Supplemental Table 1. 4062 Tumor Mutation Profile. Ge ne Protein Name M ut at io n Exp re s s io n a C lo nalit y b M utated amino acid sequence c IGSF3 Immunoglobulin superfamily, member 3 p.E296K W, R Und RLETEKRLHTVG KPVEFRCILEAQN NUDT17 Nucleoside diphosphate linked moiety X-type motif 17 p.301_302del W, R Und W LQHLGRTPPPC AAYLDPGPAKEEW SEM A6C Semaphorin-6C p.D79N W, R C LTLNR TLLVA A R N HVFSFDLQAEEE DDX59 DEAD (Asp-Glu-Ala-Asp) box polypeptide 59 p.F520Y W, R C G LDLISV R LVV N Y DM PSSM DEYVHQ TTC13 tetratricopeptide repeat domain 13 p.A150V W, R SC TDNDSTNEELAIV YVLIGSGLYDEA TTC13 tetratricopeptide repeat domain 13 p.A93V W, R SC W GDQYSAECGAIV YVLIGSGLYDEA TSSC4 tumor-suppressing subtransferable fragment 4 p.F97S W, R C M SSTFSQRSRDISDCLEGAARRAPS AHNAK Neuroblast differentiation-associated protein p.G3979D W, R C KVDVDVPDVNIED PDAKLKGPKFKM TSPAN4 Tetraspanin-4 p.I183L W, R Und VGIFGLCTALVQ LLGLTFAM TM YCQ ANAPC7 anaphase promoting complex subunit 7 p.M 570V W, R Und PTDATQEEDVDD V EGSGEEGDLEGS CLIP1 CAP-GLY domain containing linker protein 1 p.S348C W, R C LTETSSRYARKIC GTTALQEALKEK LRP6 low density lipoprotein receptor-related protein 6 p.D421A W, R C AVDW VARNLYW TA TGTDRIEVTRLN ESPL1 Extra spindle pole bodies homolog 1 p.L224F W, R C LNEADADFLDDLFSRHVIRALVGER LRP1 Low density lipoprotein receptor-related protein 1 p.L3665M W, R Und TCPLDEFQCNNTM CKPLAW KCDGED R3HDM 2 R3H domain containing 2 p.T88P W, R Und LVRSLAVCEESSPPFADGPLETQDI SYNE2 spectrin repeat containing, nuclear envelope 2 p.I6740T W, R C N SLLIKG HG ED C TEAEEKVHVIEKK ANGEL1 Protein angel homolog 1 p.R516fs W, R SC RRKYGRDFLLRFPSA A SLVSD Q UBE3A ubiquitin protein ligase E3A p.P653A W, R Und KKGTFRDLGDSHA V LYQ SLKD LLEY CLPX ATP-dependent Clp protease p.C4F W, R Und M PSFGACTCGAAAVRL CORO7,CORO7-PAM 16 Coronins p.R152K W, R Und GILSW QPM GTW C KAPSGAEM EPW W A RNM TL1 RNA methyltransferase like 1 p.R148S W, R C KAGAVPKM FFFSSLEYLKELPVDKL TP53 tumor suppressor p53 p.L111R W, R Und SQKTYQGSYGFR R GFLHSGTAKSVT ZNF121 Zinc Finger Protein 121 p.220_222del W, R Und AFAGRSGLTKHV HTGEKPYECNECG NBAS neuroblastoma amplified sequence p.K455N W, R Und FLSLEC EIKLAPN RSRLETRAGEED HEATR5B HEAT repeat containing 5B p.I1296V W, R C TN D LLVLHLSD LV RM AFM AATDHSN PTPN1 Tyrosine-protein phosphatase non-receptor type 1 p.D236Y W, R C TFC LAD TC LLLM Y KRKDPSSVDIKK PLSCR2 phospholipid scramblase 2 p.I150F W, R Und KREDVLKISGPC FVCSCIAGVDFEI ALPK1 Alpha-Kinase 1 p.A243T W, R C D KKG LSTSLGILTDIFVSM SKNDYE RBPJ Recombination signal binding protein for Immunoglobulin Kappa J region p.H204L W, R C RLRSQTVSTRYLLVEGGNFHASSQQ PDGFRA Alpha-type platelet-derived growth factor receptor p.T1044P W, R Und EDLGKRNRHSSQ PSEESA IETG SSS CDKL5 cyclin-dependent kinase-like 5 p.H32L W, R Und GEGAYGVVLKCR LKETHEIVA IKKF SEM A6C Semaphorin-6C p.D529N W C DQAGNQESM EHG N CQDGATGSQSGP LY9 T-lymphocyte surface antigen Ly-9 p.A90T W C VIWIGPKNALAFTRPKENVTIMVKS RYR2 Ryanodine receptor 2 p.C1164R W C YGRSW QAGDVVG R M VDM NEHTM M FT BAI2 brain-specific angiogenesis inhibitor 2 p.P350L W Und ELQTKLCSM AAC LVEGQW LEW GPW G DGKZ diacylglycerol kinase, zeta p.E114V W Und ETNVSGDFCYVG V QYCVARM LQKSV DGKZ diacylglycerol kinase, zeta p.E303V W Und ETNVSGDFCYVG V QYCVARM LKSVS DGKZ diacylglycerol kinase, zeta p.E119V W Und ETNVSGDFCYVG V QYCVARM LVSAR DGKZ diacylglycerol kinase, zeta p.E24V W Und ETNVSGDFCYVG V QYCVARM LINFR HIP1R huntingtin interacting protein 1 p.L465R W Und KHSELVHVHAELR RKNADTAKQLTV CHD4 Chromodomain-helicase-DNA-binding protein 4 p.1759_1766del W Und TKKTYEIWHRRHY KV SFA NANOGNB NANOG neighbor homeobox p.E16G W C ARW LTPVIPALW G AEAGRSRGQEIE SETD1A SET domain containing 1A p.P1417L W Und PPPPPPPPRAYELRSEFEQM TILYD FAM 20A Family With Sequence Similarity 20, M ember A p.C56Y W C LPSCRPSTW PPG Y LCPTPGSAPTHW RASAL3 RAS Protein Activator Like 3 p.G257R W C DVRIWPLHPSLLR EPHCFQVTW TGG CKM Creatine kinase p.D374H W C EM EKKLEKGQSIHD M IPA Q K CACNG6 Calcium Channel, Voltage-Dependent, Gamma Subunit 6 p.A86S W C AVCEAAHLGLW KSCTKRLW QADVPV USP16 Ubiquitin carboxyl-terminal hydrolase 16 p.P243T W SC NM DNDLEVLTSSTTRNLNGAYLTEG C22orf43 Aspartate-rich protein 1 p.196_197del W Und EDSLFLRCSLRHEEEED D D D IHITA M FI2 M elanotransferrin p.E32A W SC GM EVRW CATSDPA QHKCGNM SEAFR PRDM 13 PR domain zinc finger protein 13 p.P430S W C ARYAQLPPAPGLSLERCALPPLDPG FNDC1 (fibronectin type III domain containing 1 p.A1771T W SC RPPGGEPIWIPFTFKHDPSYTDCHG ZNF391 Zinc finger protein 391 p.N247I W C TIIQHQ R IHTG EIPYECSKCGKAFS BACH2 Basic Leucine Zipper Transcription Factor 2 p.S548L W C SPCSLPLCEFSSLPCSQGARFLATE M UC12 M ucin 12 p.P665T W C AFVEPSTTSHGSTSSIPTTHISA R S ST7 Suppression Of Tumorigenicity 7 p.R141C W C HQTFFTCDSDHLC PADAIMQKAW RE BM PER BM P binding endothelial regulator p.E427K W C FSW TKSVELVLG KSRVSLQQHLTVR SEM A3D Semaphorin-3D p.238_240del W Und HYIRTDISEHYW LCDFFLFTFDCLALV GRIN1 Glutamate [NM DA] receptor subunit zeta-1 p.V886M W C RPGHGPPPSPKA M ALALALVGRTGA ACO1 aconitase 1 p.V83fs W C HKNIEVPFKPARV YPAGLYGCARCG a Whole exome sequencing, W; RNA sequencing, R b Mutated sequences based on tumor whole exome sequencing. In most cases long peptides were synthesized with the mutation flanked by 12 amino acids on either side. Mutations are underlined. c Clonality: clonal, C; subclonal, SC, Undetermined, Und..