‘It's a bit of a grey area’: challenges faced by stop smoking practitioners when advising on e-cigarettes

INTRODUCTION: According to UK guidelines, stop smoking practitioners are expected to be open and supportive towards e-cigarette users. As adequate support from practitioners can be instrumental for smokers to successfully quit smoking, it is crucial to explore the challenges that stop smoking practitioners face when advising on e-cigarette use. AIM: This qualitative study explores the challenges that stop smoking practitioners face when advising patients on e-cigarettes. METHODS: A qualitative study was conducted with semi-structured interviews with 10 stop smoking practitioners from four stop smoking services in London. Face to face interviews were recorded and transcribed verbatim. Inductive thematic analysis was conducted to explore practitioners' experiences when advising on e-cigarettes. FINDINGS: Two themes were noted: practitioners' concerns and practitioner–patient interactions. Practitioners were particularly concerned regarding the lack of information, safety issues and the maintenance of addiction linked with e-cigarettes. They emphasised the difficulty of advising on a product that they cannot prescribe. Overall, practitioners expressed the lack of confidence when advising on e-cigarettes since they were often unprepared and not able to answer patients' questions on e-cigarettes. CONCLUSIONS: Stop smoking practitioners' lack of confidence and limited knowledge regarding e-cigarettes emphasises the necessity for training and guidance on e-cigarettes to improve their interactions with patients on this subject. In particular, practitioners need to be provided with clear guidance on how to counsel patients about how and where to buy e-cigarettes

ADDO: a comprehensive toolkit to detect, classify and visualise additive and non-additive Quantitative Trait Loci

MOTIVATION During the past decade, genome-wide association studies (GWAS) have been used to map quantitative trait loci (QTLs) underlying complex traits. However, most GWAS focus on additive genetic effects while ignoring non-additive effects, on the assumption that most QTL act additively. Consequently, QTLs driven by dominance and other non-additive effects could be overlooked. RESULTS We developed ADDO, a highly-efficient tool to detect, classify and visualise quantitative trait loci (QTLs) with additive and non-additive effects. ADDO implements a mixed-model transformation to control for population structure and unequal relatedness that accounts for both additive and dominant genetic covariance among individuals, and decomposes single nucleotide polymorphism (SNP) effects as either additive, partial dominant, dominant and over-dominant. A matrix multiplication approach is used to accelerate the computation: a genome scan on 13 million markers from 900 individuals takes about 5 hours with 10 CPUs. Analysis of simulated data confirms ADDO’s performance on traits with different additive and dominance genetic variance components. We showed two real examples in outbred rat where ADDO identified significant dominant QTL that were not detectable by an additive model. ADDO provides a systematic pipeline to characterize additive and non-additive QTL in whole genome sequence data, which complements current mainstream GWAS software for additive genetic effects. AVAILABILITY AND IMPLEMENTATION ADDO is customizable and convenient to install and provides extensive analytics and visualizations. The package is freely available online at https://github.com/LeileiCui/ADDO

Pathogenic variants in the CYP21A2 gene cause isolated autosomal dominant congenital posterior polar cataracts

Background: Congenital cataracts are the most common cause of visual impairment worldwide. Inherited cataract is a clinically and genetically heterogeneous disease. Here we report disease-causing variants in a novel gene, CYP21A2, causing autosomal dominant posterior polar cataract. Variants in this gene are known to cause autosomal recessive congenital adrenal hyperplasia (CAH). / Methods: Using whole-exome sequencing (WES), we have identified disease-causing sequence variants in two families of British and Irish origin, and in two isolated cases of Asian-Indian and British origin. Bioinformatics analysis confirmed these variants as rare with damaging pathogenicity scores. Segregation was tested within the families using direct Sanger sequencing. / Results: A nonsense variant NM_000500.9 c.955 C > T; p.Q319* was identified in CYP21A2 in two families with posterior polar cataract and in an isolated case with unspecified congenital cataract phenotype. This is the same variant previously linked to CAH and identified as Q318* in the literature. We have also identified a rare missense variant NM_000500.9 c.770 T > C; p.M257T in an isolated case with unspecified congenital cataract phenotype. / Conclusion: This is the first report of separate sequence variants in CYP21A2 associated with congenital cataract. Our findings extend the genetic basis for congenital cataract and add to the phenotypic spectrum of CYP21A2 variants and particularly the CAH associated Q318* variant. CYP21A2 has a significant role in mineralo- and gluco-corticoid biosynthesis. These findings suggest that CYP21A2 may be important for extra-adrenal biosynthesis of aldosterone and cortisol in the eye lens

Extending the phenotypic spectrum of PRPF8, PRPH2, RP1 and RPGR, and the genotypic spectrum of early-onset severe retinal dystrophy

PURPOSE: To present the detailed retinal phenotype of patients with Leber Congenital Amaurosis/Early-Onset Severe Retinal Dystrophy (LCA/EOSRD) caused by sequence variants in four genes, either not (n = 1) or very rarely (n = 3) previously associated with the disease. METHODS: Retrospective case series of LCA/EOSRD from four pedigrees. Chart review of clinical notes, multimodal retinal imaging, electrophysiology, and molecular genetic testing at a single tertiary referral center (Moorfields Eye Hospital, London, UK). RESULTS: The mean age of presentation was 3 months of age, with disease onset in the first year of life in all cases. Molecular genetic testing revealed the following disease-causing variants: PRPF8 (heterozygous c.5804G > A), PRPH2 (homozygous c.620_627delinsTA, novel variant), RP1 (homozygous c.4147_4151delGGATT, novel variant) and RPGR (heterozygous c.1894_1897delGACA). PRPF8, PRPH2, and RP1 variants have very rarely been reported, either as unique cases or case reports, with limited clinical data presented. RPGR variants have not previously been associated with LCA/EOSRD. Clinical history and detailed retinal imaging are presented. CONCLUSIONS: The reported cases extend the phenotypic spectrum of PRPF8-, PRPH2-, RP1-, and RPGR-associated disease, and the genotypic spectrum of LCA/EOSRD. The study highlights the importance of retinal and functional phenotyping, and the importance of specific genetic diagnosis to potential future therapy

Seqfam: A python package for analysis of Next Generation Sequencing DNA data in families [version 1]

This article introduces seqfam, a python package which is primarily designed for analysing next generation sequencing (NGS) DNA data from families with known pedigree information in order to identify rare variants that are potentially causal of a disease/trait of interest. It uses the popular and versatile Pandas library, and can be straightforwardly integrated into existing analysis code/pipelines. Seqfam can be used to verify pedigree information, to perform Monte Carlo gene dropping, to undertake regression-based gene burden testing, and to identify variants which segregate by affection status in families via user-defined pattern of occurrence rules. Additionally, it can generate scripts for running analyses in a “MapReduce pattern” on a computer cluster, something which is usually desirable in NGS data analysis and indeed “big data” analysis in general. This article summarises how seqfam’s main user functions work and motivates their use. It also provides explanatory context for example scripts and data included in the package which demonstrate use cases. With respect to verifying pedigree information, software exists for efficiently calculating kinship coefficients, so seqfam performs the necessary extra steps of mapping pedigrees and kinship coefficients to expected and observed degrees of relationship respectively. Gene dropping and the application of variant pattern of occurrence rules in families can provide evidence for a variant being causal. The authors are unaware of other software which performs these tasks in familial cohorts, so seqfam fulfils this need. Gene burden rather than single marker tests are often used to detect rare causal variants due to greater power. Seqfam may be an attractive alternative to existing gene burden testing software due to its flexibility, particularly in grouping and aggregating variants

Juvenile Batten disease (CLN3): Detailed Ocular Phenotype, Novel Observations, Delayed Diagnosis, Masquerades, and Prospects for Therapy

PURPOSE To characterize the retinal phenotype of juvenile neuronal ceroid lipofuscinosis (JNCL), highlight delayed and mistaken diagnosis, and propose an algorithm for early identification. DESIGN Retrospective case series. SUBJECTS Eight children (5 females) with JNCL. METHODS Review of clinical notes, retinal imaging including fundus autofluorescence (FAF) and optical coherence tomography (OCT), electroretinography (ERG), and both microscopy and molecular genetic testing. MAIN OUTCOME MEASUREMENTS Demographic data, signs and symptoms, visual acuity, FAF and OCT findings, ERG phenotype, and microscopy/molecular genetics. RESULTS Subjects presented with rapid bilateral vision loss over one to eighteen months, with mean visual acuity deteriorating from 0.44 LogMAR (range: 0.20 - 1.78 LogMAR) at baseline, to 1.34 LogMAR (0.30 LogMAR - light perception) at last follow-up. Age of onset ranged from 3 to 7 years (mean 5.3 years). The age at diagnosis of JNCL ranged from 7 to 10 years (mean 8.3 years). Six children displayed eccentric fixation, and six had cognitive or neurological signs at time of diagnosis (75%). Seven patients had bilateral bull’s-eye maculopathy at presentation. Coats-like exudative vasculopathy, not previously reported in JNCL, was observed in one patient. OCT imaging revealed near complete loss of outer retinal layers, and marked atrophy of the nerve fibre and ganglion cell layers, at the central macula. An ‘electronegative’ ERG was present in four patients (50%), but with additional a-wave reduction; there was an undetectable ERG in the remaining four. Blood film microscopy revealed vacuolated lymphocytes and electron microscopy showed lysosomal (fingerprint) inclusions, in all eight patients. CONCLUSIONS In a young child with bilateral rapidly progressive vision loss and macular disturbance, blood film microscopy to detect vacuolated lymphocytes is a rapid, readily accessible, and sensitive screening test for JNCL. Early suspicion of JNCL can be aided by detailed directed history and high-resolution retinal imaging, with subsequent targeted microscopy/genetic testing. Early diagnosis is critical to ensure appropriate management, counselling, support and social care for children and their families. Furthermore, although potential therapies for this group of disorders are in early phase clinical trial, realistic expectations are that successful intervention will be most effective when initiated at the earliest stage of disease

Cloud-based genomics pipelines for ophthalmology: Reviewed from research to clinical practice

Aim: To familiarize clinicians with clinical genomics, and to describe the potential of cloud computing for enabling the future routine use of genomics in eye hospital settings. Design: Review article exploring the potential for cloud-based genomic pipelines in eye hospitals. Methods: Narrative review of the literature relevant to clinical genomics and cloud computing, using PubMed and Google Scholar. A broad overview of these fields is provided, followed by key examples of their integration. Results: Cloud computing could benefit clinical genomics due to scalability of resources, potentially lower costs, and ease of data sharing between multiple institutions. Challenges include complex pricing of services, costs from mistakes or experimentation, data security, and privacy concerns. Conclusions and future perspectives: Clinical genomics is likely to become more routinely used in clinical practice. Currently this is delivered in highly specialist centers. In the future, cloud computing could enable delivery of clinical genomics services in non-specialist hospital settings, in a fast, cost-effective way, whilst enhancing collaboration between clinical and research teams

Non-Penetrance for Ocular Phenotype in Two Individuals Carrying Heterozygous Loss-of-Function ZEB1 Alleles

ZEB1 loss-of-function (LoF) alleles are known to cause a rare autosomal dominant disorder—posterior polymorphous corneal dystrophy type 3 (PPCD3). To date, 50 pathogenic LoF variants have been identified as disease-causing and familial studies have indicated that the PPCD3 phenotype is penetrant in approximately 95% of carriers. In this study, we interrogated in-house exomes (n = 3616) and genomes (n = 88) for the presence of putative heterozygous LoF variants in ZEB1. Next, we performed detailed phenotyping in a father and his son who carried a novel LoF c.1279C>T; p.(Glu427*) variant in ZEB1 (NM_030751.6) absent from the gnomAD v.2.1.1 dataset. Ocular examination of the two subjects did not show any abnormalities characteristic of PPCD3. GnomAD (n = 141,456 subjects) was also interrogated for LoF ZEB1 variants, notably 8 distinct heterozygous changes presumed to lead to ZEB1 haploinsufficiency, not reported to be associated with PPCD3, have been identified. The NM_030751.6 transcript has a pLI score ≥ 0.99, indicating extreme intolerance to haploinsufficiency. In conclusion, ZEB1 LoF variants are present in a general population at an extremely low frequency. As PPCD3 can be asymptomatic, the true penetrance of ZEB1 LoF variants remains currently unknown but is likely to be lower than estimated by the familial led approaches adopted to date