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Research by Topic: Copy Number Variations
Copy number variations are known to play a role in autism spectrum disorders. In a novel approach to study CNVs that may be present in family members, scientists look at genes in multiple generations of families affected with or without ASD as well as other psychiatric disorders. In one family, a part of chromosome 11 jumped out as being important for autism and what is known as the broader autism phenotype. (This is when a person does not have a diagnosis but meets some of the criteria for ASD.) This region contains genes for mitochondrial function and detoxification, but was found in the only family where the specific mutation was passed on beyond just parent to child. This shows that the genetic risk factors are complex and not even the same within the same family.
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.
People with autism tend to carry mutations that duplicate or delete several genes at once, according to a large study published in the American Journal of Human Genetics. Previous studies have shown that people with autism have more large deletions or duplications of DNA, also known as copy number variations (CNVs), than controls do. The new study, the largest to look at CNVs in people with autism thus far, confirms this finding. It also found that in people with autism, the CNVs are more likely to affect genes linked to intellectual disability and fragile X syndrome.
A substantial proportion of risk for developing autism spectrum disorders (ASD) resides in genes that are part of specific, interconnected biological pathways, according to researchers from the Icahn School of Medicine at Mount Sinai, who conducted a broad study of almost 2,500 families in the United States and throughout the world. The study was published in The American Journal of Human Genetics. The researchers reported numerous copy number variations (CNVS) affecting genes, and found that these genes are part of similar cellular pathways involved in brain development, synapse function and chromatin regulation. Individuals with ASD carried more of these CNVs than individuals in the control group, and some of them were inherited while others were only present in offspring with ASD.
Carrying a duplication of the 22q11.2 chromosomal region may protect against schizophrenia, suggests a study published 12 November in Molecular Psychiatry. This is the first evidence of a genetic region that lowers the risk of a disorder rather than increases it. Deletion of this part of chromosome 22 is the strongest known risk factor for schizophrenia, and is also linked to autism, attention deficit hyperactivity disorder and anxiety in childhood. Various other copy number variations (CNVs), or stretches of a chromosome that are deleted or duplicated multiple times in the genome, have been linked to schizophrenia, autism and other neurological conditions. The new study is the first to pinpoint a CNV that lowers the risk of a disorder, however.
People who carry high-risk genetic variants for schizophrenia and autism have impairments reminiscent of disorders such as dyslexia, even when they do not yet have a mental illness, a new study has found. Researchers report that people with these copy number variants (CNVs) but no diagnosis of autism or a mental illness still show subtle brain changes and impairments in cognitive function. The findings offer a window into the brain changes that precede severe mental illness and hold promise for early intervention and even prevention, researchers say.
A new study using families from the Autism Genetic Resource Exchange (AGRE) finds that individuals with autism are 20% more likely to have copy-number variations of specific genes.
Methylomic Analysis of Monozygotic Twins Discordant for Autism Spectrum Disorder and Related Behavioural TraitsPublished 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.
Penn State researchers link autism to increased genetic change in “hotspots”, regions of the genome that are highly susceptible to mutation.
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.
Identification of Rare Recurrent Copy Number Variants in High-Risk Autism Families and Their Prevalence in a Large ASD PopulationPublished January 14, 2013 in PLOS One
Researchers discover 25 new autism-linked copy number variants.
UCSD researchers suggest genes linked to autism have higher mutation rates than other genes.
Abnormally high production of neuroligins, proteins involved in synapse formation, resulted in ASD symptoms in mice. Researchers reversed ASD symptoms by reducing neuroligin synthesis.
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.
Using Large Clinical Data Sets to Infer Pathogenicity for Rare Copy Number Variants in Autism CohortsPublished 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).
New genetic variants that increase susceptibility to autism are emerging at a rapid pace from scans for copy number variants (CNVs) deletions or duplications of DNA segments and next-generation sequencing. Given the profusion of data, it seems timely to assess the availability and usefulness of mouse models in which to study these genetic risk factors.
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.
In an important test of one of the first drugs to target core symptoms of autism, researchers at Mount Sinai School of Medicine are undertaking a pilot clinical trial to evaluate insulin-like growth factor (IGF-1) in children who have SHANK3 deficiency (also known as 22q13 Deletion Syndrome or Phelan-McDermid Syndrome), a known cause of autism spectrum disorder (ASD).
Vanderbilt scientists report that a disruption in serotonin transmission in the brain may be a contributing factor for autism spectrum disorder (ASD) and other behavioral conditions.
A bone-marrow transplant can treat a mouse version of Rett syndrome, a severe autism spectrum disorder that affects roughly 1 in 10,00020,000 girls born worldwide (boys with the disease typically die within a few weeks of birth).
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
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.
New Research Might Help Explain How a Gene Mutation Found in some Autistic Individuals Leads to Difficulties in Processing Auditory Cues and Paying Spatial Attention to Sound.Published February 2, 2012 in Science Daily
New research from Cold Spring Harbor Laboratory (CSHL) might help explain how a gene mutation found in some autistic individuals leads to difficulties in processing auditory cues and paying spatial attention to sound.
The anxiety and behavioral issues associated with excess MeCP2 protein result from overexpression of two genes (Crh [corticotropin-releasing hormone] and Oprm 1 [mu-opioid receptor MOR 1]), which may point the way to treating these problems in patients with too much of the protein, said Baylor College of Medicine scientists in a report that appears online in the journal Nature Genetics.
Director of the NIMH Dr. Tom Insel shares the NIMH’s Top 10 Research Advances for 2011.
Researchers debut the SHANK2 mouse and SHANK3 rat at the 2011 Society for Neuroscience annual meeting. SHANK2 belongs to the same family as SHANK3, a well-established autism candidate gene.
Evidence found for the genetic basis of autism: Models of autism show that gene copy number controlsPublished October 5, 2011 in Science Daily
Scientists at Cold Spring Harbor Laboratory (CSHL) have discovered that one of the most common genetic alterations in autism — deletion of a 27-gene cluster on chromosome 16 — causes autism-like features. By generating mouse models of autism using a technique known as chromosome engineering, CSHL Professor Alea Mills and colleagues provide the first functional evidence that inheriting fewer copies of these genes leads to features resembling those used to diagnose children with autism.
People with autism and attention deficit hyperactivity disorder (ADHD) share some of the same underlying genetic risk factors, according to a study published this month in Science Translational Medicine. This is one of the first studies to find risk variants that are common to both disorders.In searching for rare copy number variations (CNVs) deletions and duplications in genetic material in people with ADHD, the researchers found more than a dozen regions that include genes implicated in bipolar disorder, schizophrenia, intellectual disability and autism.
A study of the genetic causes of autism confirmed that spontaneous or de novo mutations are present in a substantial number of families with only one child on the spectrum. These de novo mutations are not inherited from parents' DNA, arising instead in their egg or sperm or very early in embryonic development. Researchers compared […]
Multiple Recurrent De Novo CNVs, including Duplications of the 7q11.23 Williams Syndrome Region, are Strongly Associated with AutismPublished May 1, 2011 in Pediatrics
A recent collaborative study identified six genetic mutations that are strongly associated with autism spectrum disorder, including an area of DNA that likely holds clues to understanding the nature of human social behavior. The researchers estimate that these mutations represent only a few of the hundreds of spontaneously arising variants that are likely to increase […]
Researchers Reveal 18 Novel Subtype-Dependent Genetic Variants for Autism Spectrum Disorders and Identify Potential Genetic Markers for Diagnostic ScreeningPublished April 28, 2011 in Science Daily
By dividing individuals with autism spectrum disorders (ASD) into four subtypes according to similarity of symptoms and reanalyzing existing genome-wide genetic data on these individuals vs. controls, researchers at the George Washington University School of Medicine and Health Sciences have identified 18 novel and highly significant genetic markers for ASD. In addition, ten of the variants were associated with more than one ASD subtype, providing partial replication of these genetic markers. This study thus identifies candidate genes for ASD and potential subtype-dependent genetic markers for diagnostic screening.
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.
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.
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 […]
Researchers from Mount Sinai School of Medicine have found that when one copy of the SHANK3 gene in mice is missing, nerve cells do not effectively communicate and do not show cellular properties associated with normal learning. This discovery may explain how mutations affecting SHANK3 may lead to autism spectrum disorders (ASDs). The research is currently published in Molecular Autism.
In 1999, Baylor College of Medicine researcher Dr. Huda Zoghbi and her colleagues identified mutations in the gene called MECP2 as the culprit in a devastating neurological disorder called Rett syndrome . In new research in mice published in the current issue of the journal Nature, Zoghbi and her colleagues demonstrate that the loss of the protein MeCP2 in a special group of inhibitory nerve cells in the brain reproduces nearly all Rett syndrome features.
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).
Researchers at UCLA have discovered how an autism-risk gene rewires the brain, which could pave the way for treatments aimed at rebalancing brain circuits during early development. Dr. Geschwind and team examined the variations in brain function and connectivity resulting from two forms of the CNTNAP2 gene – one form of the gene increases the risk of autism. The researchers suspected that CNTNAP2 might have an important impact on brain activity. They used fMRI (functional magnetic resonance imaging) to scan 32 children’s brains while they were performing tasks related to learning. Only 16 of them had autism.The imaging results confirmed their suspicions. All the children with the autism-risk gene showed a disjointed brain, regardless of their diagnosis. Their frontal lobe was over-connected to itself, while connection to the rest of the brain was poor, especially with the back of the brain. There was also a difference between how the left and right sides of the brain connected with each other, depending on which CNTNAP2 version the child carried.The authors believe their findings could help identify autism risk earlier, and eventually lead to interventions that could enhance connections between the frontal lobe and the left side of the brain.
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?
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.
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, […]
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
This study analysed the genome-wide characteristics of rare (
Using microarrays, the department of molecular human genetics in Heidelberg, Germany identified de novo copy number variations in the SHANK2 synaptic scaffolding gene in two unrelated individuals with autism-spectrum disorder (ASD) and mental retardation. DNA sequencing of SHANK2 in 396 individuals with ASD, 184 individuals with mental retardation and 659 unaffected individuals (controls) revealed additional […]
IntegraGen SA, a French biotechnology company dedicated to gene discovery, announced today the publication of the results of a collaborative study reporting the use of a combined analysis of multiple genetic variants in a genetic score to help identify individuals at high risk of developing autism.
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.
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.
TIME recognized New Research on Autism as #7 of its Top 10 Medical Breakthroughs of 2009.
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.
Genome-Wide Analyses of Exonic Copy Number Variants in a Family-Based Study Point to Novel Autism Susceptibility GenesPublished 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 […]
A newly identified genetic variant could account for up to 15 percent of autism cases, say researchers who studied genes that are important in connecting brain cells. Researchers say the variant is carried by about 65 per cent of people with autism.
Rett Syndrome (RTT) is a severe form of X-linked mental retardation caused by mutations in the gene coding for methyl CpG-binding protein 2 (MECP2). Mice deficient in MeCP2 have a range of physiological and neurological abnormalities that mimic the human syndrome. Here we show that systemic treatment of MeCP2 mutant mice with an active peptide […]
A Common Genetic variant in the neurexin superfamily member CNTNAP2 increases Familial Risk of AutismPublished 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 […]
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 […]
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 […]
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 […]
Molecular Cytogenetic Analysis and Resequencing of Contactin Associate Protein-Like 2 in Autism Spectrum DisordersPublished January 10, 2008 in American Journal of Human Genetics, Bakkaloglu, O'Roak, et al
Autism spectrum disorders (ASD) are a group of related neurodevelopmental syndromes with complex genetic etiology. We identified a de novo chromosome 7q inversion disrupting Autism susceptibility candidate 2 (AUTS2) and Contactin Associated Protein-Like 2 (CNTNAP2) in a child with cognitive and social delay. We focused our initial analysis on CNTNAP2 based on our demonstration of […]
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 […]
Linkage, Association, and Gene Expression Analyses Identify CNTNAP2 as an Autism-Susceptibility GenePublished January 1, 2008 in American Journal of Human Genetics, Alarcon, Abrahams, et al.
Autism is a genetically complex neurodevelopmental syndrome in which language deficits are a core feature. We describe results from two complimentary approaches used to identify risk variants on chromosome 7 that likely contribute to the etiology of autism. A two-stage association study tested 2758 SNPs across a 10 Mb 7q35 language-related autism QTL in AGRE […]