Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Affymetrix CytoScan 750K and HD data for developmental delay and/or physical disability phenotypes samples

ABSTRACT: Affymetrix CytoScan 750K and HD data for developmental delay and/or physical disability phenotypes samples

PROVIDER: PRJNA493801 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Affymetrix CytoScan 750K and HD data for developmental delay and/or physical disability phenotypes samples

Project description:Chromosomal copy number variations (CNV) have been associated with various neurological and developmental disorders and chromosomal microarray (CMA) is a method of choice to diagnose Copy Number Gain/Loss syndromes. Recently, next-generation sequencing (NGS)-based low-coverage whole genome sequencing (LC-WGS) has been applied to detect Copy Number Gain/Loss syndromes. This dataset is intended to be used as a “Golden standard data set” for development of LC-WGS analysis method. It consists of patients (n=63) who have a mental delay and/or physical disability phenotype and normal (n=20) phenotype.

2018-09-29 | GSE120624 | GEO

CytoScan 750K array data for the ataxia patient's sample

Project description:CytoScan 750K array was performed for the detection of CNV associated with the patient's phenotype CytoScan 750K array was performed according to the manufacturer's directions on DNA extracted from peripheral blood sample.

2021-08-07 | GSE181612 | GEO

Affymetrix CytoScan 750K array data for a parthenogenetic SMA human embryonic stem cell line

Project description:A diploid 46(XX) human embryonic stem cell (HESC) line affected by Spinal muscular atrophy type 1 (SMA) due to homozygosity for a common deletion in the SMN1 gene was derived. By characterizing the methylation status of three different imprinted loci (MEST, SNRPN and H19) and carrying out genome-wide SNP analysis, we provide evidence that this cell line was established from the activation of a mutant haploid oocyte through parthenogenesis, resulting in homozygote diploidization of the entire genome. Affymetrix CytoScan 750K array analysis was performed according to the manufacturer's directions on DNA extracted from tissue culture. Copy number and LOH analysis of the Affymetrix CytoScan 750K array was performed for the SMA HESC line.

2015-09-01 | E-GEOD-72284 | biostudies-arrayexpress

CytoScan 750K array data for the ataxia patient's sample

Project description:CytoScan 750K array data for the ataxia patient's sample

| PRJNA752650 | ENA

Genetic profiling of first-trimester chorionic villus samples using Affymetrix CytoScan 750K arrays

Project description:While chromosomal microarray analysis (CMA) is increasingly utilized in prenatal diagnosis, most research focuses on mid-to-late pregnancy amniotic fluid samples. Chorionic villus samples (CVS) from the first trimester possess distinct biological characteristics. To evaluate the efficacy of CMA in early pregnancy prenatal diagnosis, we performed a genomic analysis of CVS from high-risk pregnancies.We conducted a single-center cohort study of singleton pregnancies that underwent CVS between 11⁺⁰ and 13⁺⁶ weeks of gestation. Indications for testing included advanced maternal age, ultrasound-detected soft markers or structural anomalies, abnormal first-trimester serum screening, or adverse obstetric history. All villus samples were analyzed using CMA (Affymetrix CytoScan 750K arrays). Among the samples analyzed by CMA, 16.6% showed chromosomal abnormalities, with CNVs accounting for 58.9% of these cases. Compared with other indicators, the detection rate was significantly higher in the group with ultrasound abnormalities. Complex ultrasound abnormalities, in particular, hold greater clinical significance. This study demonstrates the utility of CMA for detecting chromosomal abnormalities in first-trimester CVS. Our findings support the integration of CMA into early prenatal diagnostic protocols.

2025-12-04 | GSE306863 | GEO

CytoScan HD array for multiple myeloma samples

Project description:Affymetrix CytoScan HD array for newly diagnosed multiple myeloma patients.

2021-02-10 | GSE164554 | GEO

Genetic profiling of first-trimester chorionic villus samples using Affymetrix CytoScan 750K arrays

Project description:Genetic profiling of first-trimester chorionic villus samples using Affymetrix CytoScan 750K arrays

| PRJNA1312802 | ENA

Affymetrix CytoScan 750K data for validation of the BoBs/CNV-seq comparison study

Project description:Affymetrix CytoScan 750K data for validation of the BoBs/CNV-seq comparison study

| PRJNA638907 | ENA

affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling.

Project description:BackgroundThe well-known Genome-Wide Association Studies (GWAS) had led to many scientific discoveries using SNP data. Even so, they were not able to explain the full heritability of complex diseases. Now, other structural variants like copy number variants or DNA inversions, either germ-line or in mosaicism events, are being studies. We present the R package affy2sv to pre-process Affymetrix CytoScan HD/750k array (also for Genome-Wide SNP 5.0/6.0 and Axiom) in structural variant studies.ResultsWe illustrate the capabilities of affy2sv using two different complete pipelines on real data. The first one performing a GWAS and a mosaic alterations detection study, and the other detecting CNVs and performing an inversion calling.ConclusionBoth examples presented in the article show up how affy2sv can be used as part of more complex pipelines aimed to analyze Affymetrix SNP arrays data in genetic association studies, where different types of structural variants are considered.

| S-EPMC4438530 | biostudies-literature

Affymetrix CytoScan HD array data of iPSCs and iPSC-derived-NSPCs

Project description:Cytoscan HD analysis on DNA samples from iPSCs, iPS-derived NSPCs

2016-09-14 | GSE77995 | GEO