World's largest autism genome database shines new light on many 'autisms'

Through its research platform on the Google Cloud, Autism Speaks is making all of MSSNG's fully sequenced genomes directly available to researchers free of charge, along with analytic tools. In the coming weeks, the MSSNG team will be uploading an additional 2,000 fully sequenced autism genomes, bringing the total over 7,000.
Currently, more than 90 investigators at 40 academic and medical institutions are using the MSSNG database to advance autism research around the world."



Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder, Nature Neuroscience (2017). DOI: 10.1038/nn.4524 

Increased burden of deleterious variants in essential genes in autism spectrum disorder

Autism spectrum disorder (ASD) is a heterogeneous, highly heritable neurodevelopmental syndrome characterized by impaired social interaction, communication, and repetitive behavior. It is estimated that hundreds of genes contribute to ASD. We asked if genes with a strong effect on survival and fitness contribute to ASD risk. Human orthologs of genes with an essential role in pre- and postnatal development in the mouse [essential genes (EGs)] are enriched for disease genes and under strong purifying selection relative to human orthologs of mouse genes with a known nonlethal phenotype [nonessential genes (NEGs)]. This intolerance to deleterious mutations, commonly observed haploinsufficiency, and the importance of EGs in development suggest a possible cumulative effect of deleterious variants in EGs on complex neurodevelopmental disorders. With a comprehensive catalog of 3,915 mammalian EGs, we provide compelling evidence for a stronger contribution of EGs to ASD risk compared with NEGs. By examining the exonic de novo and inherited variants from 1,781 ASD quartet families, we show a significantly higher burden of damaging mutations in EGs in ASD probands compared with their non-ASD siblings. The analysis of EGs in the developing brain identified clusters of coexpressed EGs implicated in ASD. Finally, we suggest a high-priority list of 29 EGs with potential ASD risk as targets for future functional and behavioral studies. Overall, we show that large-scale studies of gene function in model organisms provide a powerful approach for prioritization of genes and pathogenic variants identified by sequencing studies of human disease."



'via Blog this'

SZGR2: Schizophrenia Gene Resource

SZGR2: "Schizophrenia Gene Resource 2 (SZGR 2.0) provides a comprehensive online resource for schizophrenia studies. Built in 2009, SZGR curates data from genetics studies, transcriptome studies, and epigenetics studies. Overtime, SZGR has grown from a pure genetics resource to a comprehensive, multi-omics online data house -- a one-stop shop for schizophrenia. Our long term goal is to provide resources and tools for researchers to understand schizophrenia. Our ultimate goal is to improve the life quality of schizophrenia patients and to contribute to successful therapies for patients. Please email us if there are any feedbacks. Click here to browse all data sets. Documentation can be found here."

Whole-genome sequencing of quartet families with autism spectrum disorder : Nature Medicine : Nature Publishing Group

Autism spectrum disorder (ASD) is genetically heterogeneous, with evidence for hundreds of susceptibility loci. Previous microarray and exome-sequencing studies have examined portions of the genome in simplex families (parents and one ASD-affected child) having presumed sporadic forms of the disorder. We used whole-genome sequencing (WGS) of 85 quartet families (parents and two ASD-affected siblings), consisting of 170 individuals with ASD, to generate a comprehensive data resource encompassing all classes of genetic variation (including noncoding variants) and accompanying phenotypes, in apparently familial forms of ASD. By examining de novo and rare inherited single-nucleotide and structural variations in genes previously reported to be associated with ASD or other neurodevelopmental disorders, we found that some (69.4%) of the affected siblings carried different ASD-relevant mutations. These siblings with discordant mutations tended to demonstrate more clinical variability than those who shared a risk variant. Our study emphasizes that substantial genetic heterogeneity exists in ASD, necessitating the use of WGS to delineate all genic and non-genic susceptibility variants in research and in clinical diagnostics.

Atlas shows how genes affect our metabolism - Wellcome Trust Sanger Institute

In the most comprehensive exploration of the association between genetic variation and human metabolism, researchers have provided unprecedented insights into how genetic variants influence complex disease and drug response through metabolic pathways. The team has linked 145 genetic regions with more than 400 molecules involved in human metabolism in human blood. This atlas of genetic associations with metabolism provides many new opportunities to understand the molecular pathways underlying associations with common complex diseases. Metabolic molecules, known as metabolites, include a wide range of different molecules such as vitamins, lipids, carbohydrates and nucleotides. They make up parts of, or are the products of, all biological pathways. This new compendium of associations between genetic regions and metabolite levels provides a powerful tool to identify genes that could be used in drug and diagnostic tests for a wide range of metabolic disorders.

Exclusive: 'Jaw-dropping' breakthrough hailed as landmark in fight against hereditary diseases as Crispr technique heralds genetic revolution - Science - News - The Independent

For the first time, scientists are able to engineer any part of the human genome with extreme precision using a revolutionary new technique called Crispr, which has been likened to editing the individual letters on any chosen page of an encyclopedia without creating spelling mistakes. The landmark development means it is now possible to make the most accurate and detailed alterations to any specific position on the DNA of the 23 pairs of human chromosomes without introducing unintended mutations or flaws, scientists said.

Immunity & Ageing | Full text | Variations in inflammatory genes are associated with periodontitis

Periodontitis is a multi-factorial disease and several risk-factors such as infections, inflammatory responses, oral hygiene, smoke, aging and individual predisposition are involved in the disease. Pathogens trigger chronic inflammation with cytokines release which in turn leads to the destruction of the connective and the teeth supporting bone. The identification of genetic factors controlling oral inflammation may increase our understanding of genetic predisposition to periodontitis.

Single nucleotide polymorphisms in the promoter region of Vascular Endothelial Growth Factor, Alpha-1-Antichymotripsin, hydroxy-methyl-glutaryl CoA reductase, Interferon alpha, Interleukin-1 Beta, Interleukin 10, Interleukin 6 and Tumor Necrosis Factor- alpha genes from a case/control study were investigated.

Results

The C allele of Vascular Endothelial Growth Factor, A allele of Interleukin 10 and GG genotype of Tumor Necrosis Factor-α were individually associated with chronic periodontitis. However, the concomitant presence of the three genetic markers in the same subjects appeared to play a synergistic role and increased several folds the risk of the disease.

Conclusions

Our findings offer new tools to implement the screening of unaffected subjects with an increased susceptibility of periodontitis and increase our understanding regarding the genetic inflammatory background related to familiarity of the disease.

Rapid Intrahost Evolution of Human Cytomegalovirus Is Shaped by Demography and Positive Selection.

 Populations of human cytomegalovirus (HCMV), a large DNA virus, are highly polymorphic in patient samples, which may allow for rapid evolution within human hosts. To understand HCMV evolution, longitudinally sampled genomic populations from the urine and plasma of 5 infants with symptomatic congenital HCMV infection were analyzed. Temporal and compartmental variability of viral populations were quantified using high throughput sequencing and population genetics approaches. HCMVpopulations were generally stable over time, with ∼88% of SNPs displaying similar frequencies. However, samples collected from plasma and urine of the same patient at the same time were highly differentiated with approximately 1700 consensus sequence SNPs (1.2% of the genome) identified between compartments. This inter-compartment differentiation was comparable to the differentiation observed in unrelated hosts. Models of demography (i.e., changes in population size and structure) and positive selection were evaluated to explain the observed patterns of variation. Evidence for strong bottlenecks (>90% reduction in viral population size) was consistent among all patients. From the timing of the bottlenecks, we conclude that fetal infection occurred between 13-18 weeks gestational age in patients analyzed, while colonization of the urine compartment followed roughly 2 months later. The timing of these bottlenecks is consistent with the clinical histories of congenital HCMV infections. We next inferred that positive selection plays a small but measurable role in viral evolution within a single compartment. However, positive selection appears to be a strong and pervasive driver of evolution associated with compartmentalization, affecting ≥34 of the 167 open reading frames (∼20%) of the genome. This work offers the most detailed map of HCMV in vivo evolution to date and provides evidence that viral populations can be stable or rapidly differentiate, depending on host environment. The application of population genetic methods to these data provides clinically useful information, such as the timing of infection and compartment colonization.

Mental Disorders Overlap in Genetic Etiology | The Scientist Magazine®

 "Five psychiatric disorders, whose diagnoses are based on symptoms rather than biology, share a considerable number of genetic risk factors, researchers reported in Nature Genetics last week (August 11). Schizophrenia, bipolar disorder, and major depressive disorder have the greatest commonality among one another, while depression and attention-deficit/hyperactivity disorder (ADHD) share some genetic underpinnings, as do autism spectrum disorders (ASD) and schizophrenia. “Our results will likely contribute to the efforts now under way to base psychiatric nosology on a firmer empirical footing,” the researchers wrote in their report."

The genetic and environmental bases of complex human-disease: extending the utility of twin-studies.

 Making only the assumption that twins are representative of the population from which they are drawn, we here develop a simple mathematical model (using widely available epidemiological information) that sheds considerable light on the pathogenesis of complex human diseases. Specifically, for the case of multiple sclerosis (MS), we demonstrate that the vast majority of patients (≥94%), possibly all, require genetic susceptibility in order to get MS. Nevertheless, only a tiny fraction of the population (≤2.2%) is actually susceptible to getting this disease; a finding which is highly consistent in all of the studied populations across both North America and Europe. Men are more likely to be susceptible than women although susceptible women are more than twice as likely to actually develop MS compared to susceptible men (i.e., they have a greater disease penetrance). This is because women are more responsive to the environmental factors involved in MS pathogenesis than men. These differences account for the current gender-ratio (3∶1, favoring women) and also for the increasing incidence of MS in women around the world. By contrast, the most important genetic marker for MS susceptibility (DRB1*1501) influences the likelihood of susceptibility but not the penetrance of the disease. Nevertheless, even for this major susceptibility allele, only a very small fraction of DRB1*1501carriers (<5%) are susceptible to getting MS and for only a minority of MS patients (∼41%) does this allele contribute to their susceptibility. Moreover, each copy of this allele seems to make an independent contribution to susceptibility. Finally, at least three environmental events are necessary for MS pathogenesis and, during the course of their lives, the large majority of the population (≥69%) experiences an environmental exposure, which is sufficient to produce MS in, at least, some susceptible genotypes. Also, susceptible men (compared to susceptible women) have a lower threshold, a greater hazard-rate, or both in response to the environmental factors involved in MS pathogenesis.

Cell - Genome-wide Generation and Systematic Phenotyping of Knockout Mice Reveals New Roles for Many Genes

 "Mutations in whole organisms are powerful ways of interrogating gene function in a realistic context. We describe a program, the Sanger Institute Mouse Genetics Project, that provides a step toward the aim of knocking out all genes and screening each line for a broad range of traits. We found that hitherto unpublished genes were as likely to reveal phenotypes as known genes, suggesting that novel genes represent a rich resource for investigating the molecular basis of disease. We found many unexpected phenotypes detected only because we screened for them, emphasizing the value of screening all mutants for a wide range of traits. Haploinsufficiency and pleiotropy were both surprisingly common. Forty-two percent of genes were essential for viability, and these were less likely to have a paralog and more likely to contribute to a protein complex than other genes. Phenotypic data and more than 900 mutants are openly available for further analysis."

Twin research comes of age

Thanks to thousands of volunteer twins, scientists have discovered over 400 novel genes associated with over 30 diseases over the last two decades, marking a golden era in genetic discovery.

The Interaction Of Social Amoeba And Bacteria Defined By Genes

Amoeba eat bacteria and other human pathogens, engulfing and destroying them - or being destroyed by them, but how these single-cell organisms distinguish and respond successfully to different bacterial classes has been largely unexplained. 

In a report in the journal Current Biology, researchers from Baylor College of Medicine use the model of the social amoeba -Dictyostelium discoideum - to identify the genetic controls on how the amoeba differentiate the different bacteria and respond to achieve their goal of destruction.

Exome sequencing reveals new causal mutations in children with epileptic encephalopathies - Veeramah - 2013 - Epilepsia - Wiley Online Library

The management of epilepsy in children is particularly challenging when seizures are resistant to antiepileptic medications, or undergo many changes in seizure type over time, or have comorbid cognitive, behavioral, or motor deficits. Despite efforts to classify such epilepsies based on clinical and electroencephalographic criteria, many children never receive a definitive etiologic diagnosis. Whole exome sequencing (WES) is proving to be a highly effective method for identifying de novo variants that cause neurologic disorders, especially those associated with abnormal brain development. Herein we explore the utility of WES for identifying candidate causal de novo variants in a cohort of children with heterogeneous sporadic epilepsies without etiologic diagnoses.

Methods

We performed WES (mean coverage approximately 40×) on 10 trios comprised of unaffected parents and a child with sporadic epilepsy characterized by difficult-to-control seizures and some combination of developmental delay, epileptic encephalopathy, autistic features, cognitive impairment, or motor deficits. Sequence processing and variant calling were performed using standard bioinformatics tools. A custom filtering system was used to prioritize de novo variants of possible functional significance for validation by Sanger sequencing.

Key Findings

In 9 of 10 probands, we identified one or more de novo variants predicted to alter protein function, for a total of 15. Four probands had de novo mutations in genes previously shown to harbor heterozygous mutations in patients with severe, early onset epilepsies (two inSCN1A, and one each in CDKL5 and EEF1A2). In three children, the de novo variants were in genes with functional roles that are plausibly relevant to epilepsy (KCNH5, CLCN4, and ARHGEF15). The variant in KCNH5 alters one of the highly conserved arginine residues of the voltage sensor of the encoded voltage-gated potassium channel. In vitro analyses using cell-based assays revealed that the CLCN4mutation greatly impaired ion transport by the ClC-4 2Cl⁻/H⁺-exchanger and that the mutation in ARHGEF15 reduced GEF exchange activity of the gene product, Ephexin5, by about 50%. Of interest, these seven probands all presented with seizures within the first 6 months of life, and six of these have intractable seizures.

Significance

The finding that 7 of 10 children carried de novo mutations in genes of known or plausible clinical significance to neuronal excitability suggests that WES will be of use for the molecular genetic diagnosis of sporadic epilepsies in children, especially when seizures are of early onset and difficult to control.

Genes May Explain Why Some Don't Respond To Rubella Vaccine

Genome-Wide Characterization of Transcriptional Patterns in High and Low Antibody Responders to Rubella Vaccination PlosOne 

A disease-associated PTPN22 variant promotes systemic autoimmunity in murine models.

Multiple autoimmune diseases, including type 1 diabetes, rheumatoid arthritis, Graves disease, and systemic lupus erythematosus, are associated with an allelic variant of protein tyrosine phosphatase nonreceptor 22 (PTPN22), which encodes the protein LYP. To model the human disease-linked variant LYP-R620W, we generated knockin mice expressing the analogous mutation, R619W, in the murine ortholog PEST domain phosphatase (PEP). In contrast with a previous report, we found that this variant exhibits normal protein stability, but significantly alters lymphocyte function. Aged knockin mice exhibited effector T cell expansion and transitional, germinal center, and age-related B cell expansion as well as the development of autoantibodies and systemic autoimmunity. Further, PEP-R619W affected B cell selection and B lineage-restricted variant expression and was sufficient to promote autoimmunity. Consistent with these features, PEP-R619W lymphocytes were hyperresponsive to antigen-receptor engagement with a distinct profile of tyrosine-phosphorylated substrates. Thus, PEP-R619W uniquely modulates T and B cell homeostasis, leading to a loss in tolerance and autoimmunity.

Cross-pollination of research findings, although uncommon, may accelerate discovery of human disease genes.

BACKGROUND:

Technological leaps in genome sequencing have resulted in a surge in discovery of human disease genes. These discoveries have led to increased clarity on the molecular pathology of disease and have also demonstrated considerable overlap in the genetic roots of human diseases. In light of this large genetic overlap, we tested whether cross-disease research approaches lead to faster, more impactful discoveries.

METHODS:

We leveraged several gene-disease association databases to calculate a Mutual Citation Score (MCS) for 10,853 pairs of genetically related diseases to measure the frequency of cross-citation between research fields. To assess the importance of cooperative research, we computed an Individual Disease Cooperation Score (ICS) and the average publication rate for each disease.

RESULTS:

For all disease pairs with one gene in common, we found that the degree of genetic overlap was a poor predictor of cooperation (r(2)=0.3198) and that the vast majority of disease pairs (89.56%) never cited previous discoveries of the same gene in a different disease, irrespective of the level of genetic similarity between the diseases. A fraction (0.25%) of the pairs demonstrated cross-citation in greater than 5% of their published genetic discoveries and 0.037% cross-referenced discoveries more than 10% of the time. We found strong positive correlations between ICS and publication rate (r(2)=0.7931), and an even stronger correlation between the publication rate and the number of cross-referenced diseases (r(2)=0.8585). These results suggested that cross-disease research may have the potential to yield novel discoveries at a faster pace than singular disease research.

CONCLUSIONS:

Our findings suggest that the frequency of cross-disease study is low despite the high level of genetic similarity among many human diseases, and that collaborative methods may accelerate and increase the impact of new genetic discoveries. Until we have a better understanding of the taxonomy of human diseases, cross-disease research approaches should become the rule rather than the exception.

Why does smallpox vaccine shield some, not others? It's in the genes, study finds

"How well people are protected by the smallpox vaccine depends on more than the quality of the vaccination: individual genes can alter their response, Mayo Clinic research shows. The findings, gathered using sophisticated genomic screening, appear in today's online issue of the journal Genes and Immunity."

First Mutations Leading To Leukemia Identified

MNT "The first mutations leading to leukemia in the mother's womb have been identified, according to researchers who sequenced the entire genomes of identical twins with the disease."

The genomes of four tapeworm species reveal adaptations to parasitism : Nature :

"Tapeworms (Cestoda) cause neglected diseases that can be fatal and are difficult to treat, owing to inefficient drugs. Here we present an analysis of tapeworm genome sequences using the human-infective species Echinococcus multilocularis, E. granulosus, Taenia solium and the laboratory model Hymenolepis microstoma as examples. The 115- to 141-megabase genomes offer insights into the evolution of parasitism. Synteny is maintained with distantly related blood flukes but we find extreme losses of genes and pathways that are ubiquitous in other animals, including 34 homeobox families and several determinants of stem cell fate. Tapeworms have specialized detoxification pathways, metabolism that is finely tuned to rely on nutrients scavenged from their hosts, and species-specific expansions of non-canonical heat shock proteins and families of known antigens. We identify new potential drug targets, including some on which existing pharmaceuticals may act. The genomes provide a rich resource to underpin the development of urgently needed treatments and control."