Centre d'Information et de documentation du CRA Rhône-Alpes
CRA
Informations pratiques
-
Adresse
Centre d'information et de documentation
du CRA Rhône-Alpes
Centre Hospitalier le Vinatier
bât 211
95, Bd Pinel
69678 Bron CedexHoraires
Lundi au Vendredi
9h00-12h00 13h30-16h00Contact
Tél: +33(0)4 37 91 54 65
Mail
Fax: +33(0)4 37 91 54 37
-
Résultat de la recherche
4 recherche sur le mot-clé 'Copy number variations (CNVs)'
Affiner la recherche Générer le flux rss de la recherche
Partager le résultat de cette recherche Faire une suggestion
Genome-wide analysis of copy number variations identifies PARK2 as a candidate gene for autism spectrum disorder / C. L. YIN in Molecular Autism, 7 (2016)
[article]
Titre : Genome-wide analysis of copy number variations identifies PARK2 as a candidate gene for autism spectrum disorder Type de document : Texte imprimé et/ou numérique Auteurs : C. L. YIN, Auteur ; H. I. CHEN, Auteur ; L. H. LI, Auteur ; Yi-Ling CHIEN, Auteur ; H. M. LIAO, Auteur ; Miao-Churn CHOU, Auteur ; W. J. CHOU, Auteur ; W. C. TSAI, Auteur ; Yen-Nan CHIU, Auteur ; Y. Y. WU, Auteur ; C. Z. LO, Auteur ; J. Y. WU, Auteur ; Y. T. CHEN, Auteur ; S. S. GAU, Auteur Article en page(s) : 23p. Langues : Anglais (eng) Mots-clés : Adolescent Asian Continental Ancestry Group/genetics Autism Spectrum Disorder/etiology/genetics Child China Cohort Studies DNA Copy Number Variations Down-Regulation Exons Female Genome-Wide Association Study Genotype Humans Male Odds Ratio Pedigree Phenotype Polymorphism, Single Nucleotide Ubiquitin-Protein Ligases/genetics Autism spectrum disorder (ASD) Copy number variations (CNVs) Family study Gene expression Park2 Index. décimale : PER Périodiques Résumé : BACKGROUND: Autism spectrum disorder (ASD) is an early-onset neurodevelopmental disorder with complex genetic underpinning in its etiology. Copy number variations (CNVs) as one of the genetic factors associated with ASD have been addressed in recent genome-wide association studies (GWAS). However, the significance of CNV has not been well investigated in non-Caucasian ASD population. METHODS: To identify the pathogenic CNVs responsible for ASD in Han Chinese, we performed a segment-based GWAS of CNV in 335 ASD cases and 1093 healthy controls using Affymetrix single nucleotide polymorphism (SNP) array by focusing on case-specific CNVs. PARK2 was one of the important genes with several case-specific regions overlapped on it. The findings were validated in the initial screen sample set and replicated in another sample set by real-time quantitative PCR (qPCR). RESULTS: A total of six CNVs at 6q26 that spanned different exons of PARK2 were identified. The PARK2 expression level was down-regulated at exon-dependent manner in cases with either deletion or duplication. The result revealed that the gene function might be disrupted by exonic deletion and duplication. We also observed that the ASD case with exonic duplication demonstrated a more severe interference of PARK2 expression and the clinical feature than the ones with deletion at the exons 2-4 of the PARK2 gene. CONCLUSIONS: Our finding provides evidence to support that CNVs affecting PARK2 function might contribute to genetic etiology of a proportion of cases with ASD. The intriguing results of this work warrant further study on characterizing the functional impact of various exonic CNVs on the PARK2 gene. TRIAL REGISTRATION: ClinicalTrials.gov NCT00494754. En ligne : http://dx.doi.org/10.1186/s13229-016-0087-7 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=329
in Molecular Autism > 7 (2016) . - 23p.[article] Genome-wide analysis of copy number variations identifies PARK2 as a candidate gene for autism spectrum disorder [Texte imprimé et/ou numérique] / C. L. YIN, Auteur ; H. I. CHEN, Auteur ; L. H. LI, Auteur ; Yi-Ling CHIEN, Auteur ; H. M. LIAO, Auteur ; Miao-Churn CHOU, Auteur ; W. J. CHOU, Auteur ; W. C. TSAI, Auteur ; Yen-Nan CHIU, Auteur ; Y. Y. WU, Auteur ; C. Z. LO, Auteur ; J. Y. WU, Auteur ; Y. T. CHEN, Auteur ; S. S. GAU, Auteur . - 23p.
Langues : Anglais (eng)
in Molecular Autism > 7 (2016) . - 23p.
Mots-clés : Adolescent Asian Continental Ancestry Group/genetics Autism Spectrum Disorder/etiology/genetics Child China Cohort Studies DNA Copy Number Variations Down-Regulation Exons Female Genome-Wide Association Study Genotype Humans Male Odds Ratio Pedigree Phenotype Polymorphism, Single Nucleotide Ubiquitin-Protein Ligases/genetics Autism spectrum disorder (ASD) Copy number variations (CNVs) Family study Gene expression Park2 Index. décimale : PER Périodiques Résumé : BACKGROUND: Autism spectrum disorder (ASD) is an early-onset neurodevelopmental disorder with complex genetic underpinning in its etiology. Copy number variations (CNVs) as one of the genetic factors associated with ASD have been addressed in recent genome-wide association studies (GWAS). However, the significance of CNV has not been well investigated in non-Caucasian ASD population. METHODS: To identify the pathogenic CNVs responsible for ASD in Han Chinese, we performed a segment-based GWAS of CNV in 335 ASD cases and 1093 healthy controls using Affymetrix single nucleotide polymorphism (SNP) array by focusing on case-specific CNVs. PARK2 was one of the important genes with several case-specific regions overlapped on it. The findings were validated in the initial screen sample set and replicated in another sample set by real-time quantitative PCR (qPCR). RESULTS: A total of six CNVs at 6q26 that spanned different exons of PARK2 were identified. The PARK2 expression level was down-regulated at exon-dependent manner in cases with either deletion or duplication. The result revealed that the gene function might be disrupted by exonic deletion and duplication. We also observed that the ASD case with exonic duplication demonstrated a more severe interference of PARK2 expression and the clinical feature than the ones with deletion at the exons 2-4 of the PARK2 gene. CONCLUSIONS: Our finding provides evidence to support that CNVs affecting PARK2 function might contribute to genetic etiology of a proportion of cases with ASD. The intriguing results of this work warrant further study on characterizing the functional impact of various exonic CNVs on the PARK2 gene. TRIAL REGISTRATION: ClinicalTrials.gov NCT00494754. En ligne : http://dx.doi.org/10.1186/s13229-016-0087-7 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=329 Copy number variation and neural pathway analysis of children with autism spectrum disorder from a large Han Chinese population-based cross-sectional study / You YANG in Research in Autism Spectrum Disorders, 51 (July 2018)
[article]
Titre : Copy number variation and neural pathway analysis of children with autism spectrum disorder from a large Han Chinese population-based cross-sectional study Type de document : Texte imprimé et/ou numérique Auteurs : You YANG, Auteur ; Zhijuan JIN, Auteur ; Jian WANG, Auteur ; Shijian LIU, Auteur ; Hong HUANG, Auteur ; Xingming JIN, Auteur Article en page(s) : p.66-74 Langues : Anglais (eng) Mots-clés : Autism spectrum disorder (ASD) Copy number variations (CNVs) Microarray diagnostic testing Pathway analysis Han Chinese Index. décimale : PER Périodiques Résumé : Certain genetic events can be attributed to copy number variations (CNVs). A population in Shanghai, China was screened for autism spectrum disorder (ASD), and their CNV characteristics and possible associations with neural pathways were analyzed. A multi-stage stratified cluster sampling method was used to evaluate 3- to 12-year-old children from the general population who were in kindergarten and primary school in Shanghai. DNA samples were obtained from 133 ASD cases from preparatory ASD screening. An Affymetrix Cytoscan 750k array was used for copy number variant detection. Among the 711 children who had positive results on a survey completed by both their parents and teachers, a total of 663 (93.2%) children underwent diagnostic evaluation. Of these, 203 children were confirmed to have ASD, including 163 (80.3%) children from special education schools, 29 (14.3%) children from general kindergartens, and 11 (5.4%) children from general primary schools. Final consent had been given for blood collection, and 15 CNVs that may contribute to ASD in 133 cases were identified. The mean ages at which the ASD children with and without pathogenic CNVs (pCNVs) began to speak were 45.6 months and 29.2 months, respectively (t?=?2.452, P?=?0.016), and the ages of walking alone were 33.9 months and 17.5 months, respectively (t?=?5.376, P?0.001). ASD patients with pCNVs showed more abnormal facial features and signs of ASD (long faces, large noses, irregular teeth, dental caries, excessive joint extension) than those without pCNVs. The differences in tooth irregularity and dental caries between children with and without pCNVs were statistically significant (P?0.01). These CNVs included a total of 993 genes. Pathway analysis was performed, and five statistically significant pathways were identified in online databases. This was the first population-based, pilot pathway analysis of CNVs in children with ASD under the diagnostic and statistical manual of mental disorders (DSM)-5 diagnostic criteria in China. Results indicate that ASD may be related to gamma-aminobutyric acid (GABA),dopamine, glycine and synaptic proteins. These findings are consistent with those of previous studies and provide new evidence for the role of regulation of proteolysis and endopeptidase activity in ASD. En ligne : https://doi.org/10.1016/j.rasd.2018.04.006 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=362
in Research in Autism Spectrum Disorders > 51 (July 2018) . - p.66-74[article] Copy number variation and neural pathway analysis of children with autism spectrum disorder from a large Han Chinese population-based cross-sectional study [Texte imprimé et/ou numérique] / You YANG, Auteur ; Zhijuan JIN, Auteur ; Jian WANG, Auteur ; Shijian LIU, Auteur ; Hong HUANG, Auteur ; Xingming JIN, Auteur . - p.66-74.
Langues : Anglais (eng)
in Research in Autism Spectrum Disorders > 51 (July 2018) . - p.66-74
Mots-clés : Autism spectrum disorder (ASD) Copy number variations (CNVs) Microarray diagnostic testing Pathway analysis Han Chinese Index. décimale : PER Périodiques Résumé : Certain genetic events can be attributed to copy number variations (CNVs). A population in Shanghai, China was screened for autism spectrum disorder (ASD), and their CNV characteristics and possible associations with neural pathways were analyzed. A multi-stage stratified cluster sampling method was used to evaluate 3- to 12-year-old children from the general population who were in kindergarten and primary school in Shanghai. DNA samples were obtained from 133 ASD cases from preparatory ASD screening. An Affymetrix Cytoscan 750k array was used for copy number variant detection. Among the 711 children who had positive results on a survey completed by both their parents and teachers, a total of 663 (93.2%) children underwent diagnostic evaluation. Of these, 203 children were confirmed to have ASD, including 163 (80.3%) children from special education schools, 29 (14.3%) children from general kindergartens, and 11 (5.4%) children from general primary schools. Final consent had been given for blood collection, and 15 CNVs that may contribute to ASD in 133 cases were identified. The mean ages at which the ASD children with and without pathogenic CNVs (pCNVs) began to speak were 45.6 months and 29.2 months, respectively (t?=?2.452, P?=?0.016), and the ages of walking alone were 33.9 months and 17.5 months, respectively (t?=?5.376, P?0.001). ASD patients with pCNVs showed more abnormal facial features and signs of ASD (long faces, large noses, irregular teeth, dental caries, excessive joint extension) than those without pCNVs. The differences in tooth irregularity and dental caries between children with and without pCNVs were statistically significant (P?0.01). These CNVs included a total of 993 genes. Pathway analysis was performed, and five statistically significant pathways were identified in online databases. This was the first population-based, pilot pathway analysis of CNVs in children with ASD under the diagnostic and statistical manual of mental disorders (DSM)-5 diagnostic criteria in China. Results indicate that ASD may be related to gamma-aminobutyric acid (GABA),dopamine, glycine and synaptic proteins. These findings are consistent with those of previous studies and provide new evidence for the role of regulation of proteolysis and endopeptidase activity in ASD. En ligne : https://doi.org/10.1016/j.rasd.2018.04.006 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=362 Use of clinical chromosomal microarray in Chinese patients with autism spectrum disorder-implications of a copy number variation involving DPP10 / A. S. L. MAK in Molecular Autism, 8 (2017)
[article]
Titre : Use of clinical chromosomal microarray in Chinese patients with autism spectrum disorder-implications of a copy number variation involving DPP10 Type de document : Texte imprimé et/ou numérique Auteurs : A. S. L. MAK, Auteur ; A. T. G. CHIU, Auteur ; G. K. C. LEUNG, Auteur ; C. C. Y. MAK, Auteur ; Y. W. Y. CHU, Auteur ; G. T. K. MOK, Auteur ; W. F. TANG, Auteur ; K. Y. K. CHAN, Auteur ; M. H. Y. TANG, Auteur ; E. T. LAU YIM, Auteur ; K. W. SO, Auteur ; V. Q. TAO, Auteur ; C. W. FUNG, Auteur ; Virginia C.N. WONG, Auteur ; M. UDDIN, Auteur ; S. L. LEE, Auteur ; C. R. MARSHALL, Auteur ; Stephen SCHERER, Auteur ; A. S. Y. KAN, Auteur ; B. H. Y. CHUNG, Auteur Article en page(s) : 31p. Langues : Anglais (eng) Mots-clés : Array comparative genomic hybridization (aCGH) Autism spectrum disorder (ASD) Chinese Copy number variations (CNVs) Dpp10 Index. décimale : PER Périodiques Résumé : BACKGROUND: Array comparative genomic hybridization (aCGH) is recommended as a first-tier genetic test for children with autism spectrum disorder (ASD). However, interpretation of results can often be challenging partly due to the fact that copy number variants (CNVs) in non-European ASD patients are not well studied. To address this literature gap, we report the CNV findings in a cohort of Chinese children with ASD. METHODS: DNA samples were obtained from 258 Chinese ASD patients recruited from a child assessment center between January 2011 and August 2014. aCGH was performed using NimbleGen-CGX-135k or Agilent-CGX 60k oligonucleotide array. Results were classified based on existing guidelines and literature. RESULTS: Ten pathogenic CNVs and one likely pathogenic CNV were found in nine patients, with an overall diagnostic yield of 3.5%. A 138 kb duplication involving 3' exons of DPP10 (arr[GRCh37] 2q14.1(116534689_116672358)x3), reported to be associated with ASD, was identified in one patient (0.39%). The same CNV was reported as variant of uncertain significance (VUS) in DECIPHER database. Multiple individuals of typical development carrying a similar duplication were identified among our ancestry-matched control with a frequency of 6/653 (0.92%) as well as from literature and genomic databases. CONCLUSIONS: The DPP10 duplication is likely a benign CNV polymorphism enriched in Southern Chinese with a population frequency of ~1%. This highlights the importance of using ancestry-matched controls in interpretation of aCGH findings. En ligne : http://dx.doi.org/10.1186/s13229-017-0136-x Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=330
in Molecular Autism > 8 (2017) . - 31p.[article] Use of clinical chromosomal microarray in Chinese patients with autism spectrum disorder-implications of a copy number variation involving DPP10 [Texte imprimé et/ou numérique] / A. S. L. MAK, Auteur ; A. T. G. CHIU, Auteur ; G. K. C. LEUNG, Auteur ; C. C. Y. MAK, Auteur ; Y. W. Y. CHU, Auteur ; G. T. K. MOK, Auteur ; W. F. TANG, Auteur ; K. Y. K. CHAN, Auteur ; M. H. Y. TANG, Auteur ; E. T. LAU YIM, Auteur ; K. W. SO, Auteur ; V. Q. TAO, Auteur ; C. W. FUNG, Auteur ; Virginia C.N. WONG, Auteur ; M. UDDIN, Auteur ; S. L. LEE, Auteur ; C. R. MARSHALL, Auteur ; Stephen SCHERER, Auteur ; A. S. Y. KAN, Auteur ; B. H. Y. CHUNG, Auteur . - 31p.
Langues : Anglais (eng)
in Molecular Autism > 8 (2017) . - 31p.
Mots-clés : Array comparative genomic hybridization (aCGH) Autism spectrum disorder (ASD) Chinese Copy number variations (CNVs) Dpp10 Index. décimale : PER Périodiques Résumé : BACKGROUND: Array comparative genomic hybridization (aCGH) is recommended as a first-tier genetic test for children with autism spectrum disorder (ASD). However, interpretation of results can often be challenging partly due to the fact that copy number variants (CNVs) in non-European ASD patients are not well studied. To address this literature gap, we report the CNV findings in a cohort of Chinese children with ASD. METHODS: DNA samples were obtained from 258 Chinese ASD patients recruited from a child assessment center between January 2011 and August 2014. aCGH was performed using NimbleGen-CGX-135k or Agilent-CGX 60k oligonucleotide array. Results were classified based on existing guidelines and literature. RESULTS: Ten pathogenic CNVs and one likely pathogenic CNV were found in nine patients, with an overall diagnostic yield of 3.5%. A 138 kb duplication involving 3' exons of DPP10 (arr[GRCh37] 2q14.1(116534689_116672358)x3), reported to be associated with ASD, was identified in one patient (0.39%). The same CNV was reported as variant of uncertain significance (VUS) in DECIPHER database. Multiple individuals of typical development carrying a similar duplication were identified among our ancestry-matched control with a frequency of 6/653 (0.92%) as well as from literature and genomic databases. CONCLUSIONS: The DPP10 duplication is likely a benign CNV polymorphism enriched in Southern Chinese with a population frequency of ~1%. This highlights the importance of using ancestry-matched controls in interpretation of aCGH findings. En ligne : http://dx.doi.org/10.1186/s13229-017-0136-x Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=330 Copy number variation in Han Chinese individuals with autism spectrum disorder / M. J. GAZZELLONE in Journal of Neurodevelopmental Disorders, 6-1 (December 2014)
[article]
Titre : Copy number variation in Han Chinese individuals with autism spectrum disorder Type de document : Texte imprimé et/ou numérique Auteurs : M. J. GAZZELLONE, Auteur ; X. ZHOU, Auteur ; A. C. LIONEL, Auteur ; M. UDDIN, Auteur ; B. THIRUVAHINDRAPURAM, Auteur ; S. LIANG, Auteur ; C. SUN, Auteur ; J. WANG, Auteur ; M. ZOU, Auteur ; K. TAMMIMIES, Auteur ; S. WALKER, Auteur ; T. SELVANAYAGAM, Auteur ; J. WEI, Auteur ; Z. WANG, Auteur ; L. WU, Auteur ; Stephen SCHERER, Auteur Article en page(s) : p.34 Langues : Anglais (eng) Mots-clés : Autism spectrum disorder (ASD) Copy number variations (CNVs) Han Chinese Microarray diagnostic testing Index. décimale : PER Périodiques Résumé : BACKGROUND: Autism spectrum disorders (ASDs) are a group of neurodevelopmental conditions with a demonstrated genetic etiology. Rare (<1% frequency) copy number variations (CNVs) account for a proportion of the genetic events involved, but the contribution of these events in non-European ASD populations has not been well studied. Here, we report on rare CNVs detected in a cohort of individuals with ASD of Han Chinese background. METHODS: DNA samples were obtained from 104 ASD probands and their parents who were recruited from Harbin, China. Samples were genotyped on the Affymetrix CytoScan HD platform. Rare CNVs were identified by comparing data with 873 technology-matched controls from Ontario and 1,235 additional population controls of Han Chinese ethnicity. RESULTS: Of the probands, 8.6% had at least 1 de novo CNV (overlapping the GIGYF2, SPRY1, 16p13.3, 16p11.2, 17p13.3-17p13.2, DMD, and NAP1L6 genes/loci). Rare inherited CNVs affected other plausible neurodevelopmental candidate genes including GRID2, LINGO2, and SLC39A12. A 24-kb duplication was also identified at YWHAE, a gene previously implicated in ASD and other developmental disorders. This duplication is observed at a similar frequency in cases and in population controls and is likely a benign Asian-specific copy number polymorphism. CONCLUSIONS: Our findings help define genomic features relevant to ASD in the Han Chinese and emphasize the importance of using ancestry-matched controls in medical genetic interpretations. En ligne : http://dx.doi.org/10.1186/1866-1955-6-34 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=346
in Journal of Neurodevelopmental Disorders > 6-1 (December 2014) . - p.34[article] Copy number variation in Han Chinese individuals with autism spectrum disorder [Texte imprimé et/ou numérique] / M. J. GAZZELLONE, Auteur ; X. ZHOU, Auteur ; A. C. LIONEL, Auteur ; M. UDDIN, Auteur ; B. THIRUVAHINDRAPURAM, Auteur ; S. LIANG, Auteur ; C. SUN, Auteur ; J. WANG, Auteur ; M. ZOU, Auteur ; K. TAMMIMIES, Auteur ; S. WALKER, Auteur ; T. SELVANAYAGAM, Auteur ; J. WEI, Auteur ; Z. WANG, Auteur ; L. WU, Auteur ; Stephen SCHERER, Auteur . - p.34.
Langues : Anglais (eng)
in Journal of Neurodevelopmental Disorders > 6-1 (December 2014) . - p.34
Mots-clés : Autism spectrum disorder (ASD) Copy number variations (CNVs) Han Chinese Microarray diagnostic testing Index. décimale : PER Périodiques Résumé : BACKGROUND: Autism spectrum disorders (ASDs) are a group of neurodevelopmental conditions with a demonstrated genetic etiology. Rare (<1% frequency) copy number variations (CNVs) account for a proportion of the genetic events involved, but the contribution of these events in non-European ASD populations has not been well studied. Here, we report on rare CNVs detected in a cohort of individuals with ASD of Han Chinese background. METHODS: DNA samples were obtained from 104 ASD probands and their parents who were recruited from Harbin, China. Samples were genotyped on the Affymetrix CytoScan HD platform. Rare CNVs were identified by comparing data with 873 technology-matched controls from Ontario and 1,235 additional population controls of Han Chinese ethnicity. RESULTS: Of the probands, 8.6% had at least 1 de novo CNV (overlapping the GIGYF2, SPRY1, 16p13.3, 16p11.2, 17p13.3-17p13.2, DMD, and NAP1L6 genes/loci). Rare inherited CNVs affected other plausible neurodevelopmental candidate genes including GRID2, LINGO2, and SLC39A12. A 24-kb duplication was also identified at YWHAE, a gene previously implicated in ASD and other developmental disorders. This duplication is observed at a similar frequency in cases and in population controls and is likely a benign Asian-specific copy number polymorphism. CONCLUSIONS: Our findings help define genomic features relevant to ASD in the Han Chinese and emphasize the importance of using ancestry-matched controls in medical genetic interpretations. En ligne : http://dx.doi.org/10.1186/1866-1955-6-34 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=346