Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA131535 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Schizophrenia is a severe psychiatric illness that affects ~1% of the population and has a strong genetic underpinning. Recently, genome wide analysis of copy number variation (CNV) has implicated rare and de novo events as important in schizophrenia. Here we report a genome-wide analysis of 245 schizophrenia cases and 490 controls, all of Ashkenazi Jewish descent. Since many studies have found an excess burden of large, rare deletions in cases, we limited our analysis to deletions over 500 kb in size. We observed seven large, rare deletions in cases with 57% of these being de novo. We focused on one 836 kb de novo deletion at chromosome 3q29 that falls within a 1.3–1.6 Mb deletion previously identified in children with intellectual disability (ID) and autism, as increasing evidence suggests an overlap of specific rare CNVs between autism and schizophrenia. By combining our data with prior CNV studies of schizophrenia and analysis of the data of the Genetic Association Information Network (GAIN), we identified six 3q29 deletions among 7,545 schizophrenic subjects and one among 39,748 controls, resulting in a statistically significant association with schizophrenia (p = 0.02) and an odds ratio estimate of 17 (95% CI: 1.36–1198.4). Moreover, this 3q29 deletion region contains two linkage peaks from prior schizophrenia family studies, and the minimal deletion interval implicates 20 annotated genes, including PAK2 and DLG1, both paralogous to X-linked ID genes and now strong candidates for schizophrenia susceptibility. Copy Number alanysis was performed on 245 cases and 490 controls of Ashkenazi Jewish descent. Samples were analyzed for deletions greater than 500 kb, with 20 or more snps in the interval. Three algorithms were used for analysis, GADA, GLAD and BEAST. The reference was created by using all samples processed here as the reference.
2010-08-06 | E-GEOD-23201 | biostudies-arrayexpress
Project description:Schizophrenia is a severe psychiatric illness that affects ~1% of the population and has a strong genetic underpinning. Recently, genome wide analysis of copy number variation (CNV) has implicated rare and de novo events as important in schizophrenia. Here we report a genome-wide analysis of 245 schizophrenia cases and 490 controls, all of Ashkenazi Jewish descent. Since many studies have found an excess burden of large, rare deletions in cases, we limited our analysis to deletions over 500 kb in size. We observed seven large, rare deletions in cases with 57% of these being de novo. We focused on one 836 kb de novo deletion at chromosome 3q29 that falls within a 1.3–1.6 Mb deletion previously identified in children with intellectual disability (ID) and autism, as increasing evidence suggests an overlap of specific rare CNVs between autism and schizophrenia. By combining our data with prior CNV studies of schizophrenia and analysis of the data of the Genetic Association Information Network (GAIN), we identified six 3q29 deletions among 7,545 schizophrenic subjects and one among 39,748 controls, resulting in a statistically significant association with schizophrenia (p = 0.02) and an odds ratio estimate of 17 (95% CI: 1.36–1198.4). Moreover, this 3q29 deletion region contains two linkage peaks from prior schizophrenia family studies, and the minimal deletion interval implicates 20 annotated genes, including PAK2 and DLG1, both paralogous to X-linked ID genes and now strong candidates for schizophrenia susceptibility.
2010-08-06 | GSE23201 | GEO
Project description:The Ashkenazi Jewish population has long been considered a genetic isolate and presumed to have the genetic signatures of founder effects and isolation. We genotyped a large cohort of Ashkenazi Jews and analyzed their genetic structure compared to other worldwide populations. We genotyped 471 normal control Ashkenazi Jewish individuals with the Affymetrix 6.0 array and analyzed their genetic structure relative to other Europe and worldwide populations. We measured heterozygosity, linkage disequilibrium, identity-by-descent and used extended haplotype tests of positive selection.
2010-08-16 | E-GEOD-23636 | biostudies-arrayexpress
Project description:The Ashkenazi Jewish population has long been considered a genetic isolate and presumed to have the genetic signatures of founder effects and isolation. We genotyped a large cohort of Ashkenazi Jews and analyzed their genetic structure compared to other worldwide populations.
2010-08-16 | GSE23636 | GEO
Project description:Genetics of Schizophrenia in a Ashkenazi Jewish Case-Control Cohort
| PRJNA81149 | ENA
Project description:Genetics of Schizophrenia in a Ashkenazi Jewish Case-Control Cohort
| PRJNA81147 | ENA
Project description:Whole genome, high coverage, sequencing of 128 Ashkenazi Jewish controls
| EGAD00001000781 | EGA
Project description:Individuals with Down syndrome (DS) are at an increased risk for developing congenital heart defects especially atrioventricular septal defects (AVSD). Our goal was to identify the contribution of copy number variants (CNV) to DS-associated AVSD. We used the Affymetrix SNP 6.0 genotyping platform to comprehensively characterize CNVs in 452 ethnically matched individuals with DS, comprising of 210 cases (DS + complete AVSD) and 242 controls with a structurally normal heart (DS + NH). Results from burden and region-wise analyses using PLINK revealed that despite the 2000 fold elevated risk, common CNVs of large effect (OR > 2.0) do not account for the increased risk observed in DS-associated AVSD. In contrast, cases do harbor a significantly elevated burden of large rare variants (> 100kb, < 1% frequency) (p < 0.01) and case deletions intersect genes more often than those observed in controls (p < 0.007). Gene enrichment analysis showed a trend for enrichment among deletions impacting the ciliome pathway in cases compared to controls. Our findings suggest that the etiology of AVSD is highly complex and does not arise from the action of a few common variants of large effect. Instead, our data support a multifactorial model, wherein large rare deletions play a significant role in elevating the risk of AVSD in a trisomic background.
2014-10-24 | GSE60607 | GEO
Project description:Individuals with Down syndrome (DS) are at an increased risk for developing congenital heart defects especially atrioventricular septal defects (AVSD). Our goal was to identify the contribution of copy number variants (CNV) to DS-associated AVSD. We used the Affymetrix SNP 6.0 genotyping platform to comprehensively characterize CNVs in 452 ethnically matched individuals with DS, comprising of 210 cases (DS + complete AVSD) and 242 controls with a structurally normal heart (DS + NH). Results from burden and region-wise analyses using PLINK revealed that despite the 2000 fold elevated risk, common CNVs of large effect (OR > 2.0) do not account for the increased risk observed in DS-associated AVSD. In contrast, cases do harbor a significantly elevated burden of large rare variants (> 100kb, < 1% frequency) (p < 0.01) and case deletions intersect genes more often than those observed in controls (p < 0.007). Gene enrichment analysis showed a trend for enrichment among deletions impacting the ciliome pathway in cases compared to controls. Our findings suggest that the etiology of AVSD is highly complex and does not arise from the action of a few common variants of large effect. Instead, our data support a multifactorial model, wherein large rare deletions play a significant role in elevating the risk of AVSD in a trisomic background. Copy Number Variation Analysis of individuals with DS using Affymetrix SNP 6.0 genotyping platform. A composite reference was generated using the same dataset to derive the log2 ratios using Affymetrix Power Tols (APT). Submitting here the preliminary data from 437 subjects, 15 were excluded due to privacy concerns.
2014-10-24 | E-GEOD-60607 | biostudies-arrayexpress
Project description:Population genetic structure of the Ashkenazi Jewish population
| PRJNA130941 | ENA