From 7d11a0f79b46613416f983d494a9352606c4508a Mon Sep 17 00:00:00 2001 From: Meghann Kirk Date: Fri, 26 Jun 2026 14:02:10 -0500 Subject: [PATCH 1/4] feat: sample_type update --- .../1.data-sets-and-data-access-units.md | 10 ++++++++-- .../3.metadata-and-clinical-information.md | 2 +- 2 files changed, 9 insertions(+), 3 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 f42a501..7f9d8fa 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 @@ -126,6 +126,7 @@ The following data set(s) are included within PCGP: - [Clinical Pilot](#clinical-pilot) - [DMG-H3K27a Clonal Evolution (H3K27A_EVOLUTION)](#dmg-h3k27a-clonal-evolution) - [Genome 4 Kids (G4K)](#genome-4-kids) +- [G4KF](#genome-4-kids-ffpe) - [Genomics and Transcriptomics of Relapsed Pediatric AML (RPAML)](#genomics-and-transcriptomics-of-relapsed-pediatric-aml-rpaml) - [Landscape of Pediatric Acute Myeloid Leukemia (PanpAML)](#landscape-of-pediatric-acute-myeloid-leukemia-panpaml) - [Medulloblastoma Preclinical Ribociclib and Gemcitabine (MBPRG)](#medulloblastoma-preclinical-ribociclib-and-gemcitabine-mbprg) @@ -168,7 +169,8 @@ Additional information can also be seen including which [Data Access Units (DAU) | [Clinical Pilot](#clinical-pilot) | PCGP, Clinical Genomics | Paired Tumor-Normal | WGS, WES, RNA-Seq | 155 | | [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 | 571 | +| [G4K](#genome-4-kids) | PCGP, Clinical Genomics | Paired Tumor-Normal | WGS, WES, RNA-Seq | 565 | +| [G4KF](#genome-4-kids-ffpe) | PCGP | — | WES | 33 | | [H3K27A_EVOLUTION](#dmg-h3k27a-clonal-evolution) | PCGP | — | WGS, WES | 70 | | [MBPRG](#medulloblastoma-preclinical-ribociclib-and-gemcitabine-mbprg) | PCGP | — | RNA-Seq | 70 | | [MBPRP](#medulloblastoma-preclinical-ribociclib-and-paxalisib-mbprp) | PCGP | — | RNA-Seq | 39 | @@ -178,7 +180,7 @@ Additional information can also be seen including which [Data Access Units (DAU) | [PCGP](#pediatric-cancer-genome-project) | PCGP | Paired Tumor-Normal | WGS, WES, RNA-Seq | 3,031 | | [PedAML](#pediatric-acute-myeloid-leukemia-pedaml) | PCGP | — | WES, WGS, RNA-Seq | 275 | | [RPAML](#genomics-and-transcriptomics-of-relapsed-pediatric-aml-rpaml) | PCGP, Clinical Genomics | — | WGS, RNA-Seq | 265 | -| [RTCG](#real-time-clinical-genomics) | PCGP, Clinical Genomics | Paired Tumor-Normal | WGS, WES, RNA-Seq | 2,371 | +| [RTCG](#real-time-clinical-genomics) | PCGP, Clinical Genomics | Paired Tumor-Normal | WGS, WES, RNA-Seq | 7767 | | [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 | @@ -268,6 +270,10 @@ For more information see: [http://permalinks.stjude.cloud/permalinks/h3k27a_evol The goal of the Genomes 4 Kids (G4K) prospective study was to determine whether the three-platform sequencing protocol laid out in the Clinical Pilot project could generate results on a clinical timeline in practice and to evaluate the prevalence of actionable findings. The study concluded with just over 300 patients, and the publication is currently in review. +### G4K FFPE + +**DAU**: PCGP | **Tissue Type**: - | **Sequencing Type**: WES | **Samples**: 33 | + ### Genomics and Transcriptomics of Relapsed Pediatric AML (RPAML) **DAU**: Clinical Genomics, PCGP | **Tissue Type**: — | **Sequencing Type**: RNA-seq, WGS | **Samples**: 265 diff --git a/content/3.genomics-platform/2.about-our-data/3.metadata-and-clinical-information.md b/content/3.genomics-platform/2.about-our-data/3.metadata-and-clinical-information.md index b701467..522909a 100644 --- a/content/3.genomics-platform/2.about-our-data/3.metadata-and-clinical-information.md +++ b/content/3.genomics-platform/2.about-our-data/3.metadata-and-clinical-information.md @@ -18,7 +18,7 @@ Properties with `attr` prepended are information queried from the physician or r | `file_id` | A unique identifier for the file on DNAnexus, you can see this value listed as “ID” in the DNAnexus user interface. | | `subject_name` | A unique subject identifier assigned internally at St. Jude. | | `sample_name` | A unique sample identifier assigned internally at St. Jude. | -| `sample_type` | One of Autopsy, Cell line, Diagnosis, Germline, Metastasis, Relapse, or Xenograft. | +| `sample_type` | One of Autopsy, Cell line, Diagnosis, Germline, Metastasis, Post-Transplant, Relapse, Xenograft or Other. | | `sequencing_type` | Whether the file was generated from Whole Genome (WGS), Whole Exome (WES), or RNA-Seq. | | `file_type` | Specifies the type of file. Note that index files will be labeled as the file type they accompany and will automatically be selected together in our data browser. If you wish to distinguish between the two in your project, please parse the `file_path` where index files are appended with an additional string, such as `.bai`. | | `description` | Optional field that may contain additional file information. | From b0e069228e82c8c01cf1107e14a5d2378e924980 Mon Sep 17 00:00:00 2001 From: Meghann Kirk Date: Fri, 26 Jun 2026 17:26:30 -0500 Subject: [PATCH 2/4] feat: sample_type and dau updates --- .../2.about-our-data/1.data-sets-and-data-access-units.md | 6 +++--- 1 file changed, 3 insertions(+), 3 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 7f9d8fa..9adaa01 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 @@ -126,7 +126,7 @@ The following data set(s) are included within PCGP: - [Clinical Pilot](#clinical-pilot) - [DMG-H3K27a Clonal Evolution (H3K27A_EVOLUTION)](#dmg-h3k27a-clonal-evolution) - [Genome 4 Kids (G4K)](#genome-4-kids) -- [G4KF](#genome-4-kids-ffpe) +- [G4KF](#g4kffpe) - [Genomics and Transcriptomics of Relapsed Pediatric AML (RPAML)](#genomics-and-transcriptomics-of-relapsed-pediatric-aml-rpaml) - [Landscape of Pediatric Acute Myeloid Leukemia (PanpAML)](#landscape-of-pediatric-acute-myeloid-leukemia-panpaml) - [Medulloblastoma Preclinical Ribociclib and Gemcitabine (MBPRG)](#medulloblastoma-preclinical-ribociclib-and-gemcitabine-mbprg) @@ -170,7 +170,7 @@ Additional information can also be seen including which [Data Access Units (DAU) | [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 | -| [G4KF](#genome-4-kids-ffpe) | PCGP | — | WES | 33 | +| [G4KF](#g4kffpe) | PCGP | — | WES | 33 | | [H3K27A_EVOLUTION](#dmg-h3k27a-clonal-evolution) | PCGP | — | WGS, WES | 70 | | [MBPRG](#medulloblastoma-preclinical-ribociclib-and-gemcitabine-mbprg) | PCGP | — | RNA-Seq | 70 | | [MBPRP](#medulloblastoma-preclinical-ribociclib-and-paxalisib-mbprp) | PCGP | — | RNA-Seq | 39 | @@ -270,7 +270,7 @@ For more information see: [http://permalinks.stjude.cloud/permalinks/h3k27a_evol The goal of the Genomes 4 Kids (G4K) prospective study was to determine whether the three-platform sequencing protocol laid out in the Clinical Pilot project could generate results on a clinical timeline in practice and to evaluate the prevalence of actionable findings. The study concluded with just over 300 patients, and the publication is currently in review. -### G4K FFPE +### G4KFFPE **DAU**: PCGP | **Tissue Type**: - | **Sequencing Type**: WES | **Samples**: 33 | From 12bc2792c8a8fb0b0ff281865cf7e64b2ea470b5 Mon Sep 17 00:00:00 2001 From: Meghann Kirk Date: Fri, 26 Jun 2026 17:29:57 -0500 Subject: [PATCH 3/4] Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- .../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 9adaa01..8840884 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 @@ -272,7 +272,7 @@ The study concluded with just over 300 patients, and the publication is currentl ### G4KFFPE -**DAU**: PCGP | **Tissue Type**: - | **Sequencing Type**: WES | **Samples**: 33 | +**DAU**: PCGP | **Tissue Type**: — | **Sequencing Type**: WES | **Samples**: 33 ### Genomics and Transcriptomics of Relapsed Pediatric AML (RPAML) From bf7140376638aa0450586069936a5344e960ebee Mon Sep 17 00:00:00 2001 From: Meghann Kirk Date: Fri, 26 Jun 2026 17:30:11 -0500 Subject: [PATCH 4/4] Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- .../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 8840884..21713fa 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 @@ -180,7 +180,7 @@ Additional information can also be seen including which [Data Access Units (DAU) | [PCGP](#pediatric-cancer-genome-project) | PCGP | Paired Tumor-Normal | WGS, WES, RNA-Seq | 3,031 | | [PedAML](#pediatric-acute-myeloid-leukemia-pedaml) | PCGP | — | WES, WGS, RNA-Seq | 275 | | [RPAML](#genomics-and-transcriptomics-of-relapsed-pediatric-aml-rpaml) | PCGP, Clinical Genomics | — | WGS, RNA-Seq | 265 | -| [RTCG](#real-time-clinical-genomics) | PCGP, Clinical Genomics | Paired Tumor-Normal | WGS, WES, RNA-Seq | 7767 | +| [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 |