Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Down syndrome CNVs - samples

ABSTRACT: Down syndrome CNV genotyping data

PROVIDER: EGAD00010000466 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Publications

The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome.

Sailani M Reza MR Makrythanasis Periklis P Valsesia Armand A Santoni Federico A FA Deutsch Samuel S Popadin Konstantin K Borel Christelle C Migliavacca Eugenia E Sharp Andrew J AJ Duriaux Sail Genevieve G Falconnet Emilie E Rabionet Kelly K Serra-Juhé Clara C Vicari Stefano S Laux Daniela D Grattau Yann Y Dembour Guy G Megarbane Andre A Touraine Renaud R Stora Samantha S Kitsiou Sofia S Fryssira Helena H Chatzisevastou-Loukidou Chariklia C Kanavakis Emmanouel E Merla Giuseppe G Bonnet Damien D Pérez-Jurado Luis A LA Estivill Xavier X Delabar Jean M JM Antonarakis Stylianos E SE

Genome research 20130619 9

Congenital heart defect (CHD) occurs in 40% of Down syndrome (DS) cases. While carrying three copies of chromosome 21 increases the risk for CHD, trisomy 21 itself is not sufficient to cause CHD. Thus, additional genetic variation and/or environmental factors could contribute to the CHD risk. Here we report genomic variations that in concert with trisomy 21, determine the risk for CHD in DS. This case-control GWAS includes 187 DS with CHD (AVSD = 69, ASD = 53, VSD = 65) as cases, and 151 DS with ...[more]

PMID: 23783273

Similar Datasets

Down syndrome SNPs - samples

Project description:Down syndrome SNP genotyping data

| EGAD00010000464 | EGA

Affymetrix SNP 6.0 data for individuals with Trisomy 21 or Down syndrome

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

Affymetrix SNP 6.0 data for individuals with Trisomy 21 or Down syndrome

2014-10-24 | GSE60607 | GEO

Single cell genotyping of Myeloid Leukaemia of Down Syndrome cells

Project description:Single cell genotyping of Myeloid Leukaemia of Down Syndrome cells

| PRJEB32618 | ENA

DNA methylation profiles of brain samples from Down Syndrome subjects and controls.

Project description:Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 486,000 CpGs. Dataset included 71 samples from multiple brain regions (cerebellum, temporal/occipital/frontal cortex). The goal was to evalute the effect of trisomy 21 on DNA methylation levels and epigenetic age. Explanation of characteristics variables in supplementary file Explanation_of_characteristic_variables2.docx Bisulphite converted DNA from the 71 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. Trisomy 21 (Down syndrome status) was related to CpGs.

2015-03-02 | E-GEOD-63347 | biostudies-arrayexpress

Crnic Institute Human Trisome Project - JAK inhibition in Down syndrome: PolyA RNAseq from whole blood

Project description:Analysis of steady-state mRNA levels in whole blood of subjects with Down syndrome (trisomy 21) and qualifying moderate-to-severe immune skin conditions. This dataset is part of the Human Trisome Project run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/

2024-01-23 | GSE251967 | GEO

Epigenetic changes in Down syndrome leukemogenesis

Project description:Epigenetic changes in Down syndrome leukemogenesis

| PRJNA197487 | ENA

Expression data from Down syndrome and non-Down syndrome pediatric acute lymphoblastic leukemia cases

2011-07-12 | GSE20910 | GEO

Gene Expression profiling of Down Syndrome Lungs

Project description:Gene Expression profiling of Down Syndrome Lungs

| PRJNA732691 | ENA

Expression data from Down syndrome and non-Down syndrome pediatric acute lymphoblastic leukemia cases

Project description:Gene expression profiling (GEP) can reveal characteristic signatures associated with distinct biologic subtypes of acute lymphoblastic leukemia (ALL). We performed GEP on Down syndrome (DS) and comparison non-Down syndrome (NDS) ALL cases to identify biologic differences between these groups. Ficoll-enriched, cryopreserved diagnostic bone marrow samples were obtained from patients with newly diagnosed B-precursor acute lymphoblastic leukemia.

2011-07-12 | E-GEOD-20910 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data