Therapeutically Applicable Research to Generate Effective Treatments (TARGET)

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/target-dataset")

fs.listdir("s3://gdc-target-phs000218-2-open")

Description:

Therapeutically Applicable Research to Generate Effective Treatments (TARGET) is the collaborative effort of a large, diverse consortium of extramural and NCI investigators. The goal of the effort is to accelerate molecular discoveries that drive the initiation and progression of hard-to-treat childhood cancers and facilitate rapid translation of those findings into the clinic. TARGET projects provide comprehensive molecular characterization to determine the genetic changes that drive the initiation and progression of childhood cancers.The dataset contains open Clinical Supplement, Biospecimen Supplement, RNA-Seq Gene Expression Quantification, miRNA-Seq Isoform Expression Quantification, miRNA-Seq miRNA Expression Quantification data from Genomic Data Commons (GDC), and open data from GDC Legacy Archive.

Contact:

Therapeutically Applicable Research to Generate Effective Treatments (TARGET) is the collaborative effort of a large, diverse consortium of extramural and NCI investigators. The goal of the effort is to accelerate molecular discoveries that drive the initiation and progression of hard-to-treat childhood cancers and facilitate rapid translation of those findings into the clinic. TARGET projects provide comprehensive molecular characterization to determine the genetic changes that drive the initiation and progression of childhood cancers.The dataset contains open Clinical Supplement, Biospecimen Supplement, RNA-Seq Gene Expression Quantification, miRNA-Seq Isoform Expression Quantification, miRNA-Seq miRNA Expression Quantification data from Genomic Data Commons (GDC), and open data from GDC Legacy Archive.

Update Frequency:

Genomic Data Commons (GDC) is source of truth for this dataset; GDC offers monthly data releases, although this dataset may not be updated at every release.

Managed By:

https://ctds.uchicago.edu/

Resources:

1. resource:

   • Description: Clinical Supplement, Biospecimen Supplement, RNA-Seq Gene Expression Quantification, miRNA-Seq Isoform Expression Quantification, miRNA-Seq miRNA Expression Quantification, GDC LegacyArchive

   • ARN: arn:aws:s3:::gdc-target-phs000218-2-open

   • Region: us-east-1

   • Type: S3 Bucket

Tags:

aws-pds, cancer, genomic, life sciences, whole genome sequencing, STRIDES

Tools & Applications:

1. tools & applications:

   • Title: Genomic Data Commons
   • URL: https://portal.gdc.cancer.gov/projects/
   • AuthorName: National Cancer Institute
   • AuthorURL: https://gdc.cancer.gov/

2. tools & applications:

   • Title: GDC Legacy Archive
   • URL: https://portal.gdc.cancer.gov/legacy-archive/
   • AuthorName: National Cancer Institute
   • AuthorURL: https://gdc.cancer.gov/

3. tools & applications:

   • Title: TARGET data matrix
   • URL: https://ocg.cancer.gov/programs/target/data-matrix
   • AuthorName: National Cancer Institute
   • AuthorURL: https://ocg.cancer.gov/

4. tools & applications:

   • Title: Broad Institute FireCloud
   • URL: https://firecloud.terra.bio/
   • AuthorName: The Broad Institute of MIT & Harvard
   • AuthorURL: https://www.broadinstitute.org/

5. tools & applications:

   • Title: Cancer Genomics Cloud
   • URL: https://cgc-accounts.sbgenomics.com/
   • AuthorName: Seven Bridges
   • AuthorURL: https://docs.sevenbridges.com/docs/target-data

6. tools & applications:

   • Title: ISB Cancer Genomics Cloud
   • URL: https://isb-cgc.appspot.com/
   • AuthorName: Institute for Systems Biology
   • AuthorURL: https://isb-cancer-genomics-cloud.readthedocs.io/en/latest/sections/data/TARGET_top.html

Publication:

1. publication:

   • Title: Genomic classification and identification of the cell of origin of pediatric mixed phenotype acute leukemia

   • URL: https://doi.org/10.1038/s41586-018-0436-0

   • AuthorName: Thomas B. Alexander, Zhaohui Gu, Ilaria Iacobucci, et al.

2. publication:

   • Title: The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia

   • URL: https://www.ncbi.nlm.nih.gov/pubmed/?term=28671688

   • AuthorName: Yu Liu, John Easton, Ying Shao, et al.

3. publication:

   • Title: Ancestry and pharmacogenomics of relapse in acute lymphoblastic leukemia
   • URL: https://www.ncbi.nlm.nih.gov/pubmed/21297632
   • AuthorName: Yang JJ, Cheng C, Devidas M, et al.

4. publication:

   • Title: Genomics in childhood acute myeloid leukemia comes of age
   • URL: https://www.ncbi.nlm.nih.gov/pubmed/?term=29315296
   • AuthorName: Brunner AM, Graubert TA.

5. publication:

   • Title: The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions

   • URL: https://www.ncbi.nlm.nih.gov/pubmed/?term=29227476

   • AuthorName: Bolouri H, Farrar JE, Triche T Jr, et al.

6. publication:

   • Title: MicroRNA Expression-Based Model Indicates Event-Free Survival in Pediatric Acute Myeloid Leukemia

   • URL: https://www.ncbi.nlm.nih.gov/pubmed/?term=29068783

   • AuthorName: Lim EL, Trinh DL, Ries RE, et al.

7. publication:

   • Title: CSF3R mutations have a high degree of overlap with CEBPA mutations in pediatric AM
   • URL: https://www.ncbi.nlm.nih.gov/pubmed/?term=27143256
   • AuthorName: Maxson JE, Ries RE, Wang YC, et al.

8. publication:

   • Title: TCF21 hypermethylation in genetically quiescent clear cell sarcoma of the kidney
   • URL: https://www.ncbi.nlm.nih.gov/pubmed/?term=26158413
   • AuthorName: Gooskens SL, Gadd S, Guidry Auvil JM, et al.

9. publication:

   • Title: Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism
   • URL: https://www.ncbi.nlm.nih.gov/pubmed/?term=26560027
   • AuthorName: Oldridge DA, Wood AC, Weichert-Leahey N, Crimmins I, Sussman R, Winter C, McDaniel LD, Diamond M, Hart LS, Zhu S, Durbin AD, Abraham BJ, et al.

10. publication:

    • Title: Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations
    • URL: https://www.ncbi.nlm.nih.gov/pubmed/?term=26121087
    • AuthorName: Eleveld TF, Oldridge DA, Bernard V, Koster J, et al.

11. publication:

    • Title: The genetic landscape of high-risk neuroblastoma
    • URL: https://www.ncbi.nlm.nih.gov/pubmed/?term=23334666
    • AuthorName: Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL, Cibulskis K, Hanna M, Kiezun A, Kim J, Lawrence MS, Lichenstein L, et al.

12. publication:

    • Title: Biomarker significance of plasma and tumor miR-21, miR-221, and miR-106a in osteosarcoma

    • URL: https://www.ncbi.nlm.nih.gov/pubmed/?term=29228567

    • AuthorName: Nakka M, Allen-Rhoades W, Li Y, et al.

13. publication:

    • Title: Identification and analyses of extra-cranial and cranial rhabdoid tumor molecular subgroups reveal tumors with cytotoxic T cell infiltration

    • URL: https://doi.org/10.1016/j.celrep.2019.10.013

    • AuthorName: Hye-Jung E. Chun, Pascal D. Johann, Katy Milne et al.

14. publication:

    • Title: Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways

    • URL: https://www.ncbi.nlm.nih.gov/pubmed/?term=26977886

    • AuthorName: Chun HJ, Lim EL, Heravi-Moussavi A, et al.

15. publication:

    • Title: A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor

    • URL: https://doi.org/10.1038/ng.3940

    • AuthorName: Gadd S, Huff V, Walz AL, et al.

16. publication:

    • Title: Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group

    • URL: https://www.ncbi.nlm.nih.gov/pubmed/?term=27702824

    • AuthorName: Ooms AH, Gadd S, Gerhard DS, et al.

17. publication:

    • Title: MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours

    • URL: https://www.ncbi.nlm.nih.gov/pubmed/?term=26635203

    • AuthorName: Perlman EJ, Gadd S, Arold ST, et al.

18. publication:

    • Title: Recurrent DGCR8, DROSHA, and SIX homeodomain mutations in favorable histology Wilms tumors

    • URL: https://www.ncbi.nlm.nih.gov/pubmed/?term=25670082

    • AuthorName: Walz AL, Ooms A, Gadd S, et al.