Moving towards a cure in genetics : what is needed to bring somatic gene therapy to the clinic?

Clinical trials using somatic gene editing (e.g., CRISPR-Cas9) have started in Europe and the United States and may provide safe and effective treatment and cure, not only for cancers but also for some monogenic conditions. In a workshop at the 2018 European Human Genetics Conference, the challenges of bringing somatic gene editing therapies to the clinic were discussed. The regulatory process needs to be considered early in the clinical development pathway to produce the data necessary to support the approval by the European Medicines Agency. The roles and responsibilities for geneticists may include counselling to explain the treatment possibilities and safety interpretation.Peer reviewe

Inverting Ray-Knight identity

We provide a short proof of the Ray-Knight second generalized Theorem, using a martingale which can be seen (on the positive quadrant) as the Radon-Nikodym derivative of the reversed vertex-reinforced jump process measure with respect to the Markov jump process with the same conductances. Next we show that a variant of this process provides an inversion of that Ray-Knight identity. We give a similar result for the Ray-Knight first generalized Theorem.Comment: 18 page

Domain ontology for digital marketplaces

Recently the sharing economy has emerged as a viable alternative to fulfilling a variety of consumer needs. As there is no consensus on the definition of ‘sharing economy’ we use the term ‘marketplace’ to refer more specifically to Internet/software-based sharing economy platforms connecting two different market segments. In the field of sharing economy and marketplaces we found a research gap concerning the (socio)technological aspects and the development of marketplaces. A marketplace ontology can help to have a clear account of marketplace concepts which will facilitate communication, consensus and alignment. In this paper we design this marketplace ontology in four steps. First the selection of UFO as foundation and UFO-S as core ontology. Second the search for a set of minimal conditions and properties common for marketplaces and the derivation into competency questions. Third, use the competency questions to identify fragmented sub-ontology pieces called Domain-Related Ontology Patterns (DROPs) and apply them informally by extending UFO-S concepts to design a marketplace domain ontology. This marketplace domain ontology is represented in OntoUML. The last step is the validation of the OntoUML model using expert knowledge

Impact of metabolic comorbidity on the association between body mass index and heatlh-related quality of life: a Scotland-wide cross-sectional study of 5,608 participants

<p/>Background: The prevalence of obesity is rising in Scotland and globally. Overall, obesity is associated with increased morbidity, mortality and reduced health-related quality of life. Studies suggest that "healthy obesity" (obesity without metabolic comorbidity) may not be associated with morbidity or mortality. Its impact on health-related quality of life is unknown. <p/>Methods: We extracted data from the Scottish Health Survey on self-reported health-related quality of life, body mass index (BMI), demographic information and comorbidity. SF-12 responses were converted into an overall health utility score. Linear regression analyses were used to explore the association between BMI and health utility, stratified by the presence or absence of metabolic comorbidity (diabetes, hypertension, hypercholesterolemia or cardiovascular disease), and adjusted for potential confounders (age, sex and deprivation quintile). <p/>Results: Of the 5,608 individuals, 3,744 (66.8%) were either overweight or obese and 921 (16.4%) had metabolic comorbidity. There was an inverted U-shaped relationship whereby health utility was highest among overweight individuals and fell with increasing BMI. There was a significant interaction with metabolic comorbidity (p = 0.007). Individuals with metabolic comorbidty had lower utility scores and a steeper decline in utility with increasing BMI (morbidly obese, adjusted coefficient: -0.064, 95% CI -0.115, -0.012, p = 0.015 for metabolic comorbidity versus -0.042, 95% CI -0.067, -0.018, p = 0.001 for no metabolic comorbidity). <p/>Conclusions: The adverse impact of obesity on health-related quality of life is greater among individuals with metabolic comorbidity. However, increased BMI is associated with reduced health-related quality of life even in the absence of metabolic comorbidity, casting doubt on the notion of "healthy obesity"

Cholera Epidemic in Guinea-Bissau (2008): The Importance of “Place”

As resources are limited when responding to cholera outbreaks, knowledge about where to orient interventions is crucial. We describe the cholera epidemic affecting Guinea-Bissau in 2008 focusing on the geographical spread in order to guide prevention and control activities

Effects of reallocating time in different activity intensities on health and fitness: a cross sectional study

BACKGROUND: The effects of replacing time in specific activity categories for other categories (e.g. replacing sedentary time with light activity) on health and fitness are not well known. This study used isotemporal substitution to investigate the effects of substituting activity categories in an equal time exchange fashion on health and fitness in young people. METHODS: Participants were drawn from schools in Camden, London (n = 353, mean age 9.3 ± 2.3 years). Time sedentary, in light and in moderate-to-vigorous activity (MVPA) was measured via accelerometry. The effects of substituting time in activity categories (sedentary, light and MVPA) with equivalent time in another category on health and fitness were examined using isotemporal substitution. RESULTS: In single and partition models, MVPA was favourably associated with body fat %, horizontal jump distance and flexibility. Time sedentary and in light activity were not associated with health and fitness outcomes in these models. In substitution models, replacing one hour of sedentary time with MVPA was favourably associated with body fat % (B = -4.187; 95% confidence interval (CI), -7.233, -1.142), horizontal jump distance (B = 16.093; 95% CI, 7.476, 24.710) and flexibility (B = 4.783; 95% CI, 1.910, 7.656). Replacing time in light activity with MVPA induced similar benefits but there were null effects for replacing sedentary with light intensity. CONCLUSION: Substituting time sedentary and in light activity with MVPA was associated with favourable health and fitness. Time in sedentary behaviour may only be detrimental to health and fitness when it replaces time in MVPA in young people

Genotyping Performance Assessment of Whole Genome Amplified DNA with Respect to Multiplexing Level of Assay and Its Period of Storage

Whole genome amplification can faithfully amplify genomic DNA (gDNA) with minimal bias and substantial genome coverage. Whole genome amplified DNA (wgaDNA) has been tested to be workable for high-throughput genotyping arrays. However, issues about whether wgaDNA would decrease genotyping performance at increasing multiplexing levels and whether the storage period of wgaDNA would reduce genotyping performance have not been examined. Using the Sequenom MassARRAY iPLEX Gold assays, we investigated 174 single nucleotide polymorphisms for 3 groups of matched samples: group 1 of 20 gDNA samples, group 2 of 20 freshly prepared wgaDNA samples, and group 3 of 20 stored wgaDNA samples that had been kept frozen at −70°C for 18 months. MassARRAY is a medium-throughput genotyping platform with reaction chemistry different from those of high-throughput genotyping arrays. The results showed that genotyping performance (efficiency and accuracy) of freshly prepared wgaDNA was similar to that of gDNA at various multiplexing levels (17-plex, 21-plex, 28-plex and 36-plex) of the MassARRAY assays. However, compared with gDNA or freshly prepared wgaDNA, stored wgaDNA was found to give diminished genotyping performance (efficiency and accuracy) due to potentially inferior quality. Consequently, no matter whether gDNA or wgaDNA was used, better genotyping efficiency would tend to have better genotyping accuracy

Prediction of specificity-determining residues for small-molecule kinase inhibitors

<p>Abstract</p> <p>Background</p> <p>Designing small-molecule kinase inhibitors with desirable selectivity profiles is a major challenge in drug discovery. A high-throughput screen for inhibitors of a given kinase will typically yield many compounds that inhibit more than one kinase. A series of chemical modifications are usually required before a compound exhibits an acceptable selectivity profile. Rationalizing the selectivity profile for a small-molecule inhibitor in terms of the specificity-determining kinase residues for that molecule can be an important step toward the goal of developing selective kinase inhibitors.</p> <p>Results</p> <p>Here we describe S-Filter, a method that combines sequence and structural information to predict specificity-determining residues for a small molecule and its kinase selectivity profile. Analysis was performed on seven selective kinase inhibitors where a structural basis for selectivity is known. S-Filter correctly predicts specificity determinants that were described by independent groups. S-Filter also predicts a number of novel specificity determinants that can often be justified by further structural comparison.</p> <p>Conclusion</p> <p>S-Filter is a valuable tool for analyzing kinase selectivity profiles. The method identifies potential specificity determinants that are not readily apparent, and provokes further investigation at the structural level.</p

C4B null alleles are not associated with genetic polymorphisms in the adjacent gene CYP21A2 in autism

<p>Abstract</p> <p>Background</p> <p>Research indicates that the etiology of autism has a strong genetic component, yet so far the search for genes that contribute to the disorder, including several whole genome scans, has led to few consistent findings. However, three studies indicate that the complement <it>C4B </it>gene null allele (i.e. the missing or nonfunctional <it>C4B </it>gene) is significantly more frequent in individuals with autism. Due to the close proximity of the <it>CYP21A2 </it>gene to the <it>C4B </it>locus (3 kb) it was decided to examine samples from autistic subjects, including many with known <it>C4B </it>null alleles for common <it>CYP21A2 </it>mutations.</p> <p>Methods</p> <p>Samples from subjects diagnosed with autism and non-autistic controls (controls) previously typed for <it>C4B </it>null alleles were studied. Allele specific polymerase chain reaction (PCR) methods were used to determine 8 of the most common <it>CYP21A2 </it>genetic mutations, known to completely or partially inhibit 21-hydroxylase, the enzyme encoded by the <it>CYP21A2 </it>gene.</p> <p>Results</p> <p>Although the combined autism and control study subjects had 50 <it>C4B </it>null alleles only 15 <it>CYP21A2 </it>mutations were detected in over 2250 genotypes. Eight mutations were detected in the autistic samples and 7 in the controls. The frequency of <it>CYP21A2 </it>mutations was similar between the autism and control samples. Only one individual (autistic) carried a chromosome containing both <it>C4B </it>null allele and <it>CYP21A2 </it>mutations.</p