Albinism Family Array CGH Data
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE190026 | GEO | 2021/12/03
REPOSITORIES: GEO
Similar Datasets
Project description:Albinism Family Array CGH Data
| PRJNA785601 | ENA
Project description:Albinism is genetically heterogeneous rare genetic condition affecting 1:17000 in the Western world (but more frequent in Africa) whose main feature is a profound visual impairment, characterised by foveal hypoplasia, abnormal chiasmatic connections, nystagmus and photofobia. All these features result in severly altered visual acuity (<0,1), absent depth perception and poor night vision. People with albinism are primarily visually handicapped. In addition, for some types of albinism, the visual phenotype can be presented with partial or total hypopigmentation, hence resulting in a secondary phenotype which can lead to skin cancer if skin is not adequately protected. Recently a new syndrome has been described, FHONDA, with the same visual abnormalities of albinism but without pigment alteration. The traditional classification differentiates Oculoculatenous albinism (OCA), where hypopigmentation involves hair, skin and eyes versus Ocular Albinism (OA), where hypopigmentation only affects the eyes. These are non-sydrimic types of albinism. Some syndromic forms (Hermansky-Pudlak=HPS, Chediak-Higashi=CHS) affect cells beyond pigment cells, present in the lungs, immune system, platelets and intestines, resulting in more severe phenotypes that can be fatal. Mutations in at least 19 genes are assocaited with the corresponding types of albinism. Most hospitals will only diagnose the most frequent cases using traditional Sanger, MLPA approaches. Some will use CGH arrays. We aim to diagnose all cases of albinism through the Albinochip proposal, which combines a Sequenom first step of known mutations combined with subsequent NGS approaches. In some cases we fail to find a second mutation, these are good candidates for further full exome analyses.
This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
| EGAS00001002068 | EGA
Project description:MicroRNA expression of cellular/viral microRNAs was analysed in 9 samples pCNS PTLD and 16 systemic PTLD and analyzed in 100ng of total RNA by hybridization on Agilent’s microRNA Microarray “Human microRNA-Microarray Release 16.0, 8x60K” (Ramaciotti Centre for Gene Function Analysis, Sydney, Australia). This array tests for 1262 human and viral microRNA. Labelling was performed with Agilent’s „microRNA Complete Labeling and Hyb Kit (p/n 5190-0456)“, hybridisation followed Agilent’s “microRNA Microarray System with microRNA Complete Labelling and Hyb Kit Protocol, Version 2.2, October 2009“. “Agilent high resolution scanner” and “scan control software version 8.0” were used for fluorescence detection.
2014-03-26 | E-MTAB-2453 | biostudies-arrayexpress
Project description:In this study, a high-throughput sequencing strategy was employed to identify the miRNAs involved in P. olivaceus albinism. High-throughput miRNA sequencing identified a total of 475 miRNAs, including 64 novel miRNAs. Furthermore, 33 differentially expressed miRNAs containing 13 up-regulated and 20 down-regulated miRNAs were identified in albino versus normally pigmented individuals (fold change ≥1.5 or ≤0.67 and p≤0.05).
2017-07-13 | GSE99342 | GEO
Project description:The aim of this study is to discover loss of specific miRNA loci in Wilms' tumors using array CGH. Custom arrays were designed based on the Agilent 2x105K Human Whole Genome Genomic microarray with Agilent’s eArray program (https://earray.chem.agilent.com/earray/), with additional probes that cover all miRNA regions (200 bps before, within and after each miRNA from miRBase v13, with each probe in triplicates to enhance the reliability). All custom-designed probes were designed in UCSC hg18. Probes from Agilent’s database were lifted-over from hg19 to hg18 (LiftOver tool: http://genome.ucsc.edu).
2012-03-31 | GSE28397 | GEO
Project description:In this study, a high-throughput sequencing strategy was employed to identify the mRNA involved in P. olivaceus albinism. Based on P. olivaceus genome, RNA-seq identified 21,787 know genes and 711 new genes by transcripts assembly. Of those, 235 genes exhibited significantly different expression pattern (fold change ≥2 or ≤0.5 and q-value≤0.05), including 194 down-regulated genes and 41 up-regulated genes in albino versus normally pigmented individuals. These genes were enriched to 81 GO terms and 9 KEGG pathways (p≤0.05). Among those, the pigmentation related pathways-Melanogenesis and tyrosine metabolism were contained.
2017-07-13 | GSE99341 | GEO
Project description:We introduce high-throughput and massive paired-end mapping (PEM), a large-scale genome sequencing method to identify SVs 3 kb or larger that combines the rescue and capture of paired-ends of 3 kb fragments, massive 454 Sequencing, and a computational approach to map DNA reads onto a reference genome. PEM was used to map SVs in an African and putatively European individual and identified shared and divergent SVs relative to the reference genome. Overall, we fine-mapped more than 1000 SVs and documented that the number of SVs among humans is much larger than initially hypothesized; many of the SVs potentially affect gene function. The breakpoint junction sequences of more than 200 SVs were deduced with a novel pooling strategy and computational analysis. Array-CGH was used for validation. Keywords: array CGH
2007-09-28 | GSE9002 | GEO
Project description:Capacity of exercise and performance is the most valuable in the horses. They have been selected for strength, speed, and indurance trait. Athletic pheno types are influenced markedly by environment, management, and training. However, it has long been accepted that there are underlying genetic factors. To determine altered mRNA expression in circulating leukocytes of horses induced by exercise. Healthy neutered male warmblood horses were subjected to indoor exercise (trotting with alternative cantering for 6o minutes). Peripheral blood was collected from the jugular vein before and after the exercise, and subsequently buffy coat leukocytes were isolated by centrifugation. Total RNAs was isolated. Cyanine 3-labeled cRNA (complementary RNA) was generated from Agilent’s Low RNA Input Linear Amplification kit with 500 ng total RNA. Labeled cRNA was applied microarray (Agilent technologies, 8x60K) using Agilent’s Gene Expression Hybridization Kit. The present study revealed a subset of mRNAs in equine peripheral blood leukocytes affected by exercise, providing background information for genes associated with exercise in warm-blood horses.
2015-12-24 | GSE76310 | GEO
Project description:We demonstrate that comparative genomic hybridisation (CGH) onto cDNA microarrays may be used to carry out genome-wide screens for regions of genetic loss, including homozygous (complete) deletions that may represent the possible location of tumour suppressor genes in human cancer. Screening of the prostate cancer cell lines LNCaP, PC3 and DU145 allowed the mapping of specific regions where genome copy number appeared altered and led to the identification of two novel regions of complete loss at 17q21.31 (500 kb spanning STAT3) and at 10q23.1 (50-350 kb spanning SFTPA2) in the PC3 cell line. Keywords: Tumour vs normal comparison, array CGH
2006-10-28 | GSE6138 | GEO
Project description:The aim of this study is to discover loss of specific miRNA loci in Wilms' tumors using array CGH. Custom arrays were designed based on the Agilent 2x105K Human Whole Genome Genomic microarray with Agilent’s eArray program (https://earray.chem.agilent.com/earray/), with additional probes that cover all miRNA regions (200 bps before, within and after each miRNA from miRBase v13, with each probe in triplicates to enhance the reliability). All custom-designed probes were designed in UCSC hg18. Probes from Agilent’s database were lifted-over from hg19 to hg18 (LiftOver tool: http://genome.ucsc.edu). The Agilent 2x105K custom-design whole genome microarray was used to analyze genomic alterations in Wilms' tumor samples compared to normal human genomic DNA (Promega p/n G1523).
2012-03-30 | E-GEOD-28397 | biostudies-arrayexpress