From ea1834d003c7de22c891b464216bef0aa5a7cc79 Mon Sep 17 00:00:00 2001 From: Meghann Kirk Date: Mon, 20 Jul 2026 09:45:56 -0500 Subject: [PATCH 01/14] feat: comet data release --- .../1.getting-started/3.making-a-data-request.md | 12 ++++++++++++ .../1.data-sets-and-data-access-units.md | 7 +++++++ .../2.file-formats-and-sequencing-information.md | 6 ++++++ 3 files changed, 25 insertions(+) diff --git a/content/3.genomics-platform/1.getting-started/3.making-a-data-request.md b/content/3.genomics-platform/1.getting-started/3.making-a-data-request.md index 40b17b0..a674c36 100644 --- a/content/3.genomics-platform/1.getting-started/3.making-a-data-request.md +++ b/content/3.genomics-platform/1.getting-started/3.making-a-data-request.md @@ -124,3 +124,15 @@ If you receive an email from us that your DAA is incomplete, you may edit your D ## Managing your Data Request Go to our [Managing Data Overview](/genomics-platform/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](https://platform.stjude.cloud/requests/manage) page. + +## Unrestricted Data + +Certain Data within Genomics Platform is unrestricted, meaning that access is available to all requestors and does not require a data access agreement. + +To access this data, please complete the following steps: + +1. Create an account on or log in to Genomics Platform. +2. Narrow your selection by filtering to Feature Count Files only and/or iDAT files only and then selecting Request Data at the bottom right of the screen. +3. Choose to vend the data to a new or existing project +4. Submit the request. +5. The data will be vended to your selected project in a folder labeled with the date the data was requested. diff --git a/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md b/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md index 21713fa..a1ce0c9 100644 --- a/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md +++ b/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md @@ -62,6 +62,13 @@ Publishing using any of the files _before_ the embargo date has passed is strict Some Data, including Data funded by the NIH, are not subject to embargo. Applicable Embargo Dates can be found in [Genomics Platform Metadata](https://platform.stjude.cloud/api/v1/manifest.tsv){target="_blank"} in the `SJ_Embargo_Date` column. +### Unrestricted Data + +Certain data within the Genomics Platform is unrestricted — meaning it is available to all requestors and does not require a data access agreement. The unrestricted dataset currently includes: + +- Feature count files +- COMET iDAT files + --- ## List of DAUs diff --git a/content/3.genomics-platform/2.about-our-data/2.file-formats-and-sequencing-information.md b/content/3.genomics-platform/2.about-our-data/2.file-formats-and-sequencing-information.md index 6f16b86..1fb3623 100644 --- a/content/3.genomics-platform/2.about-our-data/2.file-formats-and-sequencing-information.md +++ b/content/3.genomics-platform/2.about-our-data/2.file-formats-and-sequencing-information.md @@ -13,6 +13,7 @@ St. Jude Cloud hosts both raw genomic data files and processed results files: | Somatic VCF | Curated list of somatic variants produced by the St. Jude somatic variant analysis pipeline. | [Click here](#somatic-vcf-files) | | CNV | List of somatic copy number alterations produced by St. Jude CONSERTING pipeline. | [Click here](#cnv-files) | | Feature Counts | Curated list of read counts mapped to each gene produced by [HTSeq](https://htseq.readthedocs.io/en/master/) | [Click here](#feature-counts-files) | +| IDAT | Raw, paired intensity files output by an Illumina microarray scanner for a single sample — one per fluorescence channel — before normalization or genotype/methylation calling. | [Click here](#idat-files) | ### BAM files @@ -195,6 +196,11 @@ The files are tab-delimited text and contain the feature key and read count for [rnaseq-rfc]: https://stjudecloud.github.io/rfcs/0001-rnaseq-workflow-v2.0.0.html#specification [gencode]: https://www.gencodegenes.org/human/release_31.html +### iDAT files + +These are the raw, paired intensity files output by an Illumina microarray for a single sample. +Each sample includes two IDAT files — one per fluorescence channel (Green and Red) containing the raw, unprocessed probe intensity signal from the array before any normalization or genotype/methylation calling. + ## Sequencing Information ### Whole Genome and Whole Exome From 7d77e65fc28a3f624b653212580a9c90f96a275b Mon Sep 17 00:00:00 2001 From: stjudecloud-cloudy Date: Mon, 20 Jul 2026 09:51:51 -0500 Subject: [PATCH 02/14] ci: :rocket: creates preview environment for pr184 [skip ci] --- deployment/preview/pr184/app.yaml | 88 +++++++++++++++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 deployment/preview/pr184/app.yaml diff --git a/deployment/preview/pr184/app.yaml b/deployment/preview/pr184/app.yaml new file mode 100644 index 0000000..aca5313 --- /dev/null +++ b/deployment/preview/pr184/app.yaml @@ -0,0 +1,88 @@ +--- +apiVersion: helm.toolkit.fluxcd.io/v2 +kind: HelmRelease +metadata: + name: docs + namespace: docs-pr184 +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 # {"$imagepolicy": "flux-system:docs-pr184:tag"} + podAnnotations: + linkerd.io/inject: enabled + config.linkerd.io/proxy-cpu-request: 20m + containerPorts: + http: 3000 + service: + ports: + - name: http + protocol: TCP + port: 3000 + targetPort: http + ingress: + enabled: true + hostname: docs-pr184.staging.stjude.cloud + path: / + annotations: + cert-manager.io/cluster-issuer: letsencrypt-prod + linkerd.io/inject: ingress + nginx.ingress.kubernetes.io/auth-signin: https://$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 From 800fcc3cb4aae1608abd470d9c4fa3cd28884686 Mon Sep 17 00:00:00 2001 From: Meghann Kirk Date: Mon, 20 Jul 2026 10:01:27 -0500 Subject: [PATCH 03/14] revise: spelling update --- .spelling | 1 + 1 file changed, 1 insertion(+) diff --git a/.spelling b/.spelling index 2ee7acc..d75eb44 100644 --- a/.spelling +++ b/.spelling @@ -597,6 +597,7 @@ deconvoluting DMG-H3 gemcitabine Hematopoiesis +iDAT Illumina in-vitro in-vivo From 3fca614cc5de232f9c2092ec300d4a8b2e06be3e Mon Sep 17 00:00:00 2001 From: stjudecloud-cloudy Date: Wed, 22 Jul 2026 21:15:24 +0000 Subject: [PATCH 04/14] chore: :rocket: released pr184-5d55755-400 to pr184 [skip ci] --- deployment/preview/pr184/app.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/deployment/preview/pr184/app.yaml b/deployment/preview/pr184/app.yaml index aca5313..d5a2d6f 100644 --- a/deployment/preview/pr184/app.yaml +++ b/deployment/preview/pr184/app.yaml @@ -1,4 +1,3 @@ ---- apiVersion: helm.toolkit.fluxcd.io/v2 kind: HelmRelease metadata: @@ -58,7 +57,7 @@ spec: secretName: {{ .Values.ingress.hostname }}-tls image: repository: stjudecloud/docs - tag: latest # {"$imagepolicy": "flux-system:docs-pr184:tag"} + tag: pr184-5d55755-400 # {"$imagepolicy": "flux-system:docs-pr184:tag"} podAnnotations: linkerd.io/inject: enabled config.linkerd.io/proxy-cpu-request: 20m From 0ddb20ea391d757d5956eba93b0745ef7568d0b1 Mon Sep 17 00:00:00 2001 From: stjudecloud-cloudy Date: Wed, 22 Jul 2026 20:01:30 -0500 Subject: [PATCH 05/14] ci: :fire: removes preview environment for pr184 --- deployment/preview/pr184/app.yaml | 87 ------------------------------- 1 file changed, 87 deletions(-) delete mode 100644 deployment/preview/pr184/app.yaml diff --git a/deployment/preview/pr184/app.yaml b/deployment/preview/pr184/app.yaml deleted file mode 100644 index d5a2d6f..0000000 --- a/deployment/preview/pr184/app.yaml +++ /dev/null @@ -1,87 +0,0 @@ -apiVersion: helm.toolkit.fluxcd.io/v2 -kind: HelmRelease -metadata: - name: docs - namespace: docs-pr184 -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: pr184-5d55755-400 # {"$imagepolicy": "flux-system:docs-pr184:tag"} - podAnnotations: - linkerd.io/inject: enabled - config.linkerd.io/proxy-cpu-request: 20m - containerPorts: - http: 3000 - service: - ports: - - name: http - protocol: TCP - port: 3000 - targetPort: http - ingress: - enabled: true - hostname: docs-pr184.staging.stjude.cloud - path: / - annotations: - cert-manager.io/cluster-issuer: letsencrypt-prod - linkerd.io/inject: ingress - nginx.ingress.kubernetes.io/auth-signin: https://$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 From 93545ebb20371d577753d462ce18bcc1fddbc556 Mon Sep 17 00:00:00 2001 From: stjudecloud-cloudy Date: Wed, 22 Jul 2026 20:02:47 -0500 Subject: [PATCH 06/14] ci: :rocket: creates preview environment for pr184 [skip ci] --- deployment/preview/pr184/app.yaml | 88 +++++++++++++++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 deployment/preview/pr184/app.yaml diff --git a/deployment/preview/pr184/app.yaml b/deployment/preview/pr184/app.yaml new file mode 100644 index 0000000..aca5313 --- /dev/null +++ b/deployment/preview/pr184/app.yaml @@ -0,0 +1,88 @@ +--- +apiVersion: helm.toolkit.fluxcd.io/v2 +kind: HelmRelease +metadata: + name: docs + namespace: docs-pr184 +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 # {"$imagepolicy": "flux-system:docs-pr184:tag"} + podAnnotations: + linkerd.io/inject: enabled + config.linkerd.io/proxy-cpu-request: 20m + containerPorts: + http: 3000 + service: + ports: + - name: http + protocol: TCP + port: 3000 + targetPort: http + ingress: + enabled: true + hostname: docs-pr184.staging.stjude.cloud + path: / + annotations: + cert-manager.io/cluster-issuer: letsencrypt-prod + linkerd.io/inject: ingress + nginx.ingress.kubernetes.io/auth-signin: https://$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 From 8b5f1fc06831d8348a51ee951a319ae660f4f2c8 Mon Sep 17 00:00:00 2001 From: stjudecloud-cloudy Date: Thu, 23 Jul 2026 01:04:32 +0000 Subject: [PATCH 07/14] chore: :rocket: released pr184-5d55755-400 to pr184 [skip ci] --- deployment/preview/pr184/app.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/deployment/preview/pr184/app.yaml b/deployment/preview/pr184/app.yaml index aca5313..d5a2d6f 100644 --- a/deployment/preview/pr184/app.yaml +++ b/deployment/preview/pr184/app.yaml @@ -1,4 +1,3 @@ ---- apiVersion: helm.toolkit.fluxcd.io/v2 kind: HelmRelease metadata: @@ -58,7 +57,7 @@ spec: secretName: {{ .Values.ingress.hostname }}-tls image: repository: stjudecloud/docs - tag: latest # {"$imagepolicy": "flux-system:docs-pr184:tag"} + tag: pr184-5d55755-400 # {"$imagepolicy": "flux-system:docs-pr184:tag"} podAnnotations: linkerd.io/inject: enabled config.linkerd.io/proxy-cpu-request: 20m From 7021fa1d47009276b71f96ed4f9a914265c373a1 Mon Sep 17 00:00:00 2001 From: stjudecloud-cloudy Date: Thu, 23 Jul 2026 01:06:32 +0000 Subject: [PATCH 08/14] chore: :rocket: released pr184-0c3e51d-401 to pr184 [skip ci] --- deployment/preview/pr184/app.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployment/preview/pr184/app.yaml b/deployment/preview/pr184/app.yaml index d5a2d6f..d2d593f 100644 --- a/deployment/preview/pr184/app.yaml +++ b/deployment/preview/pr184/app.yaml @@ -57,7 +57,7 @@ spec: secretName: {{ .Values.ingress.hostname }}-tls image: repository: stjudecloud/docs - tag: pr184-5d55755-400 # {"$imagepolicy": "flux-system:docs-pr184:tag"} + tag: pr184-0c3e51d-401 # {"$imagepolicy": "flux-system:docs-pr184:tag"} podAnnotations: linkerd.io/inject: enabled config.linkerd.io/proxy-cpu-request: 20m From 033e442d8f51d5d174801e9efddee7d12e99866f Mon Sep 17 00:00:00 2001 From: Meghann Kirk Date: Mon, 27 Jul 2026 10:04:50 -0500 Subject: [PATCH 09/14] feat: COMET revisions --- .../1.data-sets-and-data-access-units.md | 2 +- ...file-formats-and-sequencing-information.md | 2 +- .../4.pecan/1.overview/1.getting-started.md | 10 +++ .../4.pecan/2.data-facets/5.epigenetics.md | 87 +++++++++++++++++++ .../{5.use-cases.md => 6.use-cases.md} | 0 5 files changed, 99 insertions(+), 2 deletions(-) create mode 100644 content/4.pecan/2.data-facets/5.epigenetics.md rename content/4.pecan/2.data-facets/{5.use-cases.md => 6.use-cases.md} (100%) diff --git a/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md b/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md index a1ce0c9..beab8b4 100644 --- a/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md +++ b/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md @@ -67,7 +67,7 @@ Applicable Embargo Dates can be found in [Genomics Platform Metadata](https://pl Certain data within the Genomics Platform is unrestricted — meaning it is available to all requestors and does not require a data access agreement. The unrestricted dataset currently includes: - Feature count files -- COMET iDAT files +- [COMET](https://comet.stjude.org/)iDAT files --- diff --git a/content/3.genomics-platform/2.about-our-data/2.file-formats-and-sequencing-information.md b/content/3.genomics-platform/2.about-our-data/2.file-formats-and-sequencing-information.md index 1fb3623..d83cff3 100644 --- a/content/3.genomics-platform/2.about-our-data/2.file-formats-and-sequencing-information.md +++ b/content/3.genomics-platform/2.about-our-data/2.file-formats-and-sequencing-information.md @@ -13,7 +13,7 @@ St. Jude Cloud hosts both raw genomic data files and processed results files: | Somatic VCF | Curated list of somatic variants produced by the St. Jude somatic variant analysis pipeline. | [Click here](#somatic-vcf-files) | | CNV | List of somatic copy number alterations produced by St. Jude CONSERTING pipeline. | [Click here](#cnv-files) | | Feature Counts | Curated list of read counts mapped to each gene produced by [HTSeq](https://htseq.readthedocs.io/en/master/) | [Click here](#feature-counts-files) | -| IDAT | Raw, paired intensity files output by an Illumina microarray scanner for a single sample — one per fluorescence channel — before normalization or genotype/methylation calling. | [Click here](#idat-files) | +| iDAT | Raw, paired intensity files output by an Illumina microarray scanner for a single sample — one per fluorescence channel — before normalization or genotype/methylation calling. | [Click here](#idat-files) | ### BAM files diff --git a/content/4.pecan/1.overview/1.getting-started.md b/content/4.pecan/1.overview/1.getting-started.md index def358a..879a1d6 100644 --- a/content/4.pecan/1.overview/1.getting-started.md +++ b/content/4.pecan/1.overview/1.getting-started.md @@ -98,6 +98,16 @@ Data Facets represent a distinct type of post-processed genomic data for collect +
+
+ Epigenetics +
+
+
Epigenetics
+

Methylation landscape of over 4,400 pediatric cancer samples in PeCan.

+
+
+ ## Tools
diff --git a/content/4.pecan/2.data-facets/5.epigenetics.md b/content/4.pecan/2.data-facets/5.epigenetics.md new file mode 100644 index 0000000..431ce34 --- /dev/null +++ b/content/4.pecan/2.data-facets/5.epigenetics.md @@ -0,0 +1,87 @@ +--- +title: Epigenetics +--- + +![Epigenetics](/img/pecan/overview/getting-started/histology.svg) +Explore the methylation landscape of over 4,400 pediatric cancer samples in PeCan. + +## Overview + +The Epigenetics facet lets you explore methylation data across 4,400+ pediatric cancer samples. +Navigate the data using a UMAP plot with gene- or probe-level overlays of β-values, or view it collectively in a data table. + +## UMAP Overlay Features + +On page load, each sample on the UMAP is colored by its cancer subtype. +When you select a gene or probe to overlay, the sample color changes to a gradient representative of the β-value for the sample. +β-value is the range in which the target is methylated, with 0 being fully unmethylated and 1 being fully methylated; values can range from 0 to 1. +You can overlay either the mean or median β-value; mean is selected by default (see β-value Toggle below). + +### Gene Overlay + +Select one or more genes to overlay their associated methylation on the UMAP. +The overlay shows the mean β-value across all probes mapped to the selected gene by default. +You can toggle to the median β-value or switch between selected genes to compare. +To narrow results, apply filters to display only probes in the promoter region, specifically TSS1500 and/or TSS200. + +### Probe Overlay + +Select one or more probe IDs to overlay their methylation values on the UMAP. +The overlay shows the mean β-value for the selected probe. +The probe overlay is only available for CpG probes that start with `cg`. + +### Overlay Considerations + +The UMAP and its overlays are drawn from the same underlying dataset, but different filters are applied depending on the view. +Understanding these filtering rules helps you interpret what you see. + +### Probe Filtering by Analysis Level + +| Level | Low Quality Filter | Common SNP Probes | Cross Reactive Probes | Sex Chromosome Probes | +|---------------------|--------------------|-------------------|-----------------------|-----------------------| +| UMAP | Yes | Yes | No | Yes | +| Gene level overlay | Yes | Yes | No | No | +| Probe level overlay | Yes | No | No | No | + +### Filter Descriptions + +- **Low Quality Filter:** Removes probes that fail quality control thresholds. +- **Common SNP Probes:** Excludes probes located at common single nucleotide polymorphisms to reduce genotype-driven variation. +- **Cross Reactive Probes:** Excludes probes known to hybridize to multiple genomic locations. +Currently not applied at any level. +Please refer to the following lists of cross-reactive probes: + - Pidsley Cross-Reactive Probes + - McCartney Supplement Probes +- **Sex Chromosome Probes:** Excludes probes on the X and Y chromosomes. +Applied only at the UMAP level to prevent sex-driven clustering. + +## Data Table Features + +Select the Data tab to view a table of samples with corresponding metadata. +Columns include Sample ID, Diagnosis Subtype Code, and Diagnosis Subtype Name. +β-value columns are sortable, allowing you to rank samples by methylation level for a given gene or probe. + +## How to Narrow and Refine the Data + +- **Filters:** Filter samples by Sample ID(s), Subtype Root, Subtype, Subtype Biomarkers, Patient Phenotype (sex, age at diagnosis, race, ethnicity), or Sample Preparation parameters. +- **Lasso and Pan/Zoom:** Use the Lasso tool to select a region of samples on the UMAP, or Pan/Zoom to focus on a specific area. +- **β-value Toggle:** In the UMAP tab header, toggle between mean and median β-values for the gene overlay. +Mean is selected by default. +- **Hover and Drawer:** + - **Sample Hover:** Hover over or click a sample on the UMAP to view its metadata (diagnosis, demographics, etc.). + - **Gene Overlay Hover:** Hover over the selected gene to view probe-level data for that gene. + +## Menu Options (⋯) + +Access additional features from the three-dot menu in the header: + +- Show or hide diagnosis category labels on the UMAP +- Copy the URL for the current UMAP view +- Copy Sample IDs for the current view +- Copy data as TSV +- Export the current UMAP as SVG + +## UMAP Generation + +Methylation β-values were generated using the Infinium MethylationEPIC BeadChip v1.0 array and normalized with subset-quantile within-array normalization (SWAN) to correct for probe-type bias between Type I and Type II probes. After normalization, the standard deviation of β-values was calculated per probe, and the 10,000 probes with the highest standard deviation were kept for UMAP generation. +Probes associated with SNPs at CpG sites, cross-reactive probes, and probes on sex chromosomes were excluded. diff --git a/content/4.pecan/2.data-facets/5.use-cases.md b/content/4.pecan/2.data-facets/6.use-cases.md similarity index 100% rename from content/4.pecan/2.data-facets/5.use-cases.md rename to content/4.pecan/2.data-facets/6.use-cases.md From 14dfb4d1e1e5f1c98927a031eaa8d7dfde659b9f Mon Sep 17 00:00:00 2001 From: Meghann Kirk Date: Tue, 28 Jul 2026 15:06:17 -0500 Subject: [PATCH 10/14] revise: unrestricted data --- .../1.data-sets-and-data-access-units.md | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md b/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md index beab8b4..424460a 100644 --- a/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md +++ b/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md @@ -9,6 +9,7 @@ title: Data Sets and Data Access Units - [Data Set](#data-set) - [Data Access Committee (DAC)](#data-access-committee-dac) - [Embargo Date](#embargo-date) + - [Unrestricted Data](#unrestricted-data) - [List of DAUs](#list-of-daus) - [List of Data Sets](#list-of-data-sets) @@ -64,10 +65,13 @@ Applicable Embargo Dates can be found in [Genomics Platform Metadata](https://pl ### Unrestricted Data -Certain data within the Genomics Platform is unrestricted — meaning it is available to all requestors and does not require a data access agreement. The unrestricted dataset currently includes: +Certain data within the Genomics Platform is unrestricted. Unrestricted data is not subject to DAC-reviewed approval before a user can obtain it. +The unrestricted dataset on St. Jude Cloud currently includes: - Feature count files -- [COMET](https://comet.stjude.org/)iDAT files +- [COMET](https://comet.stjude.org/) iDAT files + +Steps to access unrestricted data can be found [here](http://docs.stjude.cloud/genomics-platform/getting-started/making-a-data-request#unrestricted-data). --- @@ -380,3 +384,6 @@ This cohort contains unpaired germline samples and does not contain tumor sample The primary purpose of the St. Jude Lifetime Cohort Study (SJLIFE) Clonal Hematopoiesis dataset is to identify all inherited genome sequence and structural variants influencing the development of childhood cancer and occurrence of long-term adverse outcomes associated with cancer and cancer-related therapy. Additional objectives include, but are not limited to, the acquisition and analysis of additional genomic data, including epigenetic and gene expression data, data integration, and the development and validation of informatics and analytical solutions appropriate to the scale and nature of the project, as well as use of the data generated to answer important methodological and biological questions as specifically related to childhood malignancies. + + +[def]: #unrestricted-data \ No newline at end of file From bcab2d5f87069da1630359ee03200e318d2a48e2 Mon Sep 17 00:00:00 2001 From: stjudecloud-cloudy Date: Tue, 28 Jul 2026 20:12:01 +0000 Subject: [PATCH 11/14] chore: :rocket: released pr184-e10aa2c-404 to pr184 [skip ci] --- deployment/preview/pr184/app.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployment/preview/pr184/app.yaml b/deployment/preview/pr184/app.yaml index d2d593f..b8c79c4 100644 --- a/deployment/preview/pr184/app.yaml +++ b/deployment/preview/pr184/app.yaml @@ -57,7 +57,7 @@ spec: secretName: {{ .Values.ingress.hostname }}-tls image: repository: stjudecloud/docs - tag: pr184-0c3e51d-401 # {"$imagepolicy": "flux-system:docs-pr184:tag"} + tag: pr184-e10aa2c-404 # {"$imagepolicy": "flux-system:docs-pr184:tag"} podAnnotations: linkerd.io/inject: enabled config.linkerd.io/proxy-cpu-request: 20m From 54cec5561c6e14b7123f0f82daf70c9d17ade22e Mon Sep 17 00:00:00 2001 From: Meghann Kirk Date: Wed, 29 Jul 2026 15:24:26 -0500 Subject: [PATCH 12/14] revise: datasets --- .../1.data-sets-and-data-access-units.md | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md b/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md index 424460a..0621fcc 100644 --- a/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md +++ b/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md @@ -169,7 +169,7 @@ The following data set(s) are included within SJLIFE: ## List of Data Sets -We currently have 21 [Data Sets](#data-set) listed below. +We currently have 22 [Data Sets](#data-set) listed below. Additional information can also be seen including which [Data Access Units (DAU)](#data-access-unit-dau) the Data Set belongs to, tissue type, sequencing type, number of samples, additional links, and a brief description. | Data Set | DAU(s) | Tissue Type | Sequencing | Samples | @@ -178,6 +178,7 @@ Additional information can also be seen including which [Data Access Units (DAU) | [CCSS](#childhood-cancer-survivor-study) | CCSS | Germline Only | WGS | 2,912 | | [CICERO Benchmark](#cicero-benchmark) | PCGP, Clinical Genomics | Paired Tumor-Normal | RNA-Seq | 124 | | [Clinical Pilot](#clinical-pilot) | PCGP, Clinical Genomics | Paired Tumor-Normal | WGS, WES, RNA-Seq | 155 | +| [COMET](#comet) | Unrestricted | iDAT file | — | 4269 | | [CReATe](#clinical-research-in-als-and-related-disorders-for-therapeutic-development-consortium) | CReATe | PBMC Germline DNA | WGS | 705 | | [CSTN](#childhood-solid-tumor-network) | PCGP, Clinical Genomics | Paired Tumor-Normal | WGS, WES, RNA-Seq | 143 | | [G4K](#genome-4-kids) | PCGP, Clinical Genomics | Paired Tumor-Normal | WGS, WES, RNA-Seq | 565 | @@ -194,7 +195,7 @@ Additional information can also be seen including which [Data Access Units (DAU) | [RTCG](#real-time-clinical-genomics) | PCGP, Clinical Genomics | Paired Tumor-Normal | WGS, WES, RNA-Seq | 7,767 | | [SGP](#sickle-cell-genome-project) | SGP | Germline Only | WGS | 807 | | [SJLIFE](#st-jude-life) | SJLIFE | Germline Only | WGS, WES | 4,838 | -| [SJLIFE_ClonalHematopoiesis](#st-jude-life-clonal-hematopoiesis) | SJLIFE | — | Single Cell-WGS, Targeted | 3,192 | +| [SJLIFE_ClonalHematopoiesis](#st-jude-life-clonal-hematopoiesis) | PCGP | — | Single Cell-WGS, Targeted | 3,192 | | [tMN](#pediatric-therapy-related-myeloid-neoplasms-tmn) | PCGP | Paired Tumor-Normal | WGS, WES, RNA-Seq | 206 | ### Atypical Teratoid / Rhabdoid Tumor-derived Tumoroid Models @@ -265,6 +266,14 @@ In addition to patients enrolled in the PGB1 Cohort (primary participants), the This dataset includes WGS data from N=705 in PGB1, including N=472 ALS/ALS-FTD, N=20 PMA, N=47 PLS, N=162 HSP, and N=4 with other related disorders. The findings of the project were published in [Translational Neurodegeneration](https://translationalneurodegeneration.biomedcentral.com/articles/10.1186/s40035-025-00516-2). +### COMET + +**DAU**: Unrestricted | **Tissue Type**: - | **Assay Type**: Illumina Infinium 850K array | **Samples**: 4,629| **[Additional Information About COMET](https://www.stjude.org/research/departments/computational-biology/comet.html)** + +The solid tumor COmprehensive METhylation (COMET) database is a searchable repository of pediatric solid tumor DNA methylation and copy number variant (CNV) profiles, generated using the Illumina Infinium 850K array, paired with matched whole slide histology images (WSI). +It is the largest and most comprehensive extracranial pediatric solid tumor epigenetic reference dataset in the world, offering DNA methylation profiles across 20 different types of pediatric solid tumors along with a comparative collection of patient-derived orthotopic xenografts, cell lines, adult sarcomas, and normal tissues. +See [Unrestricted Data](#unrestricted-data) for more details on requesting access to this data set. + ### DMG-H3K27a Clonal Evolution **DAU**: PCGP | **Tissue Type**: — | **Sequencing Type**: WGS, WES | **Samples**: 70 @@ -384,6 +393,3 @@ This cohort contains unpaired germline samples and does not contain tumor sample The primary purpose of the St. Jude Lifetime Cohort Study (SJLIFE) Clonal Hematopoiesis dataset is to identify all inherited genome sequence and structural variants influencing the development of childhood cancer and occurrence of long-term adverse outcomes associated with cancer and cancer-related therapy. Additional objectives include, but are not limited to, the acquisition and analysis of additional genomic data, including epigenetic and gene expression data, data integration, and the development and validation of informatics and analytical solutions appropriate to the scale and nature of the project, as well as use of the data generated to answer important methodological and biological questions as specifically related to childhood malignancies. - - -[def]: #unrestricted-data \ No newline at end of file From 929a5d42aa431f1814eedaa98e2dbea87e42fb61 Mon Sep 17 00:00:00 2001 From: Meghann Kirk Date: Wed, 29 Jul 2026 15:27:45 -0500 Subject: [PATCH 13/14] revise: dau --- .../2.about-our-data/1.data-sets-and-data-access-units.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md b/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md index 0621fcc..d6cd40a 100644 --- a/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md +++ b/content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md @@ -268,7 +268,7 @@ The findings of the project were published in [Translational Neurodegeneration]( ### COMET -**DAU**: Unrestricted | **Tissue Type**: - | **Assay Type**: Illumina Infinium 850K array | **Samples**: 4,629| **[Additional Information About COMET](https://www.stjude.org/research/departments/computational-biology/comet.html)** +**DAU**: - | **Tissue Type**: - | **Assay Type**: Illumina Infinium 850K array | **Samples**: 4,629| **[Additional Information About COMET](https://www.stjude.org/research/departments/computational-biology/comet.html)** The solid tumor COmprehensive METhylation (COMET) database is a searchable repository of pediatric solid tumor DNA methylation and copy number variant (CNV) profiles, generated using the Illumina Infinium 850K array, paired with matched whole slide histology images (WSI). It is the largest and most comprehensive extracranial pediatric solid tumor epigenetic reference dataset in the world, offering DNA methylation profiles across 20 different types of pediatric solid tumors along with a comparative collection of patient-derived orthotopic xenografts, cell lines, adult sarcomas, and normal tissues. From e6c4b6302748c339fce785a585d073eb89d6a829 Mon Sep 17 00:00:00 2001 From: stjudecloud-cloudy Date: Wed, 29 Jul 2026 20:32:36 +0000 Subject: [PATCH 14/14] chore: :rocket: released pr184-318878b-406 to pr184 [skip ci] --- deployment/preview/pr184/app.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deployment/preview/pr184/app.yaml b/deployment/preview/pr184/app.yaml index b8c79c4..66fa251 100644 --- a/deployment/preview/pr184/app.yaml +++ b/deployment/preview/pr184/app.yaml @@ -57,7 +57,7 @@ spec: secretName: {{ .Values.ingress.hostname }}-tls image: repository: stjudecloud/docs - tag: pr184-e10aa2c-404 # {"$imagepolicy": "flux-system:docs-pr184:tag"} + tag: pr184-318878b-406 # {"$imagepolicy": "flux-system:docs-pr184:tag"} podAnnotations: linkerd.io/inject: enabled config.linkerd.io/proxy-cpu-request: 20m