ctsp-dlbcl.yaml

Name: Clinical Trial Sequencing Project - Diffuse Large B-Cell Lymphoma
Description: |
  The goal of the project is to identify recurrent genetic alterations (mutations, deletions,
  amplifications, rearrangements) and/or gene expression signatures. National Cancer Institute (NCI)
  utilized whole genome sequencing and/or whole exome sequencing in conjunction with transcriptome
  sequencing. The samples were processed and submitted for genomic characterization using pipelines
  and procedures established within The Cancer Genome Analysis (TCGA) project.
Documentation: |
  https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001175.v2.p2
Contact: dcf-support@datacommons.io
ManagedBy: "[Center for Translational Data Science at The University of Chicago](https://ctds.uchicago.edu/)"
UpdateFrequency: |
  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.
Tags:
  - aws-pds
  - cancer
  - genomic
  - life sciences
  - transcriptomics
  - whole genome sequencing
  - STRIDES
License: "NIH Genomic Data Sharing Policy: https://gdc.cancer.gov/access-data/data-access-policies"
Resources:
  - Description: RNA-Seq Gene Expression Quantification
    ARN: arn:aws:s3:::gdc-ctsp-phs001175-2-open
    Region: us-east-1
    Type: S3 Bucket
DataAtWork:
  Tools & Applications:
    - Title: Genomic Data Commons
      URL: https://portal.gdc.cancer.gov/projects/CTSP-DLBCL1
      AuthorName: National Cancer Institute
      AuthorURL: https://gdc.cancer.gov/
  Publications:
    - Title: A multiprotein supercomplex controlling oncogenic signalling in lymphoma
      URL: https://www.ncbi.nlm.nih.gov/pubmed?cmd=DetailsSearch&term=29925955[PMID]
      AuthorName: |
        Phelan JD, Young RM, Webster DE, Roulland S, Wright GW, Kasbekar M, Shaffer AL 3rd,
        Ceribelli M, Wang JQ, Schmitz R, Nakagawa M, Bachy E, Huang DW, Ji Y, Chen L, Yang Y, Zhao
        H, Yu X, Xu W, Palisoc MM, Valadez RR, Davies-Hill T, Wilson WH, Chan WC, Jaffe ES, Gascoyne
        RD, Campo E, Rosenwald A, Ott G, Delabie J, Rimsza LM, Rodriguez FJ, Estephan F, Holdhoff M,
        Kruhlak MJ, Hewitt SM, Thomas CJ, Pittaluga S, Oellerich T, Staudt LM
    - Title: Genetics and Pathogenesis of Diffuse Large B Cell Lymphoma
      URL: https://doi.org/10.1056/NEJMoa1801445
      AuthorName: |
        Roland Schmitz, Ph.D., George W. Wright, Ph.D., Da Wei Huang, M.D., Calvin A.  Johnson,
        Ph.D., James D. Phelan, Ph.D., James Q. Wang, Ph.D., Sandrine Roulland, Ph.D., Monica
        Kasbekar, Ph.D., Ryan M. Young, Ph.D., Arthur L. Shaffer, Ph.D., Daniel J. Hodson, M.D.,
        Ph.D., Wenming Xiao, Ph.D., et al.