{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"study_type":["Cancer Genomics"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001004786"],"host":["EGA"],"description":["EGA study EGAS00001004786"],"dataset_title":["FPKM expression values of the CUP/reference/validation cohort (H021)","subset of RNA-Seq data from umbrella study EGAS00001004338, used in EGAS00001004786","Beta values of methylation data of the CUP/reference/validation cohort (H021)","Cancer-Unknown-Primary-Array-Methylation-H021","subset of WES data from umbrella study EGAS00001004338, used in EGAS00001004786","subset of WGS data from umbrella study EGAS00001004338, used in EGAS00001004786"],"category":["restricted"],"repository":["EGA"],"name_synonyms":["primary cancer, Genomics, Malignant Neoplasm, Malignancy, Comparative, Comparative Genomics, Neoplasms, Benign Neoplasm, Benign Neoplasms, CG11181, CG31858, Cancers, Functional Genomics, Tumor, Malignant, DmelCG31858, malignant tumor, Malignant Neoplasms, Cup, CUP, DmelCG11181, i239., Neoplasias, Structural, MT, Benign, fs(1)cup, malignant neoplasm, Functional, Neoplasm, Structural Genomics, Malignancies, fs(2)cup, Neoplasia, Cancer, Tumors, cup"],"description_synonyms":["Dfr1, MTS1, HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 9, Materials, p19<ARF>, determination, D330041I19Rik, CT22273, HMERF, CFD1, Gene Expression Profile, Pctr1, Profiles, 2210013I18Rik, Tumor, Tp53, CD332, Cup, CUP, Mutations, DmelCG7223, ras, DFGF-R2, diseases, bbl, DFGF-R1, ARF-INK4a, diseases and disorders, FGF-R2, Arf, ARF, C-K-RAS, p16(INK4a), k-ras, DFR1, cup, rask2, ADY1, human disease, Genomes, BCC7, Comparative Genomics, AF006999, CT39172, MTS-1, CMYA3, AI323585, Dfr-1, Signatures, Fgfr7, genetic, set, BEK, Bek, malignant neoplasm, Expression Signature, DFR-1, Transcriptomes, svs, P14, Homo sapiens disease, Malignancies, P16, AI452089, P19, Tk1, P16-INK4A, Xin2, Tumors, close to, Cmya3, Genomics, Ki-ras, Comparative, MLM, Expression Profiles, Pfs2, familial, p16, CG7223, Functional Genomics, Fgfr-7, DmelCG31858, Fgfr-2, 2310057K23Rik, pfs2, PRETTY FEW SEEDS 2, Gene Expression, Benign, JWS, Expression Signatures, p21, Diseases, Genetic Materials, bfy, median, fs(2)cup, Expression Profile, Genetic Material, Transcriptome Profiles, HD-38, Htl, CMH9, Fr1, EMS2, BBDS, Heterogeneity, Exomes, Benign Neoplasms, D830007G01Rik, common, CG11181, whole genome, i100, TK25, Malignant Neoplasms, F2I9_12, disease, FR1, Patient, RASK2, Material, TMD, P53, p44, bhy, Cistron, DmHD-38, medical condition., inherited genetic, connectin, 2310003D02Rik, F2I9.12, other neoplasm, INK4A, A530024P18Rik, LRPDIT, DTRK(FR1), TK14, WUSCHEL RELATED HOMEOBOX 6, CDKN2, Gruppe, KI-RAS, AU043015, whole exome, other disease, CMD1G, 1100001C23Rik, localised, 2310074I15Rik, i79, Transcriptome Profile, KGFR, K-SAM, MYLK5, INK4, Neoplasms, p53, Kras2, NS3, Benign Neoplasm, EOMFC, Gene, Malignant, LFS1, fs(1)cup, 9830132L24, Structural, Genetic heterogeneity, Functional, Kras-2, disease or disorder, CEK3, KRAS2, i239, KRAS1, p21B, 2310008C07Rik, Genetic, Malignancy, AW556123, Profile, K-RAS4B, K-RAS4A, Gm352, rhabdomyosarcoma antigen MU-RMS-40.14, ECT1, Ect1, non-neoplastic, Neoplasias, Trp53, Ink4a|Arf, grupos, Clients, shru, FGFR, heterogeneity, LRP-DIT, CMM2, BFR-1, p19ARF, disorder, TRP53, constitutitional genetic, FGFR2, Cancer, HSPC037, A930002G16Rik, TP16, Transcriptome, Malignant Neoplasm, P16INK4, grupo, hspc037, K-RAS2B, DPR3, K-RAS2A, disorders, j372, K-ras, CG31858, LGMD2J, c-Ki-ras, dtk1, Cistrons, p19-lt-ARF-gt-, Client, p16INK4a, xfgfr2, WOX6, Xp53, group, near to, MT, P14ARF, HOS9, Gene Expression Signatures, chemical analysis, Neoplasm, AI956815, Ink4a/Arf, condition, i150, focal, Gene Expression Signature, mKIAA1894, mdm, AI929937, KSAM, P16INK4A, CMPD4, KGFRTr, primary cancer, 2310036G12Rik, NS, 4930500N14Rik, PSF2, ensemble, DFR1/DFGF-R2, TTN, CDK4I, AV006427, Rest, Cancers, malignant tumor, HTL/FGFR1, DmelCG11181, INK4a-ARF, DEL, Gene Expression Profiles, kras, 4833427B12Rik, approaches, L56, P19ARF, CFC2, vicinity of, xirp2, Structural Genomics, assay, Dtk1, Signature, hereditary, psf2, groupe, Neoplasia"],"additional_accession":[]},"is_claimable":false,"name":"Genomics-based personalized oncology in cancer of unknown primary (CUP, project H021)","description":"To perform a comprehensive genomic characterization of 70 patients suffering from cancer of unknown primary (CUP) we used whole-exome, whole-genome, transcriptome and methylome analysis. We detected a substantial mutational heterogeneity with genes most commonly affected by SNVs, indels and fusions being TP53, TTN, MUC16, ABCA13, COL6A3, KRAS, LRP1B, XIRP2 and CSMD3. The most common fusion involved FGFR2, the most common focal deletion affected CDKN2A. A molecular tumor board recommended genomics-based therapies in 56/70 (80%) patients which were applied in 20/56 (35.7%) cases. Entity predictions based on transcriptome and methylome data could be made in up to 62/70 (88.6%) cases but were conclusive in only 16/48 (33.3%) cases. Germline analysis revealed 6 (likely) pathogenic mutations in 5 patients. Recommended therapies translated into a mean PFS2/1 ratio of 3.61 (median=2.25) with a median PFS1 of 89 days (n=17) compared to a median PFS2 of 182.5 days (n=20). Our data emphasize the clinical benefit of comprehensive genetic approaches in diagnostic and therapeutic management and underline the need for innovative, mechanism-based clinical trials in this heterogeneous group of diseases.","dates":{"updated":"2022-03-23 15:23:49"},"accession":"EGAS00001004786","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAD00001006615","EGAD00001006614","EGAD00001008669","EGAD00010002036","EGAD00001006613","EGAD00001008638","EGAC00001000452"]}}