Research by Topic: Genomics

Podcast: Where the wild new genetic hot spots are

Published May 7, 2018

On this week’s podcast, three genetics papers featuring three ASF fellows! All three deal with using whole genome sequencing (WGS) to study non-coding regulatory regions that may be associated with autism. These regions of DNA do not code for proteins but regulate the regions that do. Mutations in the non-coding regulatory regions that regulate the […]

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Spring 2018 Autism BrainNet newsletter available now

Published April 27, 2018

The Spring 2018 issue of the Autism BrainNet newsletter is out now! Among other news, it highlights recent research using its donated brain tissue resources in autism genetics and neuroanatomy, the science campaign Brain Awareness Week, and outreach efforts through Autism Speaks walks around the country. You can view and read this issue here.

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A Novel Approach of Homozygous Haplotype Sharing Identifies Candidate Genes in Autism Spectrum Disorder

Published April 8, 2015 in Human Genetics

A large scale analysis identifies candidate genes which may contain low-frequency recessive variations contributing to ASD

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Neuronal Connectivity as a Convergent Target of Gene-environment Interactions that Confer Risk for Autism Spectrum Disorders

Published March 8, 2015 in Neurotoxicology and Teratology

This review briefly summarizes the evidence implicating dysfunctional signaling via Ca2 +-dependent mechanisms, extracellular signal-regulated kinases (ERK)/phosphatidylinositol-3-kinases (PI3K) and neuroliginneurexinSHANK as convergent molecular mechanisms in ASD, and then discusses examples of environmental chemicals for which there is emerging evidence of their potential to interfere with normal neuronal connectivity via perturbation of these signaling pathways.

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Whole-Genome Sequencing Reveals New Types of Autism Risk

Published October 20, 2014 in Simons Foundation Autism Research Initiative

Much of the genetic risk for autism may reside in regulatory regions of the genome, hidden from traditional methods of sequencing analysis. That’s the upshot of preliminary results from three studies presented at the 2014 American Society of Human Genetics Annual Meeting in San Diego. Together, the findings from these new studies show the promise of looking for autism risk in unusual places.

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Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism

Published November 21, 2013 in Cell

"As techniques for studying the human genome have advanced, an increasing number of genes are being associated with ASD; it is important to find the connections between these ASD-linked genes in order to understand how they may contribute to ASD. A new resource called the BrainSpan1 atlas provides researchers with three dimensional maps showing when […]

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Genome-Editing Tools Compose New Models of Autism

Published September 5, 2013 in Simons Foundation Autism Research Institute

New synthetic biology tools have allowed for great advances in genetic testing of many mutations. This technology known as CRISPR (clustered regularly interspaced short palindromic repeats) allows researchers to create molecular scissors that cut and paste essentially any mutation into the genome of any cell, including a human stem cell.

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FMR1 Knockout Mice Observed to have Hyperactive Neural Firing Rates

Published June 2, 2013 in Nature: Neuroscience

Researchers at UCLA observed hyperactive firing rates in the brains of FMR1 knockout mice; mice engineered to have symptoms similar to those in ASD and Fragile X syndrome.

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Methylomic Analysis of Monozygotic Twins Discordant for Autism Spectrum Disorder and Related Behavioural Traits

Published April 23, 2013 in Molecular Psychiatry

This study suggests environmentally driven changes to the epigenome may contribute to the development of ASD and ASD-related behaviors. The study, which involved identical twins who were discordant for ASD and related traits, is the first large-scale examination of the role of genome-wide DNA methylation in ASD.

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Global Increases in Both Common and Rare Copy Number Load Associated with Autism

Published March 27, 2013 in Human Molecular Genetics

Penn State researchers link autism to increased genetic change in “hotspots”, regions of the genome that are highly susceptible to mutation.

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Mother’s Drive Helps Research on Rare Autism-linked Mutation

Published March 14, 2013 in SFARI

A mother with two sons with autism helps advance research on neuroligin-4 mutations.

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Published February 21, 2013 in SFARI

SFARI Gene is an integrated resource for the autism research community. It is a publicly available, curated, web-based, searchable database for autism research. This resource is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The genetic information includes data from linkage and association studies, cytogenetic abnormalities, and specific mutations associated with ASD.

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Sex Differences in Autism Spectrum Disorders

Published February 13, 2013 in Current Opinion in Neurology

A review of current research shows that ASD affects females less frequently than males and suggests this difference may be due to several sex-differential genetic and hormonal factors.

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Stem Cell Research Focusing on Autisms Genetic Mysteries Earns $2.125 Million Grant at Robert Wood Johnson Medical School

Published February 12, 2013 in Newswise

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Sequencing Studies Implicate Inherited Mutations in Autism

Published January 23, 2013 in SFARI

SFARI: Rare, inherited mutations contribute to a significant proportion of autism cases according to two new studies published in Neuron.

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Identification of Rare Recurrent Copy Number Variants in High-Risk Autism Families and Their Prevalence in a Large ASD Population

Published January 14, 2013 in PLOS One

Researchers discover 25 new autism-linked copy number variants.

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Autism Genetic Testing: A Qualitative Study of Awareness, Attitudes, and Experiences among Parents of Children with Autism Spectrum Disorders.

Published January 3, 2013 in Genetics in Medicine

This study provides insight into awareness, perspectives and experiences of ASD genetic testing among parents of autistic children.

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Whole-Genome Sequencing in Autism Identifies Hot Spots for De Novo Germline Mutation

Published December 21, 2012 in Cell

UCSD researchers suggest genes linked to autism have higher mutation rates than other genes.

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The Autism Sequencing Consortium: Large-Scale, High-Throughput Sequencing in Autism Spectrum Disorders

Published December 20, 2012 in Neuron

Dr. Joseph Buxbaum and team discuss the current state of ASD gene discovery and the benefits of a genomic technology called high-throughput sequencing.

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Genomic Technology Reveals Hundreds of Autism Gene Mutations

Published December 20, 2012 in Laboratory Equipment

ASF SAB member Dr. Joe Buxbaum on his new gene discoveries using high-throughput sequencing: “By identifying the many genetic roots of this disorder, we can better understand its biology, which in turn will allow us to develop more tailored treatments for individuals. It is a transformative time for genetic research in autism.”

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Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders

Published November 15, 2012 in Science

De novo mutations in six genes may contribute to 1% of simplex ASD cases.

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Postmortem Brain Analysis Points to Autism Candidate Genes

Published October 16, 2012 in SFARI

Unpublished data presented at the 2012 Society for Neuroscience annual meeting show at least 30 genes show altered expression in brain tissue of people with autism. The ongoing study aims to include more samples than previous postmortem studies, and includes samples lost in Harvards freezer malfunction.

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Using Large Clinical Data Sets to Infer Pathogenicity for Rare Copy Number Variants in Autism Cohorts

Published October 9, 2012 in Molecular Psychiatry

Copy number variants (CNVs) have a major role in the etiology of autism spectrum disorders (ASD), and several of these have reached statistical significance in casecontrol analyses. Nevertheless, current ASD cohorts are not large enough to detect very rare CNVs that may be causative or contributory (that is, risk alleles).

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Predicting the Diagnosis of Autism Spectrum Disorder Using Gene Pathway Analysis

Published September 11, 2012 in Molecular Psychiatry

“The current investigation interrogated single-nucleotide polymorphisms (SNPs) of individuals with ASD from the Autism Genetic Resource Exchange (AGRE) database. SNPs were mapped to Kyoto Encyclopedia of Genes and Genomes (KEGG)-derived pathways to identify affected cellular processes and develop a diagnostic test. “

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An Integrated Encyclopedia of DNA Elements in the Human Genome

Published September 6, 2012 in Nature

“The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.”

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Levels of Select PCB and PBDE Congeners in Human Postmortem Brain Reveal Possible Environmental Involvement in 15q11-q13 Duplication Autism Spectrum Disorder.

Published August 29, 2012 in Environmental and Molecular Genetics

These results demonstrate a novel paradigm by which specific POPs may predispose to genetic copy number variation of 15q11-q13.

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Rate of De Novo Mutations and the Importance of Fathers Age to Disease Risk

Published August 23, 2012 in Nature

The diversity in mutation rate of SNP’s is dominated by the age of the father at conception of the child. The effect is an increase of about two mutations per year.

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UCLA Study Uncovers New Tools for Targeting Genes Linked to Autism

Published June 21, 2012 in

UCLA researchers compare the genes of children with autism and their typically-developing siblings to better understand the role of gene expression in the development of autism.

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Researchers at MIT Use Zebrafish to Better Understand the Genetics of Autism

Published June 19, 2012 in

Researchers at MIT use zebrafish to better understand the genetics of autism.

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Structure, Function and Diversity of The Healthy Human Microbiome

Published June 13, 2012 in Nature

“Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.”

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A Common X-linked Inborn Error of Carnitine Biosynthesis May be a Risk Factor for Nondysmorphic Autism.

Published May 22, 2012 in Proceedings of the National Academy of Sciences of the United States of America

These data suggest that dysregulation of carnitine metabolism may be important in nondysmorphic autism; that abnormalities of carnitine intake, loss, transport, or synthesis may be important in a larger fraction of nondysmorphic autism cases; and that the carnitine pathway may provide a novel target for therapy or prevention of autism.

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The Genetic Variability and Commonality of Neurodevelopmental Disease

Published May 15, 2012 in American Journal of Medical Genetics; Part C, Seminars in Medical Genetics

Copy Number Variations suggest that the distinction between milder neuropsychiatric conditions from those of severe developmental impairment may be a consequence of increased mutational burden affecting more genes

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Negative Allosteric Modulation of the mGluR5 Receptor Reduces Repetitive Behaviors and Rescues Social Deficits in Mouse Models of Autism

Published April 25, 2012 in Science Translational Medicine

Using a mouse model with behaviors relevant to the three diagnostic behavioral symptoms of autism, researchers used a genetic approach to reduce repetitive behaviors and partially reverse the striking lack of sociability in these mice.

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Sporadic Autism Exomes Reveal a Highly Interconnected Protein Network of De Novo Mutations

Published April 4, 2012 in Nature

Researchers demonstrate that de-novo point mutations are overwhelmingly paternal in origin (4:1 bias) and positively correlated with paternal age, consistent with the modest increased risk for children of older fathers to develop ASD.

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Patterns and Rates of Exonic De Novo Mutations in Autism Spectrum Disorders

Published April 4, 2012 in Nature

Results support polygenic models in which spontaneous coding mutations in any of a large number of genes increases risk by 5 to 20-fold. Despite the challenge posed by such models, results from de novo events and a large parallel case-control study provide strong evidence in favor of CHD8 and KATNAL2 as genuine autism risk factors.

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CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics.

Published March 16, 2012 in Cell

A proportion of risk for schizophrenia, bipolar disorder, and autism can be explained by rare mutations. Alleles can have specific effects on behavioral and neuroanatomical traits; however, expressivity is variable, particularly for neuropsychiatric phenotypes

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Synaptic Mutations Increase The Risk Of Autism Spectrum Disorders

Published February 13, 2012 in Medical News Today

A new study published in PLoS Genetics uses a combination of genetic and neurobiological approaches to confirm that synaptic mutations increase the risk of autism spectrum disorders (ASDs) and underlines the effect for modifier genes in these disorders.

Synaptic Mutations Increase The Risk Of Autism Spectrum Disorders

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Scientists Link Evolved, Mutated Gene Module to Syndromic Autism

Published January 26, 2012 in Science Daily

A team led by researchers at the University of California, San Diego School of Medicine reports that newly discovered mutations in an evolved assembly of genes cause Joubert syndrome, a form of syndromic autism.

Scientists Link Evolved, Mutated Gene Module to Syndromic Autism

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NIMHs Top 10 Research Advances of 2011

Published December 23, 2011 in NIMH

Director of the NIMH Dr. Tom Insel shares the NIMH’s Top 10 Research Advances for 2011.

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TBL1X Gene Involved In Autism Spectrum Disorder

Published November 6, 2011 in Medical News Today

TBL1X Gene Involved In Autism Spectrum Disorder: Dr. Eden Martin from the Hussman Institute explains, “The SNP in TBL1X is associated with an increase in risk for ASD of about 15%.

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Autism Spectrum Disorder Linked to Genetic Synaptic Behaviors

Published April 21, 2011 in Medical News Today

It seems that the place where your brain transfers electricity between synapses and how your genes determine how these processes function, are tied to autism in one way or another. There can be genetically driven disturbances in this process that lead to varying levels of autism according to a new study of DNA from approximately 1,000 autistic children and their kin.

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Gene Linked to Severity of Autism’s Social Dysfunction Identified

Published April 7, 2011 in Science Daily

With the help of two sets of brothers with autism, Johns Hopkins scientists have identified a gene associated with autism that appears to be linked very specifically to the severity of social interaction deficits. The gene, GRIP1 (glutamate receptor interacting protein 1), is a blueprint for a traffic-directing protein at synapses — those specialized contact points between brain cells across which chemical signals flow.

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A Genotype Resource for Postmortem Brain Samples from the Autism Tissue Program

Published April 1, 2011 in Autism Res, Wintle et al.

The Autism Tissue Program (ATP) is a postmortem brain tissue program created by the National Alliance for Autism Research (NAAR) for the purpose of supplying research scientists with neurological tissue samples of deceased Autistic individuals. Scientists, however, are not supplied with tissue samples from any other parts of the deceased individual, leading to frustration over […]

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Gene Variants in Autism Linked to Brain Development

Published March 7, 2011 in Science Daily

New research on the genomics of autism confirms that the genetic roots of the disorder are highly complicated, but that common biological themes underlie this complexity. In the current study, researchers have implicated several new candidate genes and genomic variants as contributors to autism, and conclude that many more remain to be discovered. While the gene alterations are individually very rare, they mostly appear to disrupt genes that play important functional roles in brain development and nerve signaling.

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Gene Variants in Autism Linked to Brain Development

Published March 1, 2011 in Journal of Molecular Psychiatry, Gai et al.

This research on the genomics of autism confirms that the genetic roots of the disorder are highly complicated, but that common biological themes underlie this complexity. In the current study, researchers have implicated several new candidate genes and genomic variants as contributors to autism, and conclude that many more remain to be discovered. While the […]

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New Genetic Risk Factor for Both Autism and Schizophrenia

Published November 4, 2010 in Science Daily

Researchers have uncovered a prominent genetic risk factor for autism spectrum disorders and schizophrenia is a small genomic deletion. Remarkably, they found the same deletion on chromosome 17 in 24 separate patients. This CNV was absent in 52,448 controls, making the finding statistically significant. Someone with this deletion is 13.58 times more likely to develop ASD or schizophrenia than is someone lacking this CNV. This gene mutation is also known to cause kidney disease (renal cysts and diabetes syndrome, RCAD).

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Gene Scan Finds Link Across Array of Childhood Brain Disorder

Published August 22, 2010 in EurekAlert

Mutations in a single gene can cause several types of developmental brain abnormalities that experts have traditionally considered different disorders. With support from the National Institutes of Health, researchers found those mutations through whole exome sequencing ? a new gene scanning technology that cuts the cost and time of searching for rare mutations. Whole exome sequencing can be applied to dozens of other rare genetic disorders where the culprit genes have so far evaded discovery. Such information can help couples assess the risk of passing on genetic disorders to their children. It can also offer insights into disease mechanisms and treatments.

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Developmental Problems, Some Exist in the Genes

Published August 18, 2010 in Medical News Today

DNA for each individual contains variants that are more or less common in the overall population.Some gene variations are actually genetic deletions, where sections of DNA ‘code’ are missing entirely. These variants are likely to have important effects on gene function and, therefore, likely to contribute to diseases associated with that gene. But what happens when multiple genes are disrupted in a single family?

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Disturbances in Certain Genes Play a Role in Autism

Published August 17, 2010 in Medical News Today

Together with colleagues from an international research group, autism researcher Christopher Gillberg of the University of Gothenburg, Sweden, has found in a new study that autism can be partially explained by abnormalities in certain genes. The group’s results could, in the long run, pave the way for more appropriate treatments for autism.In the article the group reveals that a survey of 1,000 individuals with autism and 1,300 without showed that Copy Number Variants (CNVs) sub-microscopic abnormalities in the chromosomes are heavily over-represented in autistic people.

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Functional Impact of Global Rare Copy Number Variation in Autism Spectrum Disorders

Published July 1, 2010 in Nature, Pinto et al

A genome-wide analysis reveals that people with ASDs carry a higher load of rare copy-number variants — segments of DNA for which the copy number differs between individual genomes — which are either inherited or arise de novo. The results implicate several novel genes as ASD candidates and point to the importance of cellular proliferation, […]

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New Autism Susceptibilty Genes Identified

Published June 10, 2010 in Medical News Today

Mount Sinai researchers and the Autism Genome Project Consortium (AGP) announced that they have identified new autism susceptibility genes that may lead to the development of new treatment approaches. These genes, which include SHANK2, SYNGAP1, DLGAP2 and the X-linked DDX53-PTCHD1 locus, primarily belong to synapse-related pathways, while others are involved in cellular proliferation, projection and motility, and intracellular signaling

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Functional impact of global rare copy number variation in autism spectrum disorders

Published June 7, 2010 in Nature

This study analysed the genome-wide characteristics of rare (

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Schizophrenia Shares Genetic Links with Autism, Genome Study Shows

Published May 10, 2010 in Scientific American

Schizophrenia involves some of the same genetic variations as autism and attention deficit disorders, a new whole-genome study has confirmed. In an effort to assess some of the common genetic variations that might underpin this fairly common but thorny mental illness, researchers sequenced DNA from 1,735 adults with schizophrenia and 3,485 healthy adults. Across the patients that had the disease, the researchers found many frequent variations related to copying or deleting genes, known as copy-number variations.

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Brain Development Steered By Newly Discovered RNA

Published April 16, 2010 in Medical News Today

New research from the lab of Michael Greenberg, Nathan Marsh Pusey professor and chair of neurobiology at HMS, in collaboration with bioinformatics specialist and neuroscientist Gabriel Kreiman, assistant professor of ophthalmology at Children’s Hospital, Boston, has found that a particular set of RNA molecules widely considered to be no more than a genomic oddity are actually major players in brain development – and are essential for regulating the process by which neurons absorb the outside world into their genetic machinery.

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Better Genetic Test for Autism?

Published March 15, 2010 in Science Daily

A large study from Children’s Hospital Boston and the Boston-based Autism Consortium finds that a genetic test that samples the entire genome, known as chromosomal microarray analysis, has about three times the detection rate for genetic changes related to autism spectrum disorders (ASDs) than standard tests.

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Link Between Genetic Defect And Brain Changes In Schizophrenia Demonstrated

Published October 17, 2009 in Science Daily

Researchers at the University of North Carolina at Chapel Hill School of Medicine have found that the 22q11 gene deletion — a mutation that confers the highest known genetic risk for schizophrenia — is associated with changes in the development of the brain that ultimately affect how its circuit elements are assembled.The researchers would now like to figure out how these alterations in the circuitry of the brain affect the behavior of the mouse. They also hope that understanding the “mis-wiring” of the brain in a genetic animal model of schizophrenia would help them understand the causes of the disease in the general population

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Genome Wide Study of Autism Published in Nature

Published October 7, 2009 in EurekAlert

In one of the first studies of its kind, an international team of researchers has uncovered a single-letter change in the genetic code that is associated with autism. The finding, published in the October 8 issue of the journal Nature, implicates a neuronal gene not previously tied to the disorder and more broadly, underscores a role for common DNA variation. In addition, the new research highlights two other regions of the genome, which are likely to contain rare genetic differences that may also influence autism risk.

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Genome-Wide Analyses of Exonic Copy Number Variants in a Family-Based Study Point to Novel Autism Susceptibility Genes

Published June 1, 2009 in PLOS Genetics, Bucan M, Abrahams BS, Wang K, Glessner JT, Herman EI, et al.

The study identified 27 different genetic regions where rare copy number variations – missing or extra copies of DNA segments – were found in the genes of children with autism spectrum disorders, but not in the healthy controls. The researchers, including geneticists from the University of Pennsylvania School of Medicine and The Children's Hospital of […]

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A Common Genetic variant in the neurexin superfamily member CNTNAP2 increases Familial Risk of Autism

Published December 1, 2008 in American Journal of Human Genetics, Arking, Cutler, et al

Autism is a childhood neuropsychiatric disorder that, despite exhibiting high heritability, has largely eluded efforts to identify specific genetic variants underlying its etiology. We performed a two-stage genetic study in which genome-wide linkage and family-based association mapping was followed up by association and replication studies in an independent sample. We identified a common polymorphism in […]

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Strong association of de novo copy number mutations with sporadic schizophrenia.

Published May 30, 2008 in Nature Genetics, Xu, Roose, et al

Schizophrenia is an etiologically heterogeneous psychiatric disease, which exists in familial and nonfamilial (sporadic) forms. Here, we examine the possibility that rare de novo copy number (CN) mutations with relatively high penetrance contribute to the genetic component of schizophrenia. We carried out a whole-genome scan and implemented a number of steps for finding and confirming […]

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Structural Variation of Chromosomes in Autism Spectrum Disorder

Published February 28, 2008 in American Journal of Human Genetics, Marshall, Noor, et al

Structural variation (copy number variation [CNV] including deletion and duplication, translocation, inversion) of chromosomes has been identified in some individuals with autism spectrum disorder (ASD), but the full etiologic role is unknown. We performed genome-wide assessment for structural abnormalities in 427 unrelated ASD cases via single-nucleotide polymorphism microarrays and karyotyping. With microarrays, we discovered 277 […]

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Recurrent 16p11.2 Microdeletions in Autism

Published February 15, 2008 in Human Molecular Genetics, Kumar, KaraMohamed, et al

Autism is a childhood neurodevelopmental disorder with a strong genetic component, yet the identification of autism susceptibility loci remains elusive. We investigated 180 autism probands and 372 control subjects by array comparative genomic hybridization (aCGH) using a 19K whole-genome tiling path bacterial artificial chromosome microarray to identify submicroscopic chromosomal rearrangements specific to autism. We discovered […]

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Association Between Microdeletion and Microduplication at 16p11.2 and Autism

Published January 9, 2008 in New England Journal of Medicine, Weiss, Shen, et al

We have identified a novel, recurrent microdeletion and a reciprocal microduplication that carry substantial susceptibility to autism and appear to account for approximately 1% of cases. We did not identify other regions with similar aggregations of large de novo mutations. Among the AGRE families, we observed five instances of a de novo deletion of 593 […]

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Autism: Maternally derived antibodies specific for fetal brain proteins

Published November 6, 2007 in Neurotoxicology, Braunschweig, Ashwood, et al

Autism is a profound disorder of neurodevelopment with poorly understood biological origins. A potential role for maternal autoantibodies in the etiology of some cases of autism has been proposed in previous studies To investigate this hypothesis, maternal plasma antibodies against human fetal and adult brain proteins were analyzed by western blot in 61 mothers of […]

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