Dataset features

Specifications


Application: SNP array data analysis, aCGH data analysis
Number of samples: 87
Release date: Sep 4 2012
Last update date: Aug 21 2013
Access: Public
Diseases: Adenocarcinoma, Esophageal and Gastric Varices, Gastrointestinal Neoplasms, Neoplasms, Stomach Neoplasms
Dataset link Affymetrix 250K StyI SNP array data for gastric and esophageal adenocarcinoma cancer types

Experimental Protocol


Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from 87 cancer DNAs derived from primary tumor tissues, as well as from DNA obtained from 1,480 normal DNA samples. Signal intensities were normalized to raw copy number estimates using the tangent normalization method, as described in Beroukhim et al., In Press and Mermel et al., In preparation. The 250K Sty data from this submission were combined with data for 128 colon adenocarcinomas (Firestein et al, Nature 2008) and segmented using GLAD. These segmented data were then combined with segmented SNP 6.0 data for 62 colon, 97 gastric and 112 esophageal adenocarcinomas using common markers to anchor the segments. Data analysis across samples was performed using this GISTIC 2.0 algorithm (Mermel C et al, Genome Biology 2011).

Repositories


GEO

GSE36459

ArrayExpress

E-GEOD-36459

BioProject

PRJNA155615

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Contact


Steven Schumacher
Steven E Schumacher