Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole blood gene expression profiling of multiplex multiple sclerosis family

ABSTRACT: This experiment was carried out in the context of a whole-genome sequencing study in 4 affected and 4 unaffected relatives of a consanguineous Italian family characterized by the high prevalence of multiple sclerosis. These data were used to evaluate differences in GRAMD1B gene expression in whole blood comparing healthy and affected subjects of the family. Functional experiments have been subsequently performed to evaluate the involvement of this gene in multiple sclerosis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE103005 | GEO | 2018/08/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

High-resolution array CGH profiling identifies Na-K transporting ATPase interacting 2 - NKAIN2- as a predisposing candidate gene in neuroblastoma

Project description:We studied an Italian family with three NB patients, two siblings and one of their cousins carrying the R1192P mutation in the ALK gene (that has been found mutated in a fraction of familial NBs). However, because some individuals harboring mutations in this gene do not develop this tumor, additional genetic alterations appear to be required for NB pathogenesis. In this family, a comparison between somatic and germline DNA copy number changes in the two affected siblings and their relatives by an high resolution array-based Comparative Genomic Hybridization (CGH) technique was performed.

2013-08-02 | E-MEXP-3948 | biostudies-arrayexpress

Affymetrix SNP array data for homozygosity mapping of segregating anhidrosis

2014-09-05 | GSE61122 | GEO

Identification of differential DNA methylation associated with multiple sclerosis: a family-based study

Project description:Multiple Sclerosis (MS) is known to be caused by a genetic predisposition triggered by environmental factors. Despite the knowledge of genetic factors and environmental agents involved, it is largely unclear how they interact. Epigenetics, particularly DNA methylation, represents a model for environmental factors to influence the genome. In this paper, we studied 26 affected and 26 unaffected relatives from 8 MS multiplex families (≥ 3 affected relatives) as part of a multicentric Italian cohort study using Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) run on an Illumina® HiSeq 2500 (2x100 bp). Technical validation in 6/8 of the original families and biological replication in 2 additional families (FDR < 0.1 and a concordant fold change, FC) were performed in suggestive differentially methylated regions (DMRs) between affected and unaffected relatives using SeqCap Epi Choice Enrichment (Roche®). Evidence of association from MeDIP-Seq across 8 families was combined with aggregation statistics, separately for hypo- and hyper-methylated regions with concordant FC in ≥ 6/8 families, yielding 162 DMRs at FDR ≤ 0.1. Technical validation and biological replication led to 2 hypomethylated regions, which point to NTM and BAI3 genes, and 2 hypermethylated regions in PIK3R1 and CAPN13 (mean size: 3.1 kb). Multiplex families represent a privileged setting for the study of regions of differential methylation as they reduce the impact of potential confounders like shared genetics and environmental factors. We identified 4 novel regions which contain genes of potential interest that need to be tested in larger cohorts of patients.

2021-05-01 | GSE149562 | GEO

CGH + SNP microarray analysis in consanguineous family with ovarian dysgenesis

Project description:homozygosity mapping in a family with ovarian failure Two affected and four unafected siblings from consanguineous family were studied to identify shared regions of homozygosity in affected females with gonadal dysgenesis

2014-10-16 | E-GEOD-62347 | biostudies-arrayexpress

Affymetrix SNP array data for homozygosity mapping of segregating anhidrosis

Project description:A consanguineous family segregating anhidrosis (recessive, familial) Shared homozygous regions were identified by comparing SNP genotyping results from four affected family members Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.

2014-09-05 | E-GEOD-61122 | biostudies-arrayexpress

Homo sapiens

Project description:Whole blood gene expression profiling of multiplex multiple sclerosis family

| PRJNA399733 | ENA

Homozygosity mapping in family segregating premature ovarian insufficiency (POI)

Project description:Premature ovarian insufficiency (POI) is defined as a primary ovarian defect characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles before the age of 40 (secondary amenorrhea) with hypergonadotropism and hypoestrogenism. Premature ovarian insufficiency has few known genetic causes but in familial cases a genetic link is often suspected. A large consanguineous family with three female affected with POI was investigated. All samples including 3 affected and 5 unaffecd underwent whole genome SNP genotyping using Affymetric Axiom_GW_Hu_SNP array. Linkage analysis was carried out using HomozygosityMapper and Allegro softwares.Linkage analysis mapped the disease phenotype to long arm of chromosome 20. Sequence data analysis of potential candidate genes failed to detect any pathogenic variant.

2014-03-20 | GSE56043 | GEO

Project description:Exome sequencing of multiple-sclerosis patients and their biological relatives

| PRJNA416289 | ENA

A missense mutation in TFRC, encoding transferrin receptor 1, causes combined immunodeficiency (Family A)

Project description:Affymetrix 6.0 SNP data for genome-wide linkage scans of a consanguineous Kuwaiti family with a combined immunodeficiency Peripheral blood or saliva were used for patients who had no history of hematopoietic stem cell transplant (HSCT). Fibroblasts cell lines were used as a source of DNA for individuals who received HSCT. Genomic DNA from 32 subjects (5 affected and 27 unaffected) from Family A was genotyped at 909,622 single nucleotide polymorphisms (SNPs) on the Genome-Wide Human SNP 6.0 Array (Affymetrix).

2015-11-25 | E-GEOD-75314 | biostudies-arrayexpress

Loss-of-function mutations TDRD7 lead to a rare novel syndrome combining congenital cataract and non-obstructive azoospermia in humans

Project description:Purpose: Comorbid familial non-obstructive azoospermia (NOA) and congenital cataract (CC) has not been reported previously, and no single human gene has been associated with both diseases in humans. Our purpose is to uncover novel human mutations and genes causing familial NOA and CC. Methods: We performed whole-exome sequencing for two brothers with both NOA and CC from a consanguineous family.The proband was also carried out SNP array analysis. Mutation screening of TDRD7 was performed in another similar consanguineous family and 176 patients with azoospermia or CC alone and 520 healthy controls. Histological analysis was performed for the biopsied testicle sample in one patient, and knockout mice were constructed to verify the phenotype of the mutation in TDRD7. Results: Two novel loss-of-function mutations (c.324_325insA (T110Nfs*30) and (c.688-689insA (p.Y230X), respectively) of TDRD7 were found in the affected patients from the two unrelated consanguineous families. Histological analysis demonstrated a lack of mature sperm in the male patient’s seminiferous tubules. The mutations were not detected in patients with CC or NOA alone. Mice with Tdrd7 gene disrupted at a similar position precisely replicated the human syndrome. Conclusions: We identified TDRD7 causing CC as a new pathogenic gene for male azoospermia in human, with an autosomal recessive mode of inheritance.

2017-06-15 | GSE100019 | GEO

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