Making a Data Request

Request Process Overview

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.

Helpful Things to Remember

1. Data in St. Jude Cloud is grouped into Data Access Units (DAUs), which usually correspond to large-scale sequencing initiatives at St. Jude.
2. Individuals can apply for access to DAUs on a case-by-case basis for a specific amount of time (1 year, with the opportunity to extend access).
3. Access to data in a given DAU is assessed by the corresponding Data Access Committee who reviews a variety of factors to grant access.
4. There are a number of terms of use and restrictions outlined in the Data Access Agreement. Everyone who will be working with the data must understand and agree to these terms.

Selecting Data

The primary way to make your data selection is through our Genomics Platform Data Browser. You can search our raw genomic data by diagnosis, publication, study, or individual samples by selecting a tab along the top. You may further refine your search by applying filters from three categories: Sequencing Type, Sample Type, and File Type. Please note that applying multiple filters within the same category filters using ‘OR’ logic, while applying multiple filters across different categories filters using ‘AND’ logic. For example in the overview image above, we have filtered the browser to only show data that is (either WGS OR WES) AND (Diagnosis OR Relapse) AND BAM.

As you filter and make selections, the data summary panel in the upper left hand corner will update dynamically to give you important descriptive information about the set of data you have selected. Click on an empty box to make a selection; when selected, the box will turn blue with a white check mark. Once you have completed your data selection, click on Request Data to submit your request and proceed.

Alternatively, you may be directed to the Genomics Platform Data Browser through another App to request specific samples. The PeCan homepage is one such app that allows you to select data through an interactive visualization.

Selecting a Project or Creating a New One

Now that you have selected your data, you need to choose whether to vend this data into an existing St. Jude Cloud project on DNAnexus, or to create a new St. Jude Cloud project. On the “Choose Your Data Destination” step, select to use an existing project and then which specific project you want to add data to, or select to create a new project.

On the “Name Your Project” step, you will see the name of the existing project you selected or a blank space to add a name for a new project. In either case, you also need to name a folder within the project. The text box will be pre-filled with “Data Requested (date)”, but you are able to change it here, and also can edit any names after you have created your project.

Example Use Case

Let’s quickly look at our Real-Time Clinical Genomics (RTCG) dataset as an example of how projects, folders, and files function together.

The first time you request access to RTCG from the Studies Tab of the Data Browser, you will name your new project. For this example, we’ll refer to it as RTCG Data Project. Then you’ll name the folder for this initial selection of data. Today’s date will autofill, but we’ll refer to the folder as Initial Request Folder instead. After that, complete the DAA and the rest of the process. Once you are approved, the data is delivered within your Initial Request Folder folder inside of RTCG Data Project.

The RTCG dataset is continuously updated with more Clinical Genomics data from St. Jude. When you receive an email about the latest release to the dataset, you return to the Data Browser and once again select RTCG from the Studies Tab. While you request the data, rather than create a new project, you can choose to vend data to an existing project and select RTCG Data Project from the dropdown menu. Now you may name a new folder to vend to. We’ll call this one New Release Folder and submit the request. Since you already have access, there is no need to complete a new DAA or collect any signatures. There will now be two folders within your RTCG Data Project with the Initial Request Folder having most of the data, while New Release Folder only has the new files that have been released since the first request was made. Therefore, the new files are not found in Initial Request Folder.

Completing the Data Access Agreement

Through the Electronic Data Access Agreement wizard, you will add all of the necessary information needed for the Data Access Agreement (DAA). Once you have completed the setup wizard, if you are located in the United States of America, you can opt in to using DocuSign to collect the required signatures - the form will be sent to you and necessary signatories through email via DocuSign. If you are not located in the USA, or would like to complete the form manually, you will print the DAA and collect signatures manually, then upload and submit the request. You can learn more about Filling Out The Data Access Agreement here.

Access request approval typically takes less than 2 weeks if your data access agreement is correctly and completely filled out. You will receive automated emails from notifications@stjude.cloud when your request is approved. Note that an email for each of the Data Access Units requested is sent, and they are not all approved at once, but rather as soon as each committee grants approval.

Managing your Data Request

Go to our Managing Data Overview documentation page to learn how to check the status of your data request, complete an EDAA draft, upload a revised DAA, and ultimately access your data from your My Dashboard page.