Molecular profile and clinical features of patients with gliomas using a broad targeted next generation‑sequencing panel

Romanidou,Ourania; Romanidou,Ourania; Apostolou,Paraskevi; Apostolou,Paraskevi; Kouvelakis,Kyriakos; Kouvelakis,Kyriakos; Tsangaras,Kyriakos; Tsangaras,Kyriakos; Eliades,Alexia; Eliades,Alexia; Achilleos,Achilleas; Achilleos,Achilleas; Loizides,Charalambos; Loizides,Charalambos; Lemesios,Christos; Lemesios,Christos; Ioannides,Marios; Ioannides,Marios; Kypri,Elena; Kypri,Elena; Koumbaris,George; Koumbaris,George; Papadopoulou,Kyriaki; Papadopoulou,Kyriaki; Papathanasiou,Athanasios; Papathanasiou,Athanasios; Rigakos,Georgios; Rigakos,Georgios; Xanthakis,Ioannis; Xanthakis,Ioannis; Fostira,Florentia; Fostira,Florentia; Kotoula,Vassiliki; Kotoula,Vassiliki; Fountzilas,George; Fountzilas,George; Patsalis,Philippos C.; Patsalis,Philippos C.

doi:10.3892/ol.2022.13624

Molecular profile and clinical features of patients with gliomas using a broad targeted next generation‑sequencing panel

Authors:
- Ourania Romanidou
- Paraskevi Apostolou
- Kyriakos Kouvelakis
- Kyriakos Tsangaras
- Alexia Eliades
- Achilleas Achilleos
- Charalambos Loizides
- Christos Lemesios
- Marios Ioannides
- Elena Kypri
- George Koumbaris
- Kyriaki Papadopoulou
- Athanasios Papathanasiou
- Georgios Rigakos
- Ioannis Xanthakis
- Florentia Fostira
- Vassiliki Kotoula
- George Fountzilas
- Philippos C. Patsalis
View Affiliations

Affiliations: Department of Medicine, Medical Oncology Unit, Giannitsa General Hospital, 58100 Giannitsa, Greece, Molecular Diagnostics Laboratory, InRASTES, National Centre for Scientific Research Demokritos, 15341 Athens, Greece, Section of Biostatistics, Hellenic Cooperative Oncology Group, Data Office, 11526 Athens, Greece, NIPD Genetics Ltd., 2409 Nicosia, Republic of Cyprus, Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, 54006 Thessaloniki, Greece, Third Department of Medical Oncology, Hygeia Hospital, 15123 Athens, Greece, Oncology Department, European Interbalkan Medical Center, 55535 Thessaloniki, Greece, Department of Pathology, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki, 54006 Thessaloniki, Greece
Published online on: December 8, 2022 https://doi.org/10.3892/ol.2022.13624
Article Number: 38

Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )

Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )

Cited By (CrossRef): 0 citations Loading Articles...

Abstract

Gliomas are the most common malignant primary brain tumors characterized by poor prognosis. The genotyping of tumors using next generation sequencing (NGS) platforms enables the identification of genetic alterations that constitute diagnostic, prognostic and predictive biomarkers. The present study investigated the molecular profile of 32 tumor samples from 32 patients with high‑grade gliomas by implementing a broad 80‑gene targeted NGS panel while reporting their clinicopathological characteristics and outcomes. Subsequently, 14 of 32 tumor specimens were also genotyped using a 55‑gene NGS panel to validate the diagnostic accuracy and clinical utility of the extended panel. The median follow‑up was 19.2 months. In total, 129 genetic alterations including 33 structural variants were identified in 38 distinct genes. Among 96 variants (single nucleotide variants and insertions and deletions), 38 were pathogenic and 58 variants of unknown clinical significance. TP53 was the most frequently mutated gene, followed by PTEN and IDH1 genes. Glioma patients with IDH1 mutant tumors were younger and had significantly longer overall survival compared to patients with wild‑type IDH1 tumors. Similarly, tumors with TP53 mutations were more likely observed in younger patients with glioma. Subsequently, a comparison of mutational profiles of samples analyzed by both panels was also performed. Implementation of the comprehensive pan‑cancer and the MOL panels resulted in the identification of 37 and 15 variants, respectively. Of those, 13 were common. Comprehensive pan‑cancer panel identified 24 additional variants, 22 of which were located in regions that were not targeted by the MOL panel. By contrast, the MOL panel identified two additional variants. Overall, the present study demonstrated that using an extended tumor profile assay instead of a glioma‑specific tumor profile panel identified additional genetic changes that may be taken into consideration as potential therapeutic targets for glioma diagnosis and molecular classification.

View Figures

View References

1	Schwartzbaum JA, Fisher JL, Aldape KD and Wrensch M: Epidemiology and molecular pathology of glioma. Nat Clin Pract Neurol. 2:494–503. 15162006. View Article : Google Scholar : PubMed/NCBI
2	Stupp R, Brada M, van den Bent MJ, Tonn JC and Pentheroudakis G; ESMO Guidelines Working Group, : High-grade glioma: ESMO clinical practice guidelines for diagnosis, treatment and follow-up. Ann Oncol. 25 (Suppl 3):iii93–iii101. 2014. View Article : Google Scholar : PubMed/NCBI
3	Ostrom QT, Cioffi G, Gittleman H, Patil N, Waite K, Kruchko C and Barnholtz-Sloan JS: CBTRUS statistical report: Primary brain and other central nervous system tumors diagnosed in the United States in 2012–2016. Neuro Oncol. 21 (Suppl 5):v1–v100. 2019. View Article : Google Scholar : PubMed/NCBI
4	Wesseling P and Capper D: WHO 2016 classification of gliomas. Neuropathol Appl Neurobiol. 44:139–150. 2018. View Article : Google Scholar : PubMed/NCBI
5	Louis DN, Perry A, Reifenberger G, von Deimling A, Figarella-Branger D, Cavenee WK, Ohgaki H, Wiestler OD, Kleihues P and Ellison DW: The 2016 World Health Organization classification of tumors of the central nervous system: A summary. Acta Neuropathol. 131:803–820. 2016. View Article : Google Scholar : PubMed/NCBI
6	Śledzińska P, Bebyn MG, Furtak J, Kowalewski J and Lewandowska MA: Prognostic and predictive biomarkers in gliomas. Int J Mol Sci. 22:103732021. View Article : Google Scholar : PubMed/NCBI
7	Weller M and Reifenberger G: Beyond the World Health Organization classification of central nervous system tumors 2016: What are the new developments for gliomas from a clinician' perspective? Curr Opin Neurol. 33:701–706. 2020. View Article : Google Scholar : PubMed/NCBI
8	Kristensen BW, Priesterbach-Ackley LP, Petersen JK and Wesseling P: Molecular pathology of tumors of the central nervous system. Ann Oncol. 30:1265–1278. 2019. View Article : Google Scholar : PubMed/NCBI
9	Reinhardt A, Stichel D, Schrimpf D, Sahm F, Korshunov A, Reuss DE, Koelsche C, Huang K, Wefers AK, Hovestadt V, et al: Anaplastic astrocytoma with piloid features, a novel molecular class of IDH wildtype glioma with recurrent MAPK pathway, CDKN2A/B and ATRX alterations. Acta Neuropathol. 136:273–291. 2018. View Article : Google Scholar : PubMed/NCBI
10	Ostrom QT, Kinnersley B, Wrensch MR, Eckel-Passow JE, Armstrong G, Rice T, Chen Y, Wiencke JK, McCoy LS, Hansen HM, et al: Sex-specific glioma genome-wide association study identifies new risk locus at 3p21.31 in females, and finds sex-differences in risk at 8q24.21. Sci Rep. 8:73522018. View Article : Google Scholar : PubMed/NCBI
11	Ostrom QT, Cote DJ, Ascha M, Kruchko C and Barnholtz-Sloan JS: Adult glioma incidence and survival by race or ethnicity in the united states from 2000 to 2014. JAMA Oncol. 4:1254–1262. 2018. View Article : Google Scholar : PubMed/NCBI
12	Zacher A, Kaulich K, Stepanow S, Wolter M, Köhrer K, Felsberg J, Malzkorn B and Reifenberger G: Molecular diagnostics of gliomas using next generation sequencing of a glioma-tailored gene panel. Brain Pathol. 27:146–159. 2017. View Article : Google Scholar : PubMed/NCBI
13	Kim HS, Kwon MJ, Song JH, Kim ES, Kim HY and Min KW: Clinical implications of TERT promoter mutation on IDH mutation and MGMT promoter methylation in diffuse gliomas. Pathol Res Pract. 214:881–888. 2018. View Article : Google Scholar : PubMed/NCBI
14	Razis E, Kotoula V, Koliou GA, Papadopoulou K, Vrettou E, Giannoulatou E, Tikas I, Labropoulos SV, Rigakos G, Papaemmanoyil S, et al: Is there an independent role of TERT and NF1 in high grade gliomas? Transl Oncol. 13:346–354. 2020. View Article : Google Scholar : PubMed/NCBI
15	Li H: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv. 3:130339972013.
16	Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G and Durbin R; 1000 Genome Project Data Processing Subgroup, : The sequence alignment/map format and SAMtools. Bioinformatics. 25:2078–2079. 2009. View Article : Google Scholar : PubMed/NCBI
17	Li MM, Datto M, Duncavage EJ, Kulkarni S, Lindeman NI, Roy S, Tsimberidou AM, Vnencak-Jones CL, Wolff DJ, Younes A and Nikiforova MN: Standards and guidelines for the interpretation and reporting of sequence variants in cancer: A joint consensus recommendation of the association for molecular pathology, American society of clinical oncology, and college of American pathologists. J Mol Diagn. 19:4–23. 2017. View Article : Google Scholar : PubMed/NCBI
18	McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P and Cunningham F: The ensembl variant effect predictor. Genome Biol. 17:1222016. View Article : Google Scholar : PubMed/NCBI
19	Landrum MJ, Lee JM, Benson M, Brown GR, Chao C, Chitipiralla S, Gu B, Hart J, Hoffman D, Jang W, et al: ClinVar: Improving access to variant interpretations and supporting evidence. Nucleic Acids Res. 46(D1): D1062–D1067. 2018. View Article : Google Scholar : PubMed/NCBI
20	Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, Boutselakis H, Cole CG, Creatore C, Dawson E, et al: COSMIC: The catalogue of somatic mutations in cancer. Nucleic Acids Res. 47(D1): D941–D947. 2019. View Article : Google Scholar : PubMed/NCBI
21	Seshan VE and Olshen AB: DNAcopy: A package for analyzing DNA copy data. Bioconductor Vignette. 1–7. 2014.
22	Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, Källberg M, Cox AJ, Kruglyak S and Saunders CT: Manta: Rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 32:1220–1222. 2016. View Article : Google Scholar : PubMed/NCBI
23	Cameron DL, Schröder J, Penington JS, Do H, Molania R, Dobrovic A, Speed TP and Papenfuss AT: GRIDSS: Sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly. Genome Res. 27:2050–2060. 2017. View Article : Google Scholar : PubMed/NCBI
24	Layer RM, Chiang C, Quinlan AR and Hall IM: LUMPY: A probabilistic framework for structural variant discovery. Genome Biol. 15:R842014. View Article : Google Scholar : PubMed/NCBI
25	Grech N, Dalli T, Mizzi S, Meilak L, Calleja N and Zrinzo A: Rising incidence of glioblastoma multiforme in a well-defined population. Cureus. 12:e81952020.PubMed/NCBI
26	Nie Q, Hsiao MC, Chandok H, Rowe S, Prego M, Meyers B, Omerza G, Hesse A, Uvalic J, Soucy M, et al: Molecular profiling of CNS tumors for the treatment and management of disease. J Clin Neurosci. 71:311–315. 2020. View Article : Google Scholar : PubMed/NCBI
27	Ballester LY, Fuller GN, Powell SZ, Sulman EP, Patel KP, Luthra R and Routbort MJ: Retrospective analysis of molecular and immunohistochemical characterization of 381 primary brain tumors. J Neuropathol Exp Neurol. 76:179–188. 2017.PubMed/NCBI
28	Zeng C, Wang J, Li M, Wang H, Lou F, Cao S and Lu C: Comprehensive molecular characterization of Chinese patients with glioma by extensive next-generation sequencing panel analysis. Cancer Manag Res. 13:3573–3588. 2021. View Article : Google Scholar : PubMed/NCBI
29	Zheng S, Alfaro-Munoz K, Wei W, Wang X, Wang F, Eterovic AK, Shaw KRM, Meric-Bernstam F, Fuller GN, Chen K, et al: Prospective clinical sequencing of adult glioma. Mol Cancer Ther. 18:991–1000. 2019. View Article : Google Scholar : PubMed/NCBI
30	Gillet E, Alentorn A, Doukouré B, Mundwiller E, van Thuijl HF, Reijneveld JC, Medina JA, Liou A, Marie Y, Mokhtari K, et al: TP53 and p53 statuses and their clinical impact in diffuse low grade gliomas. J Neurooncol. 118:131–139. 2014.PubMed/NCBI
31	Pessôa IA, Amorim CK, Ferreira WAS, Sagica F, Brito JR, Othman M, Meyer B, Liehr T and de Oliveira EHC: Detection and correlation of single and concomitant TP53, PTEN, and CDKN2A alterations in gliomas. Int J Mol Sci. 20:26582019. View Article : Google Scholar : PubMed/NCBI
32	Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu IM, Gallia GL, et al: An integrated genomic analysis of human glioblastoma multiforme. Science. 321:1807–1812. 2008. View Article : Google Scholar : PubMed/NCBI
33	Park C, Kim TM, Bae JM, Yun H, Kim JW, Choi SH, Lee ST, Lee JH, Park SH and Park CK: Clinical and genomic characteristics of adult diffuse midline glioma. Cancer Res Treat. 53:389–398. 2021. View Article : Google Scholar : PubMed/NCBI
34	Reis GF, Pekmezci M, Hansen HM, Rice T, Marshall RE, Molinaro AM, Phillips JJ, Vogel H, Wiencke JK, Wrensch MR, et al: CDKN2A loss is associated with shortened overall survival in lower-grade (World Health Organization grades II–III) astrocytomas. J Neuropathol Exp Neurol. 74:442–452. 2015. View Article : Google Scholar : PubMed/NCBI
35	Loriot Y, Schuler MH, Iyer G, Witt O, Doi T, Qin S, Tabernero J, Reardon DA, Massard C, Palmer D, et al: Tumor agnostic efficacy and safety of erdafitinib in patients (pts) with advanced solid tumors with prespecified fibroblast growth factor receptor alterations (FGFRalt) in RAGNAR: Interim analysis (IA) results. J Clin Oncol. 40 (16 Suppl):S30072022. View Article : Google Scholar
36	Costa R, Carneiro BA, Taxter T, Tavora FA, Kalyan A, Pai SA, Chae YK and Giles FJ: FGFR3-TACC3 fusion in solid tumors: Mini review. Oncotarget. 7:55924–55938. 2016. View Article : Google Scholar : PubMed/NCBI
37	Yang K, Wu Z, Zhang H, Zhang N, Wu W, Wang Z, Dai Z, Zhang X, Zhang L, Peng Y, et al: Glioma targeted therapy: Insight into future of molecular approaches. Mol Cancer. 21:392022. View Article : Google Scholar : PubMed/NCBI
38	Higa N, Akahane T, Hamada T, Yonezawa H, Uchida H, Makino R, Watanabe S, Takajo T, Yokoyama S, Kirishima M, et al: Detection of EGFR mutation distribution and transcriptional variants in IDH-wildtype high-grade gliomas using a next-generation sequencing oncopanel. Res Sq. 1–11. 2021.
39	Wang Y, Zhang J, Zhang P, Zhao Z, Huang Q, Yun D, Chen J, Chen H, Wang C and Lu D: LZTR1 inactivation promotes MAPK/ERK pathway activation in glioblastoma by stabilizing oncoprotein RIT1. bioRxiv. 2020.
40	Frattini V, Trifonov V, Chan JM, Castano A, Lia M, Abate F, Keir ST, Ji AX, Zoppoli P, Niola F, et al: The integrated landscape of driver genomic alterations in glioblastoma. Nat Genet. 45:1141–1149. 2013. View Article : Google Scholar : PubMed/NCBI
41	Comba A, Faisal SM, Varela ML, Hollon T, Al-Holou WN, Umemura Y, Nunez FJ, Motsch S, Castro MG and Lowenstein PR: Uncovering spatiotemporal heterogeneity of high-grade gliomas: From disease biology to therapeutic implications. Front Oncol. 11:7037642021. View Article : Google Scholar : PubMed/NCBI
42	Sottoriva A, Spiteri I, Piccirillo SG, Touloumis A, Collins VP, Marioni JC, Curtis C, Watts C and Tavaré S: Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics. Proc Natl Acad Sci USA. 110:4009–4014. 2013. View Article : Google Scholar : PubMed/NCBI
43	Tirrò E, Massimino M, Broggi G, Romano C, Minasi S, Gianno F, Antonelli M, Motta G, Certo F, Altieri R, et al: A custom DNA-based NGS panel for the molecular characterization of patients with diffuse gliomas: Diagnostic and therapeutic applications. Front Oncol. 12:8610782022. View Article : Google Scholar : PubMed/NCBI
44	Zou P, Xu H, Chen P, Yan Q, Zhao L, Zhao P and Gu A: IDH1/IDH2 mutations define the prognosis and molecular profiles of patients with gliomas: A meta-analysis. PLoS One. 8:e687822013. View Article : Google Scholar : PubMed/NCBI
45	Yan H, Parsons DW, Jin G, McLendon R, Rasheed BA, Yuan W, Kos I, Batinic-Haberle I, Jones S, Riggins GJ, et al: IDH1 and IDH2 mutations in gliomas. N Engl J Med. 360:765–773. 2009. View Article : Google Scholar : PubMed/NCBI
46	Sun H, Yin L, Li S, Han S, Song G, Liu N and Yan C: Prognostic significance of IDH mutation in adult low-grade gliomas: A meta-analysis. J Neurooncol. 113:277–284. 2013. View Article : Google Scholar : PubMed/NCBI
47	Park Y, Park J, Ahn JW, Sim JM, Kang SJ, Kim S, Hwang SJ, Han SH, Sung KS and Lim J: Transcriptomic landscape of lower grade glioma based on age-related non-silent somatic mutations. Curr Oncol. 28:2281–2295. 2021. View Article : Google Scholar : PubMed/NCBI
48	Ichimura K, Pearson DM, Kocialkowski S, Bäcklund LM, Chan R, Jones DT and Collins VP: IDH1 mutations are present in the majority of common adult gliomas but rare in primary glioblastomas. Neuro Oncol. 11:341–347. 2009. View Article : Google Scholar : PubMed/NCBI