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Study Description

This study combined whole exome (103 samples) and whole genome (22 samples) sequencing over a total of 108 breast tumors and matched normal DNA to identify novel mutations and translocations. Samples were subjected to paired-end Illumina sequencing with goal of 30x coverage of tumor/normal for whole genomes and 100x tumor/normal coverage for whole exomes. From these sequences, we used various computational techniques to identify somatic point mutations, insertion/deletions and structural rearrangements in these tumors. From these data, we identified new insights into the rates of background mutations in these cancers, novel recurrent mutated genes, and multiple gene rearrangements. One of these rearrangements appears to be a recurrent event in breast cancer.

  • Study Types: Case Set, Tumor vs. Matched-Normal, Exome Sequencing
  • Number of study subjects that have individual level data available through Authorized Access: 108

Authorized Access
Publicly Available Data (Public ftp)

Connect to the public download site. The site contains release notes and manifests. If available, the site also contains data dictionaries, variable summaries, documents, and truncated analyses.

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
Whole Genome Genotyping Affymetrix AFFY_6.0 934940 52074
Whole Genome Sequencing Illumina 101bp paired end reads N/A N/A
Whole Exome Sequencing Illumina Agilent selected, 76bp paired end reads N/A N/A
Selected publications
Diseases Related to Study (MESH terms)
Links to Other NCBI Resources
Authorized Data Access Requests
Study Attribution
  • Principal Investigators
    • Todd Golub. Broad Institute, Cambridge, MA and Dana Farber Cancer Institute, Boston, MA, USA
    • Matthew Meyerson. Broad Institute, Cambridge, MA and Dana Farber Cancer Institute, Boston, MA, USA
  • Funding Source
    • Slim Initiative for Genomic Medicine. Carlos Slim Health Institute, Mexico City, Mexico