Abstract 11: Advancing methylation profiling in neuropathology: Diagnosis and clinical management
Authors: Kannan Kasthuri S. , Tsirigos Aristotelis , Serrano Jonathan , Forrester Lynn Ann , Faustin Arline , Thomas Cheddhi , Capper David , Hovestadt Volker , Pfister Stefan M. , Jones David T. W , Sill Martin , Schrimpf Daniel , Deimling Andreas von , Heguy Adriana , Gardner Sharon L. , Allen Jeffrey , Hedvat Cyrus , Zagzag David , Snuderl Matija , Karajannis Matthias A. 
Published: May 2016

Abstract
Introduction: Although molecular profiling is increasingly being applied to improve subgroup classification and to provide novel prognostic and predictive biomarkers, clinical neuropathology practice is largely based on morphology and immunohistochemistry. Current molecular methods play only a small role in determining the diagnosis itself.
Methods: For molecular subclassification of tumors at NYU neuropathology and to improve diagnostic accuracy, we introduced genome-wide methylation profiling through Illumina Infinium HumanMethylation 450k array that can detect methylation marks from the DNA extracted from formalin-fixed paraffin embedded tissues. To this effort, an in-house pipeline was established in-house pipeline, which includes morphologic review, sample preparation, molecular profiling and bioinformatics analysis. We compared the methylation profiles to a reference cohort of 2150 cases from 77 tumor entities previously profiled and analyzed at German Cancer Research Center using a random forest algorithm and customized bioinformatics packages, which were shared between our institutions. Selected copy number variants (CNV) and mutations were confirmed by Fluorescence in situ Hybridization (FISH) or sequencing, and mutation specific immunohistochemistry, respectively.
Results: We profiled 60 difficult in-house or consult adult and pediatric brain tumors where diagnosis, grade and/or molecular subtype were not conclusive by morphology, immunohistochemistry or standard molecular studies alone. There was 100% concordance with concurrently performed molecular tests such as 1p/19q, EGFR/BRAF CNV, MGMT promoter methylation or IDH1 status testing when these tests were performed for clinical care. Methylation profiling provided additional, relevant information in 30 of 60 (50%) cases, leading to a change of diagnosis in 9 (15%), clarification of the diagnosis in 7 (12%) cases, and further molecular subgroup refinement in 14 (23%) of cases, helping to direct further molecular testing and clinical management.
Conclusion: The 450k methylation array platform represents a cost-efficient method to obtain molecular profiles of brain tumors to identify biologically relevant diagnostic subgroups, thereby improving diagnostic accuracy, and helping inform appropriate clinical management decisions.
Citation Format: Kasthuri S. Kannan, Aristotelis Tsirigos, Jonathan Serrano, Lynn Ann Forrester, Arline Faustin, Cheddhi Thomas, David Capper, Volker Hovestadt, Stefan M. Pfister, David T. W Jones, Martin Sill, Daniel Schrimpf, Andreas von Deimling, Adriana Heguy, Sharon L. Gardner, Jeffrey Allen, Cyrus Hedvat, David Zagzag, Matija Snuderl, Matthias A. Karajannis. Advancing methylation profiling in neuropathology: Diagnosis and clinical management. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 11.