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Series GSE40405 Query DataSets for GSE40405
Status Public on Aug 28, 2012
Title CNV and LOH analysis of patient sample PN11-0204
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary 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 patient’s DNA, revealing a novel homozygous missense variant in ITGA3 gene.
Overall design 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 manufacturer’s protocols. Copy numbers and “long contiguous stretches of homozygosity” (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: 6071–6079.). The average resolution of this array platform, described by McMullan et al is 150–200 kb (Mc McMullan DJ, Bonin M et al. (2009), “Molecular karyotyping of patients with unexplained mental retardation by SNP arrays: a multicenter study” Hum Mutat. Jul;30(7):1082-92).
Contributor(s) Pfundt R, Renkema KY
Citation(s) 23114595
Submission date Aug 27, 2012
Last update date Aug 14, 2019
Contact name Rolph Pfundt
Organization name RUNMC
Department Genetics
Lab Genome Diagnostics
Street address Geert Grooteplein Zuid 6
City Nijmegen
ZIP/Postal code 6525GA
Country Netherlands
Platforms (1)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
Samples (1)
GSM992930 PN11-0204
BioProject PRJNA173884

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
GSE40405_RAW.tar 28.8 Mb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file

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