Clinical impact of targeted amplicon sequencing for meningioma as a practical clinical-sequencing system.
Recent genetic analyses using next-generation sequencers have revealed numerous genetic alterations in various tumors including meningioma, which is the most common primary brain tumor. However, their use as routine laboratory examinations in clinical applications for tumor genotyping is not cost effective. To establish a clinical sequencing system for meningioma and investigate the clinical significance of genotype, we retrospectively performed targeted amplicon sequencing on 103 meningiomas and evaluated the association with clinicopathological features. We designed amplicon-sequencing panels targeting eight genes including NF2 (neurofibromin 2), TRAF7, KLF4, AKT1, and SMO. Libraries prepared with genomic DNA extracted from PAXgene-fixed paraffin-embedded tissues of 103 meningioma specimens were sequenced using the Illumina MiSeq. NF2 loss in some cases was also confirmed by interphase-fluorescent in situ hybridization. We identified NF2 loss and/or at least one mutation in NF2, TRAF7, KLF4, AKT1, and SMO in 81 out of 103 cases (79%) by targeted amplicon sequencing. On the basis of genetic status, we categorized meningiomas into three genotype groups: NF2 type, TRAKLS type harboring mutation in TRAF7, AKT1, KLF4, and/or SMO, and 'not otherwise classified' type. Genotype significantly correlated with tumor volume, tumor location, and magnetic resonance imaging findings such as adjacent bone change and heterogeneous gadolinium enhancement, as well as histopathological subtypes. In addition, multivariate analysis revealed that genotype was independently associated with risk of recurrence. In conclusion, we established a rapid clinical sequencing system that enables final confirmation of meningioma genotype within 7 days turnaround time. Our method will bring multiple benefits to neuropathologists and neurosurgeons for accurate diagnosis and appropriate postoperative management.
Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan.
Sayaka
S
Yuzawa
Department of Translational Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan.|Translational Research Laboratory, Hokkaido University Hospital, Clinical Research and Medical Innovation Center, Sapporo, Japan.
Hiroshi
H
Nishihara
Department of Neurosurgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan.
Shigeru
0000-0003-3710-5888
S
Yamaguchi
Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan.
Hiromi
H
Mohri
Department of Translational Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan.
Lei
L
Wang
Department of Translational Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan.|Translational Research Laboratory, Hokkaido University Hospital, Clinical Research and Medical Innovation Center, Sapporo, Japan.
Taichi
T
Kimura
Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan.
Masumi
M
Tsuda
Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan.
Mishie
M
Tanino
Department of Neurosurgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan.
Hiroyuki
H
Kobayashi
Department of Neurosurgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan.
Shunsuke
S
Terasaka
Translational Research Laboratory, Hokkaido University Hospital, Clinical Research and Medical Innovation Center, Sapporo, Japan.|Department of Neurosurgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan.
Kiyohiro
K
Houkin
Translational Research Laboratory, Hokkaido University Hospital, Clinical Research and Medical Innovation Center, Sapporo, Japan.
Norihiro
N
Sato
Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan.|Department of Translational Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan.
Shinya
S
Tanaka
D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D005260:Female; D023281:Genomics; D005838:Genotype; D006801:Humans; D000090062:Kruppel-Like Factor 4; D051741:Kruppel-Like Transcription Factors / Q000235:genetics; D008297:Male; D008577:Meningeal Neoplasms / Q000235:genetics* / Q000473:pathology; D008579:Meningioma / Q000235:genetics* / Q000473:pathology; D008875:Middle Aged; D009154:Mutation; D025581:Neurofibromin 2 / Q000235:genetics; D051057:Proto-Oncogene Proteins c-akt / Q000235:genetics; D000072086:Smoothened Receptor / Q000235:genetics; D047988:Tumor Necrosis Factor Receptor-Associated Peptides and Proteins / Q000235:genetics; D055815:Young Adult
C000715467:KLF4 protein, human; D000090062:Kruppel-Like Factor 4; D051741:Kruppel-Like Transcription Factors; D025581:Neurofibromin 2; C491023:SMO protein, human; D000072086:Smoothened Receptor; C486460:TRAF7 protein, human; D047988:Tumor Necrosis Factor Receptor-Associated Peptides and Proteins; C494918:AKT1 protein, human; D051057:Proto-Oncogene Proteins c-akt