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mkirk111 merged 4 commits into from
Jun 30, 2026
Merged

feat: sample_type update #182

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7d11a0f
feat: sample_type update
mkirk111 Jun 26, 2026
b0e0692
feat: sample_type and dau updates
mkirk111 Jun 26, 2026
12bc279
Potential fix for pull request finding
mkirk111 Jun 26, 2026
bf71403
Potential fix for pull request finding
mkirk111 Jun 26, 2026
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10 changes: 8 additions & 2 deletions content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md
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Expand Up @@ -126,6 +126,7 @@
- [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)

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content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md:129:3 MD051/link-fragments Link fragments should be valid [Context: "[G4KF](#genome-4-kids-ffpe)"] https://github.com/DavidAnson/markdownlint/blob/v0.37.4/doc/md051.md
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- [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)
Expand Down Expand Up @@ -168,7 +169,8 @@
| [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 |
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| [G4KF](#genome-4-kids-ffpe) | PCGP | — | WES | 33 |

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Link fragments should be valid 

content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md:173:3 MD051/link-fragments Link fragments should be valid [Context: "[G4KF](#genome-4-kids-ffpe)"] https://github.com/DavidAnson/markdownlint/blob/v0.37.4/doc/md051.md
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| [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 |
Expand All @@ -178,7 +180,7 @@
| [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 |
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| [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 |
Expand Down Expand Up @@ -268,6 +270,10 @@
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 |
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### Genomics and Transcriptomics of Relapsed Pediatric AML (RPAML)

**DAU**: Clinical Genomics, PCGP | **Tissue Type**: — | **Sequencing Type**: RNA-seq, WGS | **Samples**: 265
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2 changes: 1 addition & 1 deletion ...ent/3.genomics-platform/2.about-our-data/3.metadata-and-clinical-information.md
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Expand Up @@ -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. |
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| `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. |
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