Analysis of care-seeking pathways and factors influencing early and appropriate care-seeking for malaria patients in the Republic of Guinea: a cross-sectional study.

BACKGROUND: Malaria is a major public health issue in Guinea and care-seeking behaviour is dominated by self-medication and delayed access to appropriate care. However early and appropriate care-seeking are essential to control and reduce complicate forms and mortality, particularly for the most vulnerable. This study was conducted to analyse the diagnostic pathway, and the factors associated with early and appropriate care-seeking for malaria patients in the Republic of Guinea. METHODS: A cross-sectional study was carried out between December 2022 to March 2023 in nine health districts within health facilities and at community level. The study population was confirmed malaria patients with RDT or microscopy. Kroeger's conceptual framework was used to design the questionnaire. Conventional recourse was defined as using a healthcare facility or community services, early and appropriate care-seeking was defined as within 24 h of symptom onset in a conventional recourse, and care pathway as the sequence of recourses followed by each patient. Sankey alluvial plots were used to represent patients' diagnostic pathways, and logistic regression to identify factors associated with early and appropriate care-seeking. RESULTS: A total of 3300 malaria patients were studied, of which 1632 (49.45%) were female and 1132 (34.30%) were under 5 years of age, with a median age of 23 months. At the time of the survey, 1337 (40.52%), 1423 (43.12%), and 437 (13.85%) of patients were respectively in their first, second and third recourse. A total of 2002 (60.67%) patients had sought care from a conventional recourse as a first line. Of all patients, 1757 (53.25%) had sought care within 24 h, while 28.55% had sought early and appropriate care. In the initial stages of treatment, self-medication was the most common approach, used by 1214 (37.30%). Patients from the health districts of Boffa (Lower Guinea, coastal region) OR = 0.48 95% CI 0.33-0.70, Dabola (Upper Guinea, savanna region) OR = 0.43 95% CI 0.30-0.63 and Labe (Middle Guinea, mountain region) OR = 0.63 CI 95% 0.43-0.91 (p < 0.05) were more likely to delay appropriate care-seeking, when compared to those in Dixinn, (Conakry). However, the under 5-year-old group OR = 1.55 95% CI 1.30-1.85 (p < 0.001) and the availability of a stable monthly household income OR = 4.98 95% CI 3.03, 8.27 (p < 0.001) were positively associated with early and appropriate care seeking. CONCLUSION: A low rate of early and appropriate care-seeking was observed. Patients sought care through multiple means, often resulting in a delay in adequate management. The results show the need to deploy strategies adapted to the needs of communities.

Socioeconomic, Demographic, and Environmental Factors May Inform Malaria Intervention Prioritization in Urban Nigeria.

Urban population growth in Nigeria may exceed the availability of affordable housing and basic services, resulting in living conditions conducive to vector breeding and heterogeneous malaria transmission. Understanding the link between community-level factors and urban malaria transmission informs targeted interventions. We analyzed Demographic and Health Survey Program cluster-level data, alongside geospatial covariates, to describe variations in malaria prevalence in children under 5 years of age. Univariate and multivariable models explored the relationship between malaria test positivity rates at the cluster level and community-level factors. Generally, malaria test positivity rates in urban areas are low and declining. The factors that best predicted malaria test positivity rates within a multivariable model were post-primary education, wealth quintiles, population density, access to improved housing, child fever treatment-seeking, precipitation, and enhanced vegetation index. Malaria transmission in urban areas will likely be reduced by addressing socioeconomic and environmental factors that promote exposure to disease vectors. Enhanced regional surveillance systems in Nigeria can provide detailed data to further refine our understanding of these factors in relation to malaria transmission.

Factors associated with the ownership and use of insecticide-treated nets in Guinea: an analysis of the 2018 Demographic and Health Survey.

BACKGROUND: Malaria is a leading cause of outpatient visits and deaths among children in Guinea. Despite several mass distribution campaigns of insecticide-treated nets (ITNs) in Guinea, ITN ownership and use remain low. Identifying the underlying factors affecting household ITN ownership and ITN usage among those with access will allow the Guinea National Malaria Control Programme to develop targeted initiatives to improve bed net ownership and usage. METHODS: To understand national and regional drivers of ITN ownership and use, multivariable binary logistic regression models were applied to data from the 2018 Demographic and Health Survey to identify risk factors of household ITN ownership and risk factors of ITN use among individuals with access. Akaike Information Criterion (AIC) was used for model parameter selection. Odds ratios were estimated with corresponding 95% confidence intervals. RESULTS: The proportion of households in Guinea with at least one ITN was 44%, ranging from a low of 25% in Conakry to a high of 54% in Labé. Use of ITNs among those with access was 66.1% nationally, ranging from 35.2% in Labé to 89.7% in N'zérékoré. Risk factors for household ITN ownership were household size, marital status of the household head, education level of the household head, and region. For ITN use among those with access, risk factors were age, wealth quintile, marital status, and region. In the seven regions of Guinea and capital of Conakry, risk factors for household ITN ownership were household size in Boké, Faranah, and Kankan; education level of the household head in Boké, Faranah, and N'zérékoré; age of the household head in Conakry and Labé; children under five in the household in Kankan; and wealth quintile in Mamou. For ITN use among those with access, risk factors were marital status in Conakry, Faranah, Kindia, Labé, Mamou, and N'zérékoré; place of residence in Labé; children under five in the household in Labé; wealth quintile in Mamou; and age in Faranah and N'zérékoré. CONCLUSIONS: This analysis identified national and region-specific factors that affect ownership and use among those with access in Guinea. Future ITN and social-behavioural change campaigns in Guinea may particularly want to target larger households, households without children, and areas with lower perceived risk of malaria if universal coverage and usage are to be achieved for optimal malaria prevention.

Self-harm injury hospitalisations: an analysis of case selection criteria.

BACKGROUND: This study explores the impact of using different criteria to identify nonfatal hospitalisations with self-harm injuries using 2017-2018 Wisconsin discharge data. METHODS: Using International Classification of Diseases, 10th Revision, Clinical Modification codes, we classified records by three mutually exclusive selection criteria: subset A--principal diagnosis of injury, and any code for self-harm, initial encounter only; subset B--non-injury principal diagnosis, and any code for self-harm, initial encounter only; subset C--any principal diagnosis, and any code for self-harm, subsequent and sequelae encounters only. These categories were used to conduct two separate logistic regression models. Model 1 analysed the impact of surveillance limited to a principal diagnosis of injury, initial self-harm encounter (subset B compared with A). Model 2 analysed the impact if limited to initial encounters for self-harm, regardless of principal diagnosis (subset C compared with (A+B)). Both patient-level and visit-level analyses were conducted. RESULTS: For both patient-level models, subsets that included additional records based on an expansion of selection criteria were significantly more likely to include children (model 1: OR 2.8, model 2: OR 2.9; compared with those 25-54 years), those with mental health disorders (model 1: OR 6.5, model 2: OR 4.3) and rural residents (model 1: OR 1.2, model 2: OR 1.4). Drug-related disorder and means of self-harm were significantly different among subsets for both models. Visit-level analyses revealed similar results. DISCUSSION: Expanding case selection criteria would better capture the scale of hospitalisation for nonfatal self-harm. Using restrictive selection criteria may result in biased understanding of the affected populations, potentially impacting the development of policy and prevention programmes.

Beyond national indicators: adapting the Demographic and Health Surveys' sampling strategies and questions to better inform subnational malaria intervention policy.

In malaria-endemic countries, prioritizing intervention deployment to areas that need the most attention is crucial to ensure continued progress. Global and national policy makers increasingly rely on epidemiological data and mathematical modelling to help optimize health decisions at the sub-national level. The Demographic and Health Surveys (DHS) Program is a critical data source for understanding subnational malaria prevalence and intervention coverage, which are used for parameterizing country-specific models of malaria transmission. However, data to estimate indicators at finer resolutions are limited, and surveys questions have a narrow scope. Examples from the Nigeria DHS are used to highlight gaps in the current survey design. Proposals are then made for additional questions and expansions to the DHS and Malaria Indicator Survey sampling strategy that would advance the data analyses and modelled estimates that inform national policy recommendations. Collaboration between the DHS Program, national malaria control programmes, the malaria modelling community, and funders is needed to address the highlighted data challenges.

Antibiotic resistance surveillance systems: A review.

OBJECTIVES: Epidemiological surveillance is one critical approach to estimate and fight the burden of antibiotic resistance (AR). Here we summarise the characteristics of surveillance systems devoted to the surveillance of AR worldwide and published in the literature. METHODS: We performed a systematic review of the literature available on PubMed from January 2007 to July 2019 (12.5 years). The keywords ('surveillance system' OR 'laboratory-based surveillance' OR 'syndromic surveillance' OR 'sentinel surveillance' OR 'integrated surveillance' OR 'population-based surveillance') AND ('antibiotic resistance' OR 'antimicrobial resistance') were used. This research was completed with AR monitoring systems available on websites. RESULTS: We identified 71 AR surveillance systems described by 90 publications from 35 countries, including 64 (90.1%) national and 7 (9.9%) multinational surveillance systems. Two regions accounted for ∼72% of systems: European region (37; 52.1%) and Region of the Americas (14; 19.7%). Fifty-three focused on AR surveillance in humans, 12 studied both humans and animals, and 6 focused only on animals. The two most common bacterial species reported were Staphylococcus aureus (42; 59.2%) and Escherichia coli (39; 54.9%). Of the 71 AR surveillance systems, 20 (28.2%) used prevalence as an indicator, 3 (4.2%) used incidence and 7 (9.9%) used both. Methicillin-resistant S. aureus (MRSA), vancomycin-resistant Enterococcus spp., S. aureus and Streptococcus pneumoniae, penicillin-resistant S. pneumoniae, and extended-spectrum ß-lactamase (ESBL)-producing and carbapenem-resistant E. coli and Klebsiella pneumoniae were monitored. CONCLUSIONS: Our results showed heterogeneous surveillance systems. A 'One Health' approach is needed to monitor AR, with reference to the WHO Global Action Plan.

Major discrepancy between factual antibiotic resistance and consumption in South of France: analysis of 539,037 bacterial strains.

The burden of antibiotic resistance is currently estimated by mathematical modeling, without real count of resistance to key antibiotics. Here we report the real rate of resistance to key antibiotics in bacteria isolated from humans during a 5 years period in a large area in southeast in France. We conducted a retrospective study on antibiotic susceptibility of 539,107 clinical strains isolated from hospital and private laboratories in south of France area from January 2014 to January 2019. The resistance rate to key antibiotics as well as the proportion of bacteria classified as Difficult-to-Treat (DTR) were determined and compared with the Mann-Whitney U test, the χ2 test or the Fisher's exact test. Among 539,037 isolates, we did not observe any significant increase or decrease in resistance to key antibiotics for 5 years, (oxacillin resistance in Staphylococcus aureus, carbapenem resistance in enterobacteria and Pseudomonas aeruginosa and 3rd generation cephalosporin resistance in Escherichia coli and Klebsiella pneumoniae). However, we observed a significant decrease in imipenem resistance for Acinetobacter baumannii from 2014 to 2018 (24.19-12.27%; p = 0.005) and a significant increase of ceftriaxone resistance in Klebsiella pneumoniae (9.9-24.03%; p = 0.001) and Enterobacter cloacae (24.05-42.05%; p = 0.004). Of these 539,037 isolates, 1604 (0.3%) had a DTR phenotype. Over a 5-year period, we did not observe a burden of AR in our region despite a high rate of antibiotic consumption in our country. These results highlight the need for implementation of real-time AR surveillance systems which use factual data.

A Smart Waste Management Solution Geared towards Citizens.

Global industry is undergoing major transformations with the genesis of a new paradigm known as the Internet of Things (IoT) with its underlying technologies. Many company leaders are investing more effort and money in transforming their services to capitalize on the benefits provided by the IoT. Thereby, the decision makers in public waste management do not want to be outdone, and it is challenging to provide an efficient and real-time waste management system. This paper proposes a solution (hardware, software, and communications) that aims to optimize waste management and include a citizen in the process. The system follows an IoT-based approach where the discarded waste from the smart bin is continuously monitored by sensors that inform the filling level of each compartment, in real-time. These data are stored and processed in an IoT middleware providing information for collection with optimized routes and generating important statistical data for monitoring the waste collection accurately in terms of resource management and the provided services for the community. Citizens can easily access information about the public waste bins through the Web or a mobile application. The creation of the real prototype of the smart container, the development of the waste management application and a real-scale experiment use case for evaluation, demonstration, and validation show that the proposed system can efficiently change the way people deal with their garbage and optimize economic and material resources.

Tobacco Smoking Affects the Salivary Gram-Positive Bacterial Population.

The microbial communities of the oral fluid are in direct contact with tobacco smoke, which may thus affect these communities. Few culture-based studies have analyzed the effects of tobacco smoking on the oral fluid microbiota. Using bacterial culture we investigated whether tobacco smoking altered the microbial diversity of the oral fluid, focusing on aerobic and facultative anaerobic Gram-positive bacteria otherwise comprising of major pathogens. Among 90 oral fluid specimens collected in 19 tobacco-smokers and 71 controls, the diversity did not significantly differ with age and with sex. However, diversity was significantly lower in tobacco-smokers (nine different species) than in non-smokers (18 different species) with all the species cultured in tabocco-smokers being also cultured in non-smokers. We isolated the human pathogen Streptococcus australis for the first time from oral fluid. Tobacco smoking significantly alters the saliva Gram-positive bacterial microbiota, including pathogens with potential implication in the pathogenesis of tobacco-related diseases such as periodontitis and peri-implantitis.

Prospective head-to-head comparison of accuracy of two sequencing platforms for screening for fetal aneuploidy by cell-free DNA: the PEGASUS study.

We compared clinical validity of two non-invasive prenatal screening (NIPS) methods for fetal trisomies 13, 18, 21, and monosomy X. We recruited prospectively 2203 women at high risk of fetal aneuploidy and 1807 at baseline risk. Three-hundred and twenty-nine euploid samples were randomly removed. The remaining 1933 high risk and 1660 baseline-risk plasma aliquots were assigned randomly between four laboratories and tested with two index NIPS tests, blind to maternal variables and pregnancy outcomes. The two index tests used massively parallel shotgun sequencing (semiconductor-based and optical-based). The reference standard for all fetuses was invasive cytogenetic analysis or clinical examination at birth and postnatal follow-up. For each chromosome of interest, chromosomal ratios were calculated (number of reads for chromosome/total number of reads). Euploid samples' mean chromosomal ratio coefficients of variation were 0.48 (T21), 0.34 (T18), and 0.31 (T13). According to the reference standard, there were 155 cases of T21, 49 T18, 8 T13 and 22 45,X. Using a fetal fraction ≥4% to call results and a chromosomal ratio z-score of ≥3 to report a positive result, detection rates (DR), and false positive rates (FPR) were not statistically different between platforms: mean DR 99% (T21), 100%(T18, T13); 79%(45,X); FPR < 0.3% for T21, T18, T13, and <0.6% for 45,X. Both methods' negative predictive values in high-risk pregnancies were >99.8%, except for 45,X(>99.6%). Threshold analysis in high-risk pregnancies with different fetal fractions and z-score cut-offs suggested that a z-score cutoff to 3.5 for positive results improved test accuracy. Both sequencing platforms showed equivalent and excellent clinical validity.

Whole exome sequencing identifies novel predisposing genes in neural tube defects.

BACKGROUND: Neural tube defects (NTD) are among the most common defects affecting 1:1000 births. They are caused by a failure of neural tube closure during development. Their clinical presentation is diverse and dependent on the site and severity of the original defect on the embryonic axis. The etiology of NTD is multifactorial involving environmental factors and genetic variants that remain largely unknown. METHODS: We have conducted a whole exome sequencing (WES) study in five new NTD families and pooled the results with WES data from three NTD families and 43 trios that were previously investigated by our group. We analyzed the data using biased candidate gene and unbiased gene burden approaches. RESULTS: We identified four novel loss-of-function variants in three genes, MTHFR, DLC1, and ITGB1, previously associated with NTD. Notably, DLC1 carried two protein truncating variants in two independent cases. We also demonstrated an enrichment of variants in MYO1E involved in cytoskeletal remodeling. This enrichment reached borderline significance in a replication cohort supporting the association of this new candidate gene to NTD. CONCLUSION: These data provide some key insights into the pathogenic mechanisms of human NTD and demonstrate the power of next-generation sequencing in deciphering the genetics of this complex trait.

High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies.

Developmental and epileptic encephalopathy (DEE) is a group of conditions characterized by the co-occurrence of epilepsy and intellectual disability (ID), typically with developmental plateauing or regression associated with frequent epileptiform activity. The cause of DEE remains unknown in the majority of cases. We performed whole-genome sequencing (WGS) in 197 individuals with unexplained DEE and pharmaco-resistant seizures and in their unaffected parents. We focused our attention on de novo mutations (DNMs) and identified candidate genes containing such variants. We sought to identify additional subjects with DNMs in these genes by performing targeted sequencing in another series of individuals with DEE and by mining various sequencing datasets. We also performed meta-analyses to document enrichment of DNMs in candidate genes by leveraging our WGS dataset with those of several DEE and ID series. By combining these strategies, we were able to provide a causal link between DEE and the following genes: NTRK2, GABRB2, CLTC, DHDDS, NUS1, RAB11A, GABBR2, and SNAP25. Overall, we established a molecular diagnosis in 63/197 (32%) individuals in our WGS series. The main cause of DEE in these individuals was de novo point mutations (53/63 solved cases), followed by inherited mutations (6/63 solved cases) and de novo CNVs (4/63 solved cases). De novo missense variants explained a larger proportion of individuals in our series than in other series that were primarily ascertained because of ID. Moreover, these DNMs were more frequently recurrent than those identified in ID series. These observations indicate that the genetic landscape of DEE might be different from that of ID without epilepsy.

Spatially explicit multi-threat assessment of food tree species in Burkina Faso: A fine-scale approach.

Over the last decades agroforestry parklands in Burkina Faso have come under increasing demographic as well as climatic pressures, which are threatening indigenous tree species that contribute substantially to income generation and nutrition in rural households. Analyzing the threats as well as the species vulnerability to them is fundamental for priority setting in conservation planning. Guided by literature and local experts we selected 16 important food tree species (Acacia macrostachya, Acacia senegal, Adansonia digitata, Annona senegalensis, Balanites aegyptiaca, Bombax costatum, Boscia senegalensis, Detarium microcarpum, Lannea microcarpa, Parkia biglobosa, Sclerocarya birrea, Strychnos spinosa, Tamarindus indica, Vitellaria paradoxa, Ximenia americana, Ziziphus mauritiana) and six key threats to them (overexploitation, overgrazing, fire, cotton production, mining and climate change). We developed a species-specific and spatially explicit approach combining freely accessible datasets, species distribution models (SDMs), climate models and expert survey results to predict, at fine scale, where these threats are likely to have the greatest impact. We find that all species face serious threats throughout much of their distribution in Burkina Faso and that climate change is predicted to be the most prevalent threat in the long term, whereas overexploitation and cotton production are the most important short-term threats. Tree populations growing in areas designated as 'highly threatened' due to climate change should be used as seed sources for ex situ conservation and planting in areas where future climate is predicting suitable habitats. Assisted regeneration is suggested for populations in areas where suitable habitat under future climate conditions coincides with high threat levels due to short-term threats. In the case of Vitellaria paradoxa, we suggest collecting seed along the northern margins of its distribution and considering assisted regeneration in the central part where the current threat level is high due to overexploitation. In the same way, population-specific recommendations can be derived from the individual and combined threat maps of the other 15 food tree species. The approach can be easily transferred to other countries and can be used to analyze general and species specific threats at finer and more local as well as at broader (continental) scales in order to plan more selective and efficient conservation actions in time. The concept can be applied anywhere as long as appropriate spatial data are available as well as knowledgeable experts.

Differences in Methods of Self-Inflicted Injuries by Sex in Wisconsin, 2002-2014.

BACKGROUND: Despite suicide prevention efforts, there remains a high burden of self-inflicted injuries in Wisconsin. OBJECTIVE: Compare methods of suicide and nonfatal self-inflicted injury by sex in Wisconsin over a 12-year period. METHODS: Suicide and nonfatal self-inflicted injury rates in Wisconsin between 2002 and 2014 were compared by sex and method using data from the Wisconsin Interactive Statistics on Health. Percentages of total suicides by method of injury for each sex were calculated. RESULTS: Firearms and poisoning were the most common methods of suicide and nonfatal selfinflicted injuries, respectively. Rates of both suicide and nonfatal self-inflicted injuries differed significantly by sex and method. CONCLUSIONS: Suicide prevention strategies in Wisconsin must account for the variability of method of self-inflicted injury between sexes.

International trends in health science librarianship part 15: West Africa (Ghana, Nigeria, Senegal).

This is the 15th in a series of articles exploring international trends in health science librarianship in the 21st century. It is the third of four articles pertaining to different regions in the African continent. The present issue focuses on countries in West Africa (Ghana, Nigeria and Senegal). The next feature column will investigate trends in North Africa. JM.

Increased missense mutation burden of Fatty Acid metabolism related genes in nunavik inuit population.

BACKGROUND: Nunavik Inuit (northern Quebec, Canada) reside along the arctic coastline where for generations their daily energy intake has mainly been derived from animal fat. Given this particular diet it has been hypothesized that natural selection would lead to population specific allele frequency differences and unique variants in genes related to fatty acid metabolism. A group of genes, namely CPT1A, CPT1B, CPT1C, CPT2, CRAT and CROT, encode for three carnitine acyltransferases that are important for the oxidation of fatty acids, a critical step in their metabolism. METHODS: Exome sequencing and SNP array genotyping were used to examine the genetic variations in the six genes encoding for the carnitine acyltransferases in 113 Nunavik Inuit individuals. RESULTS: Altogether ten missense variants were found in genes CPT1A, CPT1B, CPT1C, CPT2 and CRAT, including three novel variants and one Inuit specific variant CPT1A p.P479L (rs80356779). The latter has the highest frequency (0.955) compared to other Inuit populations. We found that by comparison to Asians or Europeans, the Nunavik Inuit have an increased mutation burden in CPT1A, CPT2 and CRAT; there is also a high level of population differentiation based on carnitine acyltransferase gene variations between Nunavik Inuit and Asians. CONCLUSION: The increased number and frequency of deleterious variants in these fatty acid metabolism genes in Nunavik Inuit may be the result of genetic adaptation to their diet and/or the extremely cold climate. In addition, the identification of these variants may help to understand some of the specific health risks of Nunavik Inuit.

Loss-of-function de novo mutations play an important role in severe human neural tube defects.

BACKGROUND: Neural tube defects (NTDs) are very common and severe birth defects that are caused by failure of neural tube closure and that have a complex aetiology. Anencephaly and spina bifida are severe NTDs that affect reproductive fitness and suggest a role for de novo mutations (DNMs) in their aetiology. METHODS: We used whole-exome sequencing in 43 sporadic cases affected with myelomeningocele or anencephaly and their unaffected parents to identify DNMs in their exomes. RESULTS: We identified 42 coding DNMs in 25 cases, of which 6 were loss of function (LoF) showing a higher rate of LoF DNM in our cohort compared with control cohorts. Notably, we identified two protein-truncating DNMs in two independent cases in SHROOM3, previously associated with NTDs only in animal models. We have demonstrated a significant enrichment of LoF DNMs in this gene in NTDs compared with the gene specific DNM rate and to the DNM rate estimated from control cohorts. We also identified one nonsense DNM in PAX3 and two potentially causative missense DNMs in GRHL3 and PTPRS. CONCLUSIONS: Our study demonstrates an important role of LoF DNMs in the development of NTDs and strongly implicates SHROOM3 in its aetiology.

De novo mutations in moderate or severe intellectual disability.

Genetics is believed to have an important role in intellectual disability (ID). Recent studies have emphasized the involvement of de novo mutations (DNMs) in ID but the extent to which they contribute to its pathogenesis and the identity of the corresponding genes remain largely unknown. Here, we report a screen for DNMs in subjects with moderate or severe ID. We sequenced the exomes of 41 probands and their parents, and confirmed 81 DNMs affecting the coding sequence or consensus splice sites (1.98 DNMs/proband). We observed a significant excess of de novo single nucleotide substitutions and loss-of-function mutations in these cases compared to control subjects, suggesting that at least a subset of these variations are pathogenic. A total of 12 likely pathogenic DNMs were identified in genes previously associated with ID (ARID1B, CHD2, FOXG1, GABRB3, GATAD2B, GRIN2B, MBD5, MED13L, SETBP1, TBR1, TCF4, WDR45), resulting in a diagnostic yield of ∼29%. We also identified 12 possibly pathogenic DNMs in genes (HNRNPU, WAC, RYR2, SET, EGR1, MYH10, EIF2C1, COL4A3BP, CHMP2A, PPP1CB, VPS4A, PPP2R2B) that have not previously been causally linked to ID. Interestingly, no case was explained by inherited mutations. Protein network analysis indicated that the products of many of these known and candidate genes interact with each other or with products of other ID-associated genes further supporting their involvement in ID. We conclude that DNMs represent a major cause of moderate or severe ID.

Increased exonic de novo mutation rate in individuals with schizophrenia.

Schizophrenia is a severe psychiatric disorder that profoundly affects cognitive, behavioral and emotional processes. The wide spectrum of symptoms and clinical variability in schizophrenia suggest a complex genetic etiology, which is consistent with the numerous loci thus far identified by linkage, copy number variation and association studies. Although schizophrenia heritability may be as high as ∼80%, the genes responsible for much of this heritability remain to be identified. Here we sequenced the exomes of 14 schizophrenia probands and their parents. We identified 15 de novo mutations (DNMs) in eight probands, which is significantly more than expected considering the previously reported DNM rate. In addition, 4 of the 15 identified DNMs are nonsense mutations, which is more than what is expected by chance. Our study supports the notion that DNMs may account for some of the heritability reported for schizophrenia while providing a list of genes possibly involved in disease pathogenesis.

Excess of de novo deleterious mutations in genes associated with glutamatergic systems in nonsyndromic intellectual disability.

Little is known about the genetics of nonsyndromic intellectual disability (NSID). We hypothesized that de novo mutations (DNMs) in synaptic genes explain an important fraction of sporadic NSID cases. In order to investigate this possibility, we sequenced 197 genes encoding glutamate receptors and a large subset of their known interacting proteins in 95 sporadic cases of NSID. We found 11 DNMs, including ten potentially deleterious mutations (three nonsense, two splicing, one frameshift, four missense) and one neutral mutation (silent) in eight different genes. Calculation of point-substitution DNM rates per functional and neutral site showed significant excess of functional DNMs compared to neutral ones. De novo truncating and/or splicing mutations in SYNGAP1, STXBP1, and SHANK3 were found in six patients and are likely to be pathogenic. De novo missense mutations were found in KIF1A, GRIN1, CACNG2, and EPB41L1. Functional studies showed that all these missense mutations affect protein function in cell culture systems, suggesting that they may be pathogenic. Sequencing these four genes in 50 additional sporadic cases of NSID identified a second DNM in GRIN1 (c.1679_1681dup/p.Ser560dup). This mutation also affects protein function, consistent with structural predictions. None of these mutations or any other DNMs were identified in these genes in 285 healthy controls. This study highlights the importance of the glutamate receptor complexes in NSID and further supports the role of DNMs in this disorder.