TargetOsteoAnalysis

This package contains functionality to access the open, public genomics and clinical data from the TARGET Osteosarcoma project.

Installation

Installation from github:

install.packages('BiocManager')
BiocManager::install("seandavi/TargetOsteoAnalysis")

TARGET Osteosarcoma

The TARGET Osteosarcoma project elucidates comprehensive molecular characterization to determine the genetic changes that drive the initiation and progression of high-risk or hard-to-treat childhood cancers. Osteosarcoma (OS) is the most common type of bone cancer in children and adolescents. It is most frequently diagnosed in adolescent patients experiencing periods of rapid growth. As with other childhood cancers being studied by TARGET, improvements in survival outcomes for OS have plateaued despite attempts in refining the standard treatment protocol. Additionally, patients endure rigorous therapy regimens regardless of whether the disease is localized or metastatic. Thus, targeted therapies have the potential to enhance the survival and quality-of-life of patients with this disease. To learn more about Osteosarcoma and current treatment strategies, visit the NCI osteosarcoma website.

Datasets included

• Clinical
• Methylation (450k Illumina Arrays)
• Gene Expression (Affymetrix HuEx arrays)
• miRNA Expression (TaqMan multiplex assay)
• Purity and ploidy estimates from HTS data
• Copy Number
  • Affymetrix SNP6 arrays
  • GISTIC summary
  • Purity-corrected copy number
• DNA quality control metrics

Extra data included include:

• Sleeping beauty osteosarcoma screening data
• COSMIC consensus gene list
• Alterations defined by https://www.pnas.org/content/111/51/E5564. See get_janeway_alterations().
• SNVs from https://doi-org.ezproxy.nihlibrary.nih.gov/10.1016/j.celrep.2014.03.003. See get_stjude_snvs().