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A Novel, Internet-Based Tool to Assess the Oncogenic Potential of Genes Authors

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A Novel, Internet-Based Tool to Assess the Oncogenic Potential of Genes Authors OncoScore: a novel, Internet-based tool to assess the oncogenic potential of genes Authors: Piazza Rocco1, Ramazzotti Daniele2, Spinelli Roberta1, Pirola Alessandra3, De Sano Luca4, Ferrari Pierangelo3, Magistroni Vera1, Cordani Nicoletta1, Sharma Nitesh5, Gambacorti-Passerini Carlo1 1) University of Milano-Bicocca, Dept. of Medicine and Surgery, Monza, 20900, Italy 2) Stanford University, Dept. of Pathology, California 94305, USA 3) GalSeq s.r.l., viale Italia 46, Monza, 20900, Italy 4) University of Milano-Bicocca, Dept. of Informatics, 20125, Milano 5) University of New Mexico, Department of Pediatrics, Albuquerque Suppl. Fig. 1. Distribution of the OncoScore across all the genes with more than 10 citations as of January 2016. Suppl. Tab. 1. List of all the cancer genes comprised in the Cancer Gene Census dataset. Cancer Cancer Tumor Tumor Cancer Chr Cancer Tissue Mutation Translocation Symbol Chr Somatic Germline Types Types Molecular Band Syndrome Type Type Partner Mut Mut (Somatic) (Germline) Genetics 9q34. CML, ALL, BCR, ETV6, ABL1 9 1 yes T-ALL L Dom T, Mis NUP214 1q24- ABL2 1 q25 yes AML L Dom T ETV6 ACSL3 2 2q36 yes prostate E Dom T ETV1 AF15Q1 4 15 15q14 yes AML L Dom T MLL AF1Q 1 1q21 yes ALL L Dom T MLL AF3p21 3 3p21 yes ALL L Dom T MLL AF5q31 5 5q31 yes ALL L Dom T MLL 7q21- papillary AKAP9 7 q22 yes thyroid E Dom T BRAF breast, colorectal, 14q32 ovarian, AKT1 14 .32 yes NSCLC E Dom Mis 19q13 .1- ovarian, AKT2 19 q13.2 yes pancreatic E Dom A 12q24 leiomyom ALDH2 12 .2 yes a M Dom T HMGA2 NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALCL, ALO17, NSCLC, familial CARS, neuroblast neuroblast neuroblast EML4, ALK 2 2p23 yes yes oma oma oma L, E, M Dom T, Mis, A KIF5B, C2orf22 17q25 ALO17 17 .3 yes ALCL L Dom T ALK colorectal, colorectal, pancreatic pancreatic adenomat , desmoid, , desmoid, ous hepatobla hepatobla polyposis stoma, stoma, coli; glioma, glioma, Turcot D, Mis, APC 5 5q21 yes yes other CNS other CNS syndrome E, M, O Rec N, F, S ARHGE 11q23 F12 11 .3 yes AML L Dom T MLL ARHH 4 4p13 yes NHL L Dom T BCL6 clear cell ovarian 1p35. carcinoma Mis, N, ARID1A 1 3 yes , RCC E Rec F, S, D hepatocell ular ARID2 12 12q12 yes carcinoma E Rec N, S, F ARNT 1 1q21 yes AML L Dom T ETV6 alveolar ASPSC soft part R1 17 17q25 yes sarcoma M Dom T TFE3 20q11 MDS, ASXL1 20 .1 yes CMML L Rec F, N, Mis malignant melanoma of soft parts, angiomato id fibrous histiocyto EWSR1, ATF1 12 12q13 yes ma E, M Dom T FUS ATIC 2 2q35 yes ALCL L Dom T ALK leukemia, lymphoma , medullobl ataxia- 11q22 astoma, telangiect D, Mis, ATM 11 .3 yes yes T-PLL glioma asia L, O Rec N, F, S Pancreatic neuroendo crine tumors, Xq21. paediatric ATRX X 1 yes GBM E Rec Mis, F, N colorectal, endometri al, prostate and hepatocell ular carcinoma s, hepatobla stoma, sporadic 16p13 medullobl D, Mis, AXIN1 16 .3 yes yes astoma E, O Rec N, F, S uveal melanoma mesotheli 3p21. , breast, oma, 31- NSCLC, uveal N, Mis, BAP1 3 p21.2 yes RCC melanoma E Rec F, S, O BCL10 1 1p22 yes MALT L Dom T IGH@ BCL11A 2 2p13 yes B-CLL L Dom T IGH@ 14q32 BCL11B 14 .1 yes T-ALL L Dom T TLX3 18q21 BCL2 18 .3 yes NHL, CLL L Dom T IGH@ BCL3 19 19q13 yes CLL L Dom T IGH@ BCL5 17 17q22 yes CLL L Dom T MYC IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R, POU2AF1, ARHH, EIF4A2, BCL6 3 3q27 yes NHL, CLL L Dom T, Mis SFRS3 12q24 BCL7A 12 .1 yes BNHL L Dom T MYC BCL9 1 1q21 yes B-ALL L Dom T IGH@, IGL@ retinoblast oma, AML, APL Xp11. (translocat F, N, S, BCOR X 4 yes ion) Rec T RARA ABL1, 22q11 CML, ALL, FGFR1, BCR 22 .21 yes AML L Dom T JAK2 renal, fibrofollicul omas, Birt-Hogg- 17p11 trichodisco Dube BHD 17 .2 yes mas syndrome E, M Rec? Mis. N, F 11q22 BIRC3 11 -q23 yes MALT L Dom T MALT1 leukemia, lymphoma , skin squamous cell, other 15q26 tumor Bloom BLM 15 .1 yes types syndrome L, E Rec Mis, N, F gastrointe BMPR1 10q22 stinal juvenile A 10 .3 yes polyps polyposis E Rec Mis, N, F melanoma , colorectal, papillary thyroid, borderline ovarian, NSCLC, cholangioc arcinoma, pilocytic astrocyto AKAP9, BRAF 7 7q34 yes ma E Dom Mis, T, O KIAA1549 hereditary breast/ova breast, rian D, Mis, BRCA1 17 17q21 yes yes ovarian ovarian cancer E Rec N, F, S breast, ovarian, pancreatic hereditary breast, , leukemia breast/ova ovarian, (FANCB, rian D, Mis, BRCA2 13 13q12 yes yes pancreatic FANCD1) cancer L, E Rec N, F, S lethal midline carcinoma of young BRD3 9 9q34 yes people E Dom T C15orf55 lethal midline carcinoma 19p13 of young BRD4 19 .1 yes people E Dom T C15orf55 Fanconi anaemia J, breast AML, cancer leukemia, susceptibli BRIP1 17 17q22 yes breast ty L, E Rec F, N, Mis BTG1 12 12q22 yes BCLL L Dom T MYC mosaic variegated rhabdomy aneuploid Mis, N, BUB1B 15 15q15 yes osarcoma y M Rec F, S 12q14 C12orf9 12 .3 yes lipoma M Dom T LPP C15orf2 15q21 1 15 .1 yes prostate E Dom T ETV1 lethal C15orf5 midline 5 15 15q14 yes carcinoma E Dom T BRD3, BRD4 PMBL, C16orf7 16p13 Hodgkin 5 16 .13 yes lymphoma L Dom T CIITA 2p23. C2orf44 2 3 yes NSCLC E Dom T ALK 1p36. epithelioid 31- haemangi CAMTA p36.2 oendotheli 1 1 3 yes oma M Dom T WWTR1 CANT1 17 17q25 yes prostate E Dom T ETV4 CARD11 7 7p22 yes DLBCL L Dom Mis 11p15 CARS 11 .5 yes ALCL L Dom T ALK CBFA2T 1 8 8q22 yes AML L Dom T MLL, RUNX1 CBFA2T 3 16 16q24 yes AML L Dom T RUNX1 CBFB 16 16q22 yes AML L Dom T MYH11 AML, 11q23 JMML, T, Mis S, CBL 11 .3 yes MDS L Dom, Rec O MLL 3q13. CBLB 3 11 yes AML L Rec Mis S 19q13 CBLC 19 .2 yes AML L Rec M CCDC6 10 10q21 yes NSCLC E Dom T RET CCNB1I 14q11 leiomyom P1 14 .2 yes a M Dom T HMGA2 CLL, B- ALL, IGH@, CCND1 11 11q13 yes breast L, E Dom T FSTL3 CCND2 12 12p13 yes NHL,CLL L Dom T IGL@ CCND3 6 6p21 yes MM L Dom T IGH@ serous CCNE1 19 19q12 yes ovarian E Dom A PMBL, 9p24. Hodgkin CD273 9 2 yes lymphoma L Dom T CIITA PMBL, Hodgkin CD274 9 9p24 yes lymphoma L Dom T CIITA CD74 5 5q32 yes NSCLC E Dom T ROS1 19q13 CD79A 19 .2 yes DLBCL L Dom O, S CD79B 17 17q23 yes DLBCL L Dom Mis, O lobular familial 16q22 breast, gastric Mis, N, CDH1 16 .1 yes yes gastric gastric carcinoma E Rec F, S aneurysm 16q22 al bone CDH11 16 .1 yes cyst M Dom T USP6 serous CDK12 17 17q12 yes ovarian E Rec Mis, N, F familial malignant CDK4 12 12q14 yes melanoma melanoma E Dom Mis 7q21- CDK6 7 q22 yes ALL L Dom T MLLT10 melanoma , multiple other melanoma familial CDKN2 tumor , malignant L, E, M, D, Mis, A 9 9p21 yes yes types pancreatic melanoma O Rec N, F, S melanoma , multiple other melanoma familial CDKN2a tumor , malignant L, E, M, (p14) 9 9p21 yes yes types pancreatic melanoma O Rec D, S CDKN2 glioma, C 1 1p32 yes MM O, L Rec D 13q12 CDX2 13 .3 yes AML L Dom T ETV6 19q13 AML, CEBPA 19 .1 yes MDS L Dom Mis, N, F CEP1 9 9q33 yes MPD, NHL L Dom T FGFR1 salivary CHCHD 8q11. gland 7 8 2 yes adenoma E Dom T PLAG1 familial 22q12 breast CHEK2 22 .1 yes breast cancer E Rec F 4q11- CHIC2 4 q12 yes AML L Dom T ETV6 extraskele tal myxoid 2q31- chondrosa CHN1 2 q32.1 yes rcoma M Dom T TAF15 oligodendr oglioma, 19q13 soft tissue Mis, F, CIC 19 .2 yes sarcoma O Rec S,T DUX4 FLJ27352, CD274, CD273, RALGDS, PMBL, RUNDC2A, Hodgkin C16orf75, CIITA 16 16p13 yes lymphoma L Dom T BCL6 17q11 ALCL, CLTC 17 -qter yes renal L Dom T ALK, TFE3 22q11 CLTCL1 22 .21 yes ALCL L Dom T ? CMKOR 2q37. 1 2 3 yes lipoma M Dom T HMGA2 19q13 CNOT3 19 .4 yes T-ALL L Dom Mis, N dermatofib rosarcoma protubera ns, 17q21 aneurysm .31- al bone PDGFB, COL1A1 17 q22 yes cyst M Dom T USP6 prostate, COPEB 10 10p15 yes glioma E, O Rec Mis, N uterine 8q22- leiomyom COX6C 8 q23 yes a M Dom T HMGA2 clear cell sarcoma, angiomato id fibrous histiocyto CREB1 2 2q34 yes ma M Dom T EWSR1 CREB3L 11p11 myxofibro 1 11 .2 yes sarcoma M Dom T FUS CREB3L fibromyxoi 2 7 7q34 yes d sarcoma M Dom T FUS ALL, AML, CREBB 16p13 DLBCL, B- T, N, F, MLL, MORF, P 16 .3 yes NHL L Dom/Rec Mis, O RUNXBP2 Xp22. B-ALL, 3; Downs Yp11. associated P2RY8, CRLF2 X,Y 3 yes ALL L Dom Mis, T IGH@ salivary gland 15q26 mucoepid CRTC3 15 .1 yes ermoid E Dom T MAML2 colorectal, ovarian, hepatobla stoma, pleomorph ic salivary gland adenoma, other 3p22- tumor CTNNB1 3 p21.3 yes types E, M, O Dom H, Mis, T PLAG1 familial 16q12 cylindrom cylindrom cylindrom Mis, N, CYLD 16 -q13 yes yes a a atosis E Rec F, S papillary D10S17 thyroid, RET, 0 10 10q21 yes CML E Dom T PDGFRB pancreatic neuroendo crine tumor, paediatric 6p21.
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