Data Types

Sequencing data process

Sequencing data process

Here are a few highlights of the data types on PBTP:

Cohort-Level Data
  • Somatic mutations and differential gene expression for cohorts of patient and matched PDOX tumors in the form of interactive oncoprints and heatmaps.
  • DNA methylation classification and disease subgrouping for cohorts of patient and matched PDOX tumors in the form of TSNE plots.
  • Chemical sensitivity data (single-point, dose response, and combination therapies) for patient tumor and PDOX-derived cell lines.
Sample-Level Data
  • Sample details including sequencing types performed, patient info, material available.
  • Histology comparing patient tumor vs. PDOX tumor.
  • Somatic mutations for patient vs. PDOX tumors (static sample heatmap), Copy number variations, FISH (as applicable).
  • DNA methylation classification and disease subgrouping for patient and matched PDOX tumors.
Gene Search
  • Search genes of interest and generate custom oncoprints.
  • Explore single nucleotide variants and structural variants for patient and matched PDOX tumors.