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feat: Cc4kv0.5 1.22.25 #131

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9c32496
feat: account login
mkirk111 Jan 21, 2026
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feat: format correction
mkirk111 Jan 21, 2026
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revise: format
mkirk111 Jan 21, 2026
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revise: removed copilot .md file
mkirk111 Jan 22, 2026
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feat: cc4kv0.5
mkirk111 Jan 23, 2026
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ci: :rocket: creates preview environment for pr131 [skip ci]
stjudecloud-cloudy Jan 26, 2026
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chore: :rocket: released stjudecloud.azurecr.io/stjudecloud/docs:pr1…
Jan 26, 2026
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107 changes: 107 additions & 0 deletions content/2.cc4k/1.index.md
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title: Overview
---

## v0.5

Submitted: January xxxx, 2026

Click [here] () {target="_blank"} to download.

CC4K (Cancer Classifications for Kids) provides a harmonized, computable pediatric cancer classification framework used across [St. Jude Cloud](https://stjude.cloud) and by the [CCDI Federated API](https://github.com/CBIIT/ccdi-federation-api).
Version 0.5 delivers a major revision to the solid tumor tree, replacing the prior bespoke tissue-of-origin model with a pediatric-specific structure grounded in the WHO 5th Edition Classification of Tumours: Paediatric Tumours (WHO pediatric book).
For an informative summary of the WHO pediatric book, see [Pfister et al. (Cancer Discovery, 2022)](https://doi.org/10.1158/2159-8290.CD-21-1094).

By organizing the updated tree around the WHO pediatric book, the hierarchy reflects a pediatric-focused framework and improves consistency for pediatric entities that are often scattered across adult-oriented organ-system classifications.
Outside of CNS and hematological malignancies, the WHO organizes non-CNS solid tumor diagnoses into multiple tissue-specific blue books.
Directly translating this structure into previous versions of CC4K resulted in duplicated pediatric diagnoses appearing under multiple anatomic contexts, with examples shown below in Table 1.
Using the pediatric book’s organization as the basis for our tree structure in this update resolves these duplication issues by providing a single pediatric-oriented context or by explicitly omitting entities not yet defined for pediatric disease, while preserving extensibility for future updates.

| **Tumor Classification Terms** | **Number of WHO Books Referenced** | **Number of References in Pediatric Book** |
|:----------------------------------:|:----------------------------------:|:------------------------------------------:|
| Ewing Sarcoma | 7 | 2* |
| Inflammatory Myofibroblastic Tumor | 7 | 1 |
| Adenoid Cystic Carcinoma | 7 | 0 |
| Angiosarcoma | 10 | 2* |
| Tubular Adenoma | 4 | 0 |
| Rhabdoid Tumor | 2 | 2* |
#### Table 1. Redundant terms across WHO Books

*Includes references such as renal Ewing Sarcoma, Hepatic Angiosarcoma, and Atypical Teratoid/Rhabdoid Tumor.
Histogenic consistency was enforced across the tree, with Angiosarcoma aligned to Vascular Tumors, Inflammatory Myofibroblastic Tumor to Fibroblastic/Myofibroblastic Tumors, and Adenoid Cystic Carcinoma placed under Head and Neck Tumors, while anatomic site variation is captured through metadata attributes to deduplicate Ewing Sarcoma and Angiosarcoma.
Rhabdoid Tumors were elevated to its own entity, described below.

### Comprehensive Updates

The prior CC4K solid tumor hierarchy contained 256 total nodes (236 leaf nodes across 21 parent nodes) and was organized using a tissue-of-origin framework, initially aligned to OncoTree, but over-time, developing more into a bespoke framework.
In contrast, the updated v0.5 hierarchy contains 218 total nodes with 187 leaf nodes (Δ = −49) distributed across 31 parent nodes.
Tree depth remains four layers; however, the organization has shifted from site-centric to aligning with 11 WHO pediatric book chapters, introducing targeted subdivision where necessary, as described below.
Eight chapters were mapped directly (column A), while the structure for three chapters was intentionally modified (column B).
Using this updated hierarchy, approximately 9,474 solid tumor samples were reclassified.

| | **A** | **B** | **C** | **D** | **E** |
|:------:|:---------------------------------------------------:|:-----------------------:|:------------------:|:------------------------------:|:------------------:|
| | **WHO Chapters aligned (Under the Pediatric Book)** | **Subchapter detail** | **Levels (depth)** | **CC4K (under Solid Tumor)** | **Levels (depth)** |
| **1** | Endocrine Tumors | | 3 | Endocrine Tumors | 2 |
| **2** | Peripheral Neuroblastic Tumors | | 3 | Peripheral Neuroblastic Tumors | 1 |
| **3** | Soft Tissue and Bone Tumors | | 3 | | |
| | | Soft Tissue Sarcomas | 2 | Soft Tissue Tumors | 2 |
| | | Bone Tumors | 2 | Bone Tumors | 1 |
| | | Undifferentiated Tumors | 2 | Undifferentiated Tumors | 1 |
| **4** | Germ Cell Tumors | | 3 | Germ Cell Tumors | 1 |
| **5** | Head and Neck Tumors | | 3 | Head and Neck Tumors | 1 |
| **6** | Skin Tumors | | 3 | Skin Tumors | 1 |
| **7** | Eye Tumors | | 3 | Eye Tumors | 1 |
| **8** | Thoracic Tumors | | 3 | Thoracic Tumors | 1 |
| **9** | Digestive System Tumors | | 3 | Digestive System Tumors | 2 |
| **10** | Renal and Male Genital Tumors | | 3 | | |
| | | Renal | 2 | Renal Tumors | 1 |
| | | Male Genital | 2 | Genital Tumors | 1 |
| **11** | Female Genital Tumors | | 3 | Genital Tumors | 1 |

#### Table 2: Mapping of Pediatric WHO chapters to CC4K solid tumor domains.

For example, we split the WHO chapters “Soft Tissue and Bone Tumors” and “Renal and Male Genital Tumors” because these chapters function primarily as aggregations of distinct groups.
In the Soft Tissue and Bone chapter, tumors are subdivided into soft tissue, bone, and undifferentiated subchapters, each of which is organized according to different underlying principles.
In this update, we elevated these subchapters to top-level nodes rather than retaining the aggregate chapter as a single branch, as seen in Table 2, column D.

This change also enabled alignment with contemporary guidance to organize tumors by histogenetic lineage rather than by prior distinctions such as rhabdomyosarcoma versus non-rhabdomyosarcoma.
While the broad distinction is useful to categorize samples, this is not useful to delineate as a framework for a sample classification tree.
Bone and undifferentiated tumors are now represented as flat lists of leaf nodes to simplify handling of singleton entities and to avoid unnecessary nesting of diagnoses such as Ewing sarcoma and osteosarcoma.
Notably, rhabdoid tumors were extracted as a distinct entity under Soft Tissue Tumors.
Although rhabdoid tumors arise across multiple tissues of origin, their shared biology supports representation as a single queryable node, reducing redundancy across child leaves.

Similarly, the Renal and Male Genital Tumors chapter was restructured because many male genital tumor entities overlap with those in the female genital book.
These were consolidated under a unified Genital Tumors node, with patient sex retained as an attribute if needed to stratify.

### Challenges

Certain pediatric tumor entities span multiple anatomic sites, histogenic lineages, or fall outside the current scope of the WHO pediatric book.
In CC4K v0.5, tubular adenoma, observed in the colon, gastrointestinal tract, and breast, was assigned a single canonical placement under Digestive System Tumors → Gastrointestinal → Tubular Adenoma.
Breast cases (n=1) are classified as Adenoma, NOS with anatomic site captured via metadata, preventing duplication while preserving query flexibility. Canonical placements are periodically re-evaluated as sample volume and distribution evolve.

In total, 43 child leaf nodes in v0.5 fall outside the pediatric volume but were retained by evaluating where they might exist in a non-pediatric book.
For example, adrenal cortical adenoma and carcinoma are not explicitly defined in the WHO pediatric book but appear across other WHO books which now belong under Endocrine Tumors → Adrenal Tumors.
To see which nodes exist in non-pediatric books, we annotated this in column I in our downloadable tree for transparency.

To address over-fragmentation, five low-frequency NEC nodes were consolidated into existing NOS categories.
This decision was informed by experience with NEC/NOS usage in the CNS tumor tree and by review of WHO solid tumor classifications, which are largely not molecularly driven and do not consistently support NEC distinctions.
Given the limited sample counts and lack of defining molecular features, maintaining separate NEC nodes was not justified. These categories were therefore consolidated, pending future evidence or novel biomarkers.

Boundary conditions between the solid tumor (ST) and CNS trees were also clarified for germ cell tumors (GCTs).
Tumors explicitly defined as brain-specific germ cell entities are now placed under the CNS tree (e.g., Germ Cell Tumor, Brain).
In contrast, mixed germ cell tumors, yolk sac tumors, and germinomas with brain as the anatomic site remain under the solid tumor GCT branch.
This distinction reflects differences between WHO CNS5, which includes a single unstratified “germ cell tumor, brain” node, and the WHO pediatric book, which defines germ cell tumors as a universal chapter with resolved subtypes.
CC4K v0.5 integrates both frameworks to maintain consistency with each specific case.

Finally, the CNS tumor tree was refined to reduce overlapping vocabulary across roots.
This included adding explicit CNS prefixes to CNS terms that would otherwise overlap with solid tumor terms (e.g., CNS Soft Tissue Tumors, CNS Tumors of Uncertain Differentiation, CNS CIC-rearranged Sarcoma), as well as identification of CNS Histiocytic Tumors and CNS Vascular Tumors as distinct domains.
These changes eliminate ambiguity while preserving the historical and commonly used distinction between CNS and non-CNS solid tumors.

### Future Updates

Next, we will focus on the remaining branches under Heme (e.g., Hodgkin and Non-Hodgkin Lymphoma and Other Heme Malignancies).

### References:

1. Pfister, S. M., Reyes-Múgica, M., Chan, J. K. C., Hasle, H., Lazar, A. J., Rossi, S., Ferrari, A., Jarzembowski, J. A., Pritchard-Jones, K., Hill, D. A., Jacques, T. S., Wesseling, P., López Terrada, D. H., von Deimling, A., Kratz, C. P., Cree, I. A., & Alaggio, R. (2022). A Summary of the Inaugural WHO Classification of Pediatric Tumors: Transitioning from the Optical into the Molecular Era. Cancer Discovery, 12(2), 331-355. [https://doi.org/10.1158/2159-8290.CD-21-1094]

1. World Health Organization. (2022–2024). WHO classification of tumours (5th ed.). International Agency for Research on Cancer.


## v0.4

Submitted: September 3, 2025
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74 changes: 26 additions & 48 deletions content/3.genomics-platform/1.getting-started/2.accounts-and-billing.md
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---
title: Accounts and Billing
description: Accounts and Billing
description: Information on account creation and billing setup.
---

St. Jude Cloud is built on top of [DNAnexus](https://www.dnanexus.com/), a data-analysis and management platform that specializes in the field of bioinformatics.
All of our account management is shared between St. Jude Cloud and DNAnexus.
In other words, if you have a DNAnexus account, you automatically have a St. Jude Cloud account, and vice versa.

::callout{icon="i-heroicons-exclamation-circle" color="orange"}
**St. Jude Employees**
The account creation and login process is slightly different if you are an internal user (you work at St. Jude).
Internal users please go to the [intranet home page](https://home.stjude.org) and type 'Bioinformatics Self-Service' into the search bar.
From there, click on the link that says 'Bioinformatics Self-Service on St. Jude Cloud' to access the internal guide to creating an account.
::
### Creating a St. Jude Cloud Account

## St. Jude Employees
To create an account, simply choose Genomics Platform on [the St. Jude Cloud homepage](https://stjude.cloud/) and then select “Log In.”

### Create An Account
You will be presented with several options to choose from to setup up your account credentials.
If you are a St. Jude employee, choose the St. Jude login option and use your St. Jude credentials for account creation.
If you are not a St. Jude employee, select from any of the alternative options to create your account.

Go to the [St. Jude Employee login page](https://cloud.stjude.org/) and log in with your current St. Jude credentials.
You will then be asked to select a method to authenticate your credentials.
Select your preferred authentication method to proceed.

::callout{icon="i-heroicons-document-text-solid" color="blue"}
**Note**
If you are unable to log in at this link, and you know you have been on St. Jude Cloud before, you may have already set up a DNAnexus account through the DNAnexus log in page using your St. Jude email address.
To continue using this account, you will need to log in through the [DNAnexus log in page](https://platform.dnanexus.com/login?client_id=sjcloudplatform).
You can request that your accounts be merged by contacting [DNAnexus support](mailto:support@dnanexus.com).

> Hello DNAnexus support,
>
> I am a St. Jude employee and I would like to have my account switched over so I can use my St. Jude credentials to log in.
>
> Thank you,
**Linking Accounts**
Users who have an existing DNAnexus account must use the St. Jude Cloud account creation and login steps above to access St. Jude Cloud data.
Once you have created an account through St. Jude Cloud your DNAnexus account and St. Jude Cloud account will be linked going forward.
::

### Billing

Go to the [Bioinformatics Self Service page](https://home.stjude.org/computational-biology/Pages/bioinformatics-self-service-cloud.aspx) on the Intranet for information on how to set up your billing account.

If your account is already set up and you would like to access your Billing information:

1. Click on the drop down next to your user name in the far right of the DNAnexus navigation bar, and select 'Profile'.
2. Click on 'Billing Account' from the tabs listed just under the navigation bar.

## Non-St. Jude Employees

### Create A DNAnexus Account

1. Go to the [St. Jude Cloud log in page](https://platform.dnanexus.com/register?client_id=sjcloudplatform) on DNAnexus.
2. Click "Create an Account".
3. Fill in your information.
4. On the Create New Account page, make sure to select "Microsoft Azure (westus)" as the Default Cloud Region.
5. Click 'CREATE ACCOUNT'

![create dx account](/img/genomics-platform/getting-started/accounts-and-billing/create-DX-account.gif)

### Billing Setup

::callout{icon="i-heroicons-document-text-solid" color="blue"}
**Note**
Data from St. Jude Cloud is available for free via the DNAnexus platform, but to submit a request and access the data, your DNAnexus billing account must be setup, which includes providing a source of funds. For a more detailed explanation of what is freely available and what actions would incur costs, [see our FAQ](/genomics-platform/getting-started/faq).
::
If you are a St. Jude employee, go to the [Bioinformatics Self Service page](https://sjcrh.sharepoint.com/sites/computational-biology/SitePages/Bioinformatics-Self-Service-on-St.-Jude-Cloud.aspx) on the Intranet for information on how to set up your billing account.

To complete DNAnexus billing account setup, email DNAnexus support ([support@dnanexus.com](mailto:support@dnanexus.com)).
Use the template below, adding in the required information.
If you are not a St. Jude employee, you will need to contact DNAnexus directly to setup billing.
To complete DNAnexus billing account setup, email DNAnexus support [support@dnanexus.com](support@dnanexus.com).
DNAnexus Support will reach out directly once the email is received.
Use the template below, adding in the required information to request billing assistance.
Your DNAnexus account ID and email can be found listed on your User Account page on DNAnexus.

> Hello DNAnexus Support,
Expand All @@ -79,3 +47,13 @@ Your DNAnexus account ID and email can be found listed on your User Account page
**Note**
DNAnexus Support will reach out directly once the email has been submitted.
::
If your DNAnexus account is already set up and you would like to access your billing information:

1. Login to your St. Jude Cloud account.
2. Click on your profile in the top right corner of the navigation and select 'DNAnexus Profile'.
3. Click on 'Billing Account' from the tabs listed just under the navigation bar.

::callout{icon="i-heroicons-document-text-solid" color="blue"}
**Cost**
Data from St. Jude Cloud is available for free via the DNAnexus platform, but to submit a request and access the data, your DNAnexus billing account must be setup, which includes providing a source of funds. For a more detailed explanation of what is freely available and what actions would incur costs, [see our FAQ](/genomics-platform/getting-started/faq).
::
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