Evaluation of a novel assay for detection of the fetal marker RASSF1A: facilitating improved diagnostic reliability of noninvasive prenatal diagnosis

BackgroundAnalysis of cell free fetal (cff) DNA in maternal plasma is used routinely for non invasive prenatal diagnosis (NIPD) of fetal sex determination, fetal rhesus D status and some single gene disorders. True positive results rely on detection of the fetal target being analysed. No amplification of the target may be interpreted either as a true negative result or a false negative result due to the absence or very low levels of cffDNA. The hypermethylated RASSF1A promoter has been reported as a universal fetal marker to confirm the presence of cffDNA. Using methylation-sensitive restriction enzymes hypomethylated maternal sequences are digested leaving hypermethylated fetal sequences detectable. Complete digestion of maternal sequences is required to eliminate false positive results.MethodscfDNA was extracted from maternal plasma (n = 90) and digested with methylation-sensitive and insensitive restriction enzymes. Analysis of RASSF1A, SRY and DYS14 was performed by real-time PCR.ResultsHypermethylated RASSF1A was amplified for 79 samples (88%) indicating the presence of cffDNA. SRY real time PCR results and fetal sex at delivery were 100% accurate. Eleven samples (12%) had no detectable hypermethylated RASSF1A and 10 of these (91%) had gestational ages less than 7 weeks 2 days. Six of these samples were male at delivery, five had inconclusive results for SRY analysis and one sample had no amplifiable SRY.ConclusionUse of this assay for the detection of hypermethylated RASSF1A as a universal fetal marker has the potential to improve the diagnostic reliability of NIPD for fetal sex determination and single gene disorders

Non-invasive prenatal testing for aneuploidy, copy number variants and single gene disorders

The discovery of cell-free fetal DNA (cffDNA) in maternal plasma has enabled a paradigm shift in prenatal testing, allowing for safer, earlier detection of genetic conditions of the fetus. Non-invasive prenatal testing (NIPT) for fetal aneuploidies has provided an alternative, highly efficient approach to first-trimester aneuploidy screening, and since its inception has been rapidly adopted worldwide. Due to the genome-wide nature of some NIPT protocols, the commercial sector has widened the scope of cell-free DNA (cfDNA) screening to include sex chromosome aneuploidies, rare autosomal trisomies and sub-microscopic copy-number variants. These developments may be marketed as ‘expanded NIPT’ or ‘NIPT Plus’ and bring with them a plethora of ethical and practical considerations. Concurrently, cfDNA tests for single-gene disorders, termed non-invasive prenatal diagnosis (NIPD), have been developed for an increasing array of conditions but are less widely available. Despite the fact that all these tests utilise the same biomarker, cfDNA, there is considerable variation in key parameters such as sensitivity, specificity and positive predictive value depending on what the test is for. The distinction between diagnostics and screening has become blurred, and there is a clear need for the education of physicians and patients regarding the technical capabilities and limitations of these different forms of testing. Furthermore, there is a requirement for consistent guidelines that apply across health sectors, both public and commercial, to ensure that tests are validated and robust and that careful and appropriate pre-test and post-test counselling is provided by professionals who understand the tests offered

Neuropsychological and functional outcomes in recent-onset major depression, bipolar disorder and schizophrenia-spectrum disorders: a longitudinal cohort study

Functional disability is the lead contributor to burden of mental illness. Cognitive deficits frequently limit functional recovery, although whether changes in cognition and disability are longitudinally associated in recent-onset individuals remains unclear. Using a prospective, cohort design, 311 patients were recruited and assessed at baseline. One hundred and sixty-seven patients met eligibility criteria (M = 21.5 years old, s.d. = 4.8) and returned for follow-up (M = 20.6 months later, s.d. = 7.8). Two-hundred and thirty participants were included in the final analysis, comprising clinically stable patients with major depression (n = 71), bipolar disorder (BD; n = 61), schizophrenia-spectrum disorders (n = 35) and 63 healthy controls. Neuropsychological functioning and self-rated functional disability were examined using mixed-design, repeated-measures analysis, across diagnoses and cognitive clusters, covarying for relevant confounds. Clinical, neuropsychological and functional changes did not differ between diagnoses (all P40.05). Three reliable neuropsychological subgroups emerged through cluster analysis, characterized by psychomotor slowing, improved sustained attention, and improved verbal memory. Controlling for diagnosis and changes in residual symptoms, clusters with improved neuropsychological functioning observed greater reductions in functional disability than the psychomotor slowing cluster, which instead demonstrated a worsening in disability (Po0.01). Improved sustained attention was independently associated with greater likelihood of follow-up employment (Po0.01). Diagnosis of BD uniquely predicted both follow-up employment and independent living. Neuropsychological course appears to be independently predictive of subjective and objective functional outcomes. Importantly, cognitive phenotypes may reflect distinct pathophysiologies shared across major psychiatric conditions, and be ideal targets for personalized early intervention

Delivering genome sequencing for rapid genetic diagnosis in critically ill children: parent and professional views, experiences and challenges

Rapid genomic sequencing (RGS) is increasingly being used in the care of critically ill children. Here we describe a qualitative study exploring parent and professional perspectives around the usefulness of this test, the potential for unintended harms and the challenges for delivering a wider clinical service. The Rapid Paediatric Sequencing (RaPS) study offered trio RGS for diagnosis of critically ill children with a likely monogenic disorder. Main and actionable secondary findings were reported. Semi-structured interviews were conducted with parents of children offered RGS (n = 11) and professionals (genetic clinicians, non-genetic clinicians, scientists and consenters) (n = 19) by telephone (parents n = 10/ professionals n = 1) or face-to-face (parents n = 1/professionals n = 18). We found that participants held largely positive views about RGS, describing clinical and emotional benefits from the opportunity to obtain a rapid diagnosis. Parental stress surrounding their child’s illness complicates decision making. Parental concerns are heightened when offered RGS and while waiting for results. The importance of multidisciplinary team working to enable efficient delivery of a rapid service was emphasised. Our findings give insight into the perceived value of RGS for critically ill children. Careful pre-test counselling is needed to support informed parental decision making. Many parents would benefit from additional support while waiting for results. Education of mainstream clinicians is required to facilitate clinical implementatio

Engineering handbook

2005 handbook for the faculty of Engineerin

Using a Parallel Ensemble of Sequence-Based Selection Hyper-Heuristics for Electric Bus Scheduling

This is the author accepted manuscript. The final version is available from ACM via the DOI in this recordA Sequence-based Selection Hyper-Heuristic (SSHH) utilises a hidden Markov model (HMM) to generate sequences of low-level heuristics to apply to a given problem. The HMM represents learnt probabilistic relationships in transitioning from one heuristic to the next for generating good sequences. However, a single HMM will only represent one learnt behaviour pattern which may not be ideal. Furthermore, using a single HMM to generate sequences is sequential in manner but most processors are parallel in nature. Consequently, this paper proposes that the effectiveness and speed of SSHH can be improved by using multiple SSHH, an ensemble. These will be able to operate in parallel exploiting multi-core processor resources facilitating faster optimisation. Two methods of parallel ensemble SSHH are investigated, sharing the best found solution amongst SSHH instantiations or combining HMM information between SSHH models. The effectiveness of the methods are assessed using a real-world electric bus scheduling optimisation problem. Sharing best found solutions between ensembles of SSHH models that have differing sequence behaviours significantly improved upon sequential SSHH results with much lower run-times.Innovate UKCity Scienc

An Adaptive Sequence-Based Selection Hyper-Heuristic for Application to Electric Bus Scheduling

This is the author accepted manuscript. The final version is available from ACM via the DOI in this recordBuses are important for public transportation and beneficial for the environment. However, diesel buses are significant polluters emitting greenhouse gases and particulates. Consequently, with the advent of electric vehicles there has been a drive to transition to electric buses. Key to this transition is to optimise electric bus fleets to reduce distance travelled whilst maintaining service levels. This is complex due to the added constraint of the limited range of electric buses. This paper considers the use of a Sequence-based Selection Hyper Heuristic (SSHH) method to solve this problem. Moreover, an adaptive SSHH (A-SSHH) technique is introduced which significantly improves upon SSHH. Indeed, bus fleet non-service distances and sizes are reduced by as much as 10% using A-SSHH over SSHH. Comparing with an optimised diesel bus fleet electric buses reduce carbon dioxide emissions by over 60% and importantly for fleet operators, energy costs are similarly reduced.Innovate UKCity Scienc

Lessons learnt from prenatal exome sequencing

BACKGROUND: Prenatal exome sequencing (ES) for monogenic disorders in fetuses with structural anomalies increases diagnostic yield. In England there is a national trio ES service delivered from two laboratories. To minimise incidental findings and reduce the number of variants investigated, analysis uses a panel of 1205 genes where pathogenic variants may cause abnormalities presenting prenatally. Here we review our laboratory's early experience developing and delivering ES to identify challenges in interpretation and reporting and inform service development. METHODS: A retrospective laboratory records review from 01.04.2020 to 31.05.2021. RESULTS: Twenty-four of 116 completed cases were identified as challenging including 13 resulting in difficulties in analysis and reporting, nine where trio inheritance filtering would have missed the diagnosis, and two with no prenatal diagnosis; one due to inadequate pipeline sensitivity, the other because the gene was not on the panel. Two cases with copy number variants identified were not detectable by microarray. CONCLUSIONS: Variant interpretation requires close communication between referring clinicians, with occasional additional examination of the fetus or parents and communication of evolving phenotypes. Inheritance filtering misses ∼5% of diagnoses. Panel analysis reduces but does not exclude incidental findings. Regular review of published literature is required to identify new reports that may aid classification

The Black River: a comprehensive study of physical and chemical characteristics and their potential management implications.

An analysis of the Black River's biological and physicochemical characteristics was conducted for comparison to the model proposed by the river continuum theory. The theory specifies that the biological fauna, physical characteristics and chemical composition observed, are reflected in river order changes in terms of the presence, absence, or density of producer and consumer communities. The study reflected consistencies between the model and observed physical parameters and chemical attributes, but biological indicators were less corroborating. Physical characteristics such as temperature, depth, width, velocity, discharge, and suspended sediments increased with river mile and trends in the data became apparent. Chemical factors such as nitrates, dissolved oxygen, pH, alkalinity, and hardness, though not as clearly conclusive, show a gradient associated with river order transition. Biological indicators were not as conclusive in supporting the river continuum theory since there was no representation of shredders in the headwaters and predatory species were found at most sites. Management issues of the Black River address the control of soil erosion, species composition, and sedimentation as well as maintaining water temperature.http://deepblue.lib.umich.edu/bitstream/2027.42/54342/1/2778.pd

The Impact of Developmental and Humanitarian Aid in the Nation of Haiti

Short term aid has numerous benefits and limitations in contrast with sustainable development. For this project sustainable development is defined as: utilizing the resources in communities and encouraging indigenous leadership to promote well being for future generations. The impact of short term relief is determined by various factors. The focus of this research will be the impact of humanitarian emergency assistance and developmental assistance in the nation of Haiti. The research findings obtained through literature review educates the local community on how to effectively assist developing communities both domestically and abroad to become self-sustaining