EGAGenomicsMultiomicsAhmed Idbaihhttps://ega-archive.org/dacs/EGAC00001000513EGAEGA DAC EGAC00001000513EGAahmed.idbaih@aphp.frMolecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defined histologically. For central nervous system tumors, the current World Health Organization classification explicitly demands molecular testing, e.g., for 1p/19q-codeletion or IDH mutations, to make an integrated histomolecular diagnosis. However, a plethora of sophisticated technologies is currently needed to assess different genomic and epigenomic alterations and turnaround times are in the range of weeks, which makes standardized and widespread implementation difficult and hinders timely decision making. Here, we explored the potential of a pocket-size nanopore sequencing device for multimodal and rapid molecular diagnostics of cancer. Low-pass whole genome sequencing was used to simultaneously generate copy number (CN) and methylation profiles from native tumor DNA in the same sequencing run. Single nucleotide variants in IDH1, IDH2, TP53, H3F3A, and the TERT promoter region were identified using deep amplicon sequencing. Nanopore sequencing yielded ~0.1X genome coverage within 6 h and resulting CN and epigenetic profiles correlated well with matched microarray data. Diagnostically relevant alterations, such as 1p/19q codeletion, and focal amplifications could be recapitulated. Using ad hoc random forests, we could perform supervised pan-cancer classification to distinguish gliomas, medulloblastomas, and brain metastases of different primary sites. Single nucleotide variants in IDH1, IDH2, and H3F3A were identified using deep amplicon sequencing within minutes of sequencing. Detection of TP53 and TERT promoter mutations shows that sequencing of entire genes and GC-rich regions is feasible. Nanopore sequencing allows same-day detection of structural variants, point mutations, and methylation profiling using a single device with negligible capital cost. It outperforms hybridization-based and current sequencing technologies with respect to time to diagnosis and required laboratory equipment and expertise, aiming to make precision medicine possible for every cancer patient, even in resource-restricted settings.<h4>Background</h4>Glioblastoma (GBM) is the deadliest primary brain cancer in adults. Emerging innovative therapies hold promise for personalized cancer treatment. Improving therapeutic options depends on research relying on relevant preclinical models. In this line we have established in the setting of the GlioTex project (GBM and Experimental Therapeutics) a GBM patient-derived cell line (GBM-PDCL) library. A multi-omic approach was used to determine the molecular landscape of PDCL and the extent to which they represent GBM tumors.<h4>Methods</h4>Single nucleotide polymorphism array, expression arrays, exome sequencing, and RNA sequencing were used to measure and compare the molecular landscapes of 20 samples representing 10 human GBM tumors and paired GBM-PDCLs.<h4>Results</h4>Copy number variations were similar for a median of 85% of the genome and for 59% of the major focal events. Somatic point mutations were similar in a median of 41%. Mutations in GBM driver and "druggable" genes were maintained in 67% of events. Mutations that were not conserved in the PDCL were mainly low allelic fraction and/or non-driver mutations. Based on RNA expression profiling, PDCLs cluster closely to their parental tumor with overexpression of pathways associated with cancer progression in PDCL.<h4>Conclusions</h4>Overall, PDCLs recapitulate pivotal molecular alterations of paired-parental tumors supporting their use as a preclinical model of GBM. However, some driver aberrations are lost or gained in the passage from tumor to PDCL. Our results support using PDCL as a relevant preclinical model of GBM. Further investigations of changes between PDCLs and their parental tumor may provide insights into GBM biology.Multi-omics analysis of primary glioblastoma cell lines shows recapitulation of pivotal molecular features of parental tumors.Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing.Euskirchen Philipp P, Bielle Franck F, Labreche Karim K, Kloosterman Wigard P WP, Rosenberg Shai S, Daniau Mailys M, Schmitt Charlotte C, Masliah-Planchon Julien J, Bourdeaut Franck F, Dehais Caroline C, Marie Yannick Y, Delattre Jean-Yves JY, Idbaih Ahmed ARosenberg Shai S, Verreault Maïté M, Schmitt Charlotte C, Guegan Justine J, Guehennec Jeremy J, Levasseur Camille C, Marie Yannick Y, Bielle Franck F, Mokhtari Karima K, Hoang-Xuan Khê K, Ligon Keith K, Sanson Marc M, Delattre Jean-Yves JY, Idbaih Ahmed APanomics, Multi Omics, Integrative-Omics, Malignant Neoplasm, determination, Malignancy, Feature, Neoplasms, Benign Neoplasm, Integrative, Benign Neoplasms, Omics, Cancers, Tumor, Integrative Omics, Features, Malignant, Multi-Omics, Neoplasias, Characteristic, Benign, chemical analysis, Multi-Omic, Neoplasm, Pan Omics, Pan-Omics, Malignancies, assay, Characteristics, Neoplasia, Cancer, Tumors, Malignant Neoplasms.embryoblast, ICM, early embryoblast, embryoblastus, intermediate cell mass of Oellacher., posterior intermediate cell mass, pluriblastus senior, pluriblast, massa cellularis internaisocitrate dehydrogenase, l(4)13, Materials, Laboratory, cerebellar medulloblastoma, desmoplastic, Tumor, Diagnosis, Cost-Minimization, Long Term, hTRT, LEF-1, Mutations, Dmel_CG32005, Personal, devices, hierarchy, systematics, bbl, LEF1/TCF, Circumscribed Arachnoidal, symptoms, Medulloblastoma, Analysis, Credit Assignment, Cost Comparison, "CNS neoplasm" EXACT [CSP2005:2012-5421], infratentorial primitive neuroectodermal tumour, Id-1, PICD, treatment, Cytosolic NADP-isocitrate dehydrogenase, thymus nucleic acid, BCC7, Analyses, Molecular, Idpc, D2HGA2, Comparison, Adult Medulloblastomas, Melanocytic Medulloblastomas, suprasegmental levels of nervous system, IDPm, cTCF, D17Mit170, Epigenomic, Primary Central Nervous System Neoplasm, Cost Analysis, geographical area, IDPC, Medicine, Nucleotide, IDPM, Pan, PAN, Diagnose, Tumors, Forested Area, Diagnostic Molecular Pathologies, screening, suprasegmental structures, Assignments, Devices, Systematics, Longterm Effect, Molecular Diagnostic, l(3)L3852, Tl3, Tl2, Diagnoses, Benign, Postmortem, Central Nervous System Tumor, Pathology, Area, bfy, desoxyribose nucleic acid, finances, nucleotides, Idh-2, Idh-1, oligonucleotide random primer, Nanopore Sequencings, CT22171, instrument, TCS1, F24J5.12, Classical Polyarteritis Nodosa, Instruments and Apparatus, Panarteritis Nodosa, signs, DTCF, DTcf, salaries, Benign Neoplasms, Malignant Neoplasms, F24J5_12, 1.1.1.42, Material, DmelCG6439, Theranostics, ds DNA, bhy, DNA, financial management, Epigenetics, other neoplasm, dTCF, dTcf, Cost Analyses, CG34403, localised, Respect, DNS, (Deoxyribonucleotide)n, Effects, region or site annotation, Neoplasms, Periarteritis Nodosa, Arachnoidal Cerebellar Sarcoma, Assignment, Diagnostic Molecular Pathology, number, Prognostic Factors, Forested Areas, LFS1, h3f3a, Deoxyribonucleic Acid, Screening, central nervous system tumour, Classic Polyarteritis Nodosa, Precision, Antemortem, Molecular Pathology, TP2, Medical, Organization, positional, Complete, Whole Genome, Individualized, CNS, Diagnostic, Longterm, Cost Measures, Complete Genome Sequencing, Double Stranded, central nervous system tumors, Deoxyribonucleic acid, Diagnoses and Examinations, Long-Term, Supplies, Sequencing, Neoplasias, malignant tumor of CNS, IDH-NADP, Whole, (Deoxyribonucleotide)m, Predictive, Methylations, Childhood Medulloblastomas, Cancer, Antemortem Diagnoses, Inventories, fees, Idh-NADP, findings, Malignant Neoplasm, cou, MDB, Predictive Medicine, ICD-M, DNAn+1, Point Mutations, Factor, Primary, TRT, World Health, Personalized, medulloblastoma with extensive nodularity, encephalon, Melanocytic, medulloblastoma, Lr, MT, equipment, Long Term Effects, Neoplasm, Tcf/LEF, Mutation, INSDC_feature:regulatory, Costs and Cost Analyses, "neoplasm of central nervous system (disorder)" EXACT [SNOMEDCT_2005_07_31:126951006], periarteritis, Costs, primary cancer, Cost-Minimization Analysis, Theranostic, Cancers, Childhood, Adult Medulloblastoma, malignant tumor, primary structure of sequence macromolecule, CG32005, Longterm Effects, Forestlands, infratentorial primitive neuroectodermal tumor, P-Health, Point, Lef, Central Nervous System Tumors, Bra, Desoxyribonukleinsaeure, Central Nervous System, Cost Measure, Forest, Neoplasia, "central nervous system tumors" EXACT [NCI2004_11_17:C9293], Melanocytic Medulloblastoma, apparatus, Antemortem Diagnosis, Forestland, Polyarteritis Nodosa, Medical Devices, Individualized Medicine, FBgn0038922, central nervous system tumor, Molecular Diagnostics, mNADP-IDH, DmelCG34403, Measure, Molecular Pathologies, neoplasm of central nervous system, IA5, Tp53, Classifications, hierarchies, CPNET, AI314845, hEST2, DKCB4, Forested, Medullomyoblastomas, synganglion, Effect, Desmoplastic Medulloblastomas, Inventory, Medulloblastomas, TCF/LEF, me75, appliances, Prognoses, DKCA2, Cost-Minimization Analyses, Woodland, Adult, T1, NADP(+)-specific ICDH, H3.3A, Sarcoma, malignant neoplasm, Pathologies, disease management, Therapies, Malignancies, Double-Stranded DNA, CNS Neoplasms, deoxyribonucleic acids, Comparisons, DNAn, Affordabilities, polyarteritis, Long-Term Effects, TR, Therapy, localized primitive neuroectodermal tumor, IDH, Idh, Genome Sequencing, IDP, Double-Stranded, CNS PNET, Nanopore, LEF/TCF, CNS Neoplasm, IDCD, Dm Pan, (Deoxyribonucleotide)n+m, Taxonomies, Screenings, Complete Genome, Personalized Medicine, idh, PERIANTHIA, Examinations and Diagnoses, Areas, Supplies and Equipment, Genetic Materials, laboratory, Postmortem Diagnosis, Cerebellar, Genetic Material, Desmoplastic Medulloblastoma, Diagnoses and Examination, Postmortem Diagnoses, Diagnostics, Factors, positional polypeptide feature, Epigenetic, Circumscribed, Prognostic, Encephalon, Diagnostic Molecular, Dignity, CNS neoplasm, CG17964, Treatments, Oxalosuccinate decarboxylase, Patient, P53, Childhood Medulloblastoma, p44, microarray, Cistron, Equipment, H3F3, Prognostic Factor, the brain, taxonomy, p53, LEF/TCF-1, Benign Neoplasm, instruments, Gene, Cost Comparisons, Malignant, presence, Deoxyribonucleic acids, E430004F23, Client., Cost Minimization Analysis, Mass, Low, Primary Central Nervous System Neoplasms, HEL-216, AI788952, Central Nervous System Neoplasm, h3.3a, IDHM, h3.3b, Taxonomy, Central Nervous System Neoplasms, Woodlands, Genetic, Malignancy, Affordability, malignant neoplasm of central nervous system, Measures, Tcf-1, d-TCF, financing, E030024J03Rik, DmelCG7176, funding, Trp53, RANDOM, IDH2, CMM9, Clients, TCF/LEF1, Personal Respect, chimpanzees, Long-Term Effect, TRP53, Medical Device, Apparatus and Instruments, Dmel_CG17964, Cistrons, Examination and Diagnoses, WHO, Xp53, count in organism, Device, pan.dTCF, Mass Screenings, EST2, HEL-S-26, sequence, focal, methylation, Tcf, TCF, ds-DNA, Random selection by shearing, Lef1, LEF1, CG7176, Desmoplastic, Cost, Credit Assignments, Credit, tcf, patient, Pricing, localised primitive neuroectodermal tumour, l(4)102ABb, h3.3, cost, Medullomyoblastoma, Therapeutic, PFBMFT1, cardinality, Treatment, P Health, lef1falseGlioTex-ICMData Access Committee EGAC00001000513EGAC0000100051396062757188828638988EGAS00001002213EGAS00001001871EGAS00001003798EGAD00001002691EGAD00001003387EGAD00001002690EGAD00001003382EGAD00001009664