GEO DataSets

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL33111

39 Samples

Download data: CEL, MTX, TBI, TSV, VCF

(Submitter supplied) The mechanisms by which DNA alleles contribute to disease risk, drug response, and other human phenotypes are highly context-specific, varying across cell types and under different conditions. Human induced pluripotent stem cells (hiPSCs) are uniquely suited to study these context-dependent effects, but to do so requires cell lines from hundreds or thousands of individuals. Village cultures, where multiple hiPSC lines are cultured and differentiated in a single dish, provide an elegant solution for scaling hiPSC experiments to the necessary sample sizes required for population-scale studies. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL33111

20 Samples

Download data: CEL, TBI, VCF

(Submitter supplied) Eucalyptus urophylla is a commercially important wood crop plantation species due to its rapid growth, biomass yield, and use as bioenergy feedstock. We characterized the genetic diversity and population structure of 332 E. urophylla individuals from 19 geographically defined E. urophylla populations with a reliability of 14,468 single nucleotide polymorphisms (SNPs). We compared the patterns of genetic variation among these 19 populations. more...

Organism:

Eucalyptus urophylla

Type:

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

Platform:

GPL28143

382 Samples

Download data: IDAT, TXT

(Submitter supplied) To reveal genetic determinants of susceptibility to COVID-19 severity in the population and further explore potential immune-related factors, we performed a genome-wide association study on 284 confirmed COVID-19 patients (cases) and 95 healthy individuals (controls). We compared cases and controls of European (EUR) ancestry and African American (AFR) ancestry separately. To further exploring the linkage between HLA and COVID-19 severity, we applied fine-mapping analysis to dissect the HLA association with mild and severe cases.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platform:

GPL32596

373 Samples

Download data: CEL, TXT

(Submitter supplied) Australian working Kelpie dogs are known to be affected with an autosomal recessive form of inherited cerebellar ataxia (cerebellar abiotrophy, CA) that is characterised by a degeneration of Purkinje and granule cells in the cerebellar cortex. The clinical signs of CA include cerebellar ataxia, head tremor, motor in-coordination, wide based stance and high stepping gait, with varied clinical onset age. more...

Organism:

Canis lupus familiaris

Type:

SNP genotyping by SNP array

Platform:

GPL20953

163 Samples

Download data: IDAT, MAP, PED

(Submitter supplied) Selective breeding of domestic dogs has generated diverse breeds often optimized for performing specialized tasks. Despite the heritability of breed-typical behavioral traits, identification of causal loci has proven challenging due to the complexity of canine population structure. We overcome longstanding difficulties in identifying genetic drivers of canine behavior by developing an innovative framework for understanding relationships between breeds and the behaviors that define them utilizing genetic data for over 4,000 domestic, semi-feral and wild canids and behavioral survey data for over 46,000 dogs. more...

Organism:

Canis lupus dingo; Canis lupus; Canis lupus familiaris

Type:

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

Platform:

GPL17481

956 Samples

Download data: IDAT, TXT

(Submitter supplied) As a historical nomadic group in Central Asia, Kazaks have mainly inhabited the steppe zone from the Altay Mountains in the East to the Caspian Sea in the West. Fine scale characterization of the genetic profile and population structure of Kazaks would be invaluable for understanding their population history and modeling prehistoric human expansions across the Eurasian steppes. With this mind, we characterized the maternal lineages of 200 Kazaks from Jetisuu at mitochondrial genome level. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL32489

80 Samples

Download data: TXT, XLSX

(Submitter supplied) Diabetic kidney disease is the leading cause of end-stage kidney disease worldwide; however, the integration of high-dimensional trans-omics data to predict this diabetic complication is rare. We develop artificial intelligence (AI)-assisted models using machine learning algorithms to identify a biomarker signature that predisposes high risk patients with diabetes mellitus (DM) to diabetic kidney disease based on clinical information, untargeted metabolomics, targeted lipidomics and genome-wide single nucleotide polymorphism (SNP) datasets. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array; SNP genotyping by SNP array

Platform:

GPL32738

616 Samples

Download data: CEL, TXT

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

Organism:

Homo sapiens

Type:

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

4 related Platforms

74 Samples

Download data: IDAT

(Submitter supplied) Mammalian sex chromosomes encode homologous X/Y gene pairs that were retained on the male Y and escape X chromosome inactivation (XCI) in females. Inferred to reflect X/Y-pair dosage sensitivity, monosomy X is a leading cause of miscarriage in humans with near full penetrance. This phenotype is shared with many other mammals but not the mouse, which offers sophisticated genetic tools to generate sex chromosomal aneuploidy but also tolerates its developmental impact. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL19718

12 Samples

Download data: IDAT, TXT

(Submitter supplied) We molecularly characterized a class of histologically aggressive childhood liver cancers and showed that these tumors are clinically aggressive and that their observed histological features are associated with underlying recurrent molecular features. We proposed a diagnostic algorithm to identify these cancers using a combination of histological and molecular features, and our analysis suggested that these cancers may benefit from specialized treatment strategies that may differ from treatment guidelines for hepatoblastomas and hepatocellular carcinomas.

Organism:

Homo sapiens

Type:

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

Platform:

GPL21558

38 Samples

Download data: CEL, OSCHP

(Submitter supplied) We retrospectively reviewed 488 fetuses who diagnosed with FGR and without structural malformation during a 10-year period. A total of 19 (3.9%) cases of chromosomal anomalies were detected, including 11 cases of numerical abnormalities, 5 of structural abnormalities, and 3 of mosaicism. We classified the cohort into cases diagnosed at ≤24, 25-28, 29-32, and > 32 weeks of gestation according to the onset gestations; isolated FGR, FGR with soft markers, and FGR with nonstructural anomalies according to different ultrasound findings; high and low-risk maternal serum screening (MSS) groups based on the MSS results. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL18637

31 Samples

Download data: CEL, CYCHP

(Submitter supplied) The Illumina Infinium HumanOmni5-Quad BeadChip was used to obtain genomewide SNP profiling of 32 human couples (64 individuals), selected by their facial resemblance.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platform:

GPL27928

32 Samples

Download data: CSV, IDAT

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

Organism:

Homo sapiens

Type:

Methylation profiling by array; SNP genotyping by SNP array

Platforms:

GPL27928 GPL21145

96 Samples

Download data: IDAT

(Submitter supplied) The Illumina Infinium HumanOmni5-Quad BeadChip was used to obtain genomewide SNP profiling of 16 human couples (32 individuals), selected by their facial resemblance.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platform:

GPL27928

32 Samples

Download data: CSV, IDAT

(Submitter supplied) The molecular etiology underlying TRPS1 loss-of-function in tricho-rhino-phalangeal syndrome (TRPS) remains to be understood. Intriguingly, TRPS1 is also bioinformatically postulated as a breast cancer driver. We report here that TRPS1 is prevalently amplified in breast cancer and promotes breast carcinogenesis. We showed that the tumorigenic potential of TRPS1 is derived from its nucleation of the replication machinery and its enforced replication of H3K9me3-marked heterochromatic regions. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL6801

12 Samples

Download data: CEL, TXT

(Submitter supplied) Merkel cell carcinoma (MCC) is a rare and aggressive cutaneous neuroendocrine cancer. Management of advanced MCC is mainly based on immune-checkpoint inhibitors (ICI). The high failure rate (up to 75%) warrants investigation of new therapeutic targets. The recent identification of BRCA1 or BRCA2 (BRCA1/2) mutations in some MCC raises the issue of the use of poly-(ADP-Ribose)-polymerase inhibitors (PARPi) in selected advanced cases. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL21558

33 Samples

Download data: CEL, OSCHP, TXT

(Submitter supplied) Sex chromosomal abnormalities areare associated with multiple defects. In this study, we retrospectively analyzed the single nucleotide polymorphism (SNP) arrays of 186 early embryos with sex chromosomal abnormalities. using single nucleotide polymorphism (SNP) array. Among them, 52 cases of Turner syndrome, 21 cases of triple X syndrome, 35 cases of Klinefelter syndrome and 14 cases of XYY syndrome were detected. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL18637

185 Samples

Download data: CEL, CYCHP

(Submitter supplied) Estimating the relationships between individuals is one of the fundamental challenges in many fields. In particular, relationship estimation could provide valuable information for missing persons cases. The recently developed investigative genetic genealogy approach uses high-density single nucleotide polymorphisms (SNPs) to determine close and more distant relationships, in which hundreds of thousands to tens of millions of SNPs are generated either by microarray genotyping or whole-genome sequencing. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL30274

24 Samples

Download data: IDAT, VCF

(Submitter supplied) Vitreoretinal lymphoma is a rare subtype of diffuse large B-cell lymphoma considered a variant of primary central nervous system lymphoma. Its diagnosis requires examination of vitreous fluid, but cytologic differentiation from uveitis remains difficult. Due to its rarity and difficulty in obtaining diagnostic material, little is known about the genetic profile of the disease.

Organism:

Homo sapiens

Type:

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

Platform:

GPL18602

7 Samples

Download data: CEL, H5, XLSX