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News / Events
Jun 7, 2015: If you publish using the results found on this portal, please cite: Zack et al. Pan-cancer patterns of somatic copy number alteration. Nature Genetics (2013).
Jun 1, 2015: Today the results of two new analysis sets of the complete set of TCGA SNP 6.0 array experiments, consisting of 10844 patient tumor samples across 33 cancer types, have been published on the portal. This final data set has expanded by 274 patient samples and contains two new cancer types, Thymoma (123 patients) and Testicular germ cell tumors (150 patients). The two analysis sets differ in the method used to discriminate individual regions. One analysis set uses "arm-level peel-off" which helps specifically locate strong drivers on a chromosome arm with a potential cost of decreased sensitivity to other drivers on the arm. The other analysis set uses standard arbitrated peel-off and trades in increased sensitivity for detecting multiple drivers for less specificity.
Feb 4, 2015: Getting IGV to work on Apple Macintosh computers is becoming increasingly difficult as Apple ramps up Java application security. Here is the current work around for OS/X Mavericks.
First, make sure you are getting the IGV launcher file downloaded. It should be in your Downloads folder and be named 'igv.jnlp' or some variant like 'igv-1.jnlp'. If you can find the jnlp file, then you need to allow it to launch IGV in your Java security settings:
(1) Open System Preferences on your Mac.
(2) Select Java (bottom row). The Java Control Panel opens in a separate window.
Select the Security tab, then click on the "Edit Site List..." button to pop up the Exception Site List window.
(3) Click on the Add button in the Exception Site List window.
(4) Under Location, enter https://data.broadinstitute.org, then press the OK button to add the security exception.
(5) Press OK on the Java Control Panel to finalize the security exception.
Now you should be able to go to the Downloads folder and launch IGV with the igv.jnlp file.