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The Copy Number Variation (CNV) Project Data Index


Analysis of copy number variation in the HapMap samples using array-based comparative genome hybridization with a genome-wide Whole Genome TilePath (WGTP) array consisting of ~27000 large-insert clones.

We have produced a dataset of array-based comparative genome hybridization from EBV-transformed lymphoblastoid cell lines from all 270 HapMap individuals used in the phase I and phase II of the project (populations: CEU, CHB, JPT and YRI).

deletion map This is a collaborative effort that involves the groups of:

Groups
  • Nigel Carter
  • Matthew Hurles
  • Chris Tyler-Smith
  • Charles Lee, Harvard Medical School
  • Steve Scherer, Hospital for Sick Children

Our groups aim at performing various types of global analysis in this dataset such as :

  • generating a genome-wide map of copy number variation
  • mapping the genomic-wide CNV map onto functional annotation of the genome
  • associations to SNP and haplotype variation
  • associations to gene expression variation
  • quantify population differentiation for copy number variation
Localisation and frequency of CNVs in the Human Genome.
[Click on image for enlagement]

These data are being released freely to the scientific community and can be considered a community resource.
However, the data generators reserve the right to be the first to publish on the bulk data as indicated by the Fort Lauderdale meeting report.
(see data release policy below ).

For any questions regarding the data and the data release policy please contact:

  • Nigel Carter
  • Matthew Hurles

  • The data were generated using the WGTP array with dye-swap for each individual and using a single male reference : HapMap individual NA10851.



    DATA DOWNLOAD



    The data can be downloaded in three formats :

    • A single text file containing the mean dye-swap intensity for each clone in each individual
    • Raw extracted intensities for each image (BlueFuse format) in Excel-compatible text files
    • Normalized extracted intensities, with low intensity spots removed and log2ratios calculated.
    • Some sample image files for dye-swap experiment and a mapping file for use with the image files


    And can be downloaded from here ( data_description ).
    deletion map
    DyeSwap Intensities Ratios on Human chromosomes
    [Click on image for enlagement]

    ACKNOWLEGDMENTS

    Nigel Carter, Richard Redon, Heike Fiegler, Lyndal Montgomery, Matthew Hurles, Chris Tyler-Smith, Tatiana Zerjal,
    Daniel Andrews, Armand Valsesia, Fengtang Yang, Dimitrios Kalaitzopoulos, Charles Lee, Steve Scherer

    Funding was provided by the Wellcome Trust.


    DATA RELEASE POLICY

    The release of pre-publication data from large resource-generating scientific projects was the subject of a meeting held in January 2003, the "Fort Lauderdale meeting", sponsored by the Wellcome Trust, one of the Project funders.
    The report from that meeting can be viewed here .

    The recommendations of the Fort Lauderdale meeting address the roles and responsibilities of data producers, data users, and funders of "community resource projects", with the aim of establishing and maintaining an appropriate balance between the interests of data users in rapid access to data and the needs of data producers to receive recognition for their work.

    The conclusion of the attendees at the meeting was that responsible use of the data is necessary to ensure that first-rate data producers will continue to participate in such projects and produce and quickly release valuable large-scale data sets.
    "Responsible use" was defined as allowing the data producers to have the opportunity to publish the initial global analyses of the data, as articulated at the outset of the project.
    Doing so also will ensure that the data generated are fully described.
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    Last Modified Tue Jun 26 13:17:42 2007

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