Dataset features

Specifications


Application: SNP array data analysis, aCGH data analysis
Number of samples: 1
Release date: Aug 28 2012
Last update date: May 17 2017
Access: Public
Diseases: Nephrotic Syndrome, Respiratory Insufficiency, Lung Diseases, Interstitial
Dataset link CNV and LOH analysis of patient sample PN11-0204

Experimental Protocol


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).

Repositories


GEO

GSE40405

ArrayExpress

E-GEOD-40405

BioProject

PRJNA173884

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Contact


Rolph Pfundt