CGH + SNP microarray analysis in consanguineous family with ovarian dysgenesis
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Svetlana Yatsenko
PROVIDER: E-GEOD-62347 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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2013-01-11 | E-GEOD-29365 | biostudies-arrayexpress
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2010-04-06 | E-GEOD-14437 | biostudies-arrayexpress
Project description:We saw a patient who presented with respiratory distress from birth due to interstitial lung disease. Before the age of three months a diagnosis of nephrotic syndrome was made. Lung biopsy revealed pulmonary interstitial glycogenosis. Despite extensive investigations, no known genetic or infectious cause was found for the congenital nephrotic syndrome. The patient died at the age of 8 months due to respiratory failure. A 20 Mb homozygous region was identified on chromosome 17 in the patientM-bM-^@M-^Ys DNA, revealing a novel homozygous missense variant in ITGA3 gene. Genomic DNA was obtained from peripheral blood samples of the patient with interstitial lung fibrosis and nephrotic syndrome. Copy number variation (CNV) screening by means of microarray analyses was carried out on the Affymetrix GeneChip 250k (NspI) SNP array platform (Affymetrix, Inc., Santa Clara, CA, USA), which contains 25-mer oligonucleotides representing a total of 262,264 SNPs. Hybridizations were performed according to the manufacturerM-bM-^@M-^Ys protocols. Copy numbers and M-bM-^@M-^\long contiguous stretches of homozygosityM-bM-^@M-^] (LCSH/LOH) were determined using the 2.0 version of the CNAG (Copy Number Analyzer for Affymetrix GeneChip mapping) software package (Nannya Y, Sanada M, et al (2005) "A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays." Cancer Res; 65: 6071M-bM-^@M-^S6079.). The average resolution of this array platform, described by McMullan et al is 150M-bM-^@M-^S200 kb (Mc McMullan DJ, Bonin M et al. (2009), M-bM-^@M-^\Molecular karyotyping of patients with unexplained mental retardation by SNP arrays: a multicenter studyM-bM-^@M-^] Hum Mutat. Jul;30(7):1082-92).
2012-08-28 | E-GEOD-40405 | biostudies-arrayexpress
Project description:PHARC is a neurodegenerative disease comprising early onset cataract and hearing loss, retinitis pigmentosa, and involvement of both the central and peripheral nervous systems; including demyelinating sensorimotor polyneuropathy and cerebellar ataxia. Previously, we mapped this Refsum-like disorder to a 16 Mb region on chromosome 20. Here we report that mutations in the ABHD12 gene cause PHARC disease and we describe the clinical manifestations in a total of 19 patients from four different countries. The ABHD12 enzyme was recently shown to hydrolyse 2-arachidonoyl glycerol (2-AG), the main endocannabinoid lipid transmitter that acts on cannabinoid receptors CB1 and CB2. Our data therefore represent an example of an inherited disorder related to endocannabinoid metabolism. The endocannabinoid system is involved in a wide range of physiological processes including neurotransmission, mood, appetite, pain appreciation, addiction behaviour and inflammation, and several potential drugs targeting these pathways are in development for clinical applications. Our findings show that ABHD12 performs essential functions in both the central and peripheral nervous systems and the eye. Any future drug-mediated interference with this enzyme should consider the potential risk of long-term adverse effects. Homozygosity mapping using Affymetrix 250K SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples. This accession number contains the data for families 1-5 plus 7 in the article. Supplementary files linked below. The region of interest on chromosome 20 was found using families 1 and 2. The patients in families 3,4 and 5 were then recruited and the patients were homozygous for the same region on chromosome 20 as those in families 1 and 2, showing that all these patients are distantly related. All affected are homozygous for the same mutation. The rest of the chromosomes fall outside the scope of our study. Mutations in ABHD12 Cause the Neurodegenerative Disease PHARC: An Inborn Error of Endocannabinoid Metabolism, Fiskerstrand et al. The American Journal of Human Genetics, 26 August 2010 http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDD-50W2K9M-3&_user=6129429&_coverDate=08%2F26%2F2010&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000000150&_version=1&_urlVersion=0&_userid=6129429&md5=234296648f66debd3e2b08e795f2179f
2010-08-26 | E-GEOD-23151 | biostudies-arrayexpress
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
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
Project description:Here we have used four enchondromas and two chondrosarcomas of Maffucci patients. We also had one normal sample available for paired analysis in one of the chondrosarcoma II. We did not find any LOH or coomon copy number variation in all Maffucci enchondromas while chondrosarcomas are genetically unstable. Affymetrix SNP 6.0 array was performed using 4 EC and 2CS of Maffucci patients. Illumina expression v3 array was possible to perform using only 1 EC and 2 CS due to rarity of the disease. For SNP array, we used 29 control samples submitted previously (GSE22965) to creat baseline.
2011-07-18 | E-GEOD-26674 | biostudies-arrayexpress
Project description:Background: Moyamoya is a cerebrovascular condition of unknown mechanism characterized by a progressive stenosis of the terminal part of the internal carotid arteries (ICA) and the compensatory development of abnormal “moyamoya” vessels. It leads to ischemic and hemorrhagic stroke. We describe a novel autosomal recessive disease leading to severe moyamoya and early onset achalasia and report its cause in 3 unrelated families. Methods: We used a combination of genetic linkage and exome sequencing in 2 consanguineous to identify rare shared variants. Sanger sequencing of GUCY1A3, the sole gene mutated in both families, was then conducted in the third family. Platelets from one of the patients and controls were used to carry out functional studies. Results: Homozygous mutations of GUCY1A3 gene encoding the alpha1 subunit of soluble guanylate cyclase (sGC), the major receptor for Nitric Oxide (NO), were identified in all 3 families. Platelet analysis showed a complete loss of the mutated protein and showed an unexpected stimulatory role of sGC within platelets. Conclusion: The NO/sGC/cGMP pathway is a major pathway controlling vascular smooth muscle (VSMC) relaxation, vascular tone and vascular remodeling. Our data suggest that alterations of this pathway may lead to an abnormal vascular remodeling process in sensitive vascular areas with low blood A total of 17 samples (8 affected and 9 unaffected) were used for this study. Linkage analysis was performed in a single informative consanguine family composed of 2 unaffected parents, 4 affected siblings and 3 unaffected siblings. Two affected samples in two different families were used for the exome sequencing analysis and results were compared to 20 control exomes (in-house exomes from IntegraGen, Evry, France) and 8 HapMap exomes. All samples were used for Sanger Sequencing confirmation.
2014-06-19 | E-GEOD-48099 | biostudies-arrayexpress