ATRT-27. COST-EFFECTIVE ASSAYS TO SUBGROUP ATRT IN THE DAILY ROUTINE

Abstract

Three atypical teratoid rhabdoid tumors (ATRT) molecular subgroups with different bio-clinical characteristics have been reported (TYR, SHH and MYC). Molecular subgrouping relies on either methylation profiling (reference methods), or expression profiling. However, the cost-effectiveness of such pangenomic screening is questionable. This work aims to study the reliability of alternative techniques for subgroup classification in the daily routine. Illumina EPIC-arrays were performed on 46 samples. Among those cases, expression profiling were analysed by RNAseq (n=30). We designed a 26-gene panel to assess expression profiling using the Nanostring technology; this was applied to 35 tumors. Immunohistochemistry (IHC) was used for 20 samples; it relied on the expression of MITF, TYR, OTX2 and MYC. We first assessed the concordance between DNA methylation and RNAseq based profilings; then, between RNAseq and Nanostring and, finally, between methylation profiling and Nanostring or IHC, the two rapidest and cheapest tools. The concordance between the two expression-based profiling was 19/21. EPIC-arrays and RNAseq or Nanostring were concordant in 26/30 and 30/35 samples, respectively. The concordance was perfect for methylation-defined MYC subtype. Finally, 17/20 tumor samples were classified in the same subgroup by EPIC-arrays and IHC; the 3/20 misclassified tumors were SHH by methylation but consistently MYC by IHC, Nanostring and RNAseq. There was 90–100% of concordance for TYR subgroup (all techniques). We have designed a gene panel-based expression signature that shows promising concordance with RNAseq and methylation profiling. Nanostring assay and IHC well predict ATRT subgroup classification for MYC and TYR subclass, but less so for methylation-defined SHH ones.