ctsp-dlbcl-dataset/README.md

Clinical Trial Sequencing Project - Diffuse Large B-Cell Lymphoma

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

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

fs.listdir("s3://gdc-ctsp-phs001175-2-open")

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.

Contact:

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.

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: RNA-Seq Gene Expression Quantification
   • ARN: arn:aws:s3:::gdc-ctsp-phs001175-2-open
   • Region: us-east-1
   • Type: S3 Bucket

Tags:

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

Tools & Applications:

1. tools & applications:
   • Title: Genomic Data Commons
   • URL: https://portal.gdc.cancer.gov/projects/CTSP-DLBCL1
   • AuthorName: National Cancer Institute
   • AuthorURL: https://gdc.cancer.gov/

Publication:

1. publication:

   • 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

2. publication:

   • 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.