Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Copy Number Variations in Patients with Familial Parkinson’s Disease Compared to Their Healthy Siblings

ABSTRACT: Genomic DNA was extracted from peripheral blood from patients with familial PD and their matched healthy siblings. Genomic microarray analysis of the subjects was performed using the CytoScan HD array platform. The CytoScan HD assay was performed according to the manufacturer’s protocol. CEL files that include the intensity probe signals were produced by GeneChip Scanner 3000 7G, using the GeneChip Command Console Software (Thermo Fisher Scientific, Waltham, MA, USA).

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-9476 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Affymetrix CytoScan HD array data for patient with Intellectual Disabilities

Project description:Standard cytogenetic GTG-banding analysis (550 bands) revealed an interstitial deletion on 15q21q22 chromosomal region. Refinement of the 15q21.2 deletion intervals was conducted using aCGH (Cytoscan HD, Affymetrix) on DNA samples from the patient. This assay revealed the presence of submicroscopic alterations on chromosomes 1, 9 and 15. The result was arr[hg19] 9p24.1(6,619,823-6,749,335)x3, 1q44(248,688,586-248,795,277)x1, 15q21.2q22.2(50,848,301-61,298,006)x1. Affymetrix CytoScan HD arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.

2014-06-21 | E-GEOD-58694 | biostudies-arrayexpress

Genome-wide copy number analysis of patient-derived gliobastoma cell cultures

Project description:Genome-wide copy number variation profiles were analyzed in the patient-derived gliobastoma cell culture samples. For this purpose, gDNA was analyzed using the CytoScan® assay in combination with a one-color based labeling and hybridization protocol. Signals on the CytoScan® HD microarrays were detected using the Affymetrix GeneChip® 3000 Scanner.

2021-07-07 | E-MTAB-9341 | biostudies-arrayexpress

Copy number variants analysis of heterotaxy syndrome patients with congenital heart defects

Project description:To identify the molecular causes of heterotaxy syndrome patients with congenital heart defects, an Affymetrix CytoScan HD array was used to identify possible pathogenic CNVs in 63 patients. A total of 59 samples passed initial quality control.

2018-05-24 | E-MTAB-6820 | biostudies-arrayexpress

Genome-wide copy number analysis of patient-derived gliobastoma cell cultures

2019-02-28 | E-MTAB-7649 | biostudies-arrayexpress

CytoScan HD array for multiple myeloma samples

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

2021-02-10 | GSE164554 | GEO

Large genomic alteration of 7q in two patients with multiple primary cancers, including triple negative breast cancer, and family history of malignant neoplasms

Project description:A great percentage of patients with multiple primary cancers (MPCs) and family history of cancer are suspected to have a hereditary cancer predisposition syndrome. However, only a small proportion of these cases are explained by mutations in high-penetrance genes, suggesting the involvement of undiscovered genes in cancer predisposition. In this study, we report the molecular and clinical characterization of two unrelated patients with MPCs, a positive family history of cancer, no germline pathogenic mutations in BRCA1, BRCA2 and TP53 genes and large genomic rearrangements mapped on chromosome 7q. Genomic rearrangements were assessed with Affymetrix CytoScan HD Array platform in two unrelated patients (Patient 1 and Patient 2) with multiple primary cancers. Additionally, the mother of Patient 2 and four children (the son of Patient 1 and three children of Patient 2) were also evaluated.

2016-02-15 | E-GEOD-77138 | biostudies-arrayexpress

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

Genomic profiling of immature hematopoietic cells to obtain insights into imatinib resistance

Project description:Chronic myeloid leukemia (CML) epitomizes successful targeted therapy, with 86% of patients in the chronic phase treated with tyrosine kinase inhibitors (TKIs) attaining remission. However, resistance to TKIs occurs during treatment, and patients with resistance to TKIs progress to the acute phase called Blast Crisis (BC), wherein the survival is restricted to 7-11 months. About 80 % of patients in BC are unresponsive to TKIs. This issue can be addressed by identifying a molecular signature which can predict resistance in CML-CP prior to treatment as well as by delineating the molecular mechanism underlying resistance. Herein, we report genomic analysis of CML patients and imatinib-resistant K562 cell line to achieve the same. Thirteen CML patients (sensitive and resistant to TKIs) and 2 BMT donors (as control) were recruited for the study. DNA was isolated from an enriched CD34+ fraction for each sample as well as from K562 cells made resistant to imatinib which provided a model system for further molecular investigations. DNA was subjected to Cytoscan HD array (Affymatrix) analysis from patient samples and cell lines. Affymetrix CytoScan™ HD array (Applied Biosystems™, Cat# 901835) chip consists of 2.6 M oligonucleotide probes across the genome, including 1953K unique non-polymorphic probes and 750K bi-allelic SNP (single nucleotide polymorphism) probes. Our study identified accumulation of aberrations on chromosomes 1, 3, 7, 16 and 22 as predictive of occurrence of resistance. Further, recurrent amplification in chromosomal region 8q11.2-12.1 was detected in highly resistant K562 cells as well as CML patients. The genes present in this region were analyzed to understand molecular mechanism of imatinib resistance.

2024-01-01 | E-MTAB-11899 | biostudies-arrayexpress

two amniotic fluid sample performed by affymetrix cytoscan HD

Project description:The uploaded results of two samples were SNParray results in our research of which fetal CNVs were detected by noninvasive prenatal test (NIPT) and confirmed by microarray results. Sample ZNY162 received prenatal diagnosis because at 17 gestational week the pregnant woman received NIPT showing 23Mb microdeletion in Chr18. Later ultrasound examination showed developmental anomalies of feet and the 13th ribs. The pregnant woman received amniocentesis and SNParray at the 21st gestational week, which confirmed the existence of the microdeletion in Chr18. DNA was extracted from 10ml amniotic fluid and tested by Affymetrix CytoScan HD array to detect CNVs in whole genome, showing arr 18q22.3q23(69,461,933-78,014,123) Ã1. Sample LMQ155 received prenatal diagnosis because of advanced maternal age and NIPT result of a 2.29Mb microduplication in Chr13 at 15 gestational week. Amniocentesis was performed at the 17th gestational week. Affymetrix CytoScan HD array were used to detect fetal CNVs in whole genome, which showed arr 13q21.2(60,399,612-61,730,194) Ã3 that was consistent with NIPT result.

2016-11-16 | E-MTAB-4738 | biostudies-arrayexpress

Multi-omic analysis in patient-derived organoids unravel the impact of chromosomal instability in colorectal cancer

Project description:Cytoscan high-density (HD) chromosomal microarray analysis was conducted on PDOs and matched fresh tissue to detect copy number alterations. Due to the deepness of Cytoscan HD which goes up to gene level, we aimed at assessing intra-patient copy number heterogeneity from different metastasis of the same patient. We detected relevant differences regarding copy number gains and losses. Interestingly, we detected heterogeneity also in terms of mosaicism, confirming heterogeneity in terms of subclonal copy number variations.

2025-02-03 | E-MTAB-14074 | 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