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A genotype resource for postmortem brain samples from the Autism Tissue Program / Richard F. WINTLE in Autism Research, 4-2 (April 2011)
[article]
Titre : A genotype resource for postmortem brain samples from the Autism Tissue Program Type de document : Texte imprimé et/ou numérique Auteurs : Richard F. WINTLE, Auteur ; Anath C. LIONEL, Auteur ; Pingzhao HU, Auteur ; Stephen D. GINSBERG, Auteur ; Dalila PINTO, Auteur ; Bhooma THIRUVAHINDRAPDURAM, Auteur ; John WEI, Auteur ; Christian R. MARSHALL, Auteur ; Jane PICKETT, Auteur ; Edwin H. Jr COOK, Auteur ; Stephen SCHERER, Auteur Année de publication : 2011 Article en page(s) : p.89-97 Langues : Anglais (eng) Mots-clés : autism autism spectrum disorder brain brodmann area 19 copy number variation genome-wide microarray single nucleotide polymorphism Index. décimale : PER Périodiques Résumé : The Autism Tissue Program (ATP), a science program of Autism Speaks, provides researchers with access to well-characterized postmortem brain tissues. Researchers access these tissues through a peer-reviewed, project-based approval process, and obtain related clinical information from a secure, online informatics portal. However, few of these samples have DNA banked from other sources (such as a blood sample from the same individual), hindering genotype–phenotype correlation and interpretation of gene expression data derived from the banked brain tissue. Here, we describe an initiative to extract DNA from Brodmann Area 19, and genotype these samples using both the Affymetrix Genome-Wide Human SNP Array 6.0 and the Illumina Human1M-Duo DNA Analysis BeadChip genome-wide microarray technologies. We additionally verify reported gender, and infer ethnic background from the single nucleotide polymorphism data. We have also used a rigorous, multiple algorithm approach to identify genomic copy number variation (CNV) from these array data. Following an initial proof of principle study using two samples, 52 experimental samples, consisting of 27 subjects with confirmed or suspected autism and related disorders, 5 subjects with cytogenetically visible duplications of 15q, 2 with epilepsy and 18 age-matched normal controls were processed, yielding high-quality genotype data in all cases. The genotype and CNV data are provided via the ATP informatics portal as a resource for the autism research community. En ligne : http://dx.doi.org/10.1002/aur.173 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=121
in Autism Research > 4-2 (April 2011) . - p.89-97[article] A genotype resource for postmortem brain samples from the Autism Tissue Program [Texte imprimé et/ou numérique] / Richard F. WINTLE, Auteur ; Anath C. LIONEL, Auteur ; Pingzhao HU, Auteur ; Stephen D. GINSBERG, Auteur ; Dalila PINTO, Auteur ; Bhooma THIRUVAHINDRAPDURAM, Auteur ; John WEI, Auteur ; Christian R. MARSHALL, Auteur ; Jane PICKETT, Auteur ; Edwin H. Jr COOK, Auteur ; Stephen SCHERER, Auteur . - 2011 . - p.89-97.
Langues : Anglais (eng)
in Autism Research > 4-2 (April 2011) . - p.89-97
Mots-clés : autism autism spectrum disorder brain brodmann area 19 copy number variation genome-wide microarray single nucleotide polymorphism Index. décimale : PER Périodiques Résumé : The Autism Tissue Program (ATP), a science program of Autism Speaks, provides researchers with access to well-characterized postmortem brain tissues. Researchers access these tissues through a peer-reviewed, project-based approval process, and obtain related clinical information from a secure, online informatics portal. However, few of these samples have DNA banked from other sources (such as a blood sample from the same individual), hindering genotype–phenotype correlation and interpretation of gene expression data derived from the banked brain tissue. Here, we describe an initiative to extract DNA from Brodmann Area 19, and genotype these samples using both the Affymetrix Genome-Wide Human SNP Array 6.0 and the Illumina Human1M-Duo DNA Analysis BeadChip genome-wide microarray technologies. We additionally verify reported gender, and infer ethnic background from the single nucleotide polymorphism data. We have also used a rigorous, multiple algorithm approach to identify genomic copy number variation (CNV) from these array data. Following an initial proof of principle study using two samples, 52 experimental samples, consisting of 27 subjects with confirmed or suspected autism and related disorders, 5 subjects with cytogenetically visible duplications of 15q, 2 with epilepsy and 18 age-matched normal controls were processed, yielding high-quality genotype data in all cases. The genotype and CNV data are provided via the ATP informatics portal as a resource for the autism research community. En ligne : http://dx.doi.org/10.1002/aur.173 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=121 Impact of on-site clinical genetics consultations on diagnostic rate in children and young adults with autism spectrum disorder / A. MUNNICH in Molecular Autism, 10 (2019)
[article]
Titre : Impact of on-site clinical genetics consultations on diagnostic rate in children and young adults with autism spectrum disorder Type de document : Texte imprimé et/ou numérique Auteurs : A. MUNNICH, Auteur ; Caroline DEMILY, Auteur ; L. FRUGERE, Auteur ; C. DUWIME, Auteur ; V. MALAN, Auteur ; Giulia BARCIA, Auteur ; C. VIDAL, Auteur ; E. THROO, Auteur ; C. BESMOND, Auteur ; L. HUBERT, Auteur ; G. ROLAND-MANUEL, Auteur ; J. P. MALEN, Auteur ; M. FERRERI, Auteur ; S. HANEIN, Auteur ; J. C. THALABARD, Auteur ; Nathalie BODDAERT, Auteur ; Moïse ASSOULINE, Auteur Article en page(s) : 33 p. Langues : Anglais (eng) Mots-clés : Autism spectrum disorder Copy number variant Fragile X syndrome Gene panel Genetic counseling Genetic diagnosis Microarray Next-generation sequencing Sequence variant Index. décimale : PER Périodiques Résumé : Background: Neurogenetics investigations and diagnostic yield in patients with autism spectrum disorder (ASD) have significantly improved over the last few years. Yet, many patients still fail to be systematically investigated. Methods: To improve access to services, an ambulatory team has been established since 1998, delivering on-site clinical genetics consultations and gradually upgrading services to 502 children and young adults with ASD in their standard environment across 26 day-care hospitals and specialized institutions within the Greater Paris region. The evaluation included a clinical genetics consultation, screening for fragile X syndrome, metabolic workup, chromosomal microarray analysis, and, in a proportion of patients, next-generation sequencing of genes reported in ASD and other neurodevelopmental disorders. Results: Fragile X syndrome and pathogenic copy number variants (CNVs) accounted for the disease in 10% of cases, including 4/312 (1.3%) with fragile X syndrome and 34/388 (8.8%) with pathogenic CNVs (19 de novo and 4 inherited). Importantly, adding high-throughput resequencing of reported intellectual disability/ASD genes to the screening procedure had a major impact on diagnostic yield in the 141 patients examined most recently. Pathogenic or likely pathogenic sequence variants in 27 disease genes were identified in 33/141 patients (23.4%; 23 were de novo and 10 inherited, including five X-linked and five recessive compound heterozygous variants). Diagnosed cases presented atypical and/or syndromic ASD with moderate to severe intellectual disability. The diagnostic yield of fragile X syndrome and array CGH testing combined with next-generation sequencing was significantly higher than fragile X syndrome and array CGH alone (p value 0.009). No inborn errors of metabolism were detected with the metabolic screening. Conclusion: Based on the diagnostic rate observed in this cohort, we suggest that a stepwise procedure be considered, first screening pathogenic CNVs and a limited number of disease genes in a much larger number of patients, especially those with syndromic ASD and intellectual disability. En ligne : https://dx.doi.org/10.1186/s13229-019-0284-2 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=408
in Molecular Autism > 10 (2019) . - 33 p.[article] Impact of on-site clinical genetics consultations on diagnostic rate in children and young adults with autism spectrum disorder [Texte imprimé et/ou numérique] / A. MUNNICH, Auteur ; Caroline DEMILY, Auteur ; L. FRUGERE, Auteur ; C. DUWIME, Auteur ; V. MALAN, Auteur ; Giulia BARCIA, Auteur ; C. VIDAL, Auteur ; E. THROO, Auteur ; C. BESMOND, Auteur ; L. HUBERT, Auteur ; G. ROLAND-MANUEL, Auteur ; J. P. MALEN, Auteur ; M. FERRERI, Auteur ; S. HANEIN, Auteur ; J. C. THALABARD, Auteur ; Nathalie BODDAERT, Auteur ; Moïse ASSOULINE, Auteur . - 33 p.
Langues : Anglais (eng)
in Molecular Autism > 10 (2019) . - 33 p.
Mots-clés : Autism spectrum disorder Copy number variant Fragile X syndrome Gene panel Genetic counseling Genetic diagnosis Microarray Next-generation sequencing Sequence variant Index. décimale : PER Périodiques Résumé : Background: Neurogenetics investigations and diagnostic yield in patients with autism spectrum disorder (ASD) have significantly improved over the last few years. Yet, many patients still fail to be systematically investigated. Methods: To improve access to services, an ambulatory team has been established since 1998, delivering on-site clinical genetics consultations and gradually upgrading services to 502 children and young adults with ASD in their standard environment across 26 day-care hospitals and specialized institutions within the Greater Paris region. The evaluation included a clinical genetics consultation, screening for fragile X syndrome, metabolic workup, chromosomal microarray analysis, and, in a proportion of patients, next-generation sequencing of genes reported in ASD and other neurodevelopmental disorders. Results: Fragile X syndrome and pathogenic copy number variants (CNVs) accounted for the disease in 10% of cases, including 4/312 (1.3%) with fragile X syndrome and 34/388 (8.8%) with pathogenic CNVs (19 de novo and 4 inherited). Importantly, adding high-throughput resequencing of reported intellectual disability/ASD genes to the screening procedure had a major impact on diagnostic yield in the 141 patients examined most recently. Pathogenic or likely pathogenic sequence variants in 27 disease genes were identified in 33/141 patients (23.4%; 23 were de novo and 10 inherited, including five X-linked and five recessive compound heterozygous variants). Diagnosed cases presented atypical and/or syndromic ASD with moderate to severe intellectual disability. The diagnostic yield of fragile X syndrome and array CGH testing combined with next-generation sequencing was significantly higher than fragile X syndrome and array CGH alone (p value 0.009). No inborn errors of metabolism were detected with the metabolic screening. Conclusion: Based on the diagnostic rate observed in this cohort, we suggest that a stepwise procedure be considered, first screening pathogenic CNVs and a limited number of disease genes in a much larger number of patients, especially those with syndromic ASD and intellectual disability. En ligne : https://dx.doi.org/10.1186/s13229-019-0284-2 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=408 Meta-Analysis of Gene Expression in Autism Spectrum Disorder / Carolyn CH'NG in Autism Research, 8-5 (October 2015)
[article]
Titre : Meta-Analysis of Gene Expression in Autism Spectrum Disorder Type de document : Texte imprimé et/ou numérique Auteurs : Carolyn CH'NG, Auteur ; Willie KWOK, Auteur ; Sanja ROGIC, Auteur ; Paul PAVLIDIS, Auteur Article en page(s) : p.593-608 Langues : Anglais (eng) Mots-clés : gene expression meta-analysis molecular genetics microarray Index. décimale : PER Périodiques Résumé : Autism spectrum disorders (ASD) are clinically heterogeneous and biologically complex. In general it remains unclear, what biological factors lead to changes in the brains of autistic individuals. A considerable number of transcriptome analyses have been performed in attempts to address this question, but their findings lack a clear consensus. As a result, each of these individual studies has not led to any significant advance in understanding the autistic phenotype as a whole. Here, we report a meta-analysis of more than 1000 microarrays across twelve independent studies on expression changes in ASD compared to unaffected individuals, in both blood and brain tissues. We identified a number of known and novel genes that are consistently differentially expressed across three studies of the brain (71 samples in total). A subset of the highly ranked genes is suggestive of effects on mitochondrial function. In blood, consistent changes were more difficult to identify, despite individual studies tending to exhibit larger effects than the brain studies. Our results are the strongest evidence to date of a common transcriptome signature in the brains of individuals with ASD. Autism Res 2015, 8: 593–608. © 2015 International Society for Autism Research, Wiley Periodicals, Inc. En ligne : http://dx.doi.org/10.1002/aur.1475 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=270
in Autism Research > 8-5 (October 2015) . - p.593-608[article] Meta-Analysis of Gene Expression in Autism Spectrum Disorder [Texte imprimé et/ou numérique] / Carolyn CH'NG, Auteur ; Willie KWOK, Auteur ; Sanja ROGIC, Auteur ; Paul PAVLIDIS, Auteur . - p.593-608.
Langues : Anglais (eng)
in Autism Research > 8-5 (October 2015) . - p.593-608
Mots-clés : gene expression meta-analysis molecular genetics microarray Index. décimale : PER Périodiques Résumé : Autism spectrum disorders (ASD) are clinically heterogeneous and biologically complex. In general it remains unclear, what biological factors lead to changes in the brains of autistic individuals. A considerable number of transcriptome analyses have been performed in attempts to address this question, but their findings lack a clear consensus. As a result, each of these individual studies has not led to any significant advance in understanding the autistic phenotype as a whole. Here, we report a meta-analysis of more than 1000 microarrays across twelve independent studies on expression changes in ASD compared to unaffected individuals, in both blood and brain tissues. We identified a number of known and novel genes that are consistently differentially expressed across three studies of the brain (71 samples in total). A subset of the highly ranked genes is suggestive of effects on mitochondrial function. In blood, consistent changes were more difficult to identify, despite individual studies tending to exhibit larger effects than the brain studies. Our results are the strongest evidence to date of a common transcriptome signature in the brains of individuals with ASD. Autism Res 2015, 8: 593–608. © 2015 International Society for Autism Research, Wiley Periodicals, Inc. En ligne : http://dx.doi.org/10.1002/aur.1475 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=270 A meta-analysis of two high-risk prospective cohort studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood / C. E. MORDAUNT in Molecular Autism, 10 (2019)
[article]
Titre : A meta-analysis of two high-risk prospective cohort studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood Type de document : Texte imprimé et/ou numérique Auteurs : C. E. MORDAUNT, Auteur ; B. Y. PARK, Auteur ; K. M. BAKULSKI, Auteur ; J. I. FEINBERG, Auteur ; Lisa A. CROEN, Auteur ; Christine LADD-ACOSTA, Auteur ; C. J. NEWSCHAFFER, Auteur ; Heather E. VOLK, Auteur ; S. OZONOFF, Auteur ; I. HERTZ-PICCIOTTO, Auteur ; J. M. LASALLE, Auteur ; Rebecca J. SCHMIDT, Auteur ; M. D. FALLIN, Auteur Article en page(s) : 36 p. Langues : Anglais (eng) Mots-clés : Autism spectrum disorder Chromatin Environment Gene expression Meta-analysis Microarray Neurodevelopment Perinatal Prospective study Umbilical cord blood Index. décimale : PER Périodiques Résumé : Background: Autism spectrum disorder (ASD) is a neurodevelopmental disorder that affects more than 1% of children in the USA. ASD risk is thought to arise from both genetic and environmental factors, with the perinatal period as a critical window. Understanding early transcriptional changes in ASD would assist in clarifying disease pathogenesis and identifying biomarkers. However, little is known about umbilical cord blood gene expression profiles in babies later diagnosed with ASD compared to non-typically developing and non-ASD (Non-TD) or typically developing (TD) children. Methods: Genome-wide transcript levels were measured by Affymetrix Human Gene 2.0 array in RNA from cord blood samples from both the Markers of Autism Risk in Babies-Learning Early Signs (MARBLES) and the Early Autism Risk Longitudinal Investigation (EARLI) high-risk pregnancy cohorts that enroll younger siblings of a child previously diagnosed with ASD. Younger siblings were diagnosed based on assessments at 36 months, and 59 ASD, 92 Non-TD, and 120 TD subjects were included. Using both differential expression analysis and weighted gene correlation network analysis, gene expression between ASD and TD, and between Non-TD and TD, was compared within each study and via meta-analysis. Results: While cord blood gene expression differences comparing either ASD or Non-TD to TD did not reach genome-wide significance, 172 genes were nominally differentially expressed between ASD and TD cord blood (log2(fold change) > 0.1, p < 0.01). These genes were significantly enriched for functions in xenobiotic metabolism, chromatin regulation, and systemic lupus erythematosus (FDR q < 0.05). In contrast, 66 genes were nominally differentially expressed between Non-TD and TD, including 8 genes that were also differentially expressed in ASD. Gene coexpression modules were significantly correlated with demographic factors and cell type proportions. Limitations: ASD-associated gene expression differences identified in this study are subtle, as cord blood is not the main affected tissue, it is composed of many cell types, and ASD is a heterogeneous disorder. Conclusions: This is the first study to identify gene expression differences in cord blood specific to ASD through a meta-analysis across two prospective pregnancy cohorts. The enriched gene pathways support involvement of environmental, immune, and epigenetic mechanisms in ASD etiology. En ligne : http://dx.doi.org/10.1186/s13229-019-0287-z Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=414
in Molecular Autism > 10 (2019) . - 36 p.[article] A meta-analysis of two high-risk prospective cohort studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood [Texte imprimé et/ou numérique] / C. E. MORDAUNT, Auteur ; B. Y. PARK, Auteur ; K. M. BAKULSKI, Auteur ; J. I. FEINBERG, Auteur ; Lisa A. CROEN, Auteur ; Christine LADD-ACOSTA, Auteur ; C. J. NEWSCHAFFER, Auteur ; Heather E. VOLK, Auteur ; S. OZONOFF, Auteur ; I. HERTZ-PICCIOTTO, Auteur ; J. M. LASALLE, Auteur ; Rebecca J. SCHMIDT, Auteur ; M. D. FALLIN, Auteur . - 36 p.
Langues : Anglais (eng)
in Molecular Autism > 10 (2019) . - 36 p.
Mots-clés : Autism spectrum disorder Chromatin Environment Gene expression Meta-analysis Microarray Neurodevelopment Perinatal Prospective study Umbilical cord blood Index. décimale : PER Périodiques Résumé : Background: Autism spectrum disorder (ASD) is a neurodevelopmental disorder that affects more than 1% of children in the USA. ASD risk is thought to arise from both genetic and environmental factors, with the perinatal period as a critical window. Understanding early transcriptional changes in ASD would assist in clarifying disease pathogenesis and identifying biomarkers. However, little is known about umbilical cord blood gene expression profiles in babies later diagnosed with ASD compared to non-typically developing and non-ASD (Non-TD) or typically developing (TD) children. Methods: Genome-wide transcript levels were measured by Affymetrix Human Gene 2.0 array in RNA from cord blood samples from both the Markers of Autism Risk in Babies-Learning Early Signs (MARBLES) and the Early Autism Risk Longitudinal Investigation (EARLI) high-risk pregnancy cohorts that enroll younger siblings of a child previously diagnosed with ASD. Younger siblings were diagnosed based on assessments at 36 months, and 59 ASD, 92 Non-TD, and 120 TD subjects were included. Using both differential expression analysis and weighted gene correlation network analysis, gene expression between ASD and TD, and between Non-TD and TD, was compared within each study and via meta-analysis. Results: While cord blood gene expression differences comparing either ASD or Non-TD to TD did not reach genome-wide significance, 172 genes were nominally differentially expressed between ASD and TD cord blood (log2(fold change) > 0.1, p < 0.01). These genes were significantly enriched for functions in xenobiotic metabolism, chromatin regulation, and systemic lupus erythematosus (FDR q < 0.05). In contrast, 66 genes were nominally differentially expressed between Non-TD and TD, including 8 genes that were also differentially expressed in ASD. Gene coexpression modules were significantly correlated with demographic factors and cell type proportions. Limitations: ASD-associated gene expression differences identified in this study are subtle, as cord blood is not the main affected tissue, it is composed of many cell types, and ASD is a heterogeneous disorder. Conclusions: This is the first study to identify gene expression differences in cord blood specific to ASD through a meta-analysis across two prospective pregnancy cohorts. The enriched gene pathways support involvement of environmental, immune, and epigenetic mechanisms in ASD etiology. En ligne : http://dx.doi.org/10.1186/s13229-019-0287-z Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=414