The impact of inversions across 33,924 families with rare disease from a national genome sequencing project

Detection of structural variants (SVs) is currently biased toward those that alter copy number. The relative contribution of inversions toward genetic disease is unclear. In this study, we analyzed genome sequencing data for 33,924 families with rare disease from the 100,000 Genomes Project. From a database hosting >500 million SVs, we focused on 351 genes where haploinsufficiency is a confirmed disease mechanism and identified 47 ultra-rare rearrangements that included an inversion (24 bp to 36.4 Mb, 20/47 de novo). Validation utilized a number of orthogonal approaches, including retrospective exome analysis. RNA-seq data supported the respective diagnoses for six participants. Phenotypic blending was apparent in four probands. Diagnostic odysseys were a common theme (>50 years for one individual), and targeted analysis for the specific gene had already been performed for 30% of these individuals but with no findings. We provide formal confirmation of a European founder origin for an intragenic MSH2 inversion. For two individuals with complex SVs involving the MECP2 mutational hotspot, ambiguous SV structures were resolved using long-read sequencing, influencing clinical interpretation. A de novo inversion of HOXD11-13 was uncovered in a family with Kantaputra-type mesomelic dysplasia. Lastly, a complex translocation disrupting APC and involving nine rearranged segments confirmed a clinical diagnosis for three family members and resolved a conundrum for a sibling with a single polyp. Overall, inversions play a small but notable role in rare disease, likely explaining the etiology in around 1/750 families across heterogeneous clinical cohorts.

An evaluation of the use of individual grass species in retaining polluted soil and dust particulates in vegetated sustainable drainage devices

A sustainable means of preventing polluted particulates carried in urban storm water entering rivers, groundwater and lakes is by employing vegetated sustainable drainage system (SUDS) devices, or best management practices to trap or biodegrade them. In the UK, a mixture of grass species is recommended for use in devices such as swales or filter strips. However, there is little evidence in support of the efficiency of the individual grasses or mixtures to deal with such contaminated material. A pot-based pollutant retention study was conducted using processed street dust from central Coventry, UK, as a simulated pollutant to be applied in different quantities to a variety of recommended grasses for vegetated SUDS devices. Analysis was conducted on compost cores, roots and shoots for heavy metals (Cd, Cu, Ni, Pb and Zn). Street dust mainly concentrated in the top compost layer for all grasses with only the finer material migrating down the profile. Analysis of roots indicated little accumulation, with ANOVA statistical tests indicating significant differences in heavy metal concentrations, with less in the compost and more in the shoots. Development of root systems on or near the surface possibly explains increased uptake of heavy metals by some species. Overall Agrostis canina and Poa pratensis showed the greatest accumulations compared to their controls although Agrostis capillaris syn.tenuis and Agrostis stolonifera also demonstrated accumulation potential. On ranking, Agrostis canina and Poa pratensis were highest overall. These rankings will assist in selecting the best grasses to address pollution of the urban environment by contaminated particulates.

Phase II study of oral docetaxel and cyclosporine in canine epithelial cancer

The goal of the current study was to determine the efficacy of oral docetaxel in combination with cyclosporine in the treatment of canine epithelial cancer. Requirements for eligibility were histological confirmation of epithelial neoplasia, measurable disease, no chemotherapy treatment within 2 weeks, and a life expectancy of ≥ 3 months. Fifty-one dogs were enrolled. All dogs received 1.625 mg kg(-1) of docetaxel with 5 mg kg(-1) of cyclosporine (DT/CSA) by gavage. Ten dogs had progressive disease at 2 weeks, one dog died, and one dog was withdrawn from the study. Thirty-nine dogs were given a second dose of DT/CSA, three each receiving a third or fourth dose. Eight dogs had a dose reduction (1.5 mg kg(-1)) and six dogs had treatment delays primarily for gastrointestinal toxicity. The overall response rate was 16.7% (8/48 had a partial response there were no complete responses). The highest response rate was seen in dogs with oral squamous cell carcinoma (50%; 6/12).

Functional analysis of TCF4 missense mutations that cause Pitt-Hopkins syndrome

Pitt-Hopkins syndrome (PTHS) is a rare developmental disorder associated with severe mental retardation, facial abnormalities, and intermittent hyperventilation. Autosomal dominant PTHS is caused by mutations in the transcription factor 4 (TCF4) gene, whereas NRXN1 and CNTNAP2 mutations are associated with autosomal recessive PTHS. To determine the impact of missense mutations on TCF4 function, we tested a panel of PTHS-associated mutations using a range of quantitative techniques. Mutations in the basic helix-loop-helix (bHLH) domain of TCF4 alter the subnuclear localization of the mutant protein and can attenuate homo- and heterodimer formation in homogenous time-resolved fluorescence (HTRF) assays. By contrast, mutations proximal to the bHLH domain do not alter the location of TCF4 or impair heterodimer formation. In addition, we show that TCF4 can transactivate the NRXN1β and CNTNAP2 promoters in luciferase assays. Here we find variable, context-specific deficits in the ability of the different PTHS-associated TCF4 mutants to transactivate these promoters when coexpressed with different bHLH transcription factors. These data demonstrate that PTHS-associated missense mutations can have multiple effects on the function of the protein, and suggest that TCF4 may modulate the expression of NRXN1 and CNTNAP2 thereby defining a regulatory network in PTHS.

Search for neutrinoless double-beta decay in 136Xe with EXO-200

We report on a search for neutrinoless double-beta decay of 136Xe with EXO-200. No signal is observed for an exposure of 32.5 kg yr, with a background of ∼1.5×10(-3)  kg(-1) yr(-1)  keV(-1) in the ±1σ region of interest. This sets a lower limit on the half-life of the neutrinoless double-beta decay T(1/2)(0νββ)(136Xe)>1.6×10(25)  yr (90% C.L.), corresponding to effective Majorana masses of less than 140-380 meV, depending on the matrix element calculation.

Frequency of the C9orf72 hexanucleotide repeat expansion in patients with amyotrophic lateral sclerosis and frontotemporal dementia: a cross-sectional study

BACKGROUND

We aimed to accurately estimate the frequency of a hexanucleotide repeat expansion in C9orf72 that has been associated with a large proportion of cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD).

METHODS

We screened 4448 patients diagnosed with ALS (El Escorial criteria) and 1425 patients with FTD (Lund-Manchester criteria) from 17 regions worldwide for the GGGGCC hexanucleotide expansion using a repeat-primed PCR assay. We assessed familial disease status on the basis of self-reported family history of similar neurodegenerative diseases at the time of sample collection. We compared haplotype data for 262 patients carrying the expansion with the known Finnish founder risk haplotype across the chromosomal locus. We calculated age-related penetrance using the Kaplan-Meier method with data for 603 individuals with the expansion.

FINDINGS

In patients with sporadic ALS, we identified the repeat expansion in 236 (7·0%) of 3377 white individuals from the USA, Europe, and Australia, two (4·1%) of 49 black individuals from the USA, and six (8·3%) of 72 Hispanic individuals from the USA. The mutation was present in 217 (39·3%) of 552 white individuals with familial ALS from Europe and the USA. 59 (6·0%) of 981 white Europeans with sporadic FTD had the mutation, as did 99 (24·8%) of 400 white Europeans with familial FTD. Data for other ethnic groups were sparse, but we identified one Asian patient with familial ALS (from 20 assessed) and two with familial FTD (from three assessed) who carried the mutation. The mutation was not carried by the three Native Americans or 360 patients from Asia or the Pacific Islands with sporadic ALS who were tested, or by 41 Asian patients with sporadic FTD. All patients with the repeat expansion had (partly or fully) the founder haplotype, suggesting a one-off expansion occurring about 1500 years ago. The pathogenic expansion was non-penetrant in individuals younger than 35 years, 50% penetrant by 58 years, and almost fully penetrant by 80 years.

INTERPRETATION

A common Mendelian genetic lesion in C9orf72 is implicated in many cases of sporadic and familial ALS and FTD. Testing for this pathogenic expansion should be considered in the management and genetic counselling of patients with these fatal neurodegenerative diseases.

FUNDING

Full funding sources listed at end of paper (see Acknowledgments).

Chromosome 9 ALS and FTD locus is probably derived from a single founder

We and others have recently reported an association between amyotrophic lateral sclerosis (ALS) and single nucleotide polymorphisms on chromosome 9p21 in several populations. Here we show that the associated haplotype is the same in all populations and that several families previously shown to have genetic linkage to this region also share this haplotype. The most parsimonious explanation of these data are that there is a single founder for this form of disease.

Observation of two-neutrino double-beta decay in 136Xe with the EXO-200 detector

We report the observation of two-neutrino double-beta decay in (136)Xe with T(1/2) = 2.11 ± 0.04(stat) ± 0.21(syst) × 10(21) yr. This second-order process, predicted by the standard model, has been observed for several nuclei but not for (136)Xe. The observed decay rate provides new input to matrix element calculations and to the search for the more interesting neutrinoless double-beta decay, the most sensitive probe for the existence of Majorana particles and the measurement of the neutrino mass scale.

A gain-of-glycosylation mutation associated with myoclonus-dystonia syndrome affects trafficking and processing of mouse ε-sarcoglycan in the late secretory pathway

Missense mutations in the SGCE gene encoding ε-sarcoglycan account for approximately 15% of SGCE-positive cases of myoclonus-dystonia syndrome (MDS) in humans. In this study, we show that while the majority of MDS-associated missense mutants modeled with a murine ε-sarcoglycan cDNA are substrates for endoplasmic reticulum-associated degradation, one mutant, M68T (analogous to human c.275T>C, p.M92T), located in the Ig-like domain of ε-sarcoglycan, results in a gain-of-glycosylation mutation producing a protein that is targeted to the plasma membrane, albeit at reduced levels compared to wild-type ε-sarcoglycan. Removal of the ectopic N-linked glycan failed to restore efficient plasma membrane targeting of M68T demonstrating that the substitution rather than the glycan was responsible for the trafficking defect of this mutant. M68T also colocalized with CD63-positive vesicles in the endosomal-lysosomal system and was found to be more susceptible to lysosomal proteolysis than wild-type ε-sarcoglycan. Finally, we demonstrate impaired ectodomain shedding of M68T, a process that occurs physiologically for ε-sarcoglycan resulting in the lysosomal trafficking of the intracellular C-terminal domain of the protein. Our findings show that functional analysis of rare missense mutations can provide a mechanistic insight into the pathogenesis of MDS and the physiological role of ε-sarcoglycan.

Familial frontotemporal dementia with amyotrophic lateral sclerosis and a shared haplotype on chromosome 9p

Families with autosomal dominant frontotemporal dementia and amyotrophic lateral sclerosis (FTD/ALS) have previously been linked to a locus on chromosome 9p21. We describe the clinical phenotype and pathology of a large family with autosomal dominant FTD/ALS with nine affected members originating from Gwent in South Wales, UK. We also further refine the locus on chromosome 9p21 using a haplotype sharing approach and assess heterogeneity in 9p21 linked families. Within this family, affected individuals present with either FTD or ALS or both diseases simultaneously. In addition there was marked phenotypic variation including ataxia, Parkinsonism, psychosis and visuo-spatial cognitive deficits. The pathological features of the three cases described were consistent with type 2 FTD pathology, as previously reported in similar families. However, we also report distinctive cerebellar and glial pathology and a significant proportion of TDP-43 negative inclusions. No mutations in known genes for FTD or ALS were found. We identified a large 4.8-megabase haplotype on chromosome 9p21, which was shared by all affected family members. This haplotype overlaps and limits the previously reported FTD/ALS linkage region on chromosome 9p21. Sequencing of this region did not identify any evidence of a pathogenic exonic mutation. This suggests that the pathogenic change affects non-coding DNA and that the disease is caused by variation in gene or protein expression.

Clinically relevant doses of lidocaine and bupivacaine do not impair cutaneous wound healing in mice

BACKGROUND

Lidocaine and bupivacaine are commonly infiltrated into surgical cutaneous wounds to provide local anaesthesia after surgical procedures. However, very little is known about their effects on cutaneous wound healing. If an inhibitory effect is demonstrated, then the balance between the benefits of postoperative local anaesthesia and the negatives of impaired cutaneous wound healing may affect the decision to use local anaesthesia or not. Furthermore, if a difference in the rate of healing of lidocaine- and bupivacaine-treated cutaneous wounds is revealed, or if an inhibitory effect is found to be dose-dependent, then this may well influence the choice of agent and its concentration for clinical use.

METHODS

Immediately before incisional wounding, we administered lidocaine and bupivacaine intradermally to adult female mice, some of which had been ovariectomized to act as a model of post-menopausal women (like post-menopausal women, ovariectomized mice heal wounds poorly, with increased proteolysis and inflammation). Day 3 wound tissue was analysed histologically and tested for expression of inflammatory and proteolytic factors.

RESULTS

On day 3 post-wounding, wound areas and extent of re-epithelialization were comparable between the control and local anaesthetic-treated animals, in both intact and ovariectomized groups. Both tested drugs significantly increased wound activity of the degradative enzyme matrix metalloproteinase-2 relative to controls, while lidocaine also increased wound neutrophil numbers.

CONCLUSIONS

Although lidocaine and bupivacaine influenced local inflammatory and proteolytic factors, they did not impair the rate of healing in either of two well-established models (mimicking normal human wound healing and impaired age-related healing).

The neurobiology of the dystrophin-associated glycoprotein complex

While the function of dystrophin in muscle disease has been thoroughly investigated, dystrophin and associated proteins also have important roles in the central nervous system. Many patients with Duchenne and Becker muscular dystrophies (D/BMD) have cognitive impairment, learning disability, and an increased incidence of some neuropsychiatric disorders. Accordingly, dystrophin and members of the dystrophin-associated glycoprotein complex (DGC) are found in the brain where they participate in macromolecular assemblies that anchor receptors to specialized sites within the membrane. In neurons, dystrophin and the DGC participate in the postsynaptic clustering and stabilization of some inhibitory GABAergic synapses. During development, alpha-dystroglycan functions as an extracellular matrix receptor controlling, amongst other things, neuronal migration in the developing cortex and cerebellum. Several types of congenital muscular dystrophy caused by impaired alpha-dystroglycan glycosylation cause neuronal migration abnormalities and mental retardation. In glial cells, the DGC is involved in the organization of protein complexes that target water-channels to the plasma membrane. Finally, mutations in the gene encoding epsilon-sarcoglycan cause the neurogenic movement disorder, myoclonus-dystonia syndrome implicating epsilon-sarcoglycan in dopaminergic neurotransmission. In this review we describe the recent progress in defining the role of the DGC and associated proteins in the brain.

SGCE missense mutations that cause myoclonus-dystonia syndrome impair ε-sarcoglycan trafficking to the plasma membrane: modulation by ubiquitination and torsinA

Myoclonus-dystonia syndrome (MDS) is a genetically heterogeneous disorder characterized by myoclonic jerks often seen in combination with dystonia and psychiatric co-morbidities and epilepsy. Mutations in the gene encoding epsilon-sarcoglycan (SGCE) have been found in some patients with MDS. SGCE is a maternally imprinted gene with the disease being inherited in an autosomal dominant pattern with reduced penetrance upon maternal transmission. In the central nervous system, epsilon-sarcoglycan is widely expressed in neurons of the cerebral cortex, basal ganglia, hippocampus, cerebellum and the olfactory bulb. epsilon-Sarcoglycan is located at the plasma membrane in neurons, muscle and transfected cells. To determine the effect of MDS-associated mutations on the function of epsilon-sarcoglycan we examined the biosynthesis and trafficking of wild-type and mutant proteins in cultured cells. In contrast to the wild-type protein, disease-associated epsilon-sarcoglycan missense mutations (H36P, H36R and L172R) produce proteins that are undetectable at the cell surface and are retained intracellularly. These mutant proteins become polyubiquitinated and are rapidly degraded by the proteasome. Furthermore, torsinA, that is mutated in DYT1 dystonia, a rare type of primary dystonia, binds to and promotes the degradation of epsilon-sarcoglycan mutants when both proteins are co-expressed. These data demonstrate that some MDS-associated mutations in SGCE impair trafficking of the mutant protein to the plasma membrane and suggest a role for torsinA and the ubiquitin proteasome system in the recognition and processing of misfolded epsilon-sarcoglycan.

Repeat sudden unexpected and unexplained infant deaths: natural or unnatural?

BACKGROUND

There have been suggestions that when two or three unexpected unexplained infant deaths occur within a family they are more likely to be unnatural than natural. We aimed to estimate the probability that a second infant death is natural versus unnatural.

METHODS

The Care of Next Infant programme (CONI) supports parents who have previously had an unexpected and apparently unexplained infant death and is currently available in over 90% of health districts in England, Wales, and Northern Ireland. We studied all deaths in 6373 infants who had completed the CONI programme by December, 1999. After a CONI death, we made detailed enquiries into the previous death and the CONI death, including a family interview, a review of autopsies, and case discussion.

FINDINGS

57 (8.9 per 1000) CONI infants died. Nine deaths were inevitable, and 48 were unexpected. 44 families lost one child, and two families lost two children. Of the 46 first CONI deaths, 40 were natural; the other six were probable homicides, five committed by one or both parents (two criminally convicted). The ratio of 40 natural to six unnatural deaths is 6.7 (95% CI 2.8-19.4). Enquiries identified 18 families with two SIDS(sudden infant death syndrome) deaths and two families with probable covert double homicides (ratio 9.0 [2.2 to 80.0]). There were no convictions in 13 incomplete cases. Families with three deaths are reported.

INTERPRETATION

Repeat unexpected infant deaths are most probably natural.

The influence of group size on children's competitive behavior

The present research was designed to test the hypothesis that children would compete more in tetrads than in dyads. Twenty-two pairs of male and 14 pairs of female target children (N = 72) played a competitive game in both tetrads and dyads. Consistent with the hypothesis, male target children competed more in tetrads than in dyads. This hypothesis was not supported for females, however. Analyses of the dynamics of tetrads and dyads further demonstrated that based on a global measure of smiling, the emotional atmosphere was less positive in tetrads than in dyads. The causes and consequences of interaction in different sized social groups are discussed.

A mesoscale phytoplankton bloom in the polar Southern Ocean stimulated by iron fertilization

Changes in iron supply to oceanic plankton are thought to have a significant effect on concentrations of atmospheric carbon dioxide by altering rates of carbon sequestration, a theory known as the 'iron hypothesis'. For this reason, it is important to understand the response of pelagic biota to increased iron supply. Here we report the results of a mesoscale iron fertilization experiment in the polar Southern Ocean, where the potential to sequester iron-elevated algal carbon is probably greatest. Increased iron supply led to elevated phytoplankton biomass and rates of photosynthesis in surface waters, causing a large drawdown of carbon dioxide and macronutrients, and elevated dimethyl sulphide levels after 13 days. This drawdown was mostly due to the proliferation of diatom stocks. But downward export of biogenic carbon was not increased. Moreover, satellite observations of this massive bloom 30 days later, suggest that a sufficient proportion of the added iron was retained in surface waters. Our findings demonstrate that iron supply controls phytoplankton growth and community composition during summer in these polar Southern Ocean waters, but the fate of algal carbon remains unknown and depends on the interplay between the processes controlling export, remineralisation and timescales of water mass subduction.

Do immunoassays differentially detect different acidity glycoforms of FSH?

OBJECTIVE

The possibility of the carbohydrate residues of glycoproteins affecting their recognition in immunoassays is an important and unresolved issue. This study looked for evidence of differential recognition of FSH glycoform preparations, of variable isoelectric point (pI) and known molarity, using three routine assays employing different antibody configurations.

DESIGN

Seven glycoform preparations with differing pI bands (between 3.8 and 5.5) were produced by isoelectric focusing of recombinant human FSH and the molecular weights determined by mass spectroscopy. Three concentrations of each glycoform were assayed and the results expressed relative to unfractionated material. From the relative responses, recognition differences between the assay methods and between the glycoform preparations were investigated.

MEASUREMENTS

Three routine assays were employed: the commercially available Amerlite(R) enzyme immunoassay and Delfia(R) immunofluorometric assay, together with an in-house competitive two-site radioimmunoassay (RIA).

RESULTS

Overall, the three assays gave the same relative responses for equivalent glycoforms, with the only exceptions involving small differences between some assay pairs for the fractions at the extremes of the pI range investigated. Within each assay type, differences (P < 0.05) of up to 33% existed between glycoforms of different pI, however, these differences showed no patterns or trends across the entire acidity range examined.

CONCLUSIONS

Between the assay methods investigated in this study, few differences exist in the recognition of individual pI bands of FSH when expressed relative to a common unfractionated standard. Differences were apparent in the recognition of the different acidity glycoforms within each assay method, however, these were small and unlikely to be of clinical significance.

Case management: a week in the life of a clinical case management team

This paper describes the work of a clinical case management core team (four nurses and an occupational therapist) during the course of a week. Information was gathered through non-participant observation of the team by two independent researchers. Transcripts produced from the data recorded were examined. From this, seven categories of activity were identified: planned client contact; unplanned client contact; family/carer contact; liaison; administration; team information sharing and supervision, training and personal development. These categories were felt to encompass the range of activities practised by the team. The amount of time that case managers spent engaged in these core functions was calculated. Detailed examples are presented. Results are discussed with reference to Kanter's components and principles of clinical case management.

The comparative costs of care using apnoea monitors and scales in families with a cot death

This paper reports the findings from a programme, which provided support to families with a subsequent baby following a cot death. One hundred families participated in the study. Fifty families were randomly allocated apnoea monitors, and the remainder provided with scales and weight charts for daily weighing. The results show that the parents in both groups expressed equal satisfaction with their designated method. However, compared with families allocated scales, those using apnoea monitors attended the child health clinics more often, and the number of contacts with the paediatrician was increased. They also had slightly more home and general practitioner contacts and hospital admissions. The capital and running costs of providing monitors was also greater for this group.

Cellular mechanisms of insulin release: the effects of vitamin D deficiency and repletion on rat insulin secretion

To determine whether impaired insulin release from perifused rat islets of vitamin D-deficient (D-def) rats is a result of vitamin D-deficiency specifically or an associated decrease in food intake, we: 1) compared insulin release from islets of vitamin D-def rats with insulin release from islets of pair fed (pf) normal rats, and 2) measured the effects of 1,25(OH)2D3 treatment on food intake and insulin secretion from islets of D-def rats. Both vitamin D-def and pf normal rat islets showed significantly diminished insulin release in comparison with normal controls but were not different from each other. When D-def rats were repleted with 1,25(OH)2D3, food intake increased and insulin secretion improved during perifusion of rat islets. When D-def rats treated with 1,25(OH)2D3 were prevented from increasing their food intake in response to 1,25(OH)2D3 by pair feeding to a group of untreated D-def rats, insulin release from islets of treated rats was not significantly different from untreated D-def rats. To separate the effects of vitamin D deficiency from hypocalcemia, a group of vitamin D-def hypocalcemic rats was compared with a group of D-def normocalcemic rats. Normocalcemia did not reverse the defect in insulin release. In studies of cellular calcium uptake, both pf and D-def rat islets took up less calcium than normal islets but calcium uptake was not different between pf and D-def rat islets. Our studies suggest that vitamin D deficiency is associated with marked impairment of biphasic insulin release and that the decrease in food intake may account for this impairment at least in part.