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Tcga Data Use Agreement

All users who access the controlled access data are bound by the dbGaP TCGA DATA USE CERTIFICATION AGREEMENT (DUCA). In addition, users must comply with Terra`s Terms of Use. Initial data identification efforts often do not provide the necessary metadata. Only at the time of download are key attributes such as age, diagnosis, histology, tumor stage, and RNA-Seq methods available. Unfortunately, this information is often incomplete or flawed, creating challenges when it comes to data characterization. Of the 23 data sets we have included in our compendium, 12 come from EGA, which provides little information about the data before approval. As a general rule, only a brief summary and a title are available for all data. Once permission is given, the example name, sample access, example type, technology, and file type are provided. Only after downloading is additional information sometimes available and additional information is required. In contrast, the dbGaP repository contains a list of examples with many technical details about how the data was generated and often histological before approval. When repositories provide multiple publications for a dataset, it is up to the user to read each document (and its additions) in order to find relevant information about the data that can be described in the publication.

Often, no publications are listed in the data repository. While we understand that respecting the privacy of individuals is a legitimate characterization challenge and requires restrictions in identifying age and gender for rare diseases, for example, a standardized approach to data characterization, which adds key descriptions, would remove key characterization barriers. Open access data hosted under the PCAWG directory and its subdirectories can be downloaded without a connection. However, you must log in to the Data Portal before you can download or even view the controlled access data files. Click the Connect button in the upper right corner and follow the steps. Once you have successfully logged in, you should be able to see two green icons (next to your account name), as shown below in the top line of the portal….