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Series GSE68929 Query DataSets for GSE68929
Status Public on Oct 26, 2016
Title Genomic profiling of patient-derived xenografts identify high level “passenger” gene aberrations associated with better prognosis in non-small cell lung cancer
Platform organism Homo sapiens
Sample organism Mus musculus
Experiment type Expression profiling by array
Summary Patient-derived tumor xenografts (PDXs) increasingly are being used as preclinical models to study human cancers and to evaluate novel therapeutics, as they reflect clinical cancers more closely than established tumor cell lines. With >100 PDXs established from resected non-small cell lung carcinomas (NSCLC), we reported previously that xenograftability correlates significantly with poorer patient prognosis. In this study, genomic, transcriptomic, and proteomic profiling of 36 PDXs showed greater similarity in somatic alterations between PDX and primary tumors than with cell lines, using publicly available data on the latter. A higher number of somatic alterations among 865 frequently altered genes in the PDX tumors was associated with better overall patient survival (HR=0.15, p=0.00015) compared to patients with corresponding PDXs characterized by a lower number of alterations; this was validated with the TCGA lung cancer patient dataset (HR=0.28, p=0.000022). These passenger-like alterations, identified in PDXs, link cell-cell signaling and adhesion to patient prognosis.
 
Overall design Total RNAs from xenograftswere amplified by DASL kit and hybridized to Illumina HT12v4 chip
 
Contributor(s) Tsao M, Zhu C
Citation(s) 27750381
Submission date May 15, 2015
Last update date Aug 13, 2018
Contact name Ming Tsao
E-mail(s) ming.tsao@uhn.on.ca
Phone 4169464501
Organization name University of Toronto
Department Ontario Cancer Institute
Lab Applied Molecular Oncology
Street address 610 University Avenue
City Toronto
State/province Ontario
ZIP/Postal code M5G2M9
Country Canada
 
Platforms (2)
GPL10558 Illumina HumanHT-12 V4.0 expression beadchip
GPL14951 Illumina HumanHT-12 WG-DASL V4.0 R2 expression beadchip
Samples (36)
GSM1687221 X106
GSM1687222 X108
GSM1687223 X110
Relations
BioProject PRJNA284129

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
GSE68929_RAW.tar 26.2 Mb (http)(custom) TAR
GSE68929_non-normalized_GPL10558.txt.gz 4.9 Mb (ftp)(http) TXT
GSE68929_non-normalized_GPL14951.1.txt.gz 2.0 Mb (ftp)(http) TXT
GSE68929_non-normalized_GPL14951.2.txt.gz 1.6 Mb (ftp)(http) TXT
GSE68929_non-normalized_GPL14951.txt.gz 2.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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