Tumor-Normal PCR-Free WGS Data (HCC1187)

A variety of Illumina technologies can be used to help understand cancer markers and progression.  To illustrate this, we are publishing a series of Tumor-Normal datasets in BaseSpace analyzed using several approaches.  Read this tech note for additional details on how to visualize this particular tumor/normal data set using the integrated set of tools in BaseSpace.

Materials and Methods: The DNA was extracted from the HCC1187 breast ductal carcinoma cell line and a matching lymphoblastoid cell line. 500 ng of DNA were prepped using an early access version of Illumina’s TruSeq DNA PCR-Free kit, and sequenced on a HiSeq 2000. The data was analyzed using a pre-release version of the Cancer Sequencing Workflow. This data is being shared in accordance with the terms of a licensing agreement with UT Southwestern, the owners of the cell lines.

To access the data, click on the link below to see the project folder. You will be asked to “Accept” the Project into your BaseSpace account: this is the same mechanism you will use to share specific real-life projects or runs with your colleagues/collaborators via a dedicated URL.

  • TumorNormal_WGS_HiSeq2000_CSW_0.23: Project (Cancer Sequencing Workflow (pre-release version) output files).

Below is a preview of what can be found in the data set and the related technical note:

Summary table from the Somatic Summary Report, automatically generated using Illumina’s Cancer Sequencing Workflow (pre-release):

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Circos Plot showing HCC1187 Somatic Mutations, automatically generated using Illumina’s Cancer Sequencing Workflow (pre-release):

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Customized version of the Broad IGV, fully integrated into BaseSpace, and showing some VCF and BAM tracks for this Tumor-Normal dataset:

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Learn more about:

Note: HCC cell lines were invented by Drs. Adi F. Gazdar and John D. Minna at the University of Texas Southwestern Medical Center. Rights in and to the HCC cell lines, progeny, and unmodified derivates thereof belong to the Board of Regents of The University of Texas System. Illumina, Inc. has obtained permission from the Board of Regents of The University of Texas System through the University of Texas Southwestern Medical Center to use the HCC cell lines and publish the data and results herein displayed.

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