Rare deleterious mutations of the gene EFR3A in autism spectrum disorders

Background: Whole-exome sequencing studies in autism spectrum disorder (ASD) have identified de novo mutations in novel candidate genes, including the synaptic gene Eighty-five Requiring 3A (EFR3A). EFR3A is a critical component of a protein complex required for the synthesis of the phosphoinositide PtdIns4P, which has a variety of functions at the neural synapse. We hypothesized that deleterious mutations in EFR3A would be significantly associated with ASD. Methods: We conducted a large case/control association study by deep resequencing and analysis of whole-exome data for coding and splice site variants in EFR3A. We determined the potential impact of these variants on protein structure and function by a variety of conservation measures and analysis of the Saccharomyces cerevisiae Efr3 crystal structure. We also analyzed the expression pattern of EFR3A in human brain tissue. Results: Rare nonsynonymous mutations in EFR3A were more common among cases (16 / 2,196 = 0.73%) than matched controls (12 / 3,389 = 0.35%) and were statistically more common at conserved nucleotides based on an experiment-wide significance threshold (P = 0.0077, permutation test). Crystal structure analysis revealed that mutations likely to be deleterious were also statistically more common in cases than controls (P = 0.017, Fisher exact test). Furthermore, EFR3A is expressed in cortical neurons, including pyramidal neurons, during human fetal brain development in a pattern consistent with ASD-related genes, and it is strongly co-expressed (P < 2.2 × 10−16, Wilcoxon test) with a module of genes significantly associated with ASD. Conclusions: Rare deleterious mutations in EFR3A were found to be associated with ASD using an experiment-wide significance threshold. Synaptic phosphoinositide metabolism has been strongly implicated in syndromic forms of ASD. These data for EFR3A strengthen the evidence for the involvement of this pathway in idiopathic autism

No Evidence for Association of Autism with Rare Heterozygous Point Mutations in Contactin-Associated Protein-Like 2 (CNTNAP2), or in Other Contactin-Associated Proteins or Contactins

Contactins and Contactin-Associated Proteins, and Contactin-Associated Protein-Like 2 (CNTNAP2) in particular, have been widely cited as autism risk genes based on findings from homozygosity mapping, molecular cytogenetics, copy number variation analyses, and both common and rare single nucleotide association studies. However, data specifically with regard to the contribution of heterozygous single nucleotide variants (SNVs) have been inconsistent. In an effort to clarify the role of rare point mutations in CNTNAP2 and related gene families, we have conducted targeted next-generation sequencing and evaluated existing sequence data in cohorts totaling 2704 cases and 2747 controls. We find no evidence for statistically significant association of rare heterozygous mutations in any of the CNTN or CNTNAP genes, including CNTNAP2, placing marked limits on the scale of their plausible contribution to risk

Prevalence of normal weight obesity and its associated cardio-metabolic risk factors - Results from the baseline data of the Kerala Diabetes Prevention Program (KDPP)

BACKGROUND: Cardiometabolic disorders are frequently observed among those who have obesity as measured by body mass index (BMI). However, there is limited data available on the cardiometabolic profile of those who are non-obese by BMI but with a high body fat percentage (BFP), a phenotype frequently observed in the Indian population. We examined the prevalence of individuals with normal weight obesity (NWO) and the cardiometabolic profile of NWO individuals at high risk for type 2 diabetes(T2D) in a south Asian population. MATERIAL AND METHODS: In the Kerala Diabetes Prevention Program, individuals aged between 30 to 60 years were screened using the Indian Diabetes Risk Score(IDRS) in 60 rural communities in the Indian state of Kerala. We used data from the baseline survey of this trial for this analysis which included 1147 eligible high diabetes risk individuals(IDRS >60). NWO was defined as BMI within the normal range and a high BFP (as per Asia-pacific ethnicity based cut-off); Non-obese (NO) as normal BMI and BFP and overtly obese (OB) as BMI ≥25 kg/m2 irrespective of the BFP. Data on demographic, clinical and biochemical characteristics were collected using standardized questionnaires and protocols. Body fat percentage was assessed using TANITA body composition analyser (model SC330), based on bioelectrical impedance. RESULTS: The mean age of participants was 47.3 ± 7.5 years and 46% were women. The proportion with NWO was 32% (n = 364; 95% CI: 29.1 to 34.5%), NO was 17% (n = 200) and OB was 51% (n = 583). Among those with NWO, 19.7% had T2D, compared to 18.7% of those who were OB (p value = 0.45) and 8% with NO (p value = 0.003). Among those with NWO, mean systolic and diastolic blood pressure were 129 ± 20; 78 ± 12 mmHg, compared to 127 ± 17; 78±11 mmHg among those with OB (p value = 0.12;0.94) and 120 ± 16; 71±10 mmHg among with NO (p value<0.001; 0.001), respectively. A similar pattern of association was observed for LDL cholesterol and triglycerides. After adjusting for other risk factors, the odds of having diabetes (OR:2.72[95% CI:1.46-5.08]) and dyslipidemia (2.37[1.55-3.64]) was significantly more in individuals with NWO as compared to non-obese individuals. CONCLUSIONS: Almost one-third of this South Asian population, at high risk for T2D, had normal weight obesity. The significantly higher cardiometabolic risk associated with increased adiposity even in lower BMI individuals has important implications for recognition in clinical practice

Physical Habitat and Fish Assemblage Relationships with Landscape Variables at Multiple Spatial Scales in Wadeable Iowa Streams

Landscapes in Iowa and other midwestern states have been profoundly altered by conversion of native prairies to agriculture. We analyzed landscape data collected at multiple spatial scales to explore relationships with reach-scale physical habitat and fish assemblage data from 93 randomly selected sites on second- through fifth-order wadeable Iowa streams. Ordination of sites by physical habitat showed significant gradients of channel shape, habitat complexity, substrate composition, and stream size. Several landscape variables were significantly associated with the physical habitat ordination. Row crop land use was associated with fine substrates and steep bank angles, whereas wetland land cover and greater sinuosity and catchment land area were associated with complex channel and bank morphology and greater residual pool volume, woody debris, and canopy cover. Thirteen landscape variables were significant predictors of physical habitat variables in multiple linear regressions, with adjusted R 2 values ranging from 0.07 to 0.74. Inclusion of landscape variables with physical habitat variables in multiple regression models predicting fish assemblage metrics and a fish index of biotic integrity resulted in negligible improvements over models based on only physical habitat variables. Physical habitat in wadeable Iowa streams is strongly associated with landscape characteristics. Results of this study and previous studies suggest that (1) landscape factors directly influence physical habitat, (2) physical habitat directly influences fish assemblages, and (3) the influence of landscape factors on fish assemblages is primarily indirect. Understanding how landscape factors, such as human land use, influence physical habitat and fish assemblages will help managers make more informed decisions for improving Iowa\u27s wadeable streams

Heritability of non-speech auditory processing skills

Recent insight into the genetic bases for autism spectrum disorder, dyslexia, stuttering, and language disorders suggest that neurogenetic approaches may also reveal at least one etiology of auditory processing disorder (APD). A person with an APD typically has difficulty understanding speech in background noise despite having normal pure-tone hearing sensitivity. The estimated prevalence of APD may be as high as 10% in the pediatric population, yet the causes are unknown and have not been explored by molecular or genetic approaches. The aim of our study was to determine the heritability of frequency and temporal resolution for auditory signals and speech recognition in noise in 96 identical or fraternal twin pairs, aged 6–11 years. Measures of auditory processing (AP) of non-speech sounds included backward masking (temporal resolution), notched noise masking (spectral resolution), pure-tone frequency discrimination (temporal fine structure sensitivity), and nonsense syllable recognition in noise. We provide evidence of significant heritability, ranging from 0.32 to 0.74, for individual measures of these non-speech-based AP skills that are crucial for understanding spoken language. Identification of specific heritable AP traits such as these serve as a basis to pursue the genetic underpinnings of APD by identifying genetic variants associated with common AP disorders in children and adults

De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis

We previously established the contribution of de novo damaging sequence variants to Tourette disorder (TD) through whole-exome sequencing of 511 trios. Here, we sequence an additional 291 TD trios and analyze the combined set of 802 trios. We observe an overrepresentation of de novo damaging variants in simplex, but not multiplex, families; we identify a high-confidence TD risk gene, CELSR3 (cadherin EGF LAG seven-pass G-type receptor 3); we find that the genes mutated in TD patients are enriched for those related to cell polarity, suggesting a common pathway underlying pathobiology; and we confirm a statistically significant excess of de novo copy number variants in TD. Finally, we identify significant overlap of de novo sequence variants between TD and obsessive-compulsive disorder and de novo copy number variants between TD and autism spectrum disorder, consistent with shared genetic risk

Genome-wide association study of Tourette Syndrome

Tourette Syndrome (TS) is a developmental disorder that has one of the highest familial recurrence rates among neuropsychiatric diseases with complex inheritance. However, the identification of definitive TS susceptibility genes remains elusive. Here, we report the first genome-wide association study (GWAS) of TS in 1285 cases and 4964 ancestry-matched controls of European ancestry, including two European-derived population isolates, Ashkenazi Jews from North America and Israel, and French Canadians from Quebec, Canada. In a primary meta-analysis of GWAS data from these European ancestry samples, no markers achieved a genome-wide threshold of significance (p<5 × 10−8); the top signal was found in rs7868992 on chromosome 9q32 within COL27A1 (p=1.85 × 10−6). A secondary analysis including an additional 211 cases and 285 controls from two closely-related Latin-American population isolates from the Central Valley of Costa Rica and Antioquia, Colombia also identified rs7868992 as the top signal (p=3.6 × 10−7 for the combined sample of 1496 cases and 5249 controls following imputation with 1000 Genomes data). This study lays the groundwork for the eventual identification of common TS susceptibility variants in larger cohorts and helps to provide a more complete understanding of the full genetic architecture of this disorder

Care and communication between health professionals and patients affected by severe or chronic illness in community care settings: a qualitative study of care at the end of life

Background: Advance care planning (ACP) enables patients to consider, discuss and, if they wish, document their wishes and preferences for future care, including decisions to refuse treatment, in the event that they lose capacity to make decisions for themselves. ACP is a key component of UK health policy to improve the experience of death and dying for patients and their families. There is limited evidence about how patients and health professionals understand ACP, or when and how this is initiated. It is evident that many people find discussion of and planning for end of life care difficult, and tend to avoid the topic. Aim: To investigate how patients, their relatives and health professionals initiate and experience discussion of ACP and the outcomes of advance discussions in shaping care at the end of life. Design and data collection: Qualitative study with two workstreams: (1) interviews with 37 health professionals (general practitioners, specialist nurses and community nurses) about their experiences of ACP; and (2) longitudinal case studies of 21 patients with 6-month follow-up. Cases included a patient and, where possible, a nominated key relative and/or health professional as well as a review of medical records. Complete case triads were obtained for 11 patients. Four cases comprised the patient alone, where respondents were unable or unwilling to nominate either a family member or a professional carer they wished to include in the study. Patients were identified as likely to be within the last 6 months of life. Ninety-seven interviews were completed in total. Setting: General practices and community care settings in the East Midlands of England. Findings: The study found ACP to be uncommon and focused primarily on specific documented tasks involving decisions about preferred place of death and cardiopulmonary resuscitation, supporting earlier research. There was no evidence of ACP in nearly half (9 of 21) of patient cases. Professionals reported ACP discussions to be challenging. It was difficult to recognise when patients had entered the last year of life, or to identify their readiness to consider future planning. Patients often did not wish to do so before they had become gravely ill. Consequently, ACP discussions tended to be reactive, rather than pre-emptive, occurring in response to critical events or evidence of marked deterioration. ACP discussions intersected two parallel strands of planning: professional organisation and co-ordination of care; and the practical and emotional preparatory work that patients and families undertook to prepare themselves for death. Reference to ACP as a means of guiding decisions for patients who had lost capacity was rare. Conclusions: Advance care planning remains uncommon, is often limited to documentation of a few key decisions, is reported to be challenging by many health professionals, is not welcomed by a substantial number of patients and tends to be postponed until death is clearly imminent. Current implementation largely ignores the purpose of ACP as a means of extending personal autonomy in the event of lost capacity. Future work: Attention should be paid to public attitudes to death and dying (including those of culturally diverse and ethnic minority groups), place of death, resuscitation and the value of anticipatory planning. In addition the experiences and needs of two under-researched groups should be explored: the frail elderly, including those who manage complex comorbid conditions, unrecognised as vulnerable cases; and those patients affected by stigmatised conditions, such as substance abuse or serious mental illness who fail to engage constructively with services and are not recognised as suitable referrals for palliative and end of life care. Funding: The National Institute for Health Research Health Services and Delivery Research programme