UK survey of non-medical use of prescription drugs (NMURx) as a valuable source of general population illicit drug use data.

PURPOSE OF STUDY: The aim of the study is to describe the prevalence of illicit drug use in England and Wales using data from the UK Survey of Non-Medical Use of Prescription Drugs (NMURx) programme and to compare against the well-established Crime Survey England and Wales (CSEW). The rationale is that recreational and illicit drug use is common, but the prevalence is difficult to estimate with personal interviewing methods. STUDY DESIGN: We compared two cross-sectional population surveys (NMURx, n=8903 and CSEW, n=20 685) with data regarding self-reported recreational drug use and demographics. NMURx is an online survey using non-probability sampling methodology with preset demographical quotas based on census data. CSEW surveys drug use via computer-assisted self-interviewing as part of a computer-assisted personal-interviewing crime survey. RESULTS: Cannabis was the most frequently used drug regardless of demographics. Prevalence of drug use for specific substances was generally higher for males, younger ages and students. The relationship between income and drug misuse is less clear. Self-reported prevalence of drug use in the NMURx survey is consistently higher than CSEW (absolute difference 1%-3 % across substances and timescales) and persists after stratification for gender, age, student status and household income. CONCLUSIONS: The NMURx survey has a broad reach of participants, and a sampling scheme that achieves external validity, compared with general population demographics. NMURx's online format allows flexibility in items surveyed and in response to emerging trends. The self-reported drug use in the NMURx cohort is comparable, although slightly higher, than the CSEW estimates

Assessment of the incorporation of CNV surveillance into gene panel next-generation sequencing testing for inherited retinal diseases.

BACKGROUND: Diagnostic use of gene panel next-generation sequencing (NGS) techniques is commonplace for individuals with inherited retinal dystrophies (IRDs), a highly genetically heterogeneous group of disorders. However, these techniques have often failed to capture the complete spectrum of genomic variation causing IRD, including CNVs. This study assessed the applicability of introducing CNV surveillance into first-tier diagnostic gene panel NGS services for IRD. METHODS: Three read-depth algorithms were applied to gene panel NGS data sets for 550 referred individuals, and informatics strategies used for quality assurance and CNV filtering. CNV events were confirmed and reported to referring clinicians through an accredited diagnostic laboratory. RESULTS: We confirmed the presence of 33 deletions and 11 duplications, determining these findings to contribute to the confirmed or provisional molecular diagnosis of IRD for 25 individuals. We show that at least 7% of individuals referred for diagnostic testing for IRD have a CNV within genes relevant to their clinical diagnosis, and determined a positive predictive value of 79% for the employed CNV filtering techniques. CONCLUSION: Incorporation of CNV analysis increases diagnostic yield of gene panel NGS diagnostic tests for IRD, increases clarity in diagnostic reporting and expands the spectrum of known disease-causing mutations

Challenges in measuring measles case fatality ratios in settings without vital registration

Measles, a highly infectious vaccine-preventable viral disease, is potentially fatal. Historically, measles case-fatality ratios (CFRs) have been reported to vary from 0.1% in the developed world to as high as 30% in emergency settings. Estimates of the global burden of mortality from measles, critical to prioritizing measles vaccination among other health interventions, are highly sensitive to the CFR estimates used in modeling; however, due to the lack of reliable, up-to-date data, considerable debate exists as to what CFR estimates are appropriate to use. To determine current measles CFRs in high-burden settings without vital registration we have conducted six retrospective measles mortality studies in such settings. This paper examines the methodological challenges of this work and our solutions to these challenges, including the integration of lessons from retrospective all-cause mortality studies into CFR studies, approaches to laboratory confirmation of outbreaks, and means of obtaining a representative sample of case-patients. Our experiences are relevant to those conducting retrospective CFR studies for measles or other diseases, and to those interested in all-cause mortality studies

Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa

The cause of autosomal-dominant retinitis pigmentosa (adRP), which leads to loss of vision and blindness, was investigated in families lacking a molecular diagnosis. A refined locus for adRP on Chr17q22 (RP17) was delineated through genotyping and genome sequencing, leading to the identification of structural variants (SVs) that segregate with disease. Eight different complex SVs were characterized in 22 adRP-affected families with >300 affected individuals. All RP17 SVs had breakpoints within a genomic region spanning YPEL2 to LINC01476. To investigate the mechanism of disease, we reprogrammed fibroblasts from affected individuals and controls into induced pluripotent stem cells (iPSCs) and differentiated them into photoreceptor precursor cells (PPCs) or retinal organoids (ROs). Hi-C was performed on ROs, and differential expression of regional genes and a retinal enhancer RNA at this locus was assessed by qPCR. The epigenetic landscape of the region, and Hi-C RO data, showed that YPEL2 sits within its own topologically associating domain (TAD), rich in enhancers with binding sites for retinal transcription factors. The Hi-C map of RP17 ROs revealed creation of a neo-TAD with ectopic contacts between GDPD1 and retinal enhancers, and modeling of all RP17 SVs was consistent with neo-TADs leading to ectopic retinal-specific enhancer-GDPD1 accessibility. qPCR confirmed increased expression of GDPD1 and increased expression of the retinal enhancer that enters the neo-TAD. Altered TAD structure resulting in increased retinal expression of GDPD1 is the likely convergent mechanism of disease, consistent with a dominant gain of function. Our study highlights the importance of SVs as a genomic mechanism in unsolved Mendelian diseases

Baubles, Bangles, and Biotypes: A Critical Review of the use and Abuse of the Biotype Concept

Pest species of insects are notoriously prone to escape the weapons deployed in management efforts against them. This is particularly true in herbivorous insects. When a previously successful tactic fails the insect population has apparently adapted to it and is often considered to be a new or distinct entity, and given the non-formal category ‘biotype’. The entities falling under the umbrella term ‘biotype’ are not consistent either within or between biotypes, and their underlying genetic composition and origins, while generally unknown, are likely heterogeneous within and variable between biotypes. In some cases race or species may be more appropriate referents. Some examples of applications of the concept in the context of host plant resistance are discussed. It is argued here that the term ‘biotype’ and its applications are overly simplistic, confused, have not proved useful in current pest management, and lack predictive power for future management