diff --git a/.spelling b/.spelling index 1fea0de..856b2b6 100644 --- a/.spelling +++ b/.spelling @@ -159,6 +159,9 @@ Zhang Zhaoming Zhou # Genomics/Biology Terms +ALS-frontotemporal +ALS-FTD +amyotrophic BAM BamToGFF BAMs @@ -242,6 +245,7 @@ MethylationToActivity missense multi-omic multi-omics +multisystem MYCN-ATRX Myelodysplastic neuroblastoma @@ -257,6 +261,7 @@ PAX5-JAK2 Paxalisib PedAML plotMDS +proteinopathy ProteinPaint proteomic PolyA @@ -305,6 +310,7 @@ westus BMF_MDS-Schedule1 CCSS-Schedule1 ClinGen-Schedule1 +CReATe-Schedule1 DMG-H3K27a-Schedule1 MBPRG-Schedule1 MBPRP-Schedule1 diff --git a/content/1.overview/3.citing-stjude-cloud.md b/content/1.overview/3.citing-stjude-cloud.md index c1c1ebe..b86b717 100644 --- a/content/1.overview/3.citing-stjude-cloud.md +++ b/content/1.overview/3.citing-stjude-cloud.md @@ -32,25 +32,26 @@ Citation manager formats can be accessed [here](https://aacrjournals.org/cancerd Please download the Schedule 1(s) (linked in table below) to find dataset specific wording of acknowledgement(s). -| St. Jude Cloud Dataset | Publication(s) | Citation Info | -|----------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------| -| Pediatric Cancer Genome Project (PCGP) | [PCGP perspectives paper](https://www.ncbi.nlm.nih.gov/pubmed/22641210) and the [relevant tumor type paper(s)](https://permalinks.stjude.cloud/permalinks/pcgp) | [PCGP Schedule 1](/files/overview/citing-stjude-cloud/PCGP-Schedule1.pdf){target="_blank" download="PCGP-Schedule1.pdf"} | -| Childhood Solid Tumor Network (CSTN) | [CSTN Publication and Resources](https://cstn.stjude.cloud/resources) | [CSTN Schedule 1](/files/overview/citing-stjude-cloud/PCGP-Schedule1.pdf){target="_blank" download="PCGP-Schedule1.pdf"} | -| St. Jude Lifetime (SJLIFE) | [SJLIFE paper](https://www.ncbi.nlm.nih.gov/pubmed/?term=29847298) | [SJLIFE Schedule 1](/files/overview/citing-stjude-cloud/SJLIFE-Schedule1.pdf){target="_blank" download="SJLIFE-Schedule1.pdf"} | -| Clinical Pilot | [Clinical Pilot paper](https://www.ncbi.nlm.nih.gov/pubmed/30262806) | [Clinical Genomics Schedule 1](/files/overview/citing-stjude-cloud/ClinGen-Schedule1.pdf){target="_blank" download="ClinGen-Schedule1.pdf"} | -| Genomes for Kids (G4K) | [Genomes for Kids (G4K) Paper](https://aacrjournals.org/cancerdiscovery/article/11/12/3008/674726/Genomes-for-Kids-The-Scope-of-Pathogenic-Mutations) | [Clinical Genomics Schedule 1](/files/overview/citing-stjude-cloud/ClinGen-Schedule1.pdf){target="_blank" download="ClinGen-Schedule1.pdf"} | -| Real-Time Clinical Genomics (RTCG) | No publication yet | [Clinical Genomics Schedule 1](/files/overview/citing-stjude-cloud/ClinGen-Schedule1.pdf){target="_blank" download="ClinGen-Schedule1.pdf"} | -| Sickle Cell Genome Project (SGP) | Paper In Progress | [SGP Schedule 1](/files/overview/citing-stjude-cloud/SGP-Schedule1.pdf){target="_blank" download="SGP-Schedule1.pdf"} | -| Childhood Cancer Survivor Study (CCSS) | [CCSS study design paper](https://www.ncbi.nlm.nih.gov/pubmed/11920786) | [CCSS Schedule 1](/files/overview/citing-stjude-cloud/CCSS-Schedule1.pdf){target="_blank" download="CCSS-Schedule1.pdf"} | -| Pan-Acute Lymphoblastic Leukemia (PanALL) | Paper In Progress | [PanALL Schedule 1](/files/overview/citing-stjude-cloud/PanALL-Schedule1.pdf){target="_blank" download="PanALL-Schedule1.pdf"} | -| Pediatric therapy-related Myeloid Neoplasms (tMN) | [tMN paper](https://pubmed.ncbi.nlm.nih.gov/33579957/) | [tMN Schedule 1](/files/overview/citing-stjude-cloud/tMN-Schedule1.pdf){target="_blank" download="tMN-Schedule1.pdf"} | -| Pediatric Acute Myeloid Leukemia (PedAML) | [PedAML paper](https://pubmed.ncbi.nlm.nih.gov/34778799/) | [PedAML Schedule 1](/files/overview/citing-stjude-cloud/PedAML-Schedule1.pdf){target="_blank" download="PedAML-Schedule1.pdf"} | -| Bone Marrow Failure and Myelodysplastic Syndromes (BMF/MDS) | Paper In Progress | [BMF/MDS Schedule 1](/files/overview/citing-stjude-cloud/BMF_MDS-Schedule1.pdf){target="_blank" download="BMF_MDS-Schedule1.pdf"} | -| Genomics and transcriptomics of relapsed pediatric AML (RPAML) | Paper In Progress | [RPAML Schedule 1](/files/overview/citing-stjude-cloud/RPAML_Schedule1.pdf){target="_blank" download="RPAML-Schedule1.pdf"} | -| Medulloblastoma Preclinical Ribociclib and Gemcitabine (MBPRG) | Paper In Progress | [MBPRG Schedule 1](/files/overview/citing-stjude-cloud/MBPRG-Schedule1.pdf){target="_blank" download="MBPRG-Schedule1.pdf"} | -| Pediatric Brain Tumor Portal (PBTP) | [PBTP first set of PDOX models](https://pubmed.ncbi.nlm.nih.gov/32519082/), [second set of models](https://www.nature.com/articles/s41467-021-24168-8) and the [relevant tumor type paper(s)](https://permalinks.stjude.cloud/permalinks/pcgp) | [PBTP Schedule 1](/files/overview/citing-stjude-cloud/PBTP-Schedule1.pdf){target="_blank" download="PBTP-Schedule1.pdf"} | -| Medulloblastoma Preclinical Ribociclib and Paxalisib (MBPRP) | Paper In Progress | [MBPRP Schedule 1](/files/overview/citing-stjude-cloud/MBPRP-Schedule1.pdf){target="_blank" download="MBPRP-Schedule1.pdf"} | -| DMG-H3K27a Clonal Evolution (H3K27A_EVOLUTION) | [H3K27A_EVOLUTION Publication and Resources](https://permalinks.stjude.cloud/permalinks/h3k27a_evolution) | [H3K27A_EVOLUTION Schedule 1](/files/overview/citing-stjude-cloud/DMG-H3K27a-Schedule1.pdf){target="_blank" download="DMG-H3K27a-Schedule1.pdf"} | +| St. Jude Cloud Dataset | Publication(s) | Citation Info | +|------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------| +| Pediatric Cancer Genome Project (PCGP) | [PCGP perspectives paper](https://www.ncbi.nlm.nih.gov/pubmed/22641210) and the [relevant tumor type paper(s)](https://permalinks.stjude.cloud/permalinks/pcgp) | [PCGP Schedule 1](/files/overview/citing-stjude-cloud/PCGP-Schedule1.pdf){target="_blank" download="PCGP-Schedule1.pdf"} | +| Childhood Solid Tumor Network (CSTN) | [CSTN Publication and Resources](https://cstn.stjude.cloud/resources) | [CSTN Schedule 1](/files/overview/citing-stjude-cloud/PCGP-Schedule1.pdf){target="_blank" download="PCGP-Schedule1.pdf"} | +| St. Jude Lifetime (SJLIFE) | [SJLIFE paper](https://www.ncbi.nlm.nih.gov/pubmed/?term=29847298) | [SJLIFE Schedule 1](/files/overview/citing-stjude-cloud/SJLIFE-Schedule1.pdf){target="_blank" download="SJLIFE-Schedule1.pdf"} | +| Clinical Pilot | [Clinical Pilot paper](https://www.ncbi.nlm.nih.gov/pubmed/30262806) | [Clinical Genomics Schedule 1](/files/overview/citing-stjude-cloud/ClinGen-Schedule1.pdf){target="_blank" download="ClinGen-Schedule1.pdf"} | +| Genomes for Kids (G4K) | [Genomes for Kids (G4K) Paper](https://aacrjournals.org/cancerdiscovery/article/11/12/3008/674726/Genomes-for-Kids-The-Scope-of-Pathogenic-Mutations) | [Clinical Genomics Schedule 1](/files/overview/citing-stjude-cloud/ClinGen-Schedule1.pdf){target="_blank" download="ClinGen-Schedule1.pdf"} | +| Real-Time Clinical Genomics (RTCG) | No publication yet | [Clinical Genomics Schedule 1](/files/overview/citing-stjude-cloud/ClinGen-Schedule1.pdf){target="_blank" download="ClinGen-Schedule1.pdf"} | +| Sickle Cell Genome Project (SGP) | Paper In Progress | [SGP Schedule 1](/files/overview/citing-stjude-cloud/CReATe-Schedule1.pdf){target="_blank" download="SGP-Schedule1.pdf"} | +| Clinical Research in ALS and Related Disorders for Therapeutic Development Consortium (CReATe) | [CReATe study design paper](https://doi.org/10.1186/s40035-025-00516-2) | [CReATe Schedule 1](/files/overview/citing-stjude-cloud/CReATe-Schedule1.pdf){target="_blank" download="CReATe-Schedule1.pdf"} | +| Childhood Cancer Survivor Study (CCSS) | [CCSS study design paper](https://www.ncbi.nlm.nih.gov/pubmed/11920786) | [CCSS Schedule 1](/files/overview/citing-stjude-cloud/CCSS-Schedule1.pdf){target="_blank" download="CCSS-Schedule1.pdf"} | +| Pan-Acute Lymphoblastic Leukemia (PanALL) | Paper In Progress | [PanALL Schedule 1](/files/overview/citing-stjude-cloud/PanALL-Schedule1.pdf){target="_blank" download="PanALL-Schedule1.pdf"} | +| Pediatric therapy-related Myeloid Neoplasms (tMN) | [tMN paper](https://pubmed.ncbi.nlm.nih.gov/33579957/) | [tMN Schedule 1](/files/overview/citing-stjude-cloud/tMN-Schedule1.pdf){target="_blank" download="tMN-Schedule1.pdf"} | +| Pediatric Acute Myeloid Leukemia (PedAML) | [PedAML paper](https://pubmed.ncbi.nlm.nih.gov/34778799/) | [PedAML Schedule 1](/files/overview/citing-stjude-cloud/PedAML-Schedule1.pdf){target="_blank" download="PedAML-Schedule1.pdf"} | +| Bone Marrow Failure and Myelodysplastic Syndromes (BMF/MDS) | Paper In Progress | [BMF/MDS Schedule 1](/files/overview/citing-stjude-cloud/BMF_MDS-Schedule1.pdf){target="_blank" download="BMF_MDS-Schedule1.pdf"} | +| Genomics and transcriptomics of relapsed pediatric AML (RPAML) | Paper In Progress | [RPAML Schedule 1](/files/overview/citing-stjude-cloud/RPAML_Schedule1.pdf){target="_blank" download="RPAML-Schedule1.pdf"} | +| Medulloblastoma Preclinical Ribociclib and Gemcitabine (MBPRG) | Paper In Progress | [MBPRG Schedule 1](/files/overview/citing-stjude-cloud/MBPRG-Schedule1.pdf){target="_blank" download="MBPRG-Schedule1.pdf"} | +| Pediatric Brain Tumor Portal (PBTP) | [PBTP first set of PDOX models](https://pubmed.ncbi.nlm.nih.gov/32519082/), [second set of models](https://www.nature.com/articles/s41467-021-24168-8) and the [relevant tumor type paper(s)](https://permalinks.stjude.cloud/permalinks/pcgp) | [PBTP Schedule 1](/files/overview/citing-stjude-cloud/PBTP-Schedule1.pdf){target="_blank" download="PBTP-Schedule1.pdf"} | +| Medulloblastoma Preclinical Ribociclib and Paxalisib (MBPRP) | Paper In Progress | [MBPRP Schedule 1](/files/overview/citing-stjude-cloud/MBPRP-Schedule1.pdf){target="_blank" download="MBPRP-Schedule1.pdf"} | +| DMG-H3K27a Clonal Evolution (H3K27A_EVOLUTION) | [H3K27A_EVOLUTION Publication and Resources](https://permalinks.stjude.cloud/permalinks/h3k27a_evolution) | [H3K27A_EVOLUTION Schedule 1](/files/overview/citing-stjude-cloud/DMG-H3K27a-Schedule1.pdf){target="_blank" download="DMG-H3K27a-Schedule1.pdf"} | ::callout{icon="i-heroicons-document-text-solid" color="blue"} **Note** diff --git a/content/3.genomics-platform/1.getting-started/6.glossary.md b/content/3.genomics-platform/1.getting-started/6.glossary.md index 192bc8e..15f7ce0 100644 --- a/content/3.genomics-platform/1.getting-started/6.glossary.md +++ b/content/3.genomics-platform/1.getting-started/6.glossary.md @@ -9,7 +9,7 @@ A St. Jude Cloud **Data Access Unit (DAU)** is a grouping of data that typically Each DAU has its own governing body of researchers, the [Data Access Committee](#data-access-committee), who preside over the data and who may grant or deny access. Each Data Access Committee has its own protocols for approving access to their DAU. Please [contact us](mailto:support@stjude.cloud) if you have questions about committee approval protocols. -We currently have 6 DAUs: Pediatric Cancer Genome Project (PCGP), St. Jude Lifetime Cohort Study (SJLIFE), Genomes for Kids (G4K) and Clinical Genomics, Sickle Cell Genome Project (SGP), Childhood Cancer Survivor Study (CCSS), and Pan-Acute Lymphoblastic Leukemia (PanALL). +We currently have 7 DAUs: Pediatric Cancer Genome Project (PCGP), St. Jude Lifetime Cohort Study (SJLIFE), Genomes for Kids (G4K) and Clinical Genomics, Sickle Cell Genome Project (SGP), Childhood Cancer Survivor Study (CCSS), Pan-Acute Lymphoblastic Leukemia (PanALL), and Clinical Research in ALS and Related Disorders for Therapeutic Development Consortium (CReATe). For a brief description of each DAU see the Studies page. For a more detailed description please see the respective [Schedule 1(s)](/overview/citing-stjude-cloud#dataset-reference-table). 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 9cbc51b..e657443 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 @@ -21,7 +21,7 @@ A St. Jude Cloud **Data Access Unit (DAU)** is a grouping of data that typically Each DAU has its own governing body of researchers, the [Data Access Committee](#data-access-committee), who preside over the data and who may grant or deny access. Each Data Access Committee is responsible for only one DAU and has its own protocols for approving access to their DAU. Please [contact us](mailto:support@stjude.cloud) if you have questions about committee approval protocols. -We currently have 6 DAUs: Pediatric Cancer Genome Project (PCGP), St. Jude Lifetime Cohort Study (SJLIFE), Genomes for Kids (G4K) and Clinical Genomics, Sickle Cell Genome Project (SGP), Childhood Cancer Survivor Study (CCSS), and Pan-Acute Lymphoblastic Leukemia (PanALL). +We currently have 7 DAUs: Pediatric Cancer Genome Project (PCGP), St. Jude Lifetime Cohort Study (SJLIFE), Genomes for Kids (G4K) and Clinical Genomics, Sickle Cell Genome Project (SGP), Childhood Cancer Survivor Study (CCSS), Pan-Acute Lymphoblastic Leukemia (PanALL), and Clinical Research in ALS and Related Disorders for Therapeutic Development Consortium (CReATe). See below for a brief description of each DAU. For a more detailed description please see the respective [Schedule 1(s)](/overview/citing-stjude-cloud#dataset-reference-table). @@ -74,6 +74,12 @@ The following data set(s) are included within Clinical Genomics: - [Genome 4 Kids (G4K)](#genome-4-kids) - [Real-Time Clinical Genomics (RTCG)](#real-time-clinical-genomics) +### Clinical Research in ALS and Related Disorders for Therapeutic Development Consortium (CReATe) + +CReATe contains whole genome sequencing data with paired phenotypic data, focused on studying patients with amyotrophic lateral sclerosis (ALS) or a related disorder. The following data set(s) are included in CReATe: + +- [Clinical Research in ALS and Related Disorders for Therapeutic Development Consortium (CReATe)](#clinical-research-in-als-and-related-disorders-for-therapeutic-development-consortium) + ### Pan-Acute Lymphoblastic Leukemia (PanALL) PanALL contains tumor-only RNA-Seq data focused on the spectrum of ALL subtypes from a variety of contributing sources. @@ -154,6 +160,12 @@ The raw Data Sets from this initiative are made available via St. Jude Cloud. The CICERO Data Set contains the samples which were selected for use in the [CICERO Paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02043-x). +### Clinical Research in ALS and Related Disorders for Therapeutic Development Consortium + +**DAU**: CReATe | **Tissue Type**: PBMC germline DNA | **Sequencing Type**: WGS | **Samples**: 705 + +The Phenotype-Genotype-Biomarker (PGB, or PGB1) study (NCT02327845) of the Clinical Research in ALS and Related Disorders for Therapeutic Development (CReATe) Consortium was a natural history and biomarker study of patients with amyotrophic lateral sclerosis (ALS) or a related disorder, including but not limited to ALS-frontotemporal dementia (ALS-FTD), progressive muscular atrophy (PMA), primary lateral sclerosis (PLS), hereditary spastic paraplegia (HSP), and multisystem proteinopathy (MSP). In addition to patients enrolled in the PGB1 Cohort (primary participants), the study also enrolled family members for limited data collection (secondary participants). 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). + ### Clinical Pilot **DAU**: PCGP and Clinical Genomics | **Tissue Type**: Paired Tumor-Normal | **Sequencing Type**: WGS, WES, RNA-Seq | **Samples**: 155 | **[Additional Information About Clinical Genomics](https://www.stjude.cloud/studies/clinical-genomics)** diff --git a/public/files/overview/citing-stjude-cloud/CReATe-Schedule1.pdf b/public/files/overview/citing-stjude-cloud/CReATe-Schedule1.pdf new file mode 100644 index 0000000..c33f3d1 Binary files /dev/null and b/public/files/overview/citing-stjude-cloud/CReATe-Schedule1.pdf differ