Simple tumor sequencing data analysis

Comparing tumor and matched normal sequencing data provides insight into cancer mechanisms

Tumor-Normal Sequencing Data Analysis

Tumor sequencing experiments generate valuable data that can provide insights into the changes driving tumorigenesis. Push-button tools in BaseSpace Sequence Hub genomics computing environment, such as the Tumor-Normal Sequencing App, simplify analysis and visualization of large tumor sequencing data sets. Researchers can also explore and evaluate example data sets in BaseSpace Hub, as described on this page.

This video tutorial describes how to log into BaseSpace Hub to access tumor sequencing data. It also provides a brief description of the BaseSpace Hub Project page and describes the data contained within each section.

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This video tutorial reviews the findings in the report produced by the Tumor-Normal Sequencing App in BaseSpace Hub.

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This video tutorial shows how to load tumor sequencing data into the Broad Institute Integrative Genomics Viewer (IGV), a free app available in BaseSpace Sequence Hub.

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This video tutorial shows how to use IGV to visualize variants identified between tumor and normal samples. This example highlights an indel in TP53 and a translocation between chromosomes 1 and 8.

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Tumor sequencing data were generated from the HCC1187 breast ductal carcinoma cell line and a matching lymphoblastoid cell line from the same individual. (Note that the lymphoblastoid line HCC1187 BL does not represent a true matched normal sample from the same tissue type as the tumor, but was used so that the sequencing data could be shared publicly.)

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*Note that access to the data requires a BaseSpace Sequence Hub login. Register for BaseSpace Hub.

BaseSpace Tumor-Normal Sequencing App
  • Detects somatic variants from a tumor and matched normal sample pair
  • Designed for whole-genome sequencing data
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BaseSpace Correlation Engine

A library of genomic data to identify mechanisms, drug targets, and prognostic or predictive biomarkers from tumor sequencing data.

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Easier Analysis and Storage of Tumor Sequencing Data

Alex Dickinson, senior VP of cloud genomics, explains how BaseSpace Hub helps researchers easily run leading-edge bioinformatics tools.

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Visualizing Tumor Sequencing Data in BaseSpace Hub

Learn how to visualize tumor-normal sequencing data in BaseSpace Hub.

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References

*Shared in accordance with the terms of a licensing agreement with the University of Texas Southwestern Medical Center, the owners of the cell line.