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Introduction

TARGET data are available from different, overlapping public repositories/databases.

The NIH, NATIONAL CANCER INSTITUTE, Genomic Data Commons (GDC)

is to provide the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine.

TARGET data, and more specifically for this use case TARGET-AML data, can be accessed directly from the GDC, since it is hosting the OCG and its TARGET project (see bellow). There is also access to publication pages related to the projects, for instance here https://gdc.cancer.gov/about-data/publications/TARGET-AML-2017 where some instructions and paths to data are available.

The Office of Cancer Genomics (OCG)

is a program of the GDC aimed at supporting research programs that enhance the potential of precision oncology by improving the molecular definition of cancer subtypes—including rare and/or high-risk—and identifying potential novel strategies that can be translated into effective patient treatments.

The OCG is hosting several running or finished programs, including the running TARGET program.

Finally, TARGET is hosting several TARGET projects including the TARGET-AML we are interested in for this use case.

In the next section, we experiment one procedure to download TARGET-AML datasets, using the GDC interface. Importantly, some datasets of the GDC are tagged as controlled and are only available to validated users. This use case does not cover the download of controlled datasets. The procedure to obtain authorizations for accessing controlled data will be reviewed elsewere.