Making a Data Request
Creating a data request is the premier way to access raw St. Jude next generation sequencing data in the cloud. You can get a free copy of the data in a secure cloud environment powered by Microsoft Azure and DNAnexus, or you can elect to download the data to your local computing environment.
If you would like to download the data to local storage, there are extra steps you'll need to follow such as getting additional signatures on your data access agreement. We recommend that you work with the data in the cloud if it's feasible; the data provided by St. Jude is free, the compute charges are reasonable, and working in the cloud helps to eliminate the long, error-prone downloading process. Porting your tools to be run in the cloud is easy, as well. We recommend you follow this guide to get started.
Navigate to the Data Browser
Navigate to the data browser by clicking Access Data and Explore Data. If you would like to view the requests you have already made, you can do so under Manage Data.
Select Your Data
Next, select the cohort you are interested in requesting. You can browse our data by disease, publication, dataset, or you can use Pecan, our Pediatric Cancer portal, to find samples associated with specific genes, or mutations.
Select Your Files
Once you have selected the cohort you would like to study, you can chose what type of files you would like to receive. This step is dynamic, and shows you all of the file types we have available for the dataset you are interested in.
Submit Your Request
If you are requesting access to a dataset you have not already been approved for, you will see a section called Controlled Data. Under this section, there is a bulleted list that indicates the Data Access Units you need to request access to through our data access agreement. Please use this list to fill in the Datasets section of the Data Request Form as shown in the figure below. For more information on filling out this guide, see Filling out the DAA.
Now, you have successfully submitted your data request. Your request will be sent to the respective data access committees for evaluation. You should expect to hear from us within a week or two on average.
Data access agreement
Broadly speaking, the data access agreement (DAA) is a legal document binding the requestor and the requestor's institution to terms about how our data may be used. We do not negotiate the terms of this document unless terms are found to be in conflict with the institution's state law. Filling out the Data Access Agreement carefully and completely is crucial to having your request filled promptly.
Filling out the DAA
All Data Access Agreements require the following 5 items:
Page 5 The Data Access Unit(s) you are applying for must be marked.
- These can be found in the section Controlled Data, above the Download Data Request Form button. This can be found on the third step of the data request process under the Controlled Data section. This is a dynamic feature that allows the user to see exactly which Data Access Units (datasets) they are requesting data from.
Page 8 Signature and information of the Principal Investigator.
- This must be signed by a Principal Investigator or a faculty-level supervisor on the project.
Page 9 Signature and information of all other applicants.
- This should include any person who will have access to this data. They are legally bound to protecting and handling the data properly.
Page 10 Signature and information of Institutional or Administrative Authority.
- This individual cannot be the same Principal Investigator that signed above, as this section is to provide a second-party authority of the instituion to ensure that the institution will uphold the terms of this agreement.
Page 12 Description of contemplated use of St. Jude data.
- Here, describe your research question and it's biological significance. The Contemplated Use will be evaluated by the Data Access Committees based on their own set of protocols.
- Please contact us if you have any questions regarding the protocols of the approval process.
Data download permission
Additionally, if and only if you would like to download the data, you will also need to include the following:
Page 4 The applicant's initials in Part 2.
Page 11 Signature and information of the Information Technology Director or Chief Information Security Officer.
Frequently asked questions
Q. Why do I need to sign the DAA?
A. Although the DAA serves many purposes, the terms included in the data access agreement are ultimately in place to protect our patients. We take patient security very seriously, and we require that requestors are committed to protecting that privacy to the fullest extent.
Q. Where can I find the latest version of the DAA?
Q. Where do I submit the DAA??
A. You can submit your Data Access Agreement in the drag and drop box on the last step of submitting your request.