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PRODID:talks.ox.ac.uk
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SUMMARY:Routine molecular subgrouping of medulloblastoma: Bridging the div
 ide between research and the clinic using low-cost DNA methylomics - Dr Ed
  Schwalbe (Newcastle Cancer Centre)
DTSTART;VALUE=DATE-TIME:20150610T123000
DTEND;VALUE=DATE-TIME:20150610T133000
UID:https://talks.ox.ac.uk/talks/id/26b57b8a-97fd-4403-9f45-b33da0567c41/
DESCRIPTION:Background: DNA-methylation patterns allow the subclassificati
 on of medulloblastoma\, the most common childhood malignant brain tumour\,
  into four molecular subgroups (WNT\, SHH\, MBGrp3 and MBGrp4).  These sub
 groups have distinct molecular and clinico-pathological features\, and the
 ir distinction is now informing future treatments and risk-stratification.
  Whilst microarrays to assign subgroup are suitable for research purposes\
 , they are limited by expense\, platform-specificity\, sample quality requ
 irements and practicality. Here\, we aimed to develop a low-cost\, array-i
 ndependent\, robust subgrouping assay suitable for routine quality-control
 led subclassification\, including scant and poor-quality samples.  \nMetho
 ds:\nA minimal\, multiply-redundant\, 17-locus methylation signature was d
 erived to assign subgroup\, using Illumina 450k DNA-methylation array data
  and subgroup calls from 253 medulloblastomas. A cross-validated machine-l
 earning classifier was developed to assign subgroup using these loci. We n
 ext investigated whether bisulfite treatment of DNA could induce methylati
 on-dependent SNPs suitable for multiplexed interrogation of methylation st
 atus\, using an adaptation of Sequenom's iPlex assay. Multiplexed primer-m
 ixes were designed and quantitation validated using molar-ratios of bisulf
 ite-treated methylated:unmethylated DNA. Subsequently\, the assay was run 
 on 101 DNA extracts from fresh-frozen\, FFPE and cytospin (<30\,000 nuclei
 ) tumour material\, representing all subgroups. Subgroup assignments by Se
 quenom assay were compared to gold standard 450k array calls.\nResults:\nV
 alidation using molar-ratios of methylated:unmethylated DNA demonstrated c
 lose concordance between methylation-ratios and Sequenom methylation estim
 ates at all loci. Subsequently\, 95/103 (92%) medulloblastomas tested were
  assigned with high confidence to the same subgroup by both Sequenom and 4
 50k assays. \nConclusions:\nMedulloblastomas can be routinely subgrouped u
 sing minimal DNA-methylation signatures. The assay is suitable for reliabl
 e\, robust subgroup assignation from poor-quality\, degraded samples using
  100ng of DNA. The assay's low-cost\, rapidity (3 days from extraction to 
 result) and application to single samples demonstrate its potential for ro
 utine use. This first demonstration of multiplexed\, methylation-based Seq
 uenom subtyping holds rich promise for future molecular subclassification 
 and prognostication across diverse tumour types.\n\nSchwalbe\, E.C.1\, Hic
 ks\, D. 1 \, Rafiee\, G. 1\,Gohlke\, H. 2\, Enshaei\, A. 1\, Potluri\, S. 
 1\, Matthiesen\, J. 1\, Mather\, M. 1\, Chaston\, R.3\, Crosier\, S. 1\, S
 mith\, A.J. 1\, Williamson\, D. 1\, Bailey\, S. 1\, Clifford\, S.C. 1\n\n1
 Northern Institute for Cancer Research\, Newcastle University\, Newcastle 
 upon Tyne\, U.K.\n2Agena BioSciences\, Hamburg\, Germany\n3NewGene\, Newca
 stle upon Tyne\, U.K.\nSpeakers:\nDr Ed Schwalbe (Newcastle Cancer Centre)
LOCATION:Wellcome Trust Centre for Human Genetics (Room B)\, Headington OX
 3 7BN
TZID:Europe/London
URL:https://talks.ox.ac.uk/talks/id/26b57b8a-97fd-4403-9f45-b33da0567c41/
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DESCRIPTION:Talk:Routine molecular subgrouping of medulloblastoma: Bridgin
 g the divide between research and the clinic using low-cost DNA methylomic
 s - Dr Ed Schwalbe (Newcastle Cancer Centre)
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