Large-scale discovery of novel genetic causes of developmental disorders

Despite three decades of successful, predominantly phenotype-driven discovery of the genetic causes of monogenic disorders, up to half of children with severe developmental disorders of probable genetic origin remain without a genetic diagnosis. Particularly challenging are those disorders rare enough to have eluded recognition as a discrete clinical entity, those with highly variable clinical manifestations, and those that are difficult to distinguish from other, very similar, disorders. Here we demonstrate the power of using an unbiased genotype-driven approach to identify subsets of patients with similar disorders. By studying 1,133 children with severe, undiagnosed developmental disorders, and their parents, using a combination of exome sequencing and array-based detection of chromosomal rearrangements, we discovered 12 novel genes associated with developmental disorders. These newly implicated genes increase by 10% (from 28% to 31%) the proportion of children that could be diagnosed. Clustering of missense mutations in six of these newly implicated genes suggests that normal development is being perturbed by an activating or dominant-negative mechanism. Our findings demonstrate the value of adopting a comprehensive strategy, both genome-wide and nationwide, to elucidate the underlying causes of rare genetic disorders.

Fast segmentation of anterior segment optical coherence tomography images using graph cut

Background

Optical coherence tomography (OCT) is a non-invasive imaging system that can be used to obtain images of the anterior segment. Automatic segmentation of these images will enable them to be used to construct patient specific biomechanical models of the human eye. These models could be used to help with treatment planning and diagnosis of patients.

Methods

A novel graph cut technique using regional and shape terms was developed. It was evaluated by segmenting 39 OCT images of the anterior segment. The results of this were compared with manual segmentation and a previously reported level set segmentation technique. Three different comparison techniques were used: Dice’s similarity coefficient (DSC), mean unsigned surface positioning error (MSPE), and 95% Hausdorff distance (HD). A paired t-test was used to compare the results of different segmentation techniques.

Results

When comparison with manual segmentation was performed, a mean DSC value of 0.943 ± 0.020 was achieved, outperforming other previously published techniques. A substantial reduction in processing time was also achieved using this method.

Conclusions

We have developed a new segmentation technique that is both fast and accurate. This has the potential to be used to aid diagnostics and treatment planning.

Use of SMS and tablet computer improves the electronic collection of elective orthopaedic patient reported outcome measures

INTRODUCTION

Electronic patient reported outcome measures (PROMs) enable real time reporting back to the patient and medical team, comparison between similar patient cohorts and long-term cost effective outcome measurement. The primary objective of this three-phase pilot study was to measure uptake using a web-based PROM system following the introduction of two separate process improvements.

METHODS

Eighty consecutive new elective orthopaedic patients in a single surgeon's practice were recruited for the study. Patients in Group 1 (n=26) received only a letter reminding them to complete a symptom score. Those in Group 2 (n=31) also received a reminder SMS (short message service) message via their mobile or home telephone and those in Group 3 (n=23) also had access to a tablet computer in clinic.

RESULTS

The mean patient age in Group 1 was 55 years (range: 24-80 years), in Group 2 it was 60 years (range: 23-85 years) and in Group 3 it was 58 years (range: 37-78 years) (p>0.05). Overall, 79% of patients had internet access, and 35% of Group 1, 55% of Group 2 and 74% of Group 3 recorded an electronic PROM score (p=0.02). In Group 3, 94% of patients listed for an operation completed an electronic PROM score (p=0.006).

CONCLUSIONS

Collecting PROM data effectively in everyday clinical practice is challenging. Electronic collection should meet that challenge and improve healthcare delivery but it is in its infancy. This pilot study shows that the combination of an SMS reminder and access to a Wi-Fi enabled tablet computer in the clinic setting enabled 94% of patients listed for an operation to complete a score on a web-based clinical outcomes system. Additional staff training and telephone call reminders may further improve uptake.

Circles South East: the first 10 years 2002-2012

This article describes the first 10 years of the implementation of Circles of Support and Accountability (Circles) in the management of sexual offenders in South-East England by Circles South East (CSE). The Circles of 71 core members are reviewed in detail, with reference to demographic data, offense and sentencing histories, risk assessment data, and considerations regarding Multi-Agency Public Protection Arrangements. A group of 71 comparison subjects who were referred to CSE and deemed suitable for but did not receive the service was identified. Follow-up behaviors of both groups are examined (including all forms of reconviction, breach of orders, and prison recall). Over a comparable follow-up period of 55 months, the incidence of violent and contact sexual reconviction in the comparison group was significantly higher than for the Circles cohort. Comparisons are made between expected and actual levels of sexual reconviction, with the Circles cohort showing lower than expected rate of sexual reconviction but not to a statistically significant degree.

Reviewing the evidence base for the peripheral sensory examination

BACKGROUND

Many students find the peripheral sensory examination confusing. We set out to summarise the evidence base in order to provide guidance on the most useful manoeuvres.

METHODS

We performed a literature review starting with 5 secondary sources, supplemented by a literature search on MEDLINE.

RESULTS

A useful approach to neuropathy is to divide these into large fibre sensory neuropathy (LFSN) in which vibration and proprioception are affected, and small fibre sensory neuropathy (SFSN) in which pain and temperature are affected. Positive sensory symptoms such as burning, electric or sunburn pain point to a SFSN; negative symptoms such as loss of sensation, numbness or deep pain point to a LFSN. If LFSN is suspected, the most reproducible and best studied physical examination is a 10 g monofilament, but vibration sense is also useful. There is much less data on the best physical examination for a SFSN. The most appropriate diagnostic test for SFSN is quantitative sensory testing, whereas for LFSN a nerve conduction study is indicated.

CONCLUSIONS

A modest amount of evidence is available to guide peripheral sensory examination but more research is needed.

Delays in the stroke thrombolysis pathway--identifying areas for improvement

Despite international consensus on the benefits of thrombolysis for ischaemic stroke (IS), it remains underused. Guidelines now recommend a door-to-needle time of 60 minutes. We reviewed the rate and timeliness of thrombolysis for IS at our hospital. 323 stroke patients presented between January 2011 and April 2012.Thirty patients (10.6% of IS) were thrombolysed, mean age was 68.5 years (42 to 88) and 19 patients (63%) were male. Thirty-six patients (12.7% of IS) were not thrombolysed despite arriving within the time-window and symptom resolution was the commonest reason (15 patients; 42%). Despite most thrombolysed patients (42%) presenting to the Emergency Department during daytime working hours, there were delays at each step of the acute care pathway. The mean time for stroke team review was 23 minutes (5-50). The mean door-to-CT and the door-to-needle times were 60 minutes (25-95) and 92 minutes (46-130) respectively. In parallel with national stroke incentives, local audit can highlight barriers to uptake and efficiency within thrombolysis services.

Can audit improve patient care and treatment outcomes in endodontics?

Clinical audit is part of the NHS clinical governance framework for dentistry and is recommended as a quality improvement process for patient care, yet there is very mixed evidence supporting audit's ability to produce change in practice. Findings show evidence of changes following audit which improved patient care and practice efficiency. However, there is a general lack of dissemination of audit results, little useful feedback provided to participants, limited use of formal re-auditing of a particular topic and little reported on whether audit improves outcomes for patients. As part of its clinical governance responsibility, the Community Dental Service (CDS) is committed to ensuring that its clinical audit is robust, strategic and measures patient outcomes in its evaluation. The aim of this paper is to present a complete endodontic audit cycle; its recommendations and effects on the process and on outcomes of clinical patient endodontic care; and to evaluate if audit was a useful tool in this case.

Panda sign due to severe coughing

We present the case of a patient who developed periorbital ecchymosis (panda sign) following an exacerbation of asthma with severe coughing. There was no history of cranial trauma. Investigations for a structural or haematological cause were negative. The panda sign is typically seen following a base of skull fracture, but rarely reported due to severe coughing.

A chronological expression profile of gene activity during embryonic mouse brain development

The brain is a functionally complex organ, the patterning and development of which are key to adult health. To help elucidate the genetic networks underlying mammalian brain patterning, we conducted detailed transcriptional profiling during embryonic development of the mouse brain. A total of 2,400 genes were identified as showing differential expression between three developmental stages. Analysis of the data identified nine gene clusters to demonstrate analogous expression profiles. A significant group of novel genes of as yet undiscovered biological function were detected as being potentially relevant to brain development and function, in addition to genes that have previously identified roles in the brain. Furthermore, analysis for genes that display asymmetric expression between the left and right brain hemispheres during development revealed 35 genes as putatively asymmetric from a combined data set. Our data constitute a valuable new resource for neuroscience and neurodevelopment, exposing possible functional associations between genes, including novel loci, and encouraging their further investigation in human neurological and behavioural disorders.

The impact of trauma centre designation on open tibial fracture management

INTRODUCTION

The British Orthopaedic Association/British Association of Plastic, Reconstructive and Aesthetic Surgeons guidelines for the management of open tibial fractures recommend early senior combined orthopaedic and plastic surgical input with appropriate facilities to manage a high caseload. The aim of this study was to assess whether becoming a major trauma centre has affected the management of patients with open tibial fractures.

METHODS

Data were obtained prospectively on consecutive open tibial fractures during two eight-month periods: before and after becoming a trauma centre.

RESULTS

Overall, 29 open tibial fractures were admitted after designation as a major trauma centre compared with 15 previously. Of the 29 patients, 21 came directly or as transfers from another accident and emergency deparment (previously 8 of 15). The time to transfer patients admitted initially to local orthopaedic departments has fallen from 205.7 hours to 37.4 hours (p=0.084). Tertiary transferred patients had a longer hospital stay (16.3 vs 14.9 days) and had more operations (3.7 vs 2.6, p=0.08) than direct admissions. As a trauma centre, there were improvements in time to definitive skeletal stabilisation (4.7 vs 2.2 days, p=0.06), skin coverage (8.3 vs 3.7 days, p=0.06), average number of operations (4.2 vs 2.3, p=0.002) and average length of hospital admission (26.6 vs 15.3 days, p=0.05).

CONCLUSIONS

The volume and management of open tibial fractures, independent of fracture grade, has been directly affected by the introduction of a trauma centre enabling early combined senior orthopaedic and plastic surgical input. Our data strongly support the benefits of trauma centres and the continuing development of trauma networks in the management of open tibial fractures.

Prescribing of antidiabetic therapies in Ireland: 10-year trends 2003-2012

BACKGROUND

Over the last decade there have been significant changes in the prescribing of antidiabetic therapies. It is of interest to know about these trends and variations in the Irish population so that future prescribing patterns can be estimated.

AIMS

To examine the trends in prescribed antidiabetic treatments, including variations across age, gender, socioeconomic status and regions in the Irish population over the last 10 years.

METHODS

The Irish national pharmacy claims database was used to identify patients ≥ 16 years dispensed antidiabetic agents (oral or insulin) from January 2003 to December 2012 through the two main community drug schemes for diabetes. The rate of prescribing per 1,000 population was calculated. Logistic regression was used to examine variations in prescribing in patients with diabetes.

RESULTS

There was a significant increase in the prescribing of fast and long-acting insulin analogues with a rapid decline in the prescribing of human insulin (p < 0.0001). Increased prescribing of metformin, incretin modulators and fixed oral combination agents was observed (p < 0.0001). Females and older aged patients were more likely to be prescribed human insulin than other insulins. Metformin was less likely while sulphonylureas were more likely to be prescribed in older than younger aged patients. Socioeconomic differences were observed in increased prescribing of the newer and more expensive antidiabetic agents in the non-means tested scheme. Regional variations were observed in the prescribing of both insulin and oral antidiabetic agents.

CONCLUSION

There has been an increase over time in the prescribing of both insulin and oral antidiabetic agents in the Irish population with increasing uptake of newer antidiabetic agents. This has implications for projecting future uptake and expenditure of these agents given the rising level of diabetes in the population.

Improved estimation of the health and economic burden of chronic disease risk factors in Manitoba

INTRODUCTION

There are analytic challenges involved with estimating the aggregate burden of multiple risk factors (RFs) in a population. We describe a methodology to account for overlapping RFs in some sub-populations, a phenomenon that leads to "double-counting" the diseases and economic burden generated by those factors.

METHODS

Our method uses an efficient approach to accurately analyze the aggregate economic burden of chronic disease across a multifactorial system. In addition, it involves considering the effect of body weight as a continuous or polytomous exposure that ranges from no excess weight through overweight to obesity. We then apply this method to smoking, physical inactivity and overweight/obesity in Manitoba, a province of Canada.

RESULTS

The annual aggregate economic burden of the RFs in Manitoba in 2008 is about $1.6 billion ($557 million for smoking, $299 million for physical inactivity and $747 million for overweight/obesity). The total burden represents a 12.6% downward adjustment to account for the effect of multiple RFs in some individuals in the population.

CONCLUSION

An improved estimate of the aggregate economic burden of multiple RFs in a given population can assist in prioritizing and gaining support for primary prevention initiatives.

A semi-automated vascular access system for preclinical models

Murine models are used extensively in biological and translational research. For many of these studies it is necessary to access the vasculature for the injection of biologically active agents. Among the possible methods for accessing the mouse vasculature, tail vein injections are a routine but critical step for many experimental protocols. To perform successful tail vein injections, a high skill set and experience is required, leaving most scientists ill-suited to perform this task. This can lead to a high variability between injections, which can impact experimental results. To allow more scientists to perform tail vein injections and to decrease the variability between injections, a vascular access system (VAS) that semi-automatically inserts a needle into the tail vein of a mouse was developed. The VAS uses near infrared light, image processing techniques, computer controlled motors, and a pressure feedback system to insert the needle and to validate its proper placement within the vein. The VAS was tested by injecting a commonly used radiolabeled probe (FDG) into the tail veins of five mice. These mice were then imaged using micro-positron emission tomography to measure the percentage of the injected probe remaining in the tail. These studies showed that, on average, the VAS leaves 3.4% of the injected probe in the tail. With these preliminary results, the VAS system demonstrates the potential for improving the accuracy of tail vein injections in mice.

Penile intraepithelial neoplasia: important lessons from a case series

Summary

Seven men presenting to our genitourinary (GU) medicine clinic over a period of 22 months had a histopathological diagnosis of penile intraepithelial neoplasia (PIN). Median duration of symptoms was eight months (range 2–216 months). Macroscopic appearances were different in all cases. All histology was reviewed locally and at a tertiary centre. Six of seven had severe dysplasia (PIN III). Interestingly, only one individual was HIV-positive and one, who was immunocompetent, had multifocal disease. These cases highlight the importance of a full anogenital examination and early biopsy in patients presenting with atypical or persistent penile lesions.

Early-life hygiene-related factors affect risk of central nervous system demyelination and asthma differentially

The increasing prevalence of immune-related diseases, including multiple sclerosis, may be partly explained by reduced microbial burden during childhood. Within a multi-centre case-control study population, we examined: (i) the co-morbid immune diseases profile of adults with a first clinical diagnosis of central nervous system demyelination (FCD) and (ii) sibship structure in relation to an autoimmune (FCD) and an allergic (asthma) disease. FCD cases (n = 282) were aged 18-59 years; controls (n = 558) were matched on age, sex and region. Measures include: history of doctor-diagnosed asthma; sibling profile (number; dates of birth); and regular childcare attendance. FCD cases did not differ from controls with regard to personal or family history of allergy, but had a greater likelihood of chronic fatigue syndrome [odds ratio (OR) = 3·11; 95% confidence interval (CI) 1·11, 8·71]. Having any younger siblings showed reduced odds of FCD (OR = 0·68; 95% CI: 0·49, 0·95) but not asthma (OR = 1·47; 95% CI: 0·91, 2·38). In contrast, an increasing number of older siblings was associated with reduced risk of asthma (P trend = 0·04) but not FCD (P trend = 0·66). Allergies were not over-represented among people presenting with FCD. Sibship characteristics influence both FCD and asthma risk but the underlying mechanisms differ, possibly due to the timing of the putative 'sibling effect'.

Use of prenatal chromosomal microarray: prospective cohort study and systematic review and meta-analysis

OBJECTIVES

Chromosomal microarray analysis (CMA) is utilized in prenatal diagnosis to detect chromosomal abnormalities not visible by conventional karyotyping. A prospective cohort of women undergoing fetal CMA and karyotyping following abnormal prenatal ultrasound findings is presented in the context of a systematic review and meta-analysis of the literature describing detection rates by CMA and karyotyping.

METHODS

We performed a prospective cohort study of 243 women undergoing CMA alongside karyotyping when a structural abnormality was detected on prenatal ultrasound. A systematic review of the literature was also performed. MEDLINE (1970-Dec 2012), EMBASE (1980-Dec 2012) and CINAHL (1982-June 2012) databases were searched electronically. Selected studies included > 10 cases and prenatal CMA in addition to karyotyping. The search yielded 560 citations. Full papers were retrieved for 86, and 25 primary studies were included in the systematic review.

RESULTS

Our cohort study found an excess detection rate of abnormalities by CMA of 4.1% over conventional karyotyping when the clinical indication for testing was an abnormal fetal ultrasound finding; this was lower than the detection rate of 10% (95% CI, 8-13%) by meta-analysis. The rate of detection for variants of unknown significance (VOUS) was 2.1% (95% CI, 1.3-3.3%) when the indication for CMA was an abnormal scan finding. The VOUS detection rate was lower (1.4%; 95% CI, 0.5-3.7%) when any indication for prenatal CMA was meta-analyzed.

CONCLUSION

We present evidence for a higher detection rate by CMA than by karyotyping not just in the case of abnormal ultrasound findings but also in cases of other indications for invasive testing. It is likely that CMA will replace karyotyping in high-risk pregnancies.