Aoyagi Y, Kano Y, Tohyama K et al (2022) Clinical utility of comprehensive genomic profiling in Japan: result of PROFILE-F study. PLoS ONE 17(3):e0266112
Article CAS PubMed PubMed Central Google Scholar
Appay R, Dehais C, Maurage CA et al (2019) CDKN2A homozygous deletion is a strong adverse prognosis factor in diffuse malignant IDH-mutant gliomas. Neuro Oncol 21(12):1519–1528
CAS PubMed PubMed Central Google Scholar
Bady P, Sciuscio D, Diserens A-C et al (2012) MGMT methylation analysis of glioblastoma on the Infinium methylation BeadChip identifies two distinct CpG regions associated with gene silencing and outcome, yielding a prediction model for comparisons across datasets, tumor grades, and CIMP-status. Acta Neuropathol 124(4):547–560
Article CAS PubMed PubMed Central Google Scholar
Ballester LY, Fuller GN, Powell SZ et al (2017) Retrospective analysis of molecular and immunohistochemical characterization of 381 primary brain tumors. J Neuropathol Exp Neurol 76(3):179–188
Bell EH, Zhang P, Shaw EG et al (2020) Comprehensive genomic analysis in NRG Oncology/RTOG 9802: a Phase III trial of radiation versus radiation plus procarbazine, lomustine (CCNU), and vincristine in high-risk low-grade glioma. J Clin Oncol 38(29):3407–3417
Article CAS PubMed PubMed Central Google Scholar
Beroukhim R, Mermel CH, Porter D et al (2010) The landscape of somatic copy-number alteration across human cancers. Nature 463(7283):899–905
Article CAS PubMed PubMed Central Google Scholar
Brennan CW, Verhaak RG, McKenna A et al (2013) The somatic genomic landscape of glioblastoma. Cell 155(2):462–477
Article CAS PubMed PubMed Central Google Scholar
Cancer Genome Atlas Research Network, Brat DJ, Verhaak RG et al (2015) Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas. N Engl J Med 372(26):2481–2498
Christians A, Hartmann C, Benner A et al (2012) Prognostic value of three different methods of MGMT promoter methylation analysis in a prospective trial on newly diagnosed glioblastoma. PLoS ONE 7(3):e33449
Article CAS PubMed PubMed Central Google Scholar
Cibulskis K, Lawrence MS, Carter SL et al (2013) Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 31(3):213–219
Article CAS PubMed PubMed Central Google Scholar
Clarke M, Mackay A, Ismer B et al (2020) Infant high-grade gliomas comprise multiple subgroups characterized by novel targetable gene fusions and favorable outcomes. Cancer Discov 10(7):942–963
Article CAS PubMed PubMed Central Google Scholar
DeSisto J, Lucas JT Jr, Xu K et al (2021) Comprehensive molecular characterization of pediatric radiation-induced high-grade glioma. Nat Commun 12(1):5531
Article CAS PubMed PubMed Central Google Scholar
Do H, Dobrovic A (2015) Sequence artifacts in DNA from formalin-fixed tissues: causes and strategies for minimization. Clin Chem 61(1):64–71
Article CAS PubMed Google Scholar
Dobin A, Davis CA, Schlesinger F et al (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15–21
Article CAS PubMed Google Scholar
Ellison DW, Aldape KD, Capper D et al (2020) cIMPACT-NOW update 7: advancing the molecular classification of ependymal tumors. Brain Pathol 30(5):863–866
Article PubMed PubMed Central Google Scholar
Esteller M, Hamilton SR, Burger PC et al (1999) Inactivation of the DNA repair gene O6-methylguanine-DNA methyltransferase by promoter hypermethylation is a common event in primary human neoplasia. Cancer Res 59(4):793–797
Frattini V, Trifonov V, Chan JM et al (2013) The integrated landscape of driver genomic alterations in glioblastoma. Nat Genet 45(10):1141–1149
Article CAS PubMed PubMed Central Google Scholar
Guerreiro Stucklin AS, Ryall S, Fukuoka K et al (2019) Alterations in ALK/ROS1/NTRK/MET drive a group of infantile hemispheric gliomas. Nat Commun 10(1):4343
Article PubMed PubMed Central Google Scholar
Guo Q, Lakatos E, Bakir IA et al (2022) The mutational signatures of formalin fixation on the human genome. Nat Commun 13(1):4487
Article CAS PubMed PubMed Central Google Scholar
Hatanaka Y, Kuwata T, Morii E et al (2021) The Japanese Society of Pathology Practical Guidelines on the handling of pathological tissue samples for cancer genomic medicine. Pathol Int 71(11):725–740
Article PubMed PubMed Central Google Scholar
Hegi ME, Liu L, Herman JG et al (2008) Correlation of O6-methylguanine methyltransferase (MGMT) promoter methylation with clinical outcomes in glioblastoma and clinical strategies to modulate MGMT activity. J Clin Oncol 26(25):4189–4199
Article CAS PubMed Google Scholar
Higa N, Akahane T, Yokoyama S et al (2020) A tailored next-generation sequencing panel identified distinct subtypes of wildtype IDH and TERT promoter glioblastomas. Cancer Sci 111(10):3902–3911
Article CAS PubMed PubMed Central Google Scholar
Ji MS, Eldred BSC, Liu R et al (2020) Targeted next-generation sequencing of 565 neuro-oncology patients at UCLA: a single-institution experience. Neurooncol Adv 2(1):vdaa009
PubMed PubMed Central Google Scholar
Kohno T, Kato M, Kohsaka S et al (2022) C-CAT: the national datacenter for cancer genomic medicine in Japan. Cancer Discov 12(11):2509–2515
Article PubMed PubMed Central Google Scholar
Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27(11):1571–1572
Article CAS PubMed PubMed Central Google Scholar
Li BK, Vasiljevic A, Dufour C et al (2020) Pineoblastoma segregates into molecular sub-groups with distinct clinico-pathologic features: a Rare Brain Tumor Consortium registry study. Acta Neuropathol 139(2):223–241
Article CAS PubMed Google Scholar
Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26(5):589–595
Article PubMed PubMed Central Google Scholar
Lopez GY, Van Ziffle J, Onodera C et al (2019) The genetic landscape of gliomas arising after therapeutic radiation. Acta Neuropathol 137(1):139–150
Article CAS PubMed Google Scholar
Lorenz J, Rothhammer-Hampl T, Zoubaa S et al (2020) A comprehensive DNA panel next generation sequencing approach supporting diagnostics and therapy prediction in neurooncology. Acta Neuropathol Commun 8(1):124
Article CAS PubMed PubMed Central Google Scholar
Louis DN, Perry A, Wesseling P et al (2021) The 2021 WHO classification of tumors of the central nervous system: a summary. Neuro Oncol 23(8):1231–1251
Article CAS PubMed PubMed Central Google Scholar
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. E
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