Routine RNA sequencing of formalin-fixed paraffin-embedded specimens in neuropathology diagnostics identifies diagnostically and therapeutically relevant gene fusions

TY - JOUR

T1 - Routine RNA sequencing of formalin-fixed paraffin-embedded specimens in neuropathology diagnostics identifies diagnostically and therapeutically relevant gene fusions

AU - Stichel, Damian

AU - Schrimpf, Daniel

AU - Casalini, Belén

AU - Meyer, Jochen

AU - Wefers, Annika K

AU - Sievers, Philipp

AU - Korshunov, Andrey

AU - Koelsche, Christian

AU - Reuss, David E

AU - Reinhardt, Annekathrin

AU - Ebrahimi, Azadeh

AU - Fernández-Klett, Francisco

AU - Kessler, Tobias

AU - Sturm, Dominik

AU - Ecker, Jonas

AU - Milde, Till

AU - Herold-Mende, Christel

AU - Witt, Olaf

AU - Pfister, Stefan M

AU - Wick, Wolfgang

AU - Jones, David T W

AU - von Deimling, Andreas

AU - Sahm, Felix

PY - 2019/11

Y1 - 2019/11

N2 - Molecular markers have become pivotal in brain tumor diagnostics. Mutational analyses by targeted next-generation sequencing of DNA and array-based DNA methylation assessment with copy number analyses are increasingly being used in routine diagnostics. However, the broad variety of gene fusions occurring in brain tumors is marginally covered by these technologies and often only assessed by targeted assays. Here, we assessed the feasibility and clinical value of investigating gene fusions in formalin-fixed paraffin-embedded (FFPE) tumor tissues by next-generation mRNA sequencing in a routine diagnostic setting. After establishment and optimization of a workflow applicable in a routine setting, prospective diagnostic application in a neuropathology department for 26 months yielded relevant fusions in 66 out of 101 (65%) analyzed cases. In 43 (43%) cases, the fusions were of decisive diagnostic relevance and in 40 (40%) cases the fusion genes rendered a druggable target. A major strength of this approach was its ability to detect fusions beyond the canonical alterations for a given entity, and the unbiased search for any fusion event in cases with uncertain diagnosis and, thus, uncertain spectrum of expected fusions. This included both rare variants of established fusions which had evaded prior targeted analyses as well as the detection of previously unreported fusion events. While the impact of fusion detection on diagnostics is highly relevant, it is especially the detection of "druggable" fusions which will most likely provide direct benefit to the patients. The wider application of this approach for unbiased fusion identification therefore promises to be a major advance in identifying alterations with immediate impact on patient care.

AB - Molecular markers have become pivotal in brain tumor diagnostics. Mutational analyses by targeted next-generation sequencing of DNA and array-based DNA methylation assessment with copy number analyses are increasingly being used in routine diagnostics. However, the broad variety of gene fusions occurring in brain tumors is marginally covered by these technologies and often only assessed by targeted assays. Here, we assessed the feasibility and clinical value of investigating gene fusions in formalin-fixed paraffin-embedded (FFPE) tumor tissues by next-generation mRNA sequencing in a routine diagnostic setting. After establishment and optimization of a workflow applicable in a routine setting, prospective diagnostic application in a neuropathology department for 26 months yielded relevant fusions in 66 out of 101 (65%) analyzed cases. In 43 (43%) cases, the fusions were of decisive diagnostic relevance and in 40 (40%) cases the fusion genes rendered a druggable target. A major strength of this approach was its ability to detect fusions beyond the canonical alterations for a given entity, and the unbiased search for any fusion event in cases with uncertain diagnosis and, thus, uncertain spectrum of expected fusions. This included both rare variants of established fusions which had evaded prior targeted analyses as well as the detection of previously unreported fusion events. While the impact of fusion detection on diagnostics is highly relevant, it is especially the detection of "druggable" fusions which will most likely provide direct benefit to the patients. The wider application of this approach for unbiased fusion identification therefore promises to be a major advance in identifying alterations with immediate impact on patient care.

KW - Base Sequence

KW - Brain Neoplasms/diagnosis

KW - DNA Mutational Analysis/methods

KW - Gene Fusion/genetics

KW - High-Throughput Nucleotide Sequencing/methods

KW - Humans

KW - Mutation/genetics

KW - Neuropathology/methods

KW - Paraffin Embedding/methods

KW - Sequence Analysis, RNA

U2 - 10.1007/s00401-019-02039-3

DO - 10.1007/s00401-019-02039-3

M3 - SCORING: Journal article

C2 - 31278449

VL - 138

SP - 827

EP - 835

JO - ACTA NEUROPATHOL

JF - ACTA NEUROPATHOL

SN - 0001-6322

IS - 5

ER -