diff --git a/content/2.cc4k/1.index.md b/content/2.cc4k/1.index.md index f5d8efdc..11dccf0c 100644 --- a/content/2.cc4k/1.index.md +++ b/content/2.cc4k/1.index.md @@ -6,6 +6,58 @@ navigation: 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). +## v0.5.2 + +Submitted: xx xx, 2026 + +Click [here](){target="_blank"} to download. + +Version 0.5.2 delivers a restructuring update to the CC4K ontology, primarily within the Solid Tumor hierarchy, following pathologist recommendations and sample reclassifications. +This release renames 6 classifications, repositions 8 nodes within the tree, removes 8 ambiguous nodes, and introduces 6 new disease nodes, with approximately 104 samples reclassified as a result. +These changes correct classification inconsistencies and replace outdated or ambiguous terms to improve the accuracy of the tree. +The following sections detail each of these changes. + +### A. Renamed (6): + +- **Follicular Thyroid Carcinoma** — updated from *Follicular Thyroid, NOS* to reflect a more precise clinical classification. +- **Oncocytic Thyroid Carcinoma** — replaces *Hurthle Cell Thyroid Cancer*, adopting current WHO terminology. +- **Poorly Differentiated Thyroid Carcinoma** — updated from *Poorly Differentiated Thyroid Tumor*, adopting WHO accepted terminology. +- **Renal Cell Carcinoma, NOS** — replaces *Renal Cell Carcinoma* to remove ambiguity, as RCC encompasses many distinct subtypes. +- **Infantile Hemangioma** — replaces *Infantile Hemangioendothelioma*, a term no longer recommended, in favor of WHO accepted terminology. +- **Thymic Carcinoma** — replaces *Intrathyroidal Thymic Carcinoma*, realigned with standard clinical terminology. + +### B. Rearranged (8): + +The following nodes were misclassified and repositioned within the hierarchy following pathologist review and research validation. + +| Node | Previous Location | New Location | +|-------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------|------------------------------------------------------------------------| +| Juvenile Xanthogranuloma | Solid Tumor → Renal Tumors | Hematologic Malignancies → Other Hematologic Malignancies | +| Embryonal Sarcoma of the Liver | Solid Tumor → Undifferentiated Tumors | Solid Tumor → Digestive System Tumors → Liver Tumors | +| Spindle Cell Sarcoma, Spindle Cell Tumor, Undifferentiated Round Cell Sarcoma, and Undifferentiated Pleomorphic Sarcoma | Solid Tumor → Undifferentiated Tumors | Solid Tumor → Soft Tissue Tumors → Tumors of Uncertain Differentiation | +| Neurothekeoma | Solid Tumors → Soft Tissue Tumors → Fibroblastic and Myofibroblastic Tumors | Solid Tumors → Skin Tumors | +| Signet Ring Cell Carcinoma | Solid Tumor → Genital Tumors | Solid Tumor → Digestive System Tumors → Gastrointestinal Tumors | + +*Table 1: CC4K v0.5.2 Nodes Repositioned Within the Hierarchy.* + +### C. Deprecated (8): + +- **Solid Cancer of Unknown Primary; Epithelioid Neoplasm, NOS; Metastatic Tumor, NOS; Mesenchymal Tumor, NOS; Myxoid Neoplasm, NOS; and Primitive Round Cell Neoplasm** — removed as these classifications were deemed ambiguous and imprecise. +Samples previously tagged to these nodes have been reassigned to *Solid Tumor, NOS*. +- **Thyroid Hyperplastic Nodule** — removed as this is a subset of *Thyroid Follicular Nodular Disease*, under which its samples have been reassigned. +- **Myofibroblastic Sarcoma, NOS** — removed as this is a subset of *Myofibroblastic Neoplasm, NOS*, under which its samples have been reassigned. + +### D. New (6): + +This release adds six new disease classifications identified through curated case studies requiring formal classification within the tree: **Ganglioneuroblastoma, Nodular**; **Renal Cell Carcinoma with MiT Translocations**; **Histiocytic Neoplasm, NOS**; **Hybrid Nerve Sheath Tumor**; **Adamantinoma**; and **Fibroepithelial Tumor**. +These nodes were informed by pathologist recommendations and ongoing case review, with samples previously assigned to broader classifications found to more accurately fit these newly introduced nodes. +Their addition improves classification precision and maintains alignment with the WHO 5th Edition Classification of Tumors: Pediatric Tumors. + +A number of classifications were recommended for addition to the Solid Tumor tree but were deferred from this release as the current PeCan/Genomics Platform databases do not yet have sample representation for these nodes. +Development releases, such as this one, prioritize structural accuracy and classification consistency for nodes already represented by samples. +New nodes introduced primarily in alignment with the latest edition of WHO Pediatric Tumors are being evaluated for inclusion in upcoming releases. +We welcome feedback on prioritization as we continue to expand the hierarchy. + ## v0.5.1 Submitted: April 14, 2026 diff --git a/content/4.pecan/1.overview/1.getting-started.md b/content/4.pecan/1.overview/1.getting-started.md index 2797bf41..def358a5 100644 --- a/content/4.pecan/1.overview/1.getting-started.md +++ b/content/4.pecan/1.overview/1.getting-started.md @@ -7,7 +7,7 @@ navigation: The PeCan platform presents curated pediatric cancer genomics data including variants, mutational signatures, and gene expression data in addition to histological slide images from over 11,000 hematological, CNS, and non-CNS solid tumor patient samples. Data can be explored via a series of data facets containing both retrospective and prospective study cohorts from St. Jude Children's Research Hospital and other trusted institutions and research centers around the world such as [TARGET](https://ocg.cancer.gov/programs/target), [DKFZ](https://www.dkfz.de/en/index.html), and many others. -Learn more about the data [here](/pecan/overview/methods-and-data). +[Learn more about the data](/pecan/overview/methods-and-data). ![logos](/img/pecan/overview/getting-started/logos.png) @@ -49,7 +49,7 @@ Users can expand any node to reveal its subtypes, with sample counts displayed a A tooltip on each node provides additional details and quick navigation to each data facet to view the available data. The tree can be downloaded as an SVG for external use. -![PeCan Subtype Tree](/img/pecan/overview/getting-started/subtype_tree.png) +![PeCan Subtype Tree](/img/pecan/overview/getting-started/Subtype_Tree.png) **Figure 3: Subtype Tree** A user is able to explore the tree by selecting the interactive nodes. diff --git a/deployment/preview/pr178/app.yaml b/deployment/preview/pr178/app.yaml new file mode 100644 index 00000000..5668bf99 --- /dev/null +++ b/deployment/preview/pr178/app.yaml @@ -0,0 +1,88 @@ +--- +apiVersion: helm.toolkit.fluxcd.io/v2beta1 +kind: HelmRelease +metadata: + name: docs + namespace: docs-pr178 +spec: + interval: 30m + chart: + spec: + chart: generic + version: 1.1.x + sourceRef: + kind: HelmRepository + name: stjudecloud + namespace: flux-system + interval: 1h + values: + nameOverride: docs + extraDeploy: + - | + apiVersion: v1 + kind: Service + metadata: + name: {{ template "common.names.fullname" . }}-oauth-bridge + labels: {{- include "common.labels.standard" . | nindent 4 }} + {{- if .Values.commonLabels }} + {{- include "common.tplvalues.render" ( dict "value" .Values.commonLabels "context" $ ) | nindent 4 }} + {{- end }} + {{- if .Values.commonAnnotations }} + annotations: {{- include "common.tplvalues.render" ( dict "value" .Values.commonAnnotations "context" $ ) | nindent 4 }} + {{- end }} + spec: + type: ExternalName + externalName: oauth2-proxy.oauth2-proxy + - | + --- + apiVersion: networking.k8s.io/v1 + kind: Ingress + metadata: + name: {{ .Release.Name }}-oauth + spec: + ingressClassName: nginx + rules: + - host: {{ .Values.ingress.hostname }} + http: + paths: + - backend: + service: + name: {{ template "common.names.fullname" . }}-oauth-bridge + port: + number: 80 + path: /oauth2 + pathType: ImplementationSpecific + tls: + - hosts: + - {{ .Values.ingress.hostname }} + secretName: {{ .Values.ingress.hostname }}-tls + image: + repository: stjudecloud/docs + tag: latest # {"$imagepolicy": "flux-system:docs-pr178:tag"} + podAnnotations: + linkerd.io/inject: enabled + config.linkerd.io/proxy-cpu-request: 20m + containerPorts: + http: 3000 + service: + ports: + - name: http + protocol: TCP + port: 3000 + targetPort: http + ingress: + enabled: true + hostname: docs-pr178.staging.stjude.cloud + path: / + annotations: + cert-manager.io/cluster-issuer: letsencrypt-prod + linkerd.io/inject: ingress + nginx.ingress.kubernetes.io/auth-signin: https://$host/oauth2/start?rd=$escaped_request_uri + nginx.ingress.kubernetes.io/auth-url: https://$host/oauth2/auth + nginx.ingress.kubernetes.io/service-upstream: "true" + nginx.ingress.kubernetes.io/enable-modsecurity: "true" + nginx.ingress.kubernetes.io/enable-owasp-core-rules: "true" + tls: + enabled: true + datadog: + enabled: false diff --git a/public/img/pecan/overview/getting-started/Subtype_Tree.png b/public/img/pecan/overview/getting-started/Subtype_Tree.png index 275d20da..f21bd9ae 100644 Binary files a/public/img/pecan/overview/getting-started/Subtype_Tree.png and b/public/img/pecan/overview/getting-started/Subtype_Tree.png differ