Further delineation of dosage-sensitive K/L mediated Xq28 duplication syndrome includes incomplete penetrance.

The low copy tandem repeat area at Xq28 is prone to recurrent copy number gains, including the K/L mediated duplications of 300 kb size (herein described as the K/L mediated Xq28 duplication syndrome). We describe five families, including nine males with K/L mediated Xq28 duplications, some with regions of greater copy number variation (CNV). We summarise findings in 25 affected males reported to date. Within the five families, males were variably affected by seizures, intellectual disability, and neurological features; however, one male with a familial K/L mediated Xq28 duplication has normal intelligence, suggesting that this CNV is not 100% penetrant. Including our five families, 13 carrier females have been identified, with nine presenting phenotypically normal. Three carrier females reported mild learning difficulties, and all of them had duplications containing regions with at least four copies. Delineation of the spectrum of K/L mediated Xq28 duplication syndrome highlights GDI1 as the most likely candidate gene contributing to the phenotype. For patients identified with CNVs in this region, high-resolution microarray is required to define copy number gains and provide families with accurate information.

ClinSV: clinical grade structural and copy number variant detection from whole genome sequencing data.

Whole genome sequencing (WGS) has the potential to outperform clinical microarrays for the detection of structural variants (SV) including copy number variants (CNVs), but has been challenged by high false positive rates. Here we present ClinSV, a WGS based SV integration, annotation, prioritization, and visualization framework, which identified 99.8% of simulated pathogenic ClinVar CNVs > 10 kb and 11/11 pathogenic variants from matched microarrays. The false positive rate was low (1.5-4.5%) and reproducibility high (95-99%). In clinical practice, ClinSV identified reportable variants in 22 of 485 patients (4.7%) of which 35-63% were not detectable by current clinical microarray designs. ClinSV is available at https://github.com/KCCG/ClinSV .

Yield of comparative genomic hybridization microarray in pediatric neurology practice.

OBJECTIVE: The present study investigated the diagnostic yield of array comparative genomic hybridization (aCGH) in a large cohort of children with diverse neurologic disorders as seen in child neurology practice to test whether pathogenic copy number variants (CNVs) were more likely to be detected in specific neurologic phenotypes. METHODS: A retrospective cross-sectional analysis was performed on 555 children in whom a genetic etiology was suspected and who underwent whole-genome aCGH testing between 2006 and 2012. Neurologic phenotyping was performed using hospital medical records. An assessment of pathogenicity was made for each CNV, based on recent developments in the literature. RESULTS: Forty-seven patients were found to carry a pathogenic CNV, giving an overall diagnostic yield of 8.59%. Certain phenotypes predicted for the presence of a pathogenic CNV, including developmental delay (odds ratio [OR] 3.69 [1.30-10.51]), cortical visual impairment (OR 2.73 [1.18-6.28]), dysmorphism (OR 2.75 [1.38-5.50]), and microcephaly (OR 2.16 [1.01-4.61]). The combination of developmental delay/intellectual disability with dysmorphism and abnormal head circumference was also predictive for a pathogenic CNV (OR 2.86 [1.02-8.00]). For every additional clinical feature, there was an increased likelihood of detecting a pathogenic CNV (OR 1.18 [1.01-1.38]). CONCLUSIONS: The use of aCGH led to a pathogenic finding in 8.59% of patients. The results support the use of aCGH as a first tier investigation in children with diverse neurologic disorders, although whole-genome sequencing may replace aCGH as the detection method in the future. In particular, the yield was increased in children with developmental delay, dysmorphism, cortical visual impairment, and microcephaly.

Unintentionally retained vascular devices: improving recognition and removal.

The increased demand for minimally invasive placement of intravascular medical devices has led to increased procedure-related complications, including retention of all or part of the implanted device. A number of risk factors can predispose to unintentionally retained vascular devices (uRVD); most are technical in etiology. Despite best efforts to insert and remove vascular devices properly, uRVD still occur. Prevention or early identification of uRVD is ideal; however, procedural complications are not always recognized at the time of device insertion or removal. In these cases, early radiologic diagnosis is important to enable expeditious removal and reduction of morbidity, mortality, and medicolegal consequences. The diagnostic radiologist's role is to identify suspected uRVD and ensure proper communication of the findings to the referring clinician. The diagnostic radiologist can implement various strategies to increase detection of uRVD and advise the referring clinician regarding the use of minimally invasive percutaneous techniques for safe removal of uRVD.

Assessing burden of disease as disability adjusted life years in life cycle assessment.

Disability adjusted life years (DALYs) have been used to quantify endpoint indicators of the human burden of disease in life cycle assessment (LCA). The purpose of this paper was to examine the current use of DALYs in LCA, and also to consider whether DALYs as used in LCA have the potential to be compatible with DALYs as used in quantitative risk assessment (QRA) to facilitate direct comparison of the results of the two approaches. A literature review of current usage of DALYs in LCA was undertaken. Two prominent methods were identified: ReCiPe 2008 and LIME2. The methods and assumptions used in their calculations were then critically reviewed. The assumptions used for the derivation of characterization factors in DALYs were found to be considerably different between LCA methods. In many cases, transparency of these calculations and assumptions is lacking. Furthermore, global average DALY values are often used in these calculations, but may not be applicable for impact categories where the local factors play a significant role. The concept of DALYs seems beneficial since it enables direct comparison and aggregation of different health impacts. However, given the different assumptions used in each LCA method, it is important that LCA practitioners are aware of the differences and select the appropriate method for the focus of their study. When applying DALYs as a common metric between LCA and QRA, understanding the background information on how DALYs were derived is crucial to ensure the consistency of DALYs used in LCA and QRA for resulting DALYs to be comparable and to minimize any double counting of effects.

Global and local health burden trade-off through the hybridisation of quantitative microbial risk assessment and life cycle assessment to aid water management.

Life cycle assessment (LCA) and quantitative risk assessment (QRA) are commonly used to evaluate potential human health impacts associated with proposed or existing infrastructure and products. Each approach has a distinct objective and, consequently, their conclusions may be inconsistent or contradictory. It is proposed that the integration of elements of QRA and LCA may provide a more holistic approach to health impact assessment. Here we examine the possibility of merging LCA assessed human health impacts with quantitative microbial risk assessment (QMRA) for waterborne pathogen impacts, expressed with the common health metric, disability adjusted life years (DALYs). The example of a recent large-scale water recycling project in Sydney, Australia was used to identify and demonstrate the potential advantages and current limitations of this approach. A comparative analysis of two scenarios - with and without the development of this project - was undertaken for this purpose. LCA and QMRA were carried out independently for the two scenarios to compare human health impacts, as measured by DALYs lost per year. LCA results suggested that construction of the project would lead to an increased number of DALYs lost per year, while estimated disease burden resulting from microbial exposures indicated that it would result in the loss of fewer DALYs per year than the alternative scenario. By merging the results of the LCA and QMRA, we demonstrate the advantages in providing a more comprehensive assessment of human disease burden for the two scenarios, in particular, the importance of considering the results of both LCA and QRA in a comparative assessment of decision alternatives to avoid problem shifting. The application of DALYs as a common measure between the two approaches was found to be useful for this purpose.

Deletion of protein tyrosine phosphatase, non-receptor type 4 (PTPN4) in twins with a Rett syndrome-like phenotype.

Rett syndrome (RTT), a neurodevelopmental disorder that predominantly affects females, is primarily caused by variants in MECP2. Variants in other genes such as CDKL5 and FOXG1 are usually associated with individuals who manifest distinct phenotypes that may overlap with RTT. Individuals with phenotypes suggestive of RTT are typically screened for variants in MECP2 and then subsequently the other genes dependent on the specific phenotype. Even with this screening strategy, there are individuals in whom no causative variant can be identified, suggesting that there are other novel genes that contribute to the RTT phenotype. Here we report a de novo deletion of protein tyrosine phosphatase, non-receptor type 4 (PTPN4) in identical twins with a RTT-like phenotype. We also demonstrate the reduced expression of Ptpn4 in a Mecp2 null mouse model of RTT, as well as the activation of the PTPN4 promoter by MeCP2. Our findings suggest that PTPN4 should be considered for addition to the growing list of genes that warrant screening in individuals with a RTT-like phenotype.

Method for technical, economic and environmental assessment of advanced sludge processing routes.

The legislative framework in force in Europe entails restrictive effluent standards for sensitive areas, and quite severe restrictions on the properties of residual sewage sludge, both for landfill disposal and for agricultural use. Several technologies and management strategies have been proposed and applied in wastewater treatment plants to minimise sludge production and contamination. However, their techno-economic and environmental performance has to be carefully evaluated. The ROUTES project, funded within the EU Seventh Framework programme, aims to find new routes for wastewater treatment and sludge management and thereby guide EU members in their future choices. Within this project, the authors have developed and applied a procedure for techno-economic-environmental assessment of new wastewater and sludge processing lines in comparison to reference plants. The reference plants are model conventional plants that experience different types of problems and the new plants are modified plants in which different innovative technologies have been added to solve these problems. The procedure involves a rating of selected technical issues, estimates of operating costs and an assessment of environmental impacts from a life cycle perspective. This paper reports on the procedure and shows examples of results.

Chromosome microarrays in diagnostic testing: interpreting the genomic data.

DNA-based Chromosome MicroArrays (CMAs) are now well established as diagnostic tools in clinical genetics laboratories. Over the last decade, the primary application of CMAs has been the genome-wide detection of a particular class of mutation known as copy number variants (CNVs). Since 2010, CMA testing has been recommended as a first-tier test for detection of CNVs associated with intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies…in the post-natal setting. CNVs are now regarded as pathogenic in 14-18 % of patients referred for these (and related) disorders.Through consideration of clinical examples, and several microarray platforms, we attempt to provide an appreciation of microarray diagnostics, from the initial inspection of the microarray data, to the composing of the patient report. In CMA data interpretation, a major challenge comes from the high frequency of clinically irrelevant CNVs observed within "patient" and "normal" populations. As might be predicted, the more common and clinically insignificant CNVs tend to be the smaller ones <100 kb in length, involving few or no known genes. However, this relationship is not at all straightforward: CNV length and gene content are only very imperfect indicators of CNV pathogenicity. Presently, there are no reliable means of separating, a priori, the benign from the pathological CNV classes.This chapter also considers sources of technical "noise" within CMA data sets. Some level of noise is inevitable in diagnostic genomics, given the very large number of data points generated in any one test. Noise further limits CMA resolution, and some miscalling of CNVs is unavoidable. In this, there is no ideal solution, but various strategies for handling noise are available. Even without solutions, consideration of these diagnostic problems per se is informative, as they afford critical insights into the biological and technical underpinnings of CNV discovery. These are indispensable to any clinician or scientist practising within the field of genome diagnostics.

The hippocampus, medial prefrontal cortex, and selective memory retrieval: evidence from a rodent model of the retrieval-induced forgetting effect.

Inhibition is an important component of many cognitive functions, including memory. For example, the retrieval-induced forgetting (RIF) effect occurs when extra practice with some items from a study list inhibits the retrieval of the nonpracticed items relative to a baseline condition that does not involve extra practice. Although counterintuitive, the RIF phenomenon may be important for resolving interference by inhibiting potentially competing retrieval targets. Neuroimaging studies suggest that the hippocampus and prefrontal cortex are involved in the RIF effect, but controlled lesion studies have not yet been performed. We developed a rodent model of the RIF training procedure and trained control rats and rats with temporary inactivation of the hippocampus or medial prefrontal cortex (mPFC). Rats were trained on a list of odor cues, presented in cups of digging medium with a buried reward, followed by additional practice trials with a subset of the cues. We then tested the rats' memories for the cues and their association with reward by presenting them with unbaited cups containing the test odorants and measuring how long they persisted in digging. Control rats exhibited a robust RIF effect in which memory for the nonpracticed odors was significantly inhibited. Thus, extra practice with some odor cues inhibited memory for the others, relative to a baseline condition that involved an identical amount of training. Inactivation of either the hippocampus or the mPFC blocked the RIF effect. We also constructed a computational model of a representational learning circuit to simulate the RIF effect. We show in this model that "sideband suppression" of similar memory representations can reproduce the RIF effect and that alteration of the suppression parameters and learning rate can reproduce the lesion effects seen in our rats. Our results suggest that the RIF effect is widespread and that inhibitory processes are an important feature of memory function.

High-pressure paint gun injury: clinical presentation and imaging findings.

High-pressure paint gun injuries are potentially devastating injuries that require emergent surgical incision and drainage. They result from erroneous equipment operation and accidental injection of a variety of substances at pressures high enough to breach the skin. The largely benign superficial appearance masks the extent of the underlying injury. In the absence of an appropriate history, the radiologist must recognize the characteristic radiographic findings and suggest the diagnosis to the clinician.

pH-rate profiles support a general base mechanism for galactokinase (Lactococcus lactis).

Galactokinase (GALK), a member the Leloir pathway for normal galactose metabolism, catalyzes the conversion of α-d-galactose to galactose-1-phosphate. For this investigation, we studied the kinetic mechanism and pH profiles of the enzyme from Lactococcus lactis. Our results show that the mechanism for its reaction is sequential in both directions. Mutant proteins D183A and D183N are inactive (< 10000 fold), supporting the role of Asp183 as a catalytic base that deprotonates the C-1 hydroxyl group of galactose. The pH-kcat profile of the forward reaction has a pKa of 6.9 ± 0.2 that likely is due to Asp183. The pH-k(cat)/K(Gal) profile of the reverse reaction further substantiates this role as it is lacking a key pKa required for a direct proton transfer mechanism. The R36A and R36N mutant proteins show over 100-fold lower activity than that for the wild-type enzyme, thus suggesting that Arg36 lowers the pKa of the C-1 hydroxyl to facilitate deprotonation.

Microdeletions detected using chromosome microarray in children with suspected genetic movement disorders: a single-centre study.

AIM: Chromosome microarray (CMA) can determine copy number variants such as microdeletions or microduplications. Microdeletions of movement disorder genes including epsilon-sarcoglycan (SGCE) and thyroid transcription factor-1 (TITF1) have been described in patients with myoclonus dystonia and benign hereditary chorea respectively. We examined whether CMA is a valuable tool in the investigation of children with suspected genetic movement disorders. METHOD: A genetic movement disorder was suspected if there was a positive first-degree family history, or two or more of the following factors: normal or near-normal magnetic resonance imaging, negative history of brain injury, and negative investigations for metabolic disorders. Tic disorders were excluded. Twenty-five patients (18 males, seven females) with a mean age at movement disorder onset of 4 years 5 month (range 1 mo-14 y) were prospectively recruited with the following primary movement disorders: dystonia (n=10), paroxysmal kinesigenic dyskinesia (n=5), tremor (n=4), chorea (n=3), myoclonus (n=2), and paroxysmal non-kinesigenic dyskinesia (n=1). Comorbid associated features were common, particularly developmental delay or intellectual disability (19 out of 25) and attention-deficit-hyperactivity disorder (six out of 25). CMA was performed using Agilent aCGH 60K array. RESULTS: Seven out of twenty-five patients had a microdeletion determined by CMA. None of the microdeletions were considered benign variants. Four patients had a deletion of a known movement disorder gene including paroxysmal kinesigenic dyskinesia (PRRT2; n=2), SGCE (myoclonus dystonia, n=1), and TITF1 (benign hereditary chorea, n=1). Three patients had novel microdeletions of unknown but potential significance including 14q13.3 (chorea, n=1), 19p13.12 (tremor, n=1), and 19q13.12 (progressive dystonia). All seven patients had associated neurodevelopmental or behavioural problems. INTERPRETATION: Assays that determine copy number variants may be a valuable first-tier investigation in patients with suspected genetic movement disorders, particularly when associated with intellectual disability or developmental disorders. Microdeletion syndromes may help the search for new movement disorder genes.

Chromosome microarray in Australia: a guide for paediatricians.

Chromosomal microarray or molecular karyotype has become the first-line genetic investigation for children with intellectual disability, autistic spectrum disorder or multiple congenital anomalies. Chromosomal microarray increases the detection rate of pathogenic chromosome imbalances including submicroscopic deletions or duplications in patients with undiagnosed intellectual disability to approximately 15% compared with 3% with conventional cytogenetics. This review article summarises the diagnostic technique and highlights the advantages and limitations of chromosomal microarray. Our aim is to assist clinicians in providing pretest counselling and with interpretation of the result.

Chromosomal rearrangements and novel genes in disorders of eye development, cataract and glaucoma.

Disorders of eye development such as microphthalmia and anophthalmia (small and absent eyes respectively), anterior segment dysgenesis where there may be pupillary and iris anomalies, and associated cataract and glaucoma, often lead to visual impairment or blindness. Currently treatment options are limited, as much is unknown about the molecular pathways that control normal eye development and induce the aberrant processes that lead to ocular defects. Mutation detection rates in most of the known genes are generally low, emphasizing the genetic heterogeneity of developmental ocular defects. Identification of the disease genes in these conditions improves the clinical information available for affected individuals and families, and provides new insights into the underlying biological processes for facilitation of better treatment options. Investigation of chromosomal rearrangements associated with an ocular phenotype has been especially powerful for disease gene identification. Molecular characterization of such rearrangements, which pinpoints the region by physically disrupting the causative gene or its regulatory sequences, allows for rapid elucidation of underlying genetic factors that contribute to the phenotype. Genes including PAX6, PITX2, FOXC1, MAF, TMEM114, SOX2, OTX2 and BMP4 have been identified in this way to be associated with developmental eye disorders. More recently, new methods in chromosomal analysis such as comparative genomic hybridization (CGH) microarray, have also enhanced our ability in disease gene identification.

Resolution of trisomic mosaicism in prenatal diagnosis: estimated performance of a 50K SNP microarray.

OBJECTIVE: To evaluate the ability of a DNA single nucleotide polymorphism (SNP) microarray to detect chromosome mosaicism for trisomy in prenatal samples in order to compare this with conventional cytogenetics. METHOD: We created a dilution series of mock mosaic samples, by mixing measured amounts of fibroblast cells containing trisomy 8 from a male with aliquots of cells with a normal female karyotype. DNAs were extracted from these mosaic mixtures, then analysed on the Affymetrix 50K Xba SNP chip. Duplicate aliquots of each mosaic sample were probed using interphase FISH, with centromeric probes for chromosomes X, Y and 8, to estimate independently the proportion of male trisomy 8 in each sample. Data from the arrays were analysed using publicly available analysis tools. Statistical calculations were then performed using a Student's t-test to determine if there was a significant difference between the copy numbers of each chromosome. RESULTS: These experiments using the Affymetrix 50K Xba SNP microarray showed mosaicism to be obvious at 20% and with additional statistical calculations, the lower limit for detection is about 10%. CONCLUSION: The SNP microarray platform tested can detect mosaicism for trisomy in prenatal samples at levels comparable with conventional cytogenetic techniques in routine use.

An innocuous duplication of 11.2 Mb at 13q21 is gene poor: sub-bands of gene paucity and pervasive CNV characterize the chromosome anomalies.

A boy with autistic spectrum disorder without dysmorphisms was found to have a chromosome duplication of part of band 13q21. His mother and grandfather both of normal intellect had the same chromosomal duplication. Comparison was made with the Chromosome anomaly database www.som.soton.ac.uk/research/geneticsdiv/anomaly%20register which revealed similar cases. Mapping on DNA microarray for the proband and mother showed the duplication to be of length 11.2 Mb, encompassing the 13q21.1-13q21.32 region. The duplicated region is profoundly gene poor, with a mean gene density of 0.45 genes/Mb. We estimate, that the mean gene density in the sub-bands of the chromosome anomalies is 2.4-2.5 genes/Mb. In addition the percentages of the sub-bands reported as copy number variants (CNV) was estimated from the Database of Chromosome Genomic Variants (http://projects.tcag.ca/variation/). It was found that for some of these sub-bands, gene paucity was likely to be a major contributor to their innocuous phenotypic effect, for example, the gene densities were for: 1p31.2 (1.25 genes/Mb); 2p12 (1.7); 4p15.31 (1.3); 5p14.1 (0.22); 5p14.3 (0.8); 5q21.2 (0.6); 5q21.3 (1.2); 8p23.2 (0.25); 13q21.1 (0.9); 14q31.1 (1.4); 18q22.1 (1.4); 21q21.1 (1.2); and 21q21.2 (0.7). For other sub-bands the percentage of the band in which CNV have been reported was found to be markedly increased, for example, 8p23.2 (94.7% of the band is defined by reported CNV); 3p26.3 (81.6); 5p14.3 (59.3); 8p22 (48.8); 2p12 (44.0); 5q21.1 (43.6); 6q24.2 (41.4); 9p23 (38.8); 10q21.1 (36.5); 5q21.2 (35.4), and 11q14.3 (33.8). We argue that both gene paucity and pervasive CNV are major indicators of bands conforming to the Chromosome Anomaly phenomenon.