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Affymetrix SNP array data for family UNK-129-KW with multiple patients suffering from a lethal form of a primary immunodeficiency.

ABSTRACT: Linkage analysis and Copy Number Variation were performed on DNA isolated from the peripheral blood of the 2 affected male patients, their unaffected parents, and their unaffected 4 male siblings, according to the manufacturer's description. This allowed to narrow down the region of homozygosity specifice to the patients. This approach, in combination with Whole Exome sequencing performed on DNA isolated from the 2 affected patients and their mother, allowed to identify a homozygous missense mutation in the base excision repair enzyme NEIL3 that reduced its enzymatic activity, and a homozygous duplication of exons 48-53 of the LPS Responsive Beige-Like Anchor Protein LRBA that abolished protein expression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE85428 | GEO | 2016/08/11

SECONDARY ACCESSION(S): PRJNA338443

REPOSITORIES: GEO

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Affymetrix SNP array data for family UNK-129-KW with multiple patients suffering from a lethal form of a primary immunodeficiency.

Project description:Linkage analysis and Copy Number Variation were performed on DNA isolated from the peripheral blood of the 2 affected male patients, their unaffected parents, and their unaffected 4 male siblings, according to the manufacturer's description. This allowed to narrow down the region of homozygosity specifice to the patients. This approach, in combination with Whole Exome sequencing performed on DNA isolated from the 2 affected patients and their mother, allowed to identify a homozygous missense mutation in the base excision repair enzyme NEIL3 that reduced its enzymatic activity, and a homozygous duplication of exons 48-53 of the LPS Responsive Beige-Like Anchor Protein LRBA that abolished protein expression. Homozygozity mapping was performed with the Affymetrix genome-wide human single nucleotide polymorphism (SNP) array 6.0, and analyzed with Birdsuite version 1.4 and PLINK version 1.07.

2016-08-11 | E-GEOD-85428 | biostudies-arrayexpress

Lymphoblastoid cell lines of families with Mitochondrial Myopathy and Sideroblastic Anemia

Project description:We analyzed samples from two affected brothers (Affected 3 and 4) and their two affected female cousins (Affected 7 and 9) homozygous for the MLASA ? associated C656T mutation in the PUS1 gene; four parents ? heterozygous carriers of the C656T mutation (Parents 1, 2, 5, 6), and an unaffected female carrying wild-type genotype at the PUS1 gene (Control 8). In addition, two females and one male with normal hearing from Arab-Israeli family with nonsyndromic deafness carrying wild-type PUS1 sequence were used as controls (Controls 10, 11, 12). Keywords: Comparison of genome-wide expression in cell lines of patients and controls

2006-11-29 | GSE6374 | GEO

A knockout mutation associated with juvenile paroxysmal dyskinesia in Markiesje dogs indicates SOD1 pleiotropy

Project description:A juvenile form of paroxysmal dyskinesia segregated in the Markiesje dog breed. Affected pups exhibited clinical signs of a severe tetraparesis, dystonia, cramping and falling over when trying to walk. In most cases the presentation deteriorated within weeks and elective euthanasia was performed. Pedigree analysis indicated autosomal recessive inheritance. Genome-wide association and homozygosity mapping of 5 affected dogs from 3 litters identified the associated locus on chromosome 31 in the region of SOD1. The DNA sequence analysis of SOD1 showed that the patients were homozygous for a frameshift mutation in the fourth codon. None of the other analyzed dogs of the breed was homozygous for the mutation, indicating full penetrance of the genetic defect. Mutations in SOD1 are known to cause recessive degenerative myelopathy in middle-aged dogs with low penetrance and dominant amyotrophic lateral sclerosis in humans with variable age of onset. Our findings are similar to recent observations in human patients that a loss of function mutation in SOD1 leads to a juvenile neurologic disease distinct from amyotrophic lateral sclerosis.

2021-03-12 | GSE166712 | GEO

Quantitative Proteomics Study (iTRAQ) of Progeria Cell Lines

Project description:A quantitative proteomic study of three HGPS cell lines from affected patients and three healthy controls from unaffected progenitors

2017-10-03 | MSV000081576 | MassIVE

JAK2V617F mutant HSC microarray

Project description:Mutant JAK2V617F is found in majority of patients with myeloproliferative neoplasm. While heterozygous JAK2V617F induced an ET-like phenotype, JAK2V617F homozygosity drives an severe PV-like phenotype in knock-in mice. HSCs from mice with homozygous JAK2V617F expression show impaired self-renewal in transplants. To understand the molecular mechanisms involved this HSC functional defect, microarray was performed on isolated LT-HSCs from mice expressing wildtype, heterozygous and homozygous expression of mutant JAK2.

2018-08-06 | E-MTAB-6878 | biostudies-arrayexpress

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

Genome-wide analysis of gene expression in infarcted and non-infarcted left ventricle from NEIL3-deficient mice subjected to myocardial infarction

Project description:Myocardial infarction (MI) triggers a reparative response involving fibroblast proliferation and differentiation driving extracellular matrix modulation necessary to form a stabilizing scar. Recently, it was shown that a genetic variant of the base excision repair enzyme endonuclease VIII-like 3 (NEIL3) was associated with increased risk of MI in humans. Here, we report elevated myocardial NEIL3 expression in heart failure patients and marked myocardial upregulation of Neil3 following MI in mice, especially in a fibroblast-enriched cell fraction. Neil3-/- mice showed increased mortality after MI compared to WT, caused by myocardial rupture. Neil3-/- hearts displayed enrichment of mutations in genes involved in mitogenesis of fibroblasts and transcriptome analysis revealed dysregulated fibrosis. Correspondingly, proliferation of vimentin+ and aSMA+ (myo)fibroblasts was increased in Neil3-/- hearts following MI. We propose that NEIL3 operates in genomic regions crucial for regulation of cardiac fibroblast proliferation and thereby controls extracellular matrix modulation after MI.

2016-11-01 | GSE83350 | GEO

Whole genome epigenetic sequencing on DNA from infarcted non-infarcted left ventricle of WT and NEIL3-deficient mice subjected to myocardial infarction

Project description:Myocardial infarction (MI) triggers a reparative response involving fibroblast proliferation and differentiation driving extracellular matrix modulation necessary to form a stabilizing scar. Recently, it was shown that a genetic variant of the base excision repair enzyme endonuclease VIII-like 3 (NEIL3) was associated with increased risk of MI in humans. Here, we report elevated myocardial NEIL3 expression in heart failure patients and marked myocardial upregulation of Neil3 following MI in mice, especially in a fibroblast-enriched cell fraction. Neil3-/-mice showed increased mortality after MI compared to WT, caused by myocardial rupture. Epigenomic analysis suggested dysregulated myofibroblast proliferation and differentiation in Neil3-/-hearts and several differentially expressed genes were downstream targets of differentially methylated/hydroxymethylated transcriptional regulators. Furthermore, proliferation of Vimentin+ and SMA+ (myo)fibroblasts was increased in Neil3 -/-hearts following MI. We propose that NEIL3-dependent modulation of epigenetic DNA methylation regulates cardiac fibroblast proliferation and thereby controls extracellular matrix modulation after MI.

2017-01-01 | GSE90057 | GEO

Cytogenetics 2.7M and Cytoscan HD 2.8M Microarrays in autistic families in the Lebanese population

Project description:Autism spectrum disorder (ASD) affects these core domains: ritualistic-repetitive behaviors, impaired social interaction, and deficits in non-verbal communication/language development. Although ASD is heritable, its extreme heterogeneity defies genetic analyses. A number of ASD susceptibility genes have been identified. The Lebanese population is ideal for uncovering recessive genes because of a high rate of shared ancestry, consanguineous marriages, and high number of offspring per family. We recruited 36 ASD families (ASD: 37, unaffected parents: 36, unaffected siblings: 33). Cytogenetics 2.7M Microarrays/CytoScanâ¢ HD arrays allowed mapping of homozygous regions of the genome.

2017-07-24 | E-MTAB-4963 | biostudies-arrayexpress

Affymetrix SNP array data for ovarian dysgenesis samples

Project description:Ovarian development and maintenance are poorly understood, but diseases affecting them can offer insights into their underlying mechanisms. XX-female gonadal dysgenesis (XX-GD) is a rare, genetically heterogeneous disorder characterized by underdeveloped, dysfunctional ovaries with subsequent lack of spontaneous pubertal development, primary amenorrhea, uterine hypoplasia, and hypergonadotropic hypogonadism. We used SNP arrays to perform homozygosity mapping in order to detect informative genomic regions which are homozygous and shared among affected individuals. This analysis identified genomic regions in which the mutated gene causing the XX-GD phenotype in the affected individuals may reside. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.

2016-08-18 | GSE72159 | GEO

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