Architecture of the Genetic Risk for Autism / Pauline CHASTE in Key Issues in Mental Health, 180 (2015)

Public ISBD [article]  inKey Issues in Mental Health > 180 (2015) . - p.80-96 Titre : Architecture of the Genetic Risk for Autism Type de document : Texte imprimé et/ou numérique Auteurs : Pauline CHASTE, Auteur ; Bernie DEVLIN, Auteur Article en page(s) : p.80-96 Langues : Anglais (eng) Index. décimale : AUT-B AUT-B - L'Autisme - Ouvrages généraux et scientifiques Résumé : The past decade of investigation into the genetics of autism, marked by the identification of the first rare mutations in nonsyndromic autism and the development of genome-wide genotyping and sequencing techniques, has resulted in remarkable advances in our understanding of the genetic architecture of the risk for autism spectrum disorders (ASD). Indeed, from a population genetics perspective, it can be argued that an accurate synopsis of the genetic architecture of ASD is already in hand. Integrating all of the evidence, there can be no doubt that both rare and common variations play a role in the inherited risk for ASD. The picture of genetic risk that has emerged based on recent results is much more complex than many had imagined, and in many ways it looks like the polygenic model first proposed. Nevertheless, there seems to be some convergence on a limited number of cellular processes, which bodes well for the development of new treatments. Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=271 [article] Architecture of the Genetic Risk for Autism [Texte imprimé et/ou numérique] / Pauline CHASTE, Auteur ; Bernie DEVLIN, Auteur . - p.80-96. Langues : Anglais (eng) in Key Issues in Mental Health > 180 (2015) . - p.80-96 Index. décimale : AUT-B AUT-B - L'Autisme - Ouvrages généraux et scientifiques Résumé : The past decade of investigation into the genetics of autism, marked by the identification of the first rare mutations in nonsyndromic autism and the development of genome-wide genotyping and sequencing techniques, has resulted in remarkable advances in our understanding of the genetic architecture of the risk for autism spectrum disorders (ASD). Indeed, from a population genetics perspective, it can be argued that an accurate synopsis of the genetic architecture of ASD is already in hand. Integrating all of the evidence, there can be no doubt that both rare and common variations play a role in the inherited risk for ASD. The picture of genetic risk that has emerged based on recent results is much more complex than many had imagined, and in many ways it looks like the polygenic model first proposed. Nevertheless, there seems to be some convergence on a limited number of cellular processes, which bodes well for the development of new treatments. Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=271

Common genetic variants, acting additively, are a major source of risk for autism / Lambertus KLEI in Molecular Autism, (October 2012)  

Public ISBD [article]  inMolecular Autism > (October 2012) . - 13 p. Titre : Common genetic variants, acting additively, are a major source of risk for autism Type de document : Texte imprimé et/ou numérique Auteurs : Lambertus KLEI, Auteur ; Stephan J. SANDERS, Auteur ; Michael T. MURTHA, Auteur ; Vanessa HUS, Auteur ; Jennifer K. LOWE, Auteur ; A. J. WILLSEY, Auteur ; Daniel MORENO DE LUCA, Auteur ; Timothy W. YU, Auteur ; Eric FOMBONNE, Auteur ; Daniel H. GESCHWIND, Auteur ; Dorothy E. GRICE, Auteur ; David H. LEDBETTER, Auteur ; Catherine LORD, Auteur ; Shrikant M. MANE, Auteur ; Christa L. MARTIN, Auteur ; Donna M. MARTIN, Auteur ; Eric M. MORROW, Auteur ; Christopher A. WALSH, Auteur ; Nadine M. MELHEM, Auteur ; Pauline CHASTE, Auteur ; James S. SUTCLIFFE, Auteur ; Matthew W. STATE, Auteur ; Edwin H. Jr COOK, Auteur ; Kathryn ROEDER, Auteur ; Bernie DEVLIN, Auteur Année de publication : 2012 Article en page(s) : 13 p. Langues : Anglais (eng) Mots-clés : Narrow-sense heritability  Multiplex  Simplex  Quantitative genetics Index. décimale : PER Périodiques Résumé : Background Autism spectrum disorders (ASD) are early onset neurodevelopmental syndromes typified by impairments in reciprocal social interaction and communication, accompanied by restricted and repetitive behaviors. While rare and especially de novo genetic variation are known to affect liability, whether common genetic polymorphism plays a substantial role is an open question and the relative contribution of genes and environment is contentious. It is probable that the relative contributions of rare and common variation, as well as environment, differs between ASD families having only a single affected individual (simplex) versus multiplex families who have two or more affected individuals. Methods By using quantitative genetics techniques and the contrast of ASD subjects to controls, we estimate what portion of liability can be explained by additive genetic effects, known as narrow-sense heritability. We evaluate relatives of ASD subjects using the same methods to evaluate the assumptions of the additive model and partition families by simplex/multiplex status to determine how heritability changes with status. Results By analyzing common variation throughout the genome, we show that common genetic polymorphism exerts substantial additive genetic effects on ASD liability and that simplex/multiplex family status has an impact on the identified composition of that risk. As a fraction of the total variation in liability, the estimated narrow-sense heritability exceeds 60% for ASD individuals from multiplex families and is approximately 40% for simplex families. By analyzing parents, unaffected siblings and alleles not transmitted from parents to their affected children, we conclude that the data for simplex ASD families follow the expectation for additive models closely. The data from multiplex families deviate somewhat from an additive model, possibly due to parental assortative mating. Conclusions Our results, when viewed in the context of results from genome-wide association studies, demonstrate that a myriad of common variants of very small effect impacts ASD liability. En ligne : http://dx.doi.org/10.1186/2040-2392-3-9 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=202 [article] Common genetic variants, acting additively, are a major source of risk for autism [Texte imprimé et/ou numérique] / Lambertus KLEI, Auteur ; Stephan J. SANDERS, Auteur ; Michael T. MURTHA, Auteur ; Vanessa HUS, Auteur ; Jennifer K. LOWE, Auteur ; A. J. WILLSEY, Auteur ; Daniel MORENO DE LUCA, Auteur ; Timothy W. YU, Auteur ; Eric FOMBONNE, Auteur ; Daniel H. GESCHWIND, Auteur ; Dorothy E. GRICE, Auteur ; David H. LEDBETTER, Auteur ; Catherine LORD, Auteur ; Shrikant M. MANE, Auteur ; Christa L. MARTIN, Auteur ; Donna M. MARTIN, Auteur ; Eric M. MORROW, Auteur ; Christopher A. WALSH, Auteur ; Nadine M. MELHEM, Auteur ; Pauline CHASTE, Auteur ; James S. SUTCLIFFE, Auteur ; Matthew W. STATE, Auteur ; Edwin H. Jr COOK, Auteur ; Kathryn ROEDER, Auteur ; Bernie DEVLIN, Auteur . - 2012 . - 13 p. Langues : Anglais (eng) in Molecular Autism > (October 2012) . - 13 p. Mots-clés : Narrow-sense heritability  Multiplex  Simplex  Quantitative genetics Index. décimale : PER Périodiques Résumé : Background Autism spectrum disorders (ASD) are early onset neurodevelopmental syndromes typified by impairments in reciprocal social interaction and communication, accompanied by restricted and repetitive behaviors. While rare and especially de novo genetic variation are known to affect liability, whether common genetic polymorphism plays a substantial role is an open question and the relative contribution of genes and environment is contentious. It is probable that the relative contributions of rare and common variation, as well as environment, differs between ASD families having only a single affected individual (simplex) versus multiplex families who have two or more affected individuals. Methods By using quantitative genetics techniques and the contrast of ASD subjects to controls, we estimate what portion of liability can be explained by additive genetic effects, known as narrow-sense heritability. We evaluate relatives of ASD subjects using the same methods to evaluate the assumptions of the additive model and partition families by simplex/multiplex status to determine how heritability changes with status. Results By analyzing common variation throughout the genome, we show that common genetic polymorphism exerts substantial additive genetic effects on ASD liability and that simplex/multiplex family status has an impact on the identified composition of that risk. As a fraction of the total variation in liability, the estimated narrow-sense heritability exceeds 60% for ASD individuals from multiplex families and is approximately 40% for simplex families. By analyzing parents, unaffected siblings and alleles not transmitted from parents to their affected children, we conclude that the data for simplex ASD families follow the expectation for additive models closely. The data from multiplex families deviate somewhat from an additive model, possibly due to parental assortative mating. Conclusions Our results, when viewed in the context of results from genome-wide association studies, demonstrate that a myriad of common variants of very small effect impacts ASD liability. En ligne : http://dx.doi.org/10.1186/2040-2392-3-9 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=202

DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics / Li LIU in Molecular Autism, (March 2014)  

Public ISBD [article]  inMolecular Autism > (March 2014) . - p.1-18 Titre : DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics Type de document : Texte imprimé et/ou numérique Auteurs : Li LIU, Auteur ; Jing LEI, Auteur ; Stephan J. SANDERS, Auteur ; Arthur Jeremy WILLSEY, Auteur ; Yan KOU, Auteur ; Abdullah Ercument CICEK, Auteur ; Lambertus KLEI, Auteur ; Cong LU, Auteur ; Xin HE, Auteur ; Mingfeng LI, Auteur ; Rebecca A. MUHLE, Auteur ; Avi MA’AYAN, Auteur ; James P. NOONAN, Auteur ; Nenad ŠESTAN, Auteur ; Kathryn A. MCFADDEN, Auteur ; Matthew W. STATE, Auteur ; Joseph D. BUXBAUM, Auteur ; Bernie DEVLIN, Auteur ; Kathryn ROEDER, Auteur Article en page(s) : p.1-18 Langues : Anglais (eng) Index. décimale : PER Périodiques Résumé : De novo loss-of-function (dnLoF) mutations are found twofold more often in autism spectrum disorder (ASD) probands than their unaffected siblings. Multiple independent dnLoF mutations in the same gene implicate the gene in risk and hence provide a systematic, albeit arduous, path forward for ASD genetics. It is likely that using additional non-genetic data will enhance the ability to identify ASD genes. En ligne : http://dx.doi.org/10.1186/2040-2392-5-22 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=276 [article] DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics [Texte imprimé et/ou numérique] / Li LIU, Auteur ; Jing LEI, Auteur ; Stephan J. SANDERS, Auteur ; Arthur Jeremy WILLSEY, Auteur ; Yan KOU, Auteur ; Abdullah Ercument CICEK, Auteur ; Lambertus KLEI, Auteur ; Cong LU, Auteur ; Xin HE, Auteur ; Mingfeng LI, Auteur ; Rebecca A. MUHLE, Auteur ; Avi MA’AYAN, Auteur ; James P. NOONAN, Auteur ; Nenad ŠESTAN, Auteur ; Kathryn A. MCFADDEN, Auteur ; Matthew W. STATE, Auteur ; Joseph D. BUXBAUM, Auteur ; Bernie DEVLIN, Auteur ; Kathryn ROEDER, Auteur . - p.1-18. Langues : Anglais (eng) in Molecular Autism > (March 2014) . - p.1-18 Index. décimale : PER Périodiques Résumé : De novo loss-of-function (dnLoF) mutations are found twofold more often in autism spectrum disorder (ASD) probands than their unaffected siblings. Multiple independent dnLoF mutations in the same gene implicate the gene in risk and hence provide a systematic, albeit arduous, path forward for ASD genetics. It is likely that using additional non-genetic data will enhance the ability to identify ASD genes. En ligne : http://dx.doi.org/10.1186/2040-2392-5-22 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=276

Genetics in psychiatry: common variant association studies / Joseph D. BUXBAUM in Molecular Autism, (March 2010)  

Public ISBD [article]  inMolecular Autism > (March 2010) . - 4 p. Titre : Genetics in psychiatry: common variant association studies Type de document : Texte imprimé et/ou numérique Auteurs : Joseph D. BUXBAUM, Auteur ; Simon BARON-COHEN, Auteur ; Bernie DEVLIN, Auteur Année de publication : 2010 Article en page(s) : 4 p. Langues : Anglais (eng) Index. décimale : PER Périodiques Résumé : Many psychiatric conditions and traits are associated with significant heritability. Genetic risk for psychiatric conditions encompass rare variants, identified due to major effect, as well as common variants, the latter analyzed by association analyses. We review guidelines for common variant association analyses, undertaking after assessing evidence of heritability. We highlight the importance of: suitably large sample sizes; an experimental design that controls for ancestry; careful data cleaning; correction for multiple testing; small P values for positive findings; assessment of effect size for positive findings; and, inclusion of an independent replication sample. We also note the importance of a critical discussion of any prior findings, biological follow-up where possible, and a means of accessing the raw data. En ligne : http://dx.doi.org/10.1186/2040-2392-1-6 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=102 [article] Genetics in psychiatry: common variant association studies [Texte imprimé et/ou numérique] / Joseph D. BUXBAUM, Auteur ; Simon BARON-COHEN, Auteur ; Bernie DEVLIN, Auteur . - 2010 . - 4 p. Langues : Anglais (eng) in Molecular Autism > (March 2010) . - 4 p. Index. décimale : PER Périodiques Résumé : Many psychiatric conditions and traits are associated with significant heritability. Genetic risk for psychiatric conditions encompass rare variants, identified due to major effect, as well as common variants, the latter analyzed by association analyses. We review guidelines for common variant association analyses, undertaking after assessing evidence of heritability. We highlight the importance of: suitably large sample sizes; an experimental design that controls for ancestry; careful data cleaning; correction for multiple testing; small P values for positive findings; assessment of effect size for positive findings; and, inclusion of an independent replication sample. We also note the importance of a critical discussion of any prior findings, biological follow-up where possible, and a means of accessing the raw data. En ligne : http://dx.doi.org/10.1186/2040-2392-1-6 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=102

Modest Impact on Risk for Autism Spectrum Disorder of Rare Copy Number Variants at 15q11.2, Specifically Breakpoints 1 to 2 / Pauline CHASTE in Autism Research, 7-3 (June 2014)  

Public ISBD [article]  inAutism Research > 7-3 (June 2014) . - p.355-362 Titre : Modest Impact on Risk for Autism Spectrum Disorder of Rare Copy Number Variants at 15q11.2, Specifically Breakpoints 1 to 2 Type de document : Texte imprimé et/ou numérique Auteurs : Pauline CHASTE, Auteur ; Stephan J. SANDERS, Auteur ; Kommu N. MOHAN, Auteur ; Lambertus KLEI, Auteur ; Youeun SONG, Auteur ; Michael T. MURTHA, Auteur ; Vanessa HUS, Auteur ; Jennifer K. LOWE, Auteur ; A. Jeremy WILLSEY, Auteur ; Daniel MORENO-DE-LUCA, Auteur ; Timothy W. YU, Auteur ; Eric FOMBONNE, Auteur ; Daniel H. GESCHWIND, Auteur ; Dorothy E. GRICE, Auteur ; David H. LEDBETTER, Auteur ; Catherine LORD, Auteur ; Shrikant M. MANE, Auteur ; Donna M. MARTIN, Auteur ; Eric M. MORROW, Auteur ; Christopher A. WALSH, Auteur ; James S. SUTCLIFFE, Auteur ; Matthew W. STATE, Auteur ; Christa Lese MARTIN, Auteur ; Bernie DEVLIN, Auteur ; Arthur L. BEAUDET, Auteur ; Edwin H. Jr COOK, Auteur ; Soo-Jeong KIM, Auteur Article en page(s) : p.355-362 Langues : Anglais (eng) Mots-clés : 15q11.2  deletion  duplication  penetrance  autism Index. décimale : PER Périodiques Résumé : The proximal region of chromosome 15 is one of the genomic hotspots for copy number variants (CNVs). Among the rearrangements observed in this region, CNVs from the interval between the common breakpoints 1 and 2 (BP1 and BP2) have been reported cosegregating with autism spectrum disorder (ASD). Although evidence supporting an association between BP1-BP2 CNVs and autism accumulates, the magnitude of the effect of BP1-BP2 CNVs remains elusive, posing a great challenge to recurrence-risk counseling. To gain further insight into their pathogenicity for ASD, we estimated the penetrance of the BP1-BP2 CNVs for ASD as well as their effects on ASD-related phenotypes in a well-characterized ASD sample (n?=?2525 families). Transmission disequilibrium test revealed significant preferential transmission only for the duplicated chromosome in probands (20T:9NT). The penetrance of the BP1-BP2 CNVs for ASD was low, conferring additional risks of 0.3% (deletion) and 0.8% (duplication). Stepwise regression analyses suggest a greater effect of the CNVs on ASD-related phenotype in males and when maternally inherited. Taken together, the results are consistent with BP1-BP2 CNVs as risk factors for autism. However, their effect is modest, more akin to that seen for common variants. To be consistent with the current American College of Medical Genetics guidelines for interpretation of postnatal CNV, the BP1-BP2 deletion and duplication CNVs would probably best be classified as variants of uncertain significance (VOUS): they appear to have an impact on risk, but one so modest that these CNVs do not merit pathogenic status. Autism Res 2014, 7: 355–362. © 2014 International Society for Autism Research, Wiley Periodicals, Inc. En ligne : http://dx.doi.org/10.1002/aur.1378 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=235 [article] Modest Impact on Risk for Autism Spectrum Disorder of Rare Copy Number Variants at 15q11.2, Specifically Breakpoints 1 to 2 [Texte imprimé et/ou numérique] / Pauline CHASTE, Auteur ; Stephan J. SANDERS, Auteur ; Kommu N. MOHAN, Auteur ; Lambertus KLEI, Auteur ; Youeun SONG, Auteur ; Michael T. MURTHA, Auteur ; Vanessa HUS, Auteur ; Jennifer K. LOWE, Auteur ; A. Jeremy WILLSEY, Auteur ; Daniel MORENO-DE-LUCA, Auteur ; Timothy W. YU, Auteur ; Eric FOMBONNE, Auteur ; Daniel H. GESCHWIND, Auteur ; Dorothy E. GRICE, Auteur ; David H. LEDBETTER, Auteur ; Catherine LORD, Auteur ; Shrikant M. MANE, Auteur ; Donna M. MARTIN, Auteur ; Eric M. MORROW, Auteur ; Christopher A. WALSH, Auteur ; James S. SUTCLIFFE, Auteur ; Matthew W. STATE, Auteur ; Christa Lese MARTIN, Auteur ; Bernie DEVLIN, Auteur ; Arthur L. BEAUDET, Auteur ; Edwin H. Jr COOK, Auteur ; Soo-Jeong KIM, Auteur . - p.355-362. Langues : Anglais (eng) in Autism Research > 7-3 (June 2014) . - p.355-362 Mots-clés : 15q11.2  deletion  duplication  penetrance  autism Index. décimale : PER Périodiques Résumé : The proximal region of chromosome 15 is one of the genomic hotspots for copy number variants (CNVs). Among the rearrangements observed in this region, CNVs from the interval between the common breakpoints 1 and 2 (BP1 and BP2) have been reported cosegregating with autism spectrum disorder (ASD). Although evidence supporting an association between BP1-BP2 CNVs and autism accumulates, the magnitude of the effect of BP1-BP2 CNVs remains elusive, posing a great challenge to recurrence-risk counseling. To gain further insight into their pathogenicity for ASD, we estimated the penetrance of the BP1-BP2 CNVs for ASD as well as their effects on ASD-related phenotypes in a well-characterized ASD sample (n?=?2525 families). Transmission disequilibrium test revealed significant preferential transmission only for the duplicated chromosome in probands (20T:9NT). The penetrance of the BP1-BP2 CNVs for ASD was low, conferring additional risks of 0.3% (deletion) and 0.8% (duplication). Stepwise regression analyses suggest a greater effect of the CNVs on ASD-related phenotype in males and when maternally inherited. Taken together, the results are consistent with BP1-BP2 CNVs as risk factors for autism. However, their effect is modest, more akin to that seen for common variants. To be consistent with the current American College of Medical Genetics guidelines for interpretation of postnatal CNV, the BP1-BP2 deletion and duplication CNVs would probably best be classified as variants of uncertain significance (VOUS): they appear to have an impact on risk, but one so modest that these CNVs do not merit pathogenic status. Autism Res 2014, 7: 355–362. © 2014 International Society for Autism Research, Wiley Periodicals, Inc. En ligne : http://dx.doi.org/10.1002/aur.1378 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=235

De novo missense variants disrupting protein-protein interactions affect risk for autism through gene co-expression and protein networks in neuronal cell types / Siwei CHEN in Molecular Autism, 11 (2020)  

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