438 research outputs found

    Low load for disruptive mutations in autism genes and their biased transmission

    Get PDF
    We previously computed that genes with de novo (DN) likely gene-disruptive (LGD) mutations in children with autism spectrum disorders (ASD) have high vulnerability: disruptive mutations in many of these genes, the vulnerable autism genes, will have a high likelihood of resulting in ASD. Because individuals with ASD have lower fecundity, such mutations in autism genes would be under strong negative selection pressure. An immediate prediction is that these genes will have a lower LGD load than typical genes in the human gene pool. We confirm this hypothesis in an explicit test by measuring the load of disruptive mutations in whole-exome sequence databases from two cohorts. We use information about mutational load to show that lower and higher intelligence quotients (IQ) affected individuals can be distinguished by the mutational load in their respective gene targets, as well as to help prioritize gene targets by their likelihood of being autism genes. Moreover, we demonstrate that transmission of rare disruptions in genes with a lower LGD load occurs more often to affected offspring; we show transmission originates most often from the mother, and transmission of such variants is seen more often in offspring with lower IQ. A surprising proportion of transmission of these rare events comes from genes expressed in the embryonic brain that show sharply reduced expression shortly after birth

    Neurodevelopmental disorders: From genetics to functional pathways

    Get PDF
    Neurodevelopmental disorders (NDDs) are a class of disorders affecting brain development and function and are characterized by wide genetic and clinical variability. In this review, we discuss the multiple factors that influence the clinical presentation of NDDs, with particular attention to gene vulnerability, mutational load, and the two-hit model. Despite the complex architecture of mutational events associated with NDDs, the various proteins involved appear to converge on common pathways, such as synaptic plasticity/function, chromatin remodelers and the mammalian target of rapamycin (mTOR) pathway. A thorough understanding of the mechanisms behind these pathways will hopefully lead to the identification of candidates that could be targeted for treatment approaches

    Damaging de novo mutations diminish motor skills in children on the autism spectrum

    Get PDF
    In individuals with autism spectrum disorder (ASD), de novo mutations have previously been shown to be significantly correlated with lower IQ but not with the core characteristics of ASD: deficits in social communication and interaction and restricted interests and repetitive patterns of behavior. We extend these findings by demonstrating in the Simons Simplex Collection that damaging de novo mutations in ASD individuals are also significantly and convincingly correlated with measures of impaired motor skills. This correlation is not explained by a correlation between IQ and motor skills. We find that IQ and motor skills are distinctly associated with damaging mutations and, in particular, that motor skills are a more sensitive indicator of mutational severity than is IQ, as judged by mutational type and target gene. We use this finding to propose a combined classification of phenotypic severity: mild (little impairment of either), moderate (impairment mainly to motor skills), and severe (impairment of both IQ and motor skills)

    Essential Genes And Their Role In Autism Spectrum Disorder

    Get PDF
    Essential genes (EGs) play central roles in fundamental cellular processes and are required for the survival of an organism. EGs are enriched for human disease genes and are under strong purifying selection. This intolerance to deleterious mutations, commonly observed haploinsufficiency and the importance of EGs in pre- and postnatal development suggests a possible cumulative effect of deleterious variants in EGs on complex neurodevelopmental disorders. Autism spectrum disorder (ASD) is a heterogeneous, highly heritable neurodevelopmental syndrome characterized by impaired social interaction, communication and repetitive behavior. More and more genetic evidence points to a polygenic model of ASD and it is estimated that hundreds of genes contribute to ASD. The central question addressed in this dissertation is whether genes with a strong effect on survival and fitness (i.e. EGs) play a specific role in ASD risk. I compiled a comprehensive catalog of 3,915 mammalian EGs by combining human orthologs of lethal genes in knockout mice and genes responsible for cell-based essentiality. With an updated set of EGs, I characterized the genetic and functional properties of EGs and demonstrated the association between EGs and human diseases. Next I provided evidence for a stronger contribution of EGs to ASD risk, compared to non-essential genes (NEGs). By examining the exonic de novo and inherited variants from 1,781 ASD quartet families, I demonstrated a significantly higher burden of damaging mutations in EGs in ASD probands compared to their non-ASD siblings. Analysis of EGs in the developing brain identified clusters of co-expressed EGs implicated in ASD, among which I proposed a priority list of 29 EGs with potential ASD risk as targets for future functional and behavioral studies. Finally, I developed the essentiality burden score (EBS), which captures the burden of rare mutations in EGs as a novel polygenic predictor of individual ASD risk and a useful addition to the current tools for understanding the polygenic architecture of ASD. Overall, I show that large-scale studies of gene function in model organisms and human cell lines provide a powerful approach for prioritization of genes and pathogenic variants identified by sequencing studies of complex human disease

    Intracellular Pathways Associated with the Etiology of Autism

    Get PDF
    This chapter explores the relationship between the genes and proteins of the Akt and MAPK pathways and autism. This chapter presents the biology of these two pathways, their genes and cascading proteins, and then, it looks at the research that has connected these molecules to autism. Finally, it imparts current and future therapeutic modalities that might exploit abnormalities in these genes and proteins, change them and ultimately alter aberrant autistic behaviors

    Rare variants in the genetic background modulate cognitive and developmental phenotypes in individuals carrying disease-associated variants.

    Get PDF
    To assess the contribution of rare variants in the genetic background toward variability of neurodevelopmental phenotypes in individuals with rare copy-number variants (CNVs) and gene-disruptive variants. We analyzed quantitative clinical information, exome sequencing, and microarray data from 757 probands and 233 parents and siblings who carry disease-associated variants. The number of rare likely deleterious variants in functionally intolerant genes ("other hits") correlated with expression of neurodevelopmental phenotypes in probands with 16p12.1 deletion (n=23, p=0.004) and in autism probands carrying gene-disruptive variants (n=184, p=0.03) compared with their carrier family members. Probands with 16p12.1 deletion and a strong family history presented more severe clinical features (p=0.04) and higher burden of other hits compared with those with mild/no family history (p=0.001). The number of other hits also correlated with severity of cognitive impairment in probands carrying pathogenic CNVs (n=53) or de novo pathogenic variants in disease genes (n=290), and negatively correlated with head size among 80 probands with 16p11.2 deletion. These co-occurring hits involved known disease-associated genes such as SETD5, AUTS2, and NRXN1, and were enriched for cellular and developmental processes. Accurate genetic diagnosis of complex disorders will require complete evaluation of the genetic background even after a candidate disease-associated variant is identified

    Computational insights into the generation of chromosomal copy number changes

    Get PDF
    Deviations from a diploid configuration of the human genome, spanning single genes or entire chromosomes, can have wide-ranging impacts on the variation of human phenotypes, including Mendelian and complex forms of diseases. These chromosomal alterations — such as duplications, deletions or copy-neutral loss-of-heterozygosity — are thus important forms of genetic variation for phenotyping populations of individuals as well as populations of cells. Indeed, copy number variants (CNVs) serve as hallmarks of critical changes in the development of particular diseases such as cancer and thus may be used as biomarkers. These CNVs may be either inherited (transmitted by germ cells, originating in meiosis; “germline”) or acquired (originating in mitosis; “somatic mosaicism”). The complex structure and the diverse mechanisms generating CNVs have been studied molecularly, but this has generally not been attempted using population data. This dissertation seeks to provide insights into CNV diversity in two complementary settings: 1) the genesis of germline copy number duplications, and 2) the diversity of acquired CNVs within distinct tumor tissues. First, we develop a novel method to disentangle the haplotype (the specific alleles on an inherited chromosome) composition of de novo germline duplications to characterize the “grandparental origin” of the extra piece of a chromosome. Using large family-based genome-wide association study data, we report the ratio of “bi-allelic” duplications, from inter-chromatid non-allelic homologous recombination (NAHR), to “tri-allelic” duplications, from inter-chromosomal NAHR, as 1.07:1. In addition, our method reveals a third configuration, consisting of both tri-allelic and bi-allelic duplications, which we hypothesize arose from spontaneous inter-chromosomal and inter-chromatid NAHR. The rate of these complex duplications among all the de novo duplications is 6%. Second, we assess tumor heterogeneity of biphasic uterine carcinosarcoma (UCS) from 10 patients by analyzing the data of component-specific tumor samples (carcinomatous, sarcomatous, and normal uterine tissues), generated from multiple platforms (SNP array, DNA target sequencing, and whole transcriptome sequencing). We augment the quantification of tumor heterogeneity by considering the haplotype information within the somatic copy number alterations for each sample to more precisely annotate recurrent copy number changes. Our results imply that the carcinomatous and the sarcomatous components in UCS originate from the same clone and the heterogeneity reflects relatively advanced stages. Our work confirms that profiling of carcinomas and sarcomas separately may offer clinical utility. Overall, this dissertation shows the potential utility of incorporating haplotype information in particular settings in population science and cancer biology

    Autism Spectrum Disorders

    Get PDF
    Estimated prevalence rates of autism spectrum disorders (ASDs) have increased at an alarming rate over the past decade; current estimates stand as high as 1 in 110 persons in the population with a higher ratio of affected males to females. In addition to their emotional impact on the affected persons and their family members (in fact, the latter are often unrecognized unaffected “patients†themselves), the economic and social impacts of ASDs on society are staggering. Persons with ASDs will need interdisciplinary approaches to complex treatment and life planning, including, but not limited to, special education, speech and language therapy, vocational skills training and rehabilitation, social skills training and cognitive remediation, in addition to pharmacotherapy. The current book highlights some of the recent research on nosology, etiology, and pathophysiology. Additionally, the book touches on the implications of new research for treatment and genetic counseling. Importantly, because the field is advancing rapidly, no book can be considered the final word or finished product; thus, the availability of open access rapid publication is a mechanism that will help to assure that readers remain current and up-to-date
    corecore