feat: subtype tree documentation and release notes

.spelling

@@ -582,7 +582,45 @@ Near-Haploidy
 Low-Hypodiploidy
 
 - content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md
+Acta
+ATRT
+ATRT-SHH
+ATRT-MYC
+ATRT-TM
+ATRT_TM
+CDK4/6
+inhibitor
+Clonal
+crenolanib
+deconvoluting
+DMG-H3
+gemcitabine
+Hematopoiesis
+Illumina
+in-vitro
+in-vivo
+K27-a
+Myc
 Neurodegeneration
+Neuropathol
+pAML
+PanpAML
+paxalisib
+PDOX
+PDGFR
+PI3K/mTOR
+pontine
+orthotopic
+ribociclib
+Rhabdoid
+SJLIFE_ClonalHematopoiesis
+subclonal
+teratoid
+tumorigenesis
+tumoroid
+Tumoroid
+xenografts
+
 
 - content/3.genomics-platform/2.about-our-data/2.file-formats-and-sequencing-information.md
 bwa

content/3.genomics-platform/2.about-our-data/1.data-sets-and-data-access-units.md

@@ -135,7 +135,7 @@ The following data set(s) are included within PCGP:
 - [Pediatric Brain Tumor Program (PBTP)](#pediatric-brain-tumor-program)
 - [Pediatric Cancer Genome Project (PCGP)](#pediatric-cancer-genome-project)
 - [Pediatric therapy-related Myeloid Neoplasms (tMN)](#pediatric-therapy-related-myeloid-neoplasms-tmn)
-- [Atypical Teratoid/Rhabdoid Tumor-derived Tumoroid Models (ATRT_TM)](#atypical-teratoidrhabdoid-tumor-derived-tumoroid-models)
+- [Atypical Teratoid/Rhabdoid Tumor-derived Tumoroid Models (ATRT_TM)](#atypical-teratoid--rhabdoid-tumor-derived-tumoroid-models)
 - [Real-Time Clinical Genomics (RTCG)](#real-time-clinical-genomics)
 
 ### Sickle Cell Genome Project (SGP)
@@ -160,36 +160,36 @@ The following data set(s) are included within SJLIFE:
 We currently have 21 [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 |
-|--------------------------------------------------------------------------------------------------|-------------------------|---------------------|--------------------------|--------:|
-| [ATRT_TM](#atypical-teratoidrhabdoid-tumor-derived-tumoroid-models)                              | PCGP                    | —                   | WES, WGS, RNA-Seq        |       8 |
-| [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 |
-| [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)                                                                            | PCPG, Clinical Genomics | Paired Tumor-Normal | WGS, WES, RNA-Seq        |     571 |
-| [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 |
-| [PanALL](#pan-acute-lymphoblastic-leukemia)                                                      | PCPG, PanALL            | Paired Tumor-Normal | RNA-Seq                  |     735 |
-| [PanpAML](#landscape-of-pediatric-acute-myeloid-leukemia-panpaml)                                | PCGP                    | —                   | WES, WGS, RNA-Seq        |     272 |
-| [PBTP](#pediatric-brain-tumor-program)                                                           | PCPG, Clinical Genomics | —                   | WES, WGS, RNA-Seq        |      97 |
-| [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)                           | PCPG, Clinical Genomics | —                   | WGS, RNA-Seq             |     265 |
-| [RTCG](#real-time-clinical-genomics)                                                             | PCPG, Clinical Genomics | Paired Tumor-Normal | WGS, WES, RNA-Seq        |   2,371 |
-| [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                  | —                   | SingleCell-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
+| Data Set                                                                                         | DAU(s)                  | Tissue Type         | Sequencing                | Samples |
+|--------------------------------------------------------------------------------------------------|-------------------------|---------------------|---------------------------|--------:|
+| [ATRT_TM](#atypical-teratoid--rhabdoid-tumor-derived-tumoroid-models)                            | PCGP                    | —                   | WES, WGS, RNA-Seq         |       8 |
+| [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 |
+| [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 |
+| [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 |
+| [PanALL](#pan-acute-lymphoblastic-leukemia)                                                      | PCGP, PanALL            | Paired Tumor-Normal | RNA-Seq                   |     735 |
+| [PanpAML](#landscape-of-pediatric-acute-myeloid-leukemia-panpaml)                                | PCGP                    | —                   | WES, WGS, RNA-Seq         |     272 |
+| [PBTP](#pediatric-brain-tumor-program)                                                           | PCGP, Clinical Genomics | —                   | WES, WGS, RNA-Seq         |      97 |
+| [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 |
+| [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 |
+| [tMN](#pediatric-therapy-related-myeloid-neoplasms-tmn)                                          | PCGP                    | Paired Tumor-Normal | WGS, WES, RNA-Seq         |     206 |
+
+### Atypical Teratoid / Rhabdoid Tumor-derived Tumoroid Models
 
 **DAU**: PCGP | **Tissue Type**: — | **Sequencing Type**: WES, WGS, RNA-Seq | **Samples**: 8
 
-The ATRT-TM dataset comprises atypical teratoid/rhabdoid tumors (ATRT) of the Sonic hedgehog (ATRT-SHH) and Myc (ATRT-MYC) subgroups.
-ATRT-SHH and ATRT-MYC patient-derived orthotopic xenografts (PDOX) were used to generate pre-clinical in vitro tumoroid models.
+The ATRT-TM dataset comprises atypical teratoid / rhabdoid tumors (ATRT) of the Sonic hedgehog (ATRT-SHH) and Myc (ATRT-MYC) subgroups.
+ATRT-SHH and ATRT-MYC patient-derived orthotopic xenografts (PDOX) were used to generate pre-clinical in-vitro tumoroid models.
 The key objective of this dataset is to validate the tumoroid models by comparing them to their parental PDOX at the molecular level, including gene alterations (whole genome/whole exome sequencing), gene expression (RNA-seq), and DNA methylation (Illumina EPIC array).
 The findings of the project were published in [Oncogene](https://doi.org/10.1038/s41388-023-02681-y).
 
@@ -299,7 +299,7 @@ The key objective of this dataset is to evaluate the impact of this treatment an
 
 The MBPRP dataset comprises medulloblastoma group 3 (G3 MB) and medulloblastoma Sonic hedgehog (SHH MB) patient-derived orthotopic xenografts (PDOX).
 These human tumor models were treated with either ribociclib (CDK4/6 inhibitor), paxalisib (PI3K/mTOR inhibitor), or the combination of these two drugs in comparison to control (vehicle).
-The key objective of this dataset is to validate the synergistic effect of the combination treatment observed in vitro, and evaluate the impact of these treatments on gene expression/pathways at the transcriptional level in MB.
+The key objective of this dataset is to validate the synergistic effect of the combination treatment observed in-vitro, and evaluate the impact of these treatments on gene expression/pathways at the transcriptional level in MB.
 
 ### Pan-Acute Lymphoblastic Leukemia
 
@@ -322,7 +322,7 @@ Additional objectives include, but are not limited to, the acquisition and analy
 The Pediatric Brain Tumor Portal (PBTP) is organized by the St. Jude Children's Research Hospital Neurobiology and Brain Tumor Program.
 Investigators have access to specialized resources, such as an integrated support structure for preclinical modeling, including patient-derived xenograft samples.
 The program consists of clinicians, radiation oncologists, neurobiologists, medicinal chemists, and other research faculty and staff.
-PBTP features molecular characterization for patient-derived orthotopic xenograft (PDOX) models of pediatric CNS tumors and reflects close to 10 years of effort to generate and extensively characterize in vivo models that faithfully recapitulate pediatric brain cancer diseases.
+PBTP features molecular characterization for patient-derived orthotopic xenograft (PDOX) models of pediatric CNS tumors and reflects close to 10 years of effort to generate and extensively characterize in-vivo models that faithfully recapitulate pediatric brain cancer diseases.
 The portal offers visualization tools that allow users to interrogate curated datasets and access models from our library of PDOX for functional studies of tumorigenesis or preclinical testing.
 The findings of the project were published in [Acta Neuropathol](https://doi.org/10.1007/s00401-020-02171-5).
 
@@ -334,7 +334,7 @@ The Pediatric Cancer Genome Project (PCGP) is a collaboration between St. Jude C
 
 ### Pediatric therapy-related Myeloid Neoplasms (tMN)
 
-**DAU**: Clinical Genonics, PCGP | **Tissue Type**: Paired Tumor-Normal | **Sequencing Type**: WGS, WES, RNA-Seq | **Samples**: 206 | **[Additional Information About tMN](https://www.nature.com/articles/s41467-021-21255-8.epdf?sharing_token=OBIW5LkV7aFgSOGOTgsMy9RgN0jAjWel9jnR3ZoTv0M5OiSLUbihbK42O6ERBsqAsEXmFlmjD00oP8z36ZNOtR8gLat8utbWNUuZuH2X5F4IzuYv1CitkTK31bs0JOUmXSjFXjPfM-9GgBHGqrnQxBcRA53XXbrTagf5XbqikeA%3D)**
+**DAU**: Clinical Genomics, PCGP | **Tissue Type**: Paired Tumor-Normal | **Sequencing Type**: WGS, WES, RNA-Seq | **Samples**: 206 | **[Additional Information About tMN](https://www.nature.com/articles/s41467-021-21255-8.epdf?sharing_token=OBIW5LkV7aFgSOGOTgsMy9RgN0jAjWel9jnR3ZoTv0M5OiSLUbihbK42O6ERBsqAsEXmFlmjD00oP8z36ZNOtR8gLat8utbWNUuZuH2X5F4IzuYv1CitkTK31bs0JOUmXSjFXjPfM-9GgBHGqrnQxBcRA53XXbrTagf5XbqikeA%3D)**
 
 The primary purpose of the Pediatric therapy-related Myeloid Neoplasms (tMN) study is to define the genomic alterations in therapy-related myeloid neoplasms in children.
 The objective of the study was to define the somatic and germline alterations using WGS, WES and/or RNA-seq that drive tMN in children.
@@ -363,7 +363,7 @@ This cohort contains unpaired germline samples and does not contain tumor sample
 
 ### St. Jude Life Clonal Hematopoiesis
 
-**DAU**: PCGP | **Tissue Type**: — | **Sequencing Type**: SingleCell-WGS, Targeted | **Samples**: 3,192
+**DAU**: PCGP | **Tissue Type**: — | **Sequencing Type**: Single Cell-WGS, Targeted | **Samples**: 3,192
 
 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 informatic 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.
+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.

content/4.pecan/1.overview/1.getting-started.md

@@ -25,19 +25,35 @@ Additionally, a user can navigate by using our navigational membrane or begin se
 
 ## Diagnosis Search
 
-The sunburst plot gives an at-a-glance disease distribution and disease hierarchy where all samples have been mapped to a custom ontology (**Figure 2**).
-This interactive interface updates as a user selects a diagnoses or subtype within in the sunburst.
+PeCan's Subtype Tree and Sunburst provide a navigable hierarchy of pediatric cancer diagnoses where all samples have been mapped to the CC4K framework.
+These tools allow users to explore the full diagnosis classification structure used across St. Jude Cloud data, from broad categories down to individual pediatric cancer subtypes.
+For both the Tree and Sunburst, diagnoses are organized under three root categories: 1) HM — Hematopoietic Malignancies, 2) BT — Brain Tumor, and 3) ST — Solid Tumor.
+PeCan metadata export is also available via the download all metadata option from both views.
 
-The diseases are categorized in three main root categories: **1)** HM -Hematopoietic Malignancies, **2)** BT -Brain Tumor, and **3)** ST -Solid Tumor.
-Users are encouraged to navigate via a subtype-centric experience by selecting a subtype and then navigate to each data facet for that available data.
-This will enable custom interface views per data facet based on the sunburst selection.
-Alternatively, a user can explore all of the available data within a data facet by clicking directly on the data facet icon from the side navigation.
+### Sunburst
+
+The sunburst plot provides an at-a-glance distribution and hierarchy of pediatric cancer diagnoses, with all PeCan samples mapped to the CC4K framework (Figure 2).
+The plot updates as a user selects a diagnosis or subtype within the sunburst.
+Users are encouraged to navigate via a subtype-centric experience by selecting a subtype and then navigating to each data facet for the available data.
+This will enable custom interface views per data facet based on the sunburst selection. Alternatively, a user can explore all of the available data within a data facet by clicking directly on the icon from the side navigation.
 
 ![PeCan Sunburst](/img/pecan/overview/getting-started/diagnosis_search_sidenav.png)
 
 **Figure 2: Diagnosis Search Interface and Facet Navigation**
 A user is able to filter by diagnoses and/or subtype by selecting the interactive sunburst or by navigating directly into a data facet for the available data by using the side navigation.
 
+### Subtype Tree
+
+The Subtype Tree allows users to explore the full diagnostic classification structure, [CC4K](https://docs.stjude.cloud/cc4k), used across St. Jude Cloud data, from broad categories down to individual subtypes.
+Users can expand any node to reveal its subtypes, with sample counts displayed at each level to indicate data availability.
+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)
+
+**Figure 3: Subtype Tree**
+A user is able to explore the tree by selecting the interactive nodes.
+
 ## Data Facets
 
 Data Facets represent a distinct type of post-processed genomic data for collections of pediatric cancer samples via a designated interface.