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Title: Affymetrix SNP array data for NSCLC and CRC      
keywords:
Variation
ID:
PRJNA125169
description:
Cancer is a heterogeneous disease caused by genomic aberrations and characterized by significant variability in clinical outcome and response to therapies. Several subtypes of common cancer types have been identified based on alterations of individual cancer genes, such as HER2, EGFR, and others. However, cancer is a complex disease driven by the interaction of multiple genes, so the copy number status of individual genes is not sufficient to define cancer subtypes and predict the response to treatments. A classification based on genome-wide copy number patterns would be better suited for this purpose. To develop a more comprehensive cancer taxonomy based on genome-wide patterns of copy number abnormalities, we designed an unsupervised gNMF-based classification algorithm that identifies genomic subgroups of tumors. The algorithm was subjected to a stability test and validated by demonstrating clinical differences between samples assigned to different clusters. Our algorithm demonstrated better performance in the stability test when compared with other clustering methods. Most importantly, it yielded better separation between groups of samples with distinct clinical outcomes, implying that it classifies samples into clinically relevant subgroups. We propose using this methodology to identify unknown subtypes of cancers and to assemble panels of pre-clinical testing models that would represent different subtypes of cancers. Overall design: Affymetrix SNP arrays were performed according to the manufacturer's directions. Copy number analysis of Affymetrix 100K SNP arrays was performed for 40 non-small cell lung carcinoma cell lines, 205 non-small cell lung carcinoma primary tumors, 35 colorectal cancer cell lines, and 101 colorectal cancer primary tumors.
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA125169
authentication:
none
authorization:
none
ID:
pmid:20569491
dateReleased:
08-06-2010
name:
Homo sapiens
ncbiID:
ncbitax:9606
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject