title: 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: The Arthur and Sonia Labatt Brain Tumour Research Center, Hospital for Sick Children, Toronto, ON, Canada.
authors: Paul A
authors: PA
authors: Northcott
authors: David J H
authors: DJ
authors: Shih
authors: Marc
authors: M
authors: Remke
authors: Yoon-Jae
authors: YJ
authors: Cho
authors: Marcel
authors: M
authors: Kool
authors: Cynthia
authors: C
authors: Hawkins
authors: Charles G
authors: CG
authors: Eberhart
authors: Adrian
authors: A
authors: Dubuc
authors: Toumy
authors: T
authors: Guettouche
authors: Yoslayma
authors: Y
authors: Cardentey
authors: Eric
authors: E
authors: Bouffet
authors: Scott L
authors: SL
authors: Pomeroy
authors: Marco
authors: M
authors: Marra
authors: David
authors: D
authors: Malkin
authors: James T
authors: JT
authors: Rutka
authors: Andrey
authors: A
authors: Korshunov
authors: Stefan
authors: S
authors: Pfister
authors: Michael D
authors: MD
authors: Taylor
mesh_terms: D000293:Adolescent; D000328:Adult; D002528:Cerebellar Neoplasms / Q000145:classification* / Q000175:diagnosis* / Q000235:genetics; D002648:Child; D015331:Cohort Studies; D019295:Computational Biology; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D053263:Gene Regulatory Networks / Q000235:genetics; D053823:Hedgehog Proteins; D006801:Humans; D051662:Kv1.1 Potassium Channel / Q000378:metabolism; D016015:Logistic Models; D008297:Male; D008527:Medulloblastoma / Q000145:classification* / Q000175:diagnosis* / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D011336:Probability; D011509:Proteoglycans / Q000378:metabolism; D012044:Regression Analysis; D015203:Reproducibility of Results; D051153:Wnt Proteins; D055815:Young Adult
chemical_list: D053823:Hedgehog Proteins; C412522:IMPG2 protein, human; C496946:KCNA1 protein, human; D011509:Proteoglycans; C509239:SHH protein, human; D051153:Wnt Proteins; D051662:Kv1.1 Potassium Channel