Rapid, reliable, and reproducible molecular sub-grouping of clinical medulloblastoma samples.

Abstract

The diagnosis of medulloblastoma likely encompasses several distinct entities, with recent evidence for the existence of at least four unique molecular subgroups that exhibit distinct genetic, transcriptional, demographic, and clinical features. Assignment of molecular subgroup through routine profiling of high-quality RNA on expression microarrays is likely impractical in the clinical setting. The planning and execution of medulloblastoma clinical trials that stratify by subgroup, or which are targeted to a specific subgroup requires technologies that can be economically, rapidly, reliably, and reproducibly applied to formalin-fixed paraffin embedded (FFPE) specimens. In the current study, we have developed an assay that accurately measures the expression level of 22 medulloblastoma subgroup-specific signature genes (CodeSet) using nanoString nCounter Technology. Comparison of the nanoString assay with Affymetrix expression array data on a training series of 101 medulloblastomas of known subgroup demonstrated a high concordance (Pearson correlation r = 0.86). The assay was validated on a second set of 130 non-overlapping medulloblastomas of known subgroup, correctly assigning 98% (127/130) of tumors to the appropriate subgroup. Reproducibility was demonstrated by repeating the assay in three independent laboratories in Canada, the United States, and Switzerland. Finally, the nanoString assay could confidently predict subgroup in 88% of recent FFPE cases, of which 100% had accurate subgroup assignment. We present an assay based on nanoString technology that is capable of rapidly, reliably, and reproducibly assigning clinical FFPE medulloblastoma samples to their molecular subgroup, and which is highly suited for future medulloblastoma clinical trials.

• Authors: Paul A Northcott, David J H Shih, Marc Remke, Yoon-Jae Cho, Marcel Kool, Cynthia Hawkins, Charles G Eberhart, Adrian Dubuc, Toumy Guettouche, Yoslayma Cardentey, Eric Bouffet, Scott L Pomeroy, Marco Marra, David Malkin, James T Rutka, Andrey Korshunov, Stefan Pfister, Michael D Taylor
• Journal: Acta neuropathologica (Acta Neuropathol) Vol. 123 Issue 4 Pg. 615-26 (Apr 2012) ISSN: 1432-0533 [Electronic] Germany
• PMID: 22057785 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't)

Chemical References

• Hedgehog Proteins
• IMPG2 protein, human
• KCNA1 protein, human
• Proteoglycans
• SHH protein, human
• Wnt Proteins
• Kv1.1 Potassium Channel

Topics

• Adolescent
• Adult
• Cerebellar Neoplasms (classification, diagnosis, genetics)
• Child
• Cohort Studies
• Computational Biology
• Female
• Gene Expression Profiling (methods)
• Gene Regulatory Networks (genetics)
• Hedgehog Proteins
• Humans
• Kv1.1 Potassium Channel (metabolism)
• Logistic Models
• Male
• Medulloblastoma (classification, diagnosis, genetics)
• Oligonucleotide Array Sequence Analysis (methods)
• Probability
• Proteoglycans (metabolism)
• Regression Analysis
• Reproducibility of Results
• Wnt Proteins
• Young Adult