Medulloblastoma (Broad, Nature 2012)

Overview

The Broad medulloblastoma dataset comprises 92 primary medulloblastoma tumor/normal pairs from pediatric patients, profiled by whole-exome sequencing (Pugh et al., Nature 2012). Samples were collected from Children’s Hospital Boston, Hospital for Sick Children Toronto, and Children’s Oncology Group/CHTN. The cohort spans all four molecular subgroups of medulloblastoma (WNT, SHH, Group 3, Group 4) and is characterized by one of the lowest somatic mutation rates across cancer types (median 0.35/Mb), consistent with other pediatric tumors.

Composition

  • 92 primary medulloblastoma tumor/normal pairs
  • Cancer type: MBL (medulloblastoma)
  • Molecular subgroups: 6 WNT, 23 SHH, 33 Group 3, 30 Group 4
  • Median age and institutional breakdown not specified but samples from three major pediatric oncology centers
  • Median somatic mutation rate: 0.35 non-silent mutations per megabase (median 12 non-silent mutations per tumor)

Assays / panels (linked)

  • whole-exome-seq — hybrid capture of 193,094 exons from 18,863 genes; median 106X coverage
  • mutsig — significance testing for somatic mutations (q < 0.1 threshold)
  • Validation: microfluidic PCR (Fluidigm) + single-molecule real-time sequencing (Pacific Biosciences); 19/20 mutations confirmed

Papers using this cohort

Notable findings derived from this cohort

Sources

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