The integration of SNP genomic microarray analysis into pediatric solid tumour analysis
Dr. Mary Shago
Thursday, July 28, 2016
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Chapters
Introduction
Distribution of new cancer cases – Ages 0 to 14 years – Canada 2006-2010
Development of SNP array technology for pediatric cancer
Affymetrix CytoScanHD analysis parameters for Oncology cases
Comparison of SNP array technology and FISH results to date
Solid tumor types
Medulloblastoma
Medulloblastoma expression profiling
Molecular Subgrouping and Cytogenetic Features
Risk stratification for childhood medulloblastoma – consensus 2015
How can we determine molecular subgroup?
NanoString Technology
NanoString CodeSet design
Medulloblastoma subtyping: 8 cases
Anaplastic Medulloblastoma with MYCN amp (FISH)
G-banding -> tetraploid
G-banding -> no double minute chromosome visible
G-banding -> sequential FISH for MYCN
Whole Genome View Diploid baseline
Whole Genome View Tetraploid baseline correction
Chromosome 2 MYCN amplification
Chromosome 17 Likely isochromosome 17q
Medulloblastoma SNP array report
Pathology of neuroblastoma
Risk Groups (COG)
Neuroblastoma Testing Algorithm
Example 1 – (mostly) aneuploid tumor – good prognosis
Neuroblastoma SNP array report
Example 2 – MYCN amplification and Segmental losses & gains – poor prognosis
Chromosome 2 MYCN amplification
Example 3 – (mostly) segmental losses & gains – poor prognosis
Chromosome X 112kb Deletion of one copy of ATRX from exon 02 to exon 15
Pediatric low-grade gliomas - Distribution by location
Pilocytic astrocytomas frequently present with BRAF–KIAA1549 fusion
Low grade glioma – 7q34 duplication leading to BRAF-KIAA1549 fusion – FISH test
FISH reults
Posterior fossa tumour - Pilocytic Astrocytoma, WHO grade 1: Chromosome 7
sterior fossa tumour - Pilocytic Astrocytoma, WHO grade 1
Other applications for NanoString at SickKids
Nanostring Pediatric Low Grade Glioma Panel
Pediatric low grade gliomas: the KIAA1549-BRAF fusions
Low Grade Glioma Testing Algorithm
Acknowledgements
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