Comment[ArrayExpressAccession]	E-MTAB-1088
Investigation Title	17 Breast Cancer Genome Illumina Expression Data		
Comment[Submitted Name]	17 Breast Cancer Genome Illumina Expression Data
Experiment Description	Cancer evolves dynamically, as clonal expansions supersede or overlap one another, driven by shifting selective pressures, mutational processes and disrupted cancer genes. These processes mark the genome, such that a cancerÕs life history is encrypted in the timing, ploidy, clonality and patterns of somatic mutation. We developed bioinformatic algorithms to decipher this narrative, and applied them to 21 breast cancer genomes. We find that mutational processes evolve across the lifespan of a breast tumor, with cancer-specific signatures of point mutations and chromosomal instability often emerging late but contributing extensive genetic variation. Subclonal diversification is prominent, providing insight into the dynamics of clonal expansion in breast cancer. Most point mutations are found in just a fraction of tumor cells, together with frequent variegation in chromosomal copy number. Every tumor studied here has a dominant subclonal lineage, representing more than 50% of tumor cells. Minimal expansion of these subclones occurs until many hundreds to thousands of mutations have accumulated, implying the existence of long-lived, quiescent lineages of cells that are capable of substantial proliferation upon acquisition of enabling genomic changes. Expansion of the dominant subclone to an appreciable mass may therefore represent the final rate-limiting step in a breast cancer's development, triggering diagnosis. 		
Experimental Design	individual_genetic_characteristics_design	reference_design	co-expression_design
Comment[AEExperimentType]	transcription profiling by array		
Comment[AEExperimentDisplayName]	Transcription profiling by array of 17 human breast cancer samples		
Experimental Factor Name	INDIVIDUAL		
Experimental Factor Type	individual		
Quality Control Type			
Public Release Date	2013-04-16
Person Last Name	McLaren
Person First Name	Stuart
Person Mid Initials	R
Person Email	sm2@sanger.ac.uk
Person Phone	+44 (0) 1223 494753
Person Address	The wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Person Affiliation	The Wellcome Trust Sanger Institute 
Person Roles	submitter
Protocol Name	P-MTAB-26609
Protocol Description	Samples were selected on the basis of a pathological review and DNA/RNA was extracted using a traditional phenol or TRIzol method by which ever institute held the tissue. The subsequent genomic DNA and RNA samples were shipped to the Sanger Institute for array analysis.
SDRF File	E-MTAB-1088.sdrf.txt