status: Curated disease: Cancer species: Homo sapiens citation:
Molecular characterization of breast cancer with high-resolution oligonucleotide comparative genomic hybridization array. Andre F, Job B, Dessen P, Tordai A, Michiels S, Liedtke C, Richon C, Yan K, Wang B, Vassal G, Delaloge S, Hortobagyi GN, Symmans WF, Lazar V, Pusztai L. Clin Cancer Res. 2009 Jan 15;15(2):441-51.PMID:19147748
Pharmacogenomic predictor discovery in phase II clinical trials for breast cancer.
Pusztai L, Anderson K, Hess KR. Clin Cancer Res. 2007 Oct 15;13(20):6080-6.PMID: 17947471 SampleType: Tumor Tissue numSamples: 112 tissueType: Breast Institution: Institut Gustave Roussy Investigator: Fabrice Andre release_notes: Curation notes: Patients studied all had stage II-III breast cancer which had been previously treated with preoperative chemotherapy. Expression profiling was done on the Affymetrix U133A gene array. CNV was done using Agilent Human 4x44K arrays. It is of note that the Affy *.CEL files were not available and the preprocessing methods for the gene array data are unknown to the curator. Genome builds: Expression- annotated with R version 2.11.1 and the Bioconductor suite of annotation packages CNV- NCBI36 version of the human genome per file annotation provided with data MORE INFORMATION IS AVAILABLE FROM: Andre et al. Clinical Cancer Research 2009 (PMID: 17947471) ***************** FILE DESCRIPTIONS ***************** files under each directory individuals.txt individuals description file ******** cnv data ******** platform: Agilent Human 4x44K array (G4426A) files under ./cnv/*/ cnv_bkgrd_g_signal.txt background signal of channel 1 (Cy3) cnv_bkgrd_r_signal.txt background signal of channel 2 (Cy5) cnv_g_signal.txt spot signal channel 1 (Cy3) cnv_nreplic.txt number of replicates are each spot cnv_r_signal.txt spot signal channel 2 (Cy5) probe.txt probe description files with the following descriptors: probe_id column (Coordinate for probe column) row (Coordinate for probe row) ProbeUID (Agilent probe ID - not necessarily unique) ProbeName (Agilent probe name - not necessarily unique) Database_Entry_hugo (gene name) Sequence (probe sequence) Comment (probe specific comments) chromosome (from which probe belongs) location_start (bp location on chromosome where probe begins) location_stop (bp location on chromosome where probe ends) *************** expression data *************** platform: Affymetrix U133A gene array files under ./expression/ expression.txt probeset level data for each sample - exact preprocessing / normalization / summarization unknown ** paper suggests that dChip V1.3 software was used to normalize to a single reference array with default parameters used ** feature.txt feature description file with the following descriptors: feature_id Symbol (gene symbol) Description Chromosome Chromosome_Location GenBank (accession number) Gene Cytoband UniGene Gene_Ontology Pathway ************** phenotype data ************** files under ./phenotype/ phenotype.txt phenotype trait values for each individual features.txt description of each phenotype trait syn47254 syn88643 syn47253