKGROUND: Second-generation immigrants have an increased risk of schizophrenia, a finding that still lacks a satisfactory explanation. Various operational definitions of second-generation immigrants have been used, including foreign parental country of birth. However, with increasing global migration, it is not clear that parental country of birth necessarily is informative with regard to ethnicity. We compare two independently collected measures of parental foreign ethnicity, parental foreign country of birth versus genetic divergence, based on genome-wide genotypic data, to access which measure most efficiently captures the increased risk of schizophrenia among second-generation immigrants residing in Denmark. METHOD: A case-control study covering all children born in Denmark since 1981 included 892 cases of schizophrenia and 883 matched controls. Genetic divergence was assessed using principal component analyses of the genotypic data. Independently, parental foreign country of birth was assessed using information recorded prospectively in the Danish Civil Registration System. We compared incidence rate ratios of schizophrenia associated with these two independently collected measures of parental foreign ethnicity. RESULTS: People with foreign-born parents had a significantly increased risk of schizophrenia [relative risk (RR) 1.94 (95% confidence intervals (CI) 1.41-2.65)]. Genetically divergent persons also had a significant increased risk [RR 2.43 (95% CI 1.55-3.82)]. Mutual adjustment of parental foreign country of birth and genetic divergence showed no difference between these measures with regard to their potential impact on the results. CONCLUSIONS: In terms of RR of schizophrenia, genetic divergence and parental foreign country of birth are interchangeable entities, and both entities have validity with regard to identifying second-generation immigrants.

[Simultaneous occurrence of trigger fingers and carpal tunnel syndrome]. / Samtidig forekomst af springfingre og karpaltunnelsyndrom.

We report an unusual case of trigger fingers and carpal tunnel syndrome occurring simultaneously; both conditions were caused by space-occupying fibrosis of the flexor tendon sheath. Following operation the patient was relieved of his symptoms. In case of simultaneously occurring trigger fingers and carpal tunnel syndrome, one should be aware that both conditions can be caused by space-occupying lesions beneath the carpal tunnel. Endoscopic surgery should be avoided in these cases.

Observer variation in the radiographic classification of fractures of the neck of the femur using Garden's system.

By means of Kappa statistics, we calculated the inter- and intra-observer variation in the classification of fractures of the neck of the femur according to Garden's system. Radiographs of 96 consecutive patients were assessed independently by six observers who agreed on classification for only 14 fractures (15%). The level of agreement was poor for the overall classification (Kappa = 0.39). When reducing Garden's system into non-displaced (Stage I and II) and displaced fractures (Stage III and IV) the level of agreement became acceptable (Kappa = 0.68). However, problems remain in distinguishing Stage II and Stage III fractures, and further improvements in the classification system are necessary.

The effect of bone drilling on pain in gonarthrosis.

Seventy-seven patients with mild to moderate gonarthrosis of the knee were treated by subchondral bone drilling, and followed for from 2 to 7 years. Patients with generalised arthrosis benefited more than those with unicompartmental involvement. Pain, assessed by a visual analogue scale, was significantly reduced compared with a control group of 16 patients who had a diagnostic arthroscopy only. Drilling is a safe procedure with few complications and can be used in patients when more extensive surgery is not yet indicated or possible.

[Conservative treatment of clavicular fractures]. / Konservativt behandlede claviculafrakturer.

The outcome of 99 clavicular fractures was examined retrospectively through a questionnaire and, in 20 cases, clinical examination. Primary treatment was in all cases a simple sling or a figure of eight bandage. The aim of the study was to examine prognostic factors in relation to the end-result. The fractures were classified, according to the roentgenograms, and the primary dislocation, primary shortening and secondary shortening of the shoulder were recorded. The end-result was expressed as the degree of pain. Statistically significantly more patients with group two type two fractures had a poor result. No other prognostic factors were found.

The human ubiquitin multigene family: some genes contain multiple directly repeated ubiquitin coding sequences.

Ubiquitin coding sequences were isolated from a human genomic library and two cDNA libraries. One human ubiquitin gene consists of 2055 nucleotides and codes for a polyprotein consisting of 685 amino acid residues. The polyprotein contains nine direct repeats of the ubiquitin amino acid sequence and the last ubiquitin sequence is extended with an additional valyl residue at the C-terminal end. No spacer sequences separate the ubiquitin repeats and the coding regions are not interrupted by intervening sequences. This particular gene is transcribed since cDNAs corresponding to the genomic sequence have been isolated. At least two more types of ubiquitin genes are encoded in the human genome, one coding for an ubiquitin monomer while another presumably codes for three or four direct repeats of the ubiquitin sequence. Human DNA contains many copies of the ubiquitin sequence. Ubiquitin is therefore encoded in the human genome as a multigene family.