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Series GSE50573 Query DataSets for GSE50573
Status Public on Jun 04, 2014
Title Posterior Amorphous Corneal Dystrophy Is Associated with a Deletion of Small Leucine-rich Proteoglycans on Chromosome 12
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Genome variation profiling by SNP array
Summary Posterior amorphous corneal dystrophy (PACD) is a rare, autosomal dominant disorder affecting the cornea and iris. After next-generation sequencing of the family in which linkage analysis identified a chromosomal locus for PACD on 12q21.33 failed to yield a pathogenic mutation, array-based copy number analysis and qPCR detected a deletion on 12q21.33 containing four genes encoding small leucine-rich proteoglycans (SLRPs): KERA, LUM, DCN, and EPYC. Two other families with PACD also demonstrated deletion of these SLRPs, which together with murine models of KERA, LUM, and DCN deficiency provide convincing evidence that PACD is caused by haploinsufficiency of these SLRPs.
 
Overall design Copy number analysis of 750K SNP and 1.9 non-polymorphic probes present on the Affymetrix CytoScan HD array. Samples were separated by affection status. Eight unaffected and 5 affected samples from across 3 families were analyzed. Analysis was performed using the Affymetrix Chromosome Analysis Suite (ChAS) v.2.0 software.
 
Contributor(s) Kim MJ, Frausto RF, Aldave AJ
Citation(s) 24759697
Submission date Sep 04, 2013
Last update date Jul 13, 2018
Contact name Anthony J. Aldave
E-mail(s) Aldave@jsei.ucla.edu
Organization name Stein Eye Institute, UCLA
Department Ophthalmology
Lab Cornea Genetics Laboratory
Street address 200 Stein Plaza DSERC 3-143
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platforms (1)
GPL16131 [CytoScanHD_Array] Affymetrix CytoScan HD Array
Samples (13)
GSM1223764 PACD Affected 1_5
GSM1223765 PACD Unaffected 1_7
GSM1223766 PACD Unaffected 1_11
Relations
BioProject PRJNA217967

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE50573_RAW.tar 1.4 Gb (http)(custom) TAR (of CEL, CYCHP)
Processed data included within Sample table
Processed data provided as supplementary file
Raw data provided as supplementary file

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