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Autism Genome Project (AGP) Consortium - Whole Genome Association and Copy Number Variation Study of over 1,500 Parent-Offspring Trios - Stage I

ABSTRACT:

Autism spectrum disorders (ASDs) are highly heritable (~90%), yet the underlying genetic determinants are largely unknown. To understand the genetic and phenotypic heterogeneity in ASDs, we analyzed over 1,500 strictly defined ASD families with over 1,000,000 single nucleotide polymorphisms (SNPs), and applied multiple analytical strategies to examine these families for SNPs and Copy Number Variation (CNVs) affecting risk for ASDs. Secondary analyses examined associations in more homogenous subgroups. Furthermore, the use of large control datasets permitted contrasting case and control samples and addressed the potential increased burden of rare CNVs in ASD. Our data have allowed us to discern key features of the ASD genomic architecture, find new susceptibility loci, and chart a course for future studies in ASDs.

PROVIDER: phs000267.v1.p1 | EGA |

REPOSITORIES: EGA

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Genome-wide linkage analyses of quantitative and categorical autism subphenotypes.

Liu Xiao-Qing XQ Paterson Andrew D AD Szatmari Peter P

Biological psychiatry 20080716 7

<h4>Background</h4>The search for susceptibility genes in autism and autism spectrum disorders (ASD) has been hindered by the possible small effects of individual genes and by genetic (locus) heterogeneity. To overcome these obstacles, one method is to use autism-related subphenotypes instead of the categorical diagnosis of autism since they may be more directly related to the underlying susceptibility loci. Another strategy is to analyze subsets of families that meet certain clinical criteria t ...[more]

PMID: 18632090

Publication: 1/5

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Autism Genome Project (AGP) Consortium - GWAS - Stage I and II

Project description:<p>Autism spectrum disorders (ASDs) are highly heritable (~90%), yet the underlying genetic determinants are largely unknown. To understand the genetic and phenotypic heterogeneity in ASDs, we analyzed 2,611 strictly defined ASD families with over 1,000,000 single nucleotide polymorphisms (SNPs), and applied multiple analytical strategies to examine these families for SNPs and Copy Number Variation (CNVs) affecting risk for ASDs. Secondary analyses examined associations in more homogenous subgroups. Furthermore, the use of large control datasets permitted contrasting case and control samples and addressed the potential increased burden of rare CNVs in ASD. Our data have allowed us to discern key features of the ASD genomic architecture, find new susceptibility loci, and chart a course for future studies in ASDs.</p>

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Genome-wide copy number variation in Chinese schizophrenia trios

Project description:To reveal the risk CNVs of SZ in Chinese population, we recrited and enrolled 100 Chinese family trios with a schizophrenia affected children and both of their father and mother. SZ was diagnosed according to DSM-IV criteria by two independent psychiatrists. There gDNA we screen the genome-wide CNV using Agilent SurePrint G3 Human CGH Microarray Kit (1x1M) and Agilent sex-matched human DNA was used as reference. The CNV were called by ADM-2 statistical algorithms with a threshold of 6.0. We compared the burden of large rare CNVs and found that SZ probands carried more duplications and less deletions. Furtherly, we performed familial inheritance analysis of transmission disequilibrium and de novo CNV detection, validated several associated CNV loci with SZ susceptibility and also identify eight novel loci conferring risk of SZ

2021-10-01 | E-MTAB-8075 | biostudies-arrayexpress

Whole-genome gene expression variation in 210 unrelated HapMap individuals

Project description:Extensive studies are currently being performed to associate disease susceptibility with one form of genetic variation, namely single nucleotide polymorphisms (SNPs). In recent years another type of common genetic variation has been characterised, namely structural variation, including copy number variations (CNVs). To determine the overall contribution of CNVs to complex phenotypes we have performed association analyses of expression levels of 14,925 transcripts with SNPs and CNVs in individuals who are part of the International HapMap project. SNPs and CNVs captured 83.6% and 17.7% of the total detected genetic variation in gene expression, respectively, but the signals from the two types of variation had little overlap. Interrogation of the genome for both types of variants may be an effective way to elucidate the causes of complex phenotypes and disease in humans. Keywords: gene expression

2007-02-09 | GSE6536 | GEO

CGH analysis of inbred mouses strains

Project description:The contribution to genetic diversity of genomic segmental copy number variations (CNVs) is less well understood than that of single-nucleotide polymorphisms (SNPs). While less frequent than SNPs, CNVs have greater potential to affect phenotype. In this study, we have performed the most comprehensive survey to date of CNVs in mice, analyzing the genomes of 42 Mouse Phenome Consortium priority strains. This microarray comparative genomic hybridization (CGH)-based analysis has identified 2094 putative CNVs, with an average of 10 Mb of DNA in 51 CNVs when individual mouse strains were compared to the reference strain C57BL/6J. This amount of variation results in gene content that can differ by hundreds of genes between strains. These genes include members of large families such as the major histocompatibility and pheromone receptor genes, but there are also many singleton genes including genes with expected phenotypic consequences from their deletion or amplification. Using a whole-genome association analysis, we demonstrate that complex multigenic phenotypes, such as food intake, can be associated with specific copy number changes. Keywords: comparative genomic hybridization

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Genotyping data from 120 trios with unexplained mental retardation

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2009-04-01 | GSE13117 | GEO

Rare germline copy number variations and disease susceptibility in familial melanoma

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2016-12-01 | GSE85010 | GEO

Cytogenetics 2.7M and Cytoscan HD 2.8M Microarrays in autistic families in the Lebanese population

Project description:Autism spectrum disorder (ASD) affects these core domains: ritualistic-repetitive behaviors, impaired social interaction, and deficits in non-verbal communication/language development. Although ASD is heritable, its extreme heterogeneity defies genetic analyses. A number of ASD susceptibility genes have been identified. The Lebanese population is ideal for uncovering recessive genes because of a high rate of shared ancestry, consanguineous marriages, and high number of offspring per family. We recruited 36 ASD families (ASD: 37, unaffected parents: 36, unaffected siblings: 33). Cytogenetics 2.7M Microarrays/CytoScanâ¢ HD arrays allowed mapping of homozygous regions of the genome.

2017-07-24 | E-MTAB-4963 | biostudies-arrayexpress

Use of clinical chromosomal microarray in Chinese patients with autism spectrum disorder - implications of a copy number variation involving dpp10 (CGX-12)

Project description:Background: Array-Comparative-Genomic-Hybridization (aCGH) is recommended as first-tier genetic test for children with autism spectrum disorder (ASD). However, result interpretation can be challenging as copy number variants (CNVs) in non-European ASD patients is 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 and one likely-pathogenic CNVs were found in nine patients, with an overall diagnostic yield of 3.5%. A 138kb duplication involving 3â exons of DPP10 (hg[19]chr2:116534689-116672358), reported to be associated with ASD, was identified in one patient (0.39%). The same CNV was reported as variant of unknown significance (VUS) in DECIPHER database. Multiple individuals of typical development carrying a similar duplication were identified amongst our ancestry-matched control with frequency of 6/653 (0.92%) as well as from literature and genomic databases. Conclusions: DPP10 duplication is likely a benign CNV polymorphism enriched in Southern Chinese with population frequency of ~1%. This highlights the importance of using ancestry-matched controls in interpretation of aCGH findings.

2017-04-07 | E-MTAB-5665 | biostudies-arrayexpress

Use of clinical chromosomal microarray in Chinese patients with autism spectrum disorder - implications of a copy number variation involving dpp10 (Perkin Elmer CGX)

Project description:Background Array-Comparative-Genomic-Hybridization (aCGH) is recommended as first-tier genetic test for children with autism spectrum disorder (ASD). However, result interpretation can be challenging as copy number variants (CNVs) in non-European ASD patients is 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 and one likely-pathogenic CNVs were found in nine patients, with an overall diagnostic yield of 3.5%. A 138kb duplication involving 3â exons of DPP10 (hg[19]chr2:116534689-116672358), reported to be associated with ASD, was identified in one patient (0.39%). The same CNV was reported as variant of unknown significance (VUS) in DECIPHER database. Multiple individuals of typical development carrying a similar duplication were identified amongst our ancestry-matched control with frequency of 6/653 (0.92%) as well as from literature and genomic databases. Conclusions DPP10 duplication is likely a benign CNV polymorphism enriched in Southern Chinese with population frequency of ~1%. This highlights the importance of using ancestry-matched controls in interpretation of aCGH findings.

2017-04-07 | E-MTAB-5672 | biostudies-arrayexpress

Individuals with excess numbers of germline de novo CNVs [Agilent]

Project description:We describe a multiple de novo CNV (MdnCNV) phenomenon in which individuals with genomic disorders carry five to ten constitutional de novo CNVs. Five such families are studied, which consists of four trios and one singleton. Various array platforms are used to interogate these families to identify de novo CNVs.

2016-10-14 | GSE87913 | GEO

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