Data Types

Sample-Level Data

  • Interactive heatmaps showing somatic genetic alterations comparing primary patient and corresponding PDX(s)
  • Extensive metadata including clinical information, mouse models tested, engraftment latency, links to publications
  • Explore small variant and structural variant of patient samples and PDXs
  • Links to request and download primary genomic data.
  • Table summarizing types of sequencing performed
  • Expression plots depicting sequencing coverage

Cohort-Level Data

  • Clustering of subtypes and PDXs with subtypes using tSNE plots derived from transcriptome sequencing data.
  • Interactive heatmaps to visualize somatic mutations of multiple samples in a cohort

Genomic Coverage

  • Genomic Coverage displays a genomepaint view showing UCSC RefSeq track as well as raw coverage of WGS, WES and RNAseq data, where available
  • Pediatric mutation data from Pediatric Cancer Genome Project (PCGP) phase II as well as B-ALL mutation and expression data in Pan-ALL study can be viewed

Genomic Data

  • Genomic data for select samples is displayed in the form of Onco print/heatmap displaying genomic changes such as mutations, structural variants (SV), fusions, and copy number variation (CNV)
  • For single patient, genes with higher frequency of changes among all related samples in the above-mentioned genomic changes will be selected for display

TSNE data

  • TSNE is a two-dimensional t-distributed stochastic neighbor embedding plot showing gene expression profiling of B-ALL samples. Each dot represents a sample
  • Adapted from Gu Z. et al. “PAX5-driven subtypes of B-progenitor acute lymphoblastic leukemia.” Nat Genetics, 51: 296-307, 2019