GEO DataSets

(Submitter supplied) Eukaryotic genomes are structured in zones that replicate predominantly early or late. Besides these genome-wide patterns of replication timing (RT), some genes display asynchronous replication between the two alleles in certain stem cells, brought about by stochastic processes and genetic polymorphisms. To what extent epigenetic modifications control asynchronous replication remains unclear. As a paradigm to address this question we explored imprinted chromosomal domains, at which parental DNA methylation imprints mediate parental allele-specific gene expression. more...

Organism:

Mus musculus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10449

12 Samples

Download data: TXT

(Submitter supplied) Objective This study presents a rare case of father-to-offspring mosaic transmission of a supernumerary marker chromosome (SMC) and, through integration of literature analysis and computational modeling, proposes a novel embryonic selection-based regulatory mechanism. Methods Karyotyping and SNP-array were performed on amniotic fluid, cord blood, and parental samples. A systematic review identified 35 additional mosaic SMC transmission cases. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL18637

2 Samples

Download data: CEL, TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL18637

28 Samples

Download data: CEL, CYCHP, TXT

(Submitter supplied) Background. Recurrent pregnancy loss (RPL) is often associated with genetic factors. This study investigates chromosomal abnormalities in RPL by analyzing copy number variations (CNVs) and single nucleotide variants (SNVs). Methods. We conducted a retrospective analysis of 400 RPL patients, with 393 successfully analyzed using CNV-seq and SNP-array after excluding maternal cell contamination (MCC). more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL18637

66 Samples

Download data: CEL, CYCHP, TXT

(Submitter supplied) PluriTest score for iPSCs cultured for 7 days in a small bioreactor received a pluripotency score of 36.87 ± 0.12. n = 3. PluriTest score for iPSCs cultured in a standard bioreactor for 6 or 7 days was 41.28 ± 0.32. n = 3. KaryoStat assays revealed no chromosomal or genetic mutations occurred in the iPSCs cultured in the small and standard bioreactors. n = 3.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL32641

6 Samples

Download data: CEL, CYCHP

(Submitter supplied) Schizophrenia is a polygenic, multifactorial chronic neuropsychiatric disorde. Due to its polygenic and complex nature, traditional genetic approaches like GWAS or candidate gene studies are often insufficient to capture rare or novel mutations. We have used genomic microarray to find large deletion in the Schizophrenic patients which are difficult to find from whole exome sequencing

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array; SNP genotyping by SNP array

Platform:

GPL18637

2 Samples

Download data: CEL, CYCHP

(Submitter supplied) We analyzed 13 samples of primary cold agglutinin disease (CAD) for copy number variations (CNVs). In 12/13 cases complete or partial trisomy 3/3q was detected. Most of the cases (9/13) had a trisomy 12 or 18 but never both together. 4 cases had trisomy 12 and 5 case had trisomy 18. In addition there were only small recurrent gains and losses. Our data indicate that trisomy 3 or at least +3q is present in almost all cases of CAD and therefore testing for it could aid diagnosis. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL18602

13 Samples

Download data: CEL, OSCHP

(Submitter supplied) We compared the genomic copy number profiles of liver tissues of wild type mice with that of ATF6-transgenic mice after 3 and 12 months, respectively.

Organism:

Mus musculus

Type:

Genome variation profiling by array

Platform:

GPL24320

16 Samples

Download data: TXT

(Submitter supplied) The 2q31 region is commonly associated with pathogenic alleles of the HOXD cluster leading to various clinical phenotypes related to skeletal development. We present a patient with short stature, tetralogy of Fallot, and multiple congenital anomalies. Initial array comparative genomic hybridization (aCGH) revealed a de novo complex genomic rearrangement (CGR) spanning 2q31 in proband characterized as a triplication (TRP)-duplication (DUP)-triplication (TRP). more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL35825

3 Samples

Download data: TXT

(Submitter supplied) Comparative Genomic Hybridization study of Severe vs Uncomplicated P. vivax malaria

Organism:

Plasmodium vivax

Type:

Genome variation profiling by genome tiling array

Platform:

GPL35337

1 Sample

Download data: TXT

(Submitter supplied) In this study, we investigated the production of white-shelled eggs at physiological and molecular levels using a F2 resource population as major samples.

Organism:

Gallus gallus

Type:

Genome variation profiling by SNP array

Platform:

GPL23815

200 Samples

Download data: CEL, VCF

(Submitter supplied) Despite decades of research, brain tumours remain among the deadliest of all forms of cancer. As recurrence in glioblastoma is locally generated around the resection cavity, the ability of these tumours to resist almost all conventional and novel treatments relates, in part, to the unique cell-intrinsic and microenvironmental properties of neural tissues. Photodynamic therapy (PDT) relies on photo-toxic effects induced by specific molecules (photosensitisers) upon absorption of photons from a light source. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL21558

16 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by SNP array

Platforms:

GPL23159 GPL16131

98 Samples

Download data: CEL, CHP, CYCHP

(Submitter supplied) IL3 expression and reactive eosinophils

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; Expression profiling by high throughput sequencing; Other

Platform:

GPL16131

2 Samples

Download data: CEL, CYCHP

(Submitter supplied) Copy-number and loss of heterozygosity analysis of salivary gland tumors in a proband with attenuated familial adenomatous polyposis (AFAP), using Affymetrix OncoScan and CytoScan HD arrays

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL21558

3 Samples

Download data: CEL, OSCHP

(Submitter supplied) To investigate the clinical phenotype, genetic etiology, and diagnosis of 11q deletion (11q-) syndrome. The differences and severity of fetal phenotypes may depend on the types and quantities of functional genes contained in fragments of different sizes.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL18637 GPL32641

4 Samples

Download data: CEL, CYCHP

(Submitter supplied) Fenton reaction-based repeated oxidative stress via ferric nitrilotriacetate (Fe-NTA) causes renal cell carcinoma (RCC) with genetic alterations similar to those in humans. We conducted high-resolution microarray comparative genomic hybridization with Fe-NTA induced RCC obtained from both wild-type and BRCA2+/- rats to evaluate the involvement of BRCA2 haploinsufficiency in carcinogenesis.

Organism:

Rattus norvegicus

Type:

Genome variation profiling by array

Platform:

GPL10451

16 Samples

Download data: TXT

(Submitter supplied) Jumping translocations are cytogenetic abnormalities associated with poor clinical outcome and progression in Myelodysplastic Syndromes/Acute Myeloid Leukemia (MDS/AML).Typically a donor chromosome, often a trisomic 1q, is transferred onto 2 or more recipient chromosomes. Previous studies have demonstrated the crosstalk between DNA hypomethylation and 1q trisomy. Here, we used an epi-genomic approach in sequential samples from a cohort of MDS and AML with the appearance of 1q jumping translocations after 5’-azacytidine (AZA) treatment.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array; Genome variation profiling by SNP array

Platform:

GPL16131

7 Samples

Download data: CEL, CYCHP

(Submitter supplied) Objective: Analyze the ultrasound features, single nucleotide polymorphism microarray (SNP-array) outcomes, pregnancy results, and follow-up data of fetuses with Xp22.31 deletions or duplications in mid to late pregnancy. Methods: A retrospective analysis was carried out on 10 cases diagnosed with Xp22.31 deletions and 11 cases with duplications, identified through single nucleotide polymorphism microarray (SNP-array) testing. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL18637

21 Samples

Download data: CEL, CYCHP

(Submitter supplied) Gene chip analysis was performed using the Infinium OmniZhongHua-8 v1.3 BeadChip (Ilumina, Inc.). This method is used to detect ~240 CNV-affected genetic diseases/regions, including uniparental disomy and polyploidy. To identify copy number and CNV variations on chromosome 3 and in the vicinity of VHL, compared to a new assay called MLPA-NGS, we analysed individual hybridizations conducted on Infinium OmniZhongHua-8 v1.3 BeadChip (Ilumina, Inc.). more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL20166

3 Samples

Download data: IDAT, TXT