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Supplemental Table 1: Genes Targeted in OncoPanelFull-length exons for detection of SNVs, indels and copy number alterationsGenomic regions for structural rearrangementsABL1CDK2EXT2KDM6ANTRK3SETBP1ABL1AKT1CDK4EZH2KDM6BPALB2SETD2AKT3AKT2CDK5FAM46CKDRPARK2SF1ALKAKT3CDK6FANCAKITPAX5SF3B1BCL2ALKCDK9FANCCKRASPDCD1LG2SH2B3BCL6ALOX12BCDKN1AFANCD2LMO1PDGFRASMAD2BRAFAPCCDKN1BFANCELMO2PDGFRBSMAD4CIITAARCDKN1CFANCFLMO3PHF6SMARCA4EGFRARAFCDKN2AFANCGMAP2K1PHOX2BSMARCB1ETV1ARID1ACDKN2BFASMAP2K4PIK3C2BSMC1AEWSR1ARID1BCDKN2CFBXW7MAP3K1PIK3CASMC3FGFR1ARID2CEBPAFGFR1MAPK1PIK3R1SMOFGFR3ASXL1CHEK2FGFR2MCL1PIM1SOCS1FUSATMCIITAFGFR3MDM2PMS1SOX2IgHATRXCREBBPFGFR4MDM4PMS2SOX9IgKAURKACRKLFHMECOMPNRC1SRCIgLAURKBCRLF2FKBP9MEF2BPRAMESRSF2JAK2AXLCRTC1FLCNMEN1PRDM1STAG1MLLB2MCRTC2FLT1METPRF1STAG2MYCBAP1CTNNB1FLT3MITFPRKAR1ASTAT3NPM1BCL2CUX1FLT4MLH1PRKCISTAT6PAX5BCL2L1CYLDFUSMLLPRKCZSTK11PDGFRABCL2L12DDB2GATA3MLL2PRKDCSUFUPDGFRBBCL6DDR2GATA4MPLPRPF40BSUZ12RAF1BCORDICER1GATA6MSH2PRPF8SYKRARABCORL1DIS3GLI1MSH6PSMD13TCF3RETBLMDMDGLI2MTORPTCH1TCF7L1ROS1BMPR1ADNMT3AGLI3MUTYHPTENTCF7L2TRABRAFEGFRGNA11MYBPTK2TERTTRBBRCA1EP300GNAQMYBL1PTPN11TET2TRGBRCA2EPHA3GNASMYCRAD21TNFAIP3?BRD4EPHA5GPC3MYCL1RAF1TP53?BRIP1EPHA7GSTM5MYCNRARATRA?BUB1BERBB2H3F3AMYD88RB1TRB?CARD11ERBB3HNF1ANBNRBL2TRG?CBLERBB4HRASNF1RELTSC1?CBLBERCC2ID3NF2RETTSC2?CCND1ERCC3IDH1NFE2L2RFWD2U2AF1?CCND2ERCC4IDH2NFKBIARHPN2VHL?CCND3ERCC5IGF1RNFKBIZROS1WRN?CCNE1ESR1IGHNKX2-1RPL26WT1?CD274ETV1IGKNOTCH1RUNX1XPA?CD58ETV4IGLNOTCH2SBDSXPC?CD79BETV5IKZF1NPM1SDHAF2XPO1?CDC73ETV6IKZF3NRASSDHBZNF217?CDH1EWSR1JAK2NTRK1SDHCZNF708?CDK1EXT1JAK3NTRK2SDHDZRSR2?Supplemental Table 2: Tumor Diagnoses in the Sequencing CohortDiagnosisNumberDiagnosisNumberAdrenal Gland20Nasopharynx11Adenoma7Adenocarcinoma1Adrenocortical carcinoma10Carcinoma2Pheochromocytoma2DLBCL1Primitive neuroectodermal tumor1Neuroblastoma1Ampulla of Vater3Nut Midline Carcinoma1Adenocarcinoma3Squamous cell carcinoma4Anus10Undifferentiated carcinoma1Adenocarcinoma1Nerve1Squamous cell carcinoma9Schwannoma1Appendix11Nose2Adenocarcinoma3Carcinoma1Goblet cell carcinoid1Neuroblastoma1Mucinous adenocarcinoma2Oral Cavity44Mucinous neoplasm2Adenoid cystic carcinoma1Neuroendocrine tumor3Nut Midline Carcinoma1Bile Duct9Squamous cell carcinoma42Cholangiocarcinoma9Oropharynx and hypopharynx47Bone5Adenoid cystic carcinoma1Chondroblastoma1Squamous cell carcinoma46Chondrosarcoma1Other14Osteosarcoma2B-cell Lymphoma1Sarcoma1Blastoma1Bone Marrow336Carcinoma1Acute Leukemia58Follicular lymphoma1ALL10Leiomyosarcoma2AML64Liposarcoma2B-ALL37Neoplasm1B-cell Lymphoma3Peripheral nerve sheath tumor1CLL/SLL26Rhabdomyosarcoma1CML14Squamous cell carcinoma2CMML3Wilms tumor1Essential thrombocythemia1Ovary191Hairy cell leukemia5Adenocarcinoma139Histiocytic Sarcoma1Borderline serous tumor4Idiopathic hypereosinophilic syndrome1Carcinoma1Lymphoma1Carcinosarcoma4Malignancy1Clear cell carcinoma6Mastocytosis1Endometrioid adenocarcinoma2Myelodysplastic/myeloproliferative neoplasm88Granulosa cell tumor9Myeloma4Mucinous adenocarcinoma1NK/T-cell Lymphoma1Serous carcinoma20Other6Sex-cord stromal tumor1Plasmacytoma1Small cell carcinoma1Polycythemia vera2Teratoma2Refractory cytopenia1Undifferentiated carcinoma1T-ALL4Pancreas55T-cell lymphoma2Adenocarcinoma34T-LGL1IPMN4Brain429Neuroendocrine carcinoma1Choroid plexus papilloma1Neuroendocrine tumor14Craniopharyngioma1Pancreatoblastoma1DLBCL10Solid pseudopapillary neoplasm1Ependymoma8Penis2Ganglioglioma4Squamous cell carcinoma2Glioblastoma173Peritoneum5Glioma66Carcinoma1Hemangioblastoma5Desmoid1Medulloblastoma9Liposarcoma1Medullomyoblastoma1Mesothelioma2Melanocytoma1Pituitary32Meningioma34Adenoma32Neuroblastoma4Pleura55Neurocytoma1DLBCL1Neuroepithelial tumor1Ewing sarcoma1Oligoastrocytoma27Mesothelioma53Oligodendroglioma72Prostate184Pilocytic astrocytoma5Adenocarcinoma183Pineoblastoma2Adenoid cystic carcinoma1Pleomorphic xanthoastrocytoma2Retroperitoneum8Schwannoma1Leiomyosarcoma4Subependymoma1Liposarcoma3Breast298Myxoma1Angiosarcoma2Salivary gland39Carcinoma291Adenocarcinoma1Carcinosarcoma1Adenoid cystic carcinoma15Neuroendocrine carcinoma2Carcinoma13Phyllodes tumour1Carcinoma ex pleomorphic adenoma1Squamous cell carcinoma1Merkel Cell Carcinoma1Cervix28Mucoepidermoid carcinoma1Adenocarcinoma12Myoepithelioma1Squamous cell carcinoma16Neoplasm1Colon210Pleomorphic adenoma2Adenocarcinoma209Squamous cell carcinoma3Liposarcoma1Skin95Endometrium168Adenocarcinoma2Adenocarcinoma148Angiosarcoma2Carcinosarcoma16Apocrine carcinoma1Mucinous adenocarcinoma1B-cell Lymphoma2Sarcoma1Carcinoma3Serous carcinoma2Cutaneous T cell lymphoma1Esophagus45Lymphoma2Adenocarcinoma40Malignancy1Carcinoma1Melanoma42Squamous cell carcinoma4Merkel Cell Carcinoma10Fallopian Tube30Other1Adenocarcinoma30Squamous cell carcinoma19Female genital tract167T-cell lymphoma9Adenocarcinoma73Small intestine14Adenosarcoma1Adenocarcinoma4Borderline serous tumor6Gastrointestinal Stromal Tumor1Carcinoma3Leiomyosarcoma1Carcinosarcoma10Neuroendocrine carcinoma1Choriocarcinoma1Neuroendocrine tumor7Endometrioid adenocarcinoma4Soft tissue130Ewing sarcoma1Alveolar rhabdomyosarcoma1Leiomyoma1Angiosarcoma3Leiomyosarcoma11Chondrosarcoma2Malignancy1Chondrosarcoma, extraskeletal myxoid1Mesothelioma1Dermatofibrosarcoma protuberans1Mucinous adenocarcinoma2Desmoid3Sarcoma2Desmoplastic small round cell tumor1Serous carcinoma47Ewing sarcoma1Solitary fibrous tumor1Gastrointestinal Stromal Tumor31Squamous cell carcinoma1Giant cell tumor2Trophoblastic tumor1Glomus tumor1Gall Bladder5Hemangioendothelioma2Adenocarcinoma1Leiomyosarcoma17Merkel Cell Carcinoma1Lipomatous tumor1Ganglion1Liposarcoma15Neuroblastoma1Lymphangioma1Gastrointestinal tract7Myoepithelioma1Adenocarcinoma5Myxofibrosarcoma2Gastrointestinal Stromal Tumor1Myxoma1Tumor1Osteosarcoma3Head and neck1Perineurioma1Squamous cell carcinoma1Peripheral nerve sheath tumor3Ileum1Rhabdomyosarcoma3Neuroepithelial tumor1Sarcoma20Kidney107Schwannoma2Angiomyolipoma1Small round cell tumor1Angiosarcoma1Solitary fibrous tumor5Clear cell sarcoma1Synovial sarcoma3Myelolipoma1Tumor1Neoplasm1Wilms tumor1Oncocytoma6Soft tissue 2Renal cell carcinoma88Myxofibrosarcoma1Sarcoma1Synovial sarcoma1Urothelial neoplasm2Spinal Cord4Wilms tumor5Astroblastoma1Larynx6Ependymoma1Adenoid cystic carcinoma1Hemangioma1Squamous cell carcinoma5Neurofibroma1Liver21Spleen1Adenocarcinoma1Lymphoma1Cholangiocarcinoma6Stomach31Hepatoblastoma2Adenocarcinoma21Hepatocellular carcinoma11Gastrointestinal Stromal Tumor9Liposarcoma1Leiomyosarcoma1Lung661Testis42Adenocarcinoma495Germ cell tumor24Adenoid cystic carcinoma1Leydig cell tumor2Atypical carcinoid2Liposarcoma1B-cell Lymphoma1Seminoma13Carcinoid-adenocarcinoma1Serous carcinoma1Carcinoma34Sertoli cell tumor1Hemangioma1Throat1Lymphoma2Squamous cell carcinoma1Neuroendocrine carcinoma8Thymus15Neuroendocrine tumor11Carcinoma11Non-small cell carcinoma12Thymoma4Small cell carcinoma18Thyroid104Squamous cell carcinoma75Anaplastic thyroid carcinoma5Lymph node22Carcinoma1B-cell Lymphoma6Follicular adenoma1Burkitt Lymphoma1Follicular thyroid carcinoma9DLBCL4Medullary thyroid carcinoma5Follicular lymphoma4Papillary thyroid carcinoma81Hodgkin lymphoma1Poorly differentiated carcinoma1Langerhans cell sarcoma1Undifferentiated carcinoma1Lymphoma2Unknown22NK/T-cell Lymphoma1Adenocarcinoma3Sarcoma1Carcinoma10T-cell lymphoma1Malignancy2Mediastinum4Sarcoma1Carcinoma1Squamous cell carcinoma6DLBCL1Urinary tract127Liposarcoma1Adenocarcinoma4Squamous cell carcinoma1Bladder Carcinoma1Nasopharynx11Ewing sarcoma1Adenocarcinoma1Leiomyosarcoma1Carcinoma2Paget's disease1DLBCL1Sarcoma3Neuroblastoma1Small cell carcinoma2Nut Midline Carcinoma1Urothelial carcinoma113Squamous cell carcinoma4Urothelial neoplasm1Undifferentiated carcinoma1Vagina1Nerve1Melanoma1Schwannoma1Vulva11Nose2Melanoma1Carcinoma1Squamous cell carcinoma9Neuroblastoma1Yolk sac tumor1Grand Total3892Supplemental Table 3. OncoPanel assay performance for detection of KRAS point mutations and EGFR insertion-deletion mutations.\s\s\sSupplemental Table 4. OncoPanel assay performance for detection of low and high copy number changes.* In one case with a complex karyotype, segmental 1p loss and monosomy 19 was detected by Oncopanel but not by clinical aCGH. In another case, monosomy 19 was detected by Oncopanel but not by clinical aCGH.?In one case, low mean target coverage and high signal dispersion (noise) precluded accurate copy calls by Oncopanel.Supplemental Table 5. OncoPanel assay performance for detection of ALK rearrangements.\s*One case considered a false negative by Oncopanel was estimated to have <20% tumor content and thus was below the limit of detection for this assay. ?After elimination of one tumor with a concurrent KRAS activating mutation considered falsely positive by FISH, and inclusion of one tumor originally called negative by FISH but found to have ALK rearrangement by OncoPanel as well as ALK protein overexpression. ................
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