Abyzov A, Urban AE, Snyder M, Gerstein M (2011) CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 21:974–984. https://doi.org/10.1101/gr.114876.110

Article  CAS  PubMed  PubMed Central  Google Scholar 

Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A et al (2012) methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol 13:R87. https://doi.org/10.1186/gb-2012-13-10-r87

Article  PubMed  PubMed Central  Google Scholar 

Burger L, Gaidatzis D, Schübeler D, Stadler MB (2013) Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res 41:e155–e155. https://doi.org/10.1093/nar/gkt599

Article  CAS  PubMed  PubMed Central  Google Scholar 

Choudhury A, Chen WC, Lucas C-HG, Bayley JC, Harmanci AS, Maas SLN et al (2022) Hypermitotic meningiomas harbor DNA methylation subgroups with distinct biological and clinical features. Neuro Oncol. https://doi.org/10.1093/neuonc/noac224

Article  PubMed  PubMed Central  Google Scholar 

Choudhury A, Magill ST, Eaton CD, Prager BC, Chen WC, Cady MA et al (2022) Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities. Nat Genet 54:649–659. https://doi.org/10.1038/s41588-022-01061-8

Article  CAS  PubMed  PubMed Central  Google Scholar 

Choudhury A, Raleigh DR (2020) Preclinical models of meningioma: cell culture and animal systems. Handb Clin Neurol 169:131–136. https://doi.org/10.1016/b978-0-12-804280-9.00008-1

Article  PubMed  Google Scholar 

Kim D, Paggi JM, Park C, Bennett C, Salzberg SL (2019) Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37:907–915. https://doi.org/10.1038/s41587-019-0201-4

Article  CAS  PubMed  PubMed Central  Google Scholar 

Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27:1571–1572. https://doi.org/10.1093/bioinformatics/btr167

Article  CAS  PubMed  PubMed Central  Google Scholar 

LeBlanc AK, Mazcko C, Brown DE, Koehler JW, Miller AD, Miller CR et al (2016) Creation of an NCI comparative brain tumor consortium: informing the translation of new knowledge from canine to human brain tumor patients. Neuro Oncol 18:1209–1218. https://doi.org/10.1093/neuonc/now051

Article  PubMed  PubMed Central  Google Scholar 

Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923–930. https://doi.org/10.1093/bioinformatics/btt656

Article  CAS  PubMed  Google Scholar 

Louis DN, Perry A, Wesseling P, Brat DJ, Cree IA, Figarella-Branger D et al (2021) The 2021 WHO classification of tumors of the central nervous system: a summary. Neuro Oncol 23:1231–1251. https://doi.org/10.1093/neuonc/noab106

Article  CAS  PubMed  PubMed Central  Google Scholar 

Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. https://doi.org/10.1186/s13059-014-0550-8

Article  CAS  PubMed  PubMed Central  Google Scholar 

Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetJ 17:10–12. https://doi.org/10.14806/ej.17.1.200

Article  Google Scholar 

Miller AD, Miller CR, Rossmeisl JH (2019) Canine primary intracranial cancer: a clinicopathologic and comparative review of glioma, meningioma, and choroid plexus tumors. Front Oncol 9:1151. https://doi.org/10.3389/fonc.2019.01151

Article  PubMed  PubMed Central  Google Scholar 

Nassiri F, Liu J, Patil V, Mamatjan Y, Wang JZ, Hugh-White R et al (2021) A clinically applicable integrative molecular classification of meningiomas. Nature 597:119–125. https://doi.org/10.1038/s41586-021-03850-3

Article  ADS  CAS  PubMed  Google Scholar 

Ostrom QT, Price M, Neff C, Cioffi G, Waite KA, Kruchko C et al (2023) CBTRUS statistical report: primary brain and other central nervous system tumors diagnosed in the United States in 2016–2020. Neuro Oncol 25:iv1–iv99. https://doi.org/10.1093/neuonc/noad149

Article  PubMed  Google Scholar 

Patel AJ, Wan Y-W, Al-Ouran R, Revelli J-P, Cardenas MF, Oneissi M et al (2019) Molecular profiling predicts meningioma recurrence and reveals loss of DREAM complex repression in aggressive tumors. Proc Natl Acad Sci USA 116:21715–21726. https://doi.org/10.1073/pnas.1912858116

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

Priester WA, McKay FW (1980) The occurrence of tumors in domestic animals. Natl Cancer Inst Monogr 1–210. https://pubmed.ncbi.nlm.nih.gov/7254313/

Rechache NS, Wang Y, Stevenson HS, Killian JK, Edelman DC, Merino M et al (2012) DNA methylation profiling identifies global methylation differences and markers of adrenocortical tumors. J Clin Endocrinol Metab 97:E1004–E1013. https://doi.org/10.1210/jc.2011-3298

Article  CAS  PubMed  PubMed Central  Google Scholar 

Song RB, Vite CH, Bradley CW, Cross JR (2013) Postmortem evaluation of 435 cases of intracranial neoplasia in dogs and relationship of neoplasm with breed, age, and body weight. J Vet Intern Med 27:1143–1152. https://doi.org/10.1111/jvim.12136

Article  CAS  PubMed  Google Scholar