Supplemental Figure 1. Outline of Personalized Screening Strategy

i. Isolation of T cells PD-1- PD-1+ va. Bulk Blood expansion iii. Screening for iv. Sort 4-1BB vi. DNA/RNA vii. Clone into viii. Viral & Generation of reactivity against expressing extraction & Retroviral vector production autologous APCs neoantigens lymphocytes TRB / TRA sequencing MHC-I T cell MHC-II TCR ii. WES /RNAseq V D J C Peptides ix. Transduction of PBL Identification of NSM TRB

vb. Single V J C 1BB

- TRA 4 cell isolation CD8/CD4 + APCs GI Cancer & synthesis of mutated Patient peptides or TMGs

Tumor biopsy

Supplemental Figure 1. Outline of personalized screening strategy used to identify and isolate neoantigen specific T-cell receptors circulating in the blood of GI cancer patients. (i) Lymphocytes were sorted from a pre-treatment peripheral blood sample or leukapheresis product based on PD-1 expression and expanded in vitro for 14 days, and autologous antigen presenting cells (APCs) were established. (ii) Fresh or archive formalin fixed paraffin embedded tumor biopsies were used to perform tumor WES and, when possible, RNA sequencing to identify non-synonymous mutations (NSM), and this information was used to synthesize mutated 25-mers or concatenated mutated minigenes encoding for all the candidate neoantigens. (ii) T cells were screened for recognition of putative neaontigens by co-culturing the effector T cells subsets with autologous APCs pulsed with or encoding for all the NSM identified. (iv) Cells upregulating 4-1BB following co-culture with a specific neoantigen were sorted to high purity and either (va) expanded non-specifically in vitro or (vb) isolated at the single cell level. (vi) DNA or RNA was extracted from ex vivo expanded and/or single cells from (va) and (vb) and TRA and TRB sequencing was performed to identify candidate neoantigen-reactive TCR-αβ pairs. (vii) Variable TRA and TRB pairs identified were cloned into a retroviral vector to (viii) generate a retrovirus used to (ix) infect and express the candidate neoantigen-specific TCR in peripheral blood lymphocytes. independent were position Spots from CD mers and ELISPOT cells Representative biopsy encoding specified CD blood Supplemental 4 8 C A E + + individual PD . PP from and IFN-γ/ IFN-γ/ IFN-γ/ Numbers per performed . of 4 4 4

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+ Supplemental Figure 3. Identification of KRASp.G12D specific CD8 lymphocytes and candidate TCR- αβ pairs in the peripheral blood of a patient with colon cancer NCI-4095. (A) IFN-γ ELISPOT assay of in vitro expanded peripheral blood CD8+ and CD4+ lymphocytes subsets co-cultured overnight with DCs pulsed with an irrelevant peptide pool (PP) or the indicated PP containing the various mutated 25-mers identified by whole exome sequencing. (B) Reactivity of the CD8+PD-1+ cells to autologous DCs pulsed with individual 25-mers from PP1. IFN-γ spots per 2e4 effector cells are plotted. (C) IFN-γ ELISPOT assay and (D) flow cytometric detection of 4-1BB expression after co- culture of the CD8+PD-1+ cells with APCs pulsed with HLA-C*08:02 restricted wild type (WT) and mutated (MUT) KRASp.G12D 9-mers and 10-mers. Representative plot displays the percentage of 4- 1BB upregulation on the CD8+PD-1+-derived cells when co-cultured with DCs pulsed with the mutated KRASp.G12D 10-mer. (E) Candidate KRASp.G12D reactive TCR-αβ pairs identified by single cell TRA and TRB sequencing from CD8+4-1BB+ T cells isolated in (D). The number of times each TCR-αβ pair was detected and the CDR3α and CDR3β amino acid sequences are specified. (F) IFN-γ ELISPOT assay and flow cytometric analysis of 4-1BB expression on in vitro expanded KRASp.G12D-reactive CD8+ T cells isolated in (D) following overnight co-culture with DCs pulsed with WT and mut

KRASp.G12D 10-mers or electroporated with RNA encoding for full-length wt and mutated KRASp.G12D. The mean number of spots per 2x104 effector cells and percentage of CD8+ cells that are 4-1BB are plotted. The individual neoantigens recognized and the amino acid position and change are noted. ‘>’ denotes greater than 500 spots/2 x 104 cells. Except in (F), experiments were performed without technical duplicates. Data from A-F are representative of at least two independent experiments. vitro peripheral Supplemental Data greater and culture on plotted an MMP 1 cytometric 3 CD 25 culture reproducible identified pulsed + E - - derived 3 irrelevant but mers A in D + percentage from 14 expanded lymphocytes IFN-γ/ CD8 vitro is .

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0 P3 P26 i P13 P30 LP#22 + - + h P15 4 1 1 P4 P27 D - - -1 P14 P31 LP#23 C + D D D P16 P + P + P P15 P32 4 4 4 P5 P28 LP#24 D D D P17 C C C P16 Anti-CD3 P6 P18 P29 LP#25 P7 P19 P30 LP#26 P8 P20 P31 LP#27 P9 P21 P32 LP#28 Supplemental Figure 6. IdentificationP10 of personalizedP22 neoantigenAnti-CD3 -specific lymphocytes in theLP#29 peripheral blood of a patient with metastatic pancreatic cancer NCI-MM. (A) IFN-γ ELISPOT assayLP#30 of in vitro expanded peripheral blood CD8+ (top panel) and CD4+ (bottom panel) lymphocyteLP#31 subsets co-cultured overnight with DCs pulsed with the individual mutated 25-mers identifiedLP#32by whole exome sequencing. (B) IFN-γ ELISPOT assay of CD4+PD-1hi lymphocytes following co-cultureAnti-CD3 with autologous DCs pulsed with wt or mutated TARP 25-mers. Spots per 2x104 cells effector cells. Plate bound anti-CD3 was used as a positive control in all co-culture assays. Experiments were performed without technical duplicates. Data are representative of at least two independent experiments. A 4078 B 4166 C 4177

TMPRSS4 SUN1 DLAT GBAS NPLOC4 PSMD2 MMP14

D 4095-1 4095-2A 4095-2B

KRAS KRAS KRAS

E 4110-A 4110-B

DNAJB1

Supplemental Figure 7. Intra- and inter-tumoral heterogeneity of mutated genes that resulted in neoantigens recognized by circulating lymphocytes in patients with GI cancer (n=5). Clonal architecture of the resected tumors from patients (A) NCI-4078, (B) NCI-4166, (C) NCI-4177, (D) NCI-4095, and (E) NCI-4110. Each plot represents and individual tumor sequenced. Each dot represents one non-synonymous somatic mutation identified. The fraction of tumor cells with each variant and coverage is plotted. Non-synonymous mutations encoding for a neoepitope recognized by peripheral blood T cells are highlighted in red.

A 4078 4095 4110 4114 4166

p.I312V p.Q236H

p.E207K p.G12D CD8 p.G294L

p.K62N TIL-derived reactivity

DLAT GBAS KRAS DNAJB1 TES NPLOC4 Neoepitopes Peripheral blood-derived reactivity Conv. TILs PD-1+ TILs Not tested Pher. PD-1+/hi No detectable reactivity

Supplemental Figure 8. Comparison of neoepitopes targeted by ex vivo expanded CD8+ tumor- infiltrating lymphocytes and peripheral blood lymphocytes (n=5). (A) Neoepitopes recognized by conventional TILs derived from tumor fragments expanded in IL-2 (Conv. TILs), ex vivo expanded CD8+PD-1+ lymphocytes sorted from the fresh tumor (Tumor PD-1+), and peripheral blood-derived CD8+PD-1+/hi (Pher. PD-1+/hi). The patient ID as well as the individual neoantigens recognized and the amino acid position and change are specified above. Blue and red squares indicate that reactivity was detected in the TILs or peripheral blood, respectively. CD4+ lymphocytes CD4+ CD4+lymphocytes diff A + + + Phenotype CD4 T cells CD4 CD4 Differentiation Status CD4CD4++ 100

100 100CD4+PD1- CD4CD4+PD1neg+PD1-

l l

l + + + +

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Supplemental Figure 9. Phenotypic characterization of ex vivo expanded peripheral blood CD4+ and CD8+ T-cell subsets. Ex vivo expanded peripheral blood (A) CD4+ and (B) CD8+ lymphocytes subsets from n=4 patients (NCI-4166, NCI-4095, NCI-4078 and MM) were thawed, rested overnight in media containing IL-2, washed and stained to evaluate the expression of selected co-stimulatory and co-inhibitory receptors specified (left panel) or the differentiation status based on expression + - + + - of CCR7 and CD45RO (right panel; Naïve=CCR7 /CD45RO ; TCM=CCR7 /CD45RO ; TEM=CCR7 + - - /CD45RO ; TEMRA=CCR7 /CD45RO ). Percentages of lymphocytes derived from the different peripheral blood T-cell subsets expressing individual or combinations of markers are shown (mean ± SEM; n=4 patients). Each dot represents one sample analysed. *P<0.05 CD8+PD-1- vs. CD8+PD-1+ using 1-way ANOVA and Dunn’s test for multiple comparisons, P value adjusted for number of comparisons. Immunophenotyping experiment was performed once.

Supplemental Table 1. Patient Characteristics Patient ID Age/Sex Tumor Type Prior Therapies % PD-1+ of % PD-1+ of CD8+ PBMCs CD4+ PBMCs NCI-MM 60/M Pancreatic Pancreatectomy and 5.4% 2.62% splenectomy, adjuvant gemcitabine NCI-4078 48/M Gastro- Neoadjuvant chemotherapy 2.80% 2.95% esophageal (mitomycin C, Abraxane, Oxaliplatin, 5-Fluorouracil, Carboplatin, Avastin), Ivor Lewis esophagectomy NCI-4095 50/F Colon Sigmoid colectomy and partial 0.37% 0.80% cystectomy, adjuvant FOLFOX NCI-4110 67/F Bile duct Gemcitabine/cisplatin, radiation 2.76% 2.64%

NCI-4114 45/F Pancreatic Neoadjuvant FOLFIRINOX, 2.94% 1.99% neoadjuvant gemcitabine, whipple procedure, adjuvant FOLFOX NCI-4166 45/F Colon Surgery, FOLFOX and 0.41% 0.57% Bevacizumab, 5-Fluorouracil and Bevacizumab, FOLFIRI and Cetuximab, Trifluridine/Tipiracil NCI-4177 40/M Pancreatic Surgery, Folfirinox, Radiation 19% 15.5% and Capecitabine, Gemzar and Abraxane,

Supplemental Table 2. Amino acid sequence of the functional mutation-reactive T-cell receptors isolated from the peripheral blood CD8+PD-1+/hi or CD4+PD-1hi subsets of NCI-4078, NCI-4110 and NCI-4095 Patient Reactivity TRAV/TRAJ TCR alpha chain V-J amino TRBV/TRBJ TCR beta chain V-D-J amino ID acid sequence (CDR3 acid sequence (CD3 highlighted) highlighted) 4078 DLATp.G294L TRAV10*01 MKKHLTTFLVILWLYFYRGNGK TRBV5- MGSRLLCWVLLCLLGAGPVKAGV / NQVEQSPQSLIILEGKNCTLQCN 1*01/ TQTPRYLIKTRGQQVTLSCSPISGH TRAJ35*01 YTVSPFSNLRWYKQDTGRGPVS TRBJ2*01 RSVSWYQQTPGQGLQFLFEYFSE LTIMTFSENTKSNGRYTATLDA TQRNKGNFPGRFSGRQFSNSRSE DTKQSSLHITASQLSDSASYICVV MNVSTLELGDSALYLCASSLETSGL GFGNVLHCGSGTQVIVLP VGEQFFGPGTRLTVL

GBASp.E207K TRAV5*01/ MKTFAGFSFLFLWLQLDCMSR TRBV27*01/ MGPQLLGYVVLCLLGAGPLEAQV TRAJ3*01 GEDVEQSLFLSVREGDSSVINCT TRBJ2-1*01 TQNPRYLITVTGKKLTVTCSQNM YTDSSSTYLYWYKQEPGAGLQL NHEYMSWYRQDPGLGLRQIYYS LTYIFSNMDMKQDQRLTVLLNK MNVEVTDKGDVPEGYKVSRKEKR KDKHLSLRIADTQTGDSAIYFCA NFPLILESPSPNQTSLYFCASSLIPG YSSASKIIFGSGTRLSIRP AGDEQFFGPGTRLTVL

TMPRSS4p.H23 TRAV41*01 MVKIRQFLLAILWLQLSCVSAAK TRBV7- MGTRLLFWVAFCLLGADHTGAG 3Y / NEVEQSPQNLTAQEGEFITINCS 2*01/ VSQSPSNKVTEKGKDVELRCDPIS TRAJ57*01 YSVGISALHWLQQHPGGGIVSL TRBJ1-5*01 GHTALYWYRQSLGQGLEFLIYFQG FMLSSGKKKHGRLIATINIQEKH NSAPDKSGLPSDRFSAERPGGSVS SSLHITASHPRDSAVYICAGSGG TLTIQRTQQEDSAVYLCASSSSGAF SEKLVFGKGTKLTVNPD QPQHFGDGTRLSIL

PSMD2p.G644A TRAV39*01 MKKLLAMILWLQLDRLSGELKV TRBV11- MGTRLLCWAALCLLGAELTEAGV / EQNPLFLSMQEGKNYTIYCNYS 2*01/ AQSPRYKIIEKRQSVAFWCNPISG TRAJ40*01 TTSDRLYWYRQDPGKSLESLFVL TRBJ2-1*01 HATLYWYQQILGQGPKLLIQFQN LSNGAVKQEGRLMASLDTKARL NGVVDDSQLPKDRFSAERLKGVD STLHITAAVHDLSATYFCAVVSG STLKIQPAKLEDSAVYLCASSVGLA TYKYIFGTGTRLKVLA GAYEQFFGPGTRLTVL

4110 DNAJB1p.Q336R TRAV30*01 METLLKVLSGTLLWQLTWVRS TRBV7- MGTSLLCWVVLGFLGTDHTGAG / QQPVQSPQAVILREGEDAVINC 6*01/ VSQSPRYKVTKRGQDVALRCDPIS TRAJ34*01 SSSKALYSVHWYRQKHGEAPVF TRBJ1-4*01 GHVSLYWYRQALGQGPEFLTYFN LMILLKGGEQKGHEKISASFNEK YEAQQDKSGLPNDRFSAERPEGSI KQQSSLYLTASQLSYSGTYFCGT STLTIQRTEQRDSAMYRCASSADR EVDTDKLIFGTGTRLQVFP GWDEKLFFGSGTQLSVL

4095 KRASp.G12D TRAV12- MKSLRVLLVILWLQLSWVWSQ TRBV10- MGTRLFFYVALCLLWAGHRDAGI 2*01/ QKEVEQNSGPLSVPEGAIASLN 2*01/ TQSPRYKITETGRQVTLMCHQTW TRAJ12*01 CTYSDRGSQSFFWYRQYSGKSP TRJ10-3*01 SHSYMFWYRQDLGHGLRLIYYSA ELIMFIYSNGDKEDGRFTAQLN AADITDKGEVPDGYVVSRSKTENF KASQYVSLLIRDSQPSDSATYLC PLTLESATRSQTSVYFCASSDPGTE AAAMDSSYKLIFGSGTRLLVRP AFFGQGTRLTVV The amino acid sequences of the TRAV-TRAJ or the TRBV-TRBJ rearrangements, encoding for the hypervariable region of the TRA and TRB genes, used to construct each TCR are shown. The amino acid sequence of the complementarity determining region 3 (CDR3) important for peptide recognition is highlighted in grey.

Supplemental Table 3. Detection of peripheral blood neoantigen-specific TRB CDR3 amino acid sequences in the blood and metastatic tumor deposits from GI patients NCI-4078, NCI-4110, and NCI-4095 Blood Tumor CD8+ Bulk CD8+ CD8+PD-1- CD8+PD-1+ Peripheral blood T-cell Neoantigen 4078 CDR3 TCRB subset targeted rank freq rank freq rank freq rank freq rank freq

+ hi CASSLETSGLVGEQFF CD8 PD-1 DLATp.G294L 8803 0.0074 1192 0.0094 429 0.0363 - - 24 0.5906

4078 + hi

- CASSLIPGAGDEQFF CD8 PD-1 GBASp.E207K - - 11780 0.0019 - - - - 88 0.1969

NCI CD4+ Bulk CD4+ CD4+PD-1- CD4+PD-1+ Peripheral blood T-cell Neoantigen 4078 CDR3 TCRB subset targeted rank freq rank freq rank freq rank freq rank freq

+ hi CASSSSGAFQPQHF CD4 PD-1 TMPRSS4p.H233Y - - 2015 0.0057 - - - - 12 0.765

+ hi CASSVGLAGAYEQFF CD4 PD-1 PSMD2p.G644A - - 5150 0.0038 ------

Blood Tumor 4110-A Tumor 4110-B

CD8+ Bulk Bulk

4110 Peripheral - blood T-cell Neoantigen NCI 4110 CDR3 TCRB subset targeted rank freq rank freq rank freq

+ + CASSADRGWDEKLFF CD8 PD-1 DNAJB1p.Q336R ------Blood Tumor 4095-1 Tumor 4095-2A Tumor 4095-2B CD8+ Bulk Bulk Bulk Peripheral

blood T-cell Neoantigen

4095 CDR3 TCRB subset targeted rank freq rank freq rank freq rank freq

4095 - + +

CASSDPGTEAFF CD8 PD-1 KRASp.G12D - - 1 2.6800 1 2.8100 2 2.7100 NCI

CASSLGEGRVDGYTF* - KRASp.G12D - - 20 0.2100 26 0.2000 33 0.1600

CASSFGQSSTYGYTF* - KRASp.G12D ------

CASSLGRASNQPQHF* - KRASp.G12D - - 917 0.0200 1589 0.0100 2243 0.0080 We mined the tumor TRB deep sequencing data (bulk sequencing or T-cell subsets sorted to high purity from tumor) for the presence of the amino acid (AA) sequence of the TRB complementarity determining region 3 (CDR3) from each of the circulating neoantigen-specific TCRs identified. The frequency (percentage) and the rank of the specific CDR3 AA sequence in each population is shown. For patients NCI-4110 and NCI-4095, multiple tumors were resected and interrogated for the presence of the specific CDR3 AA sequences. – Not detected.*TRB CDR3 AA sequences exclusively detected in TILs, not in peripheral blood (15).

Supplemental Table 4. Immunohistochemical quantification of T cells infiltrating the gastrointestinal tumor specimens from the cancer patients studied Patient ID Tumor type Biopsy/ Infiltrating lymphocytes surgical site Description tumor periphery NCI-4078 Gastro- Adrenal CD4 2+ 3+ esophageal gland predominant NCI-4095* Colon Lung CD4 and CD8 1+ 2+ NCI-4110 Bile duct Omental CD4 only 1+ 1+ mass NCI-4114 Pancreatic Lung CD4 and CD8 1+ 2+ NCI-4166 Colon Lung CD4 and CD8 1+ 3+ NCI-4177 Pancreatic Liver CD8 1+ 2+ predominant T-cell infiltration was measured in 6 of the 7 patients studied. The level of T-cell infiltration was reported as: 3+ abundant, 2+ moderate, 1+ occasional, 0 none.

Supplemental Table 5. Expansion of neoantigen-specific lymphocytes enriched from peripheral blood of GI cancer patients Patient population Est. freq. neoantigen- Neoantigen Fold Est. freq. neoantigen- ID reactive (%4-1BB+) recognized expansion reactive (%4-1BB+) cells cells REP2 day 14 After REP2 After REP 1 + hi 4078 CD8 PD-1 6.5% *DLATp.G294L 7100 9.23%

+ hi CD4 PD-1 5.6% *PSMD2p.G644A 94000 92.1%

+ + $ 4095 CD8 PD-1 1.6% KRASp.G12D 12000 42.8%

CD8+ or CD4+ lymphocytes were sorted from peripheral blood of the patients indicated based on PD-1 expression as described in materials and methods and expanded using a rapid expansion protocol (REP) for 14 days. The estimated frequency of neoantigen-reactive cells after REP 1 based on 4-1BB+ expression within the populations indicated is shown. Next, CD8+PD-1+, CD8+PD-1hi or CD4+PD-1hi from the indicated patients were co-cultured with autologous B cells pulsed with long peptides* or $ + minimal epitopes derived from DLATp.G294L, PSMD2p.G644A or KRASp.G12D, respectively. Sorted 4-1BB lymphocytes were expanded in a second REP (REP2) for 14 days. The fold-expansion and the estimated frequency of neoantigen-specific cells based on 4-1BB expression is shown. Est. freq.=Estimated frequency.

Supplemental Table 6. Mutated epitopes screened for subjects 4078, 4095, 4110, 4114, 4166, 4177, and MM Patient Peptide Pos. Gene Mutated Amino Acid Sequence ID Pool within (PP) PP 4078 PP1 1 ACAP3 LCSVKPCEDIERSFCFEVLSPTKSC 2 NBPF9 YKVLVHSQERELMQLKEKLQEGRDA 3 NBPF15 TKITFEEDKVDSALIGSSSHVEWED 4 FAM171A1 SMSHINLLFSRRSSEFPGPLSVTSH 5 ZNF518A MQSPLLNSEQKKNIIVQTSKGFLIP 6 DLAT PTPSAPCPATPALPKGRVFVSPLAK 7 TMPRSS4 KQHVCGGSILDPYWVLTAAHCFRKH 8 OSBPL5 ESGSDQSETPGALVRRGTTYVEQVQ 9 SHANK2 EIDGSHLPNLQKDDLIDLGVTRVGH 10 FBRSL1 HRHTPQPPPPQPRLLPTHVPASLGA 11 G2E3 LAIPITNTYKEFHENMDFTIRNTLR 12 LRRC49 TVCPIINGEDHLCLLNFQHNFITRI 13 TBL3 LWALQDFSCLKTIEGHDASVLKVAF 14 SH2B1 RQQEPTTSHDPPPPPEPPSWTDPPQ 15 ZNF768 DSSYLLRHQRTHYGQKPYKCPHCGK PP2 1 ENSG00000135722 RVCRAWAAAATCSVWHDTKIRFHPV 2 ENSG00000135722 RVCRAWAAAATCSVWHDTKISQPSP 3 ENSG00000135722 RVCRAWAAAATCSVWHDTKIRRPTR 4 PIEZO1 GPTNCSSPHALVFNTGLDWPVYASP 5 TCF25 PRQRQRVYPKCTCLTTPKSTWPRYS 6 TP53 RCSDSDGLAPPQNLIRVEGNLRVEY 7 KMT2B PSQGLTASPADPPRTFAWLPGAPGV 8 ZNF180 CGKSFSQSYVLVEHQRTHTGEKPYE 9 GULP1 RIQDLETENMELKIKYKIWKTN 10 DNAH7 DLQDVQRYLKKARILNGKLDLAADK 11 CUL3 RYGCIRDHLRQTVLDMIARERKGEV 12 THUMPD2 SKDSHTDEPGIKKVLES 13 GGCX ELNPSNTDSSHSKPPESNPDPVHSE 14 ABHD16B PELGALVLDATFEDLVPLALKVMPH 15 PSMD2 VRLAQGLTHLGKATLTLCPYHSDRQ PP3 1 AIMP1 GDEKKAKEKIEKNGEKKEKKQQSIA 2 PCDHB12 TVTDLGTPRLKTKHNITVLVSDVND 3 TRIO QFQHAIEKTHQSTLQVQQKAEAMLQ 4 RICTOR RGYVAKQLEKWHGEYNSKYVDLIEE 5 MSH5-SAPCD1 EVARKELENLDSCIPSCSVIYIPLI 6 FAXC FSFYSRTETFEDAGAENSFSRTPDT 7 TSPAN12 LTHAWNFFQREFTCCGVVYFTDWLE 8 ING3 KSKNNNKSSSQQTSSSSSSSSLSSC 9 URGCP RNTTMVLDVLPDTRPVEKESQMEEE 10 GBAS HHLWAYRDLQTRKDIRNAAWHKHGW 11 BCL7B PSPQQSESLSPAYTSDFRTDDSQPP 12 ENSG00000147687 TNGILIFLLPKKN 13 HMBOX1 RYHANSMGQRSYRFEASEEDLDVDD 14 HSPA5 LEEIVQPIISKLDGSAGPPPTGEED 15 ANGPTL2 PSARPVPQPPPAGPPRVYQPPTYNR 16 POLA1 LKKKKYAALVVEATSDGNYVTKQEL PP4 1 IGFN1 EAGYRKDLGAPEGIGSGSKAGFRDG 2 ENSG00000116883 PAHLLPTSSLPIFPGLICCLLTCLL 3 ELTD1 VVGVIYNKGFLHTNFYIFGYLSPAV 4 WDFY4 CTQLTFFPALHERLHSEDFLELCRE 5 ENSG00000148926 KGASRSPEDSCLCSPSPRPQQSGCR 6 ENSG00000184956 MDTSRTQSVCRETGGAALS 7 OTOG PQLSQESPRTPTPRPALTPAAPLTT 8 RAG2 LPLGSPAVNCTVFPGGISVSSAILT 9 GALNT9 VSGDGVRASAATESGDGVRASAAMA 10 VWF QGDDFLTPSGLAGPRVEDFGNAWKL 11 GOLGA8CP GSPHDKPTAQPIMQDHQEHPGLGSN 12 PDILT SCKGVVESAALVIWLRRQISQKAFL 13 HS3ST4 GVEPHFFDRNYEEGLEWYRNVMPKT 14 NARR GTPRPRVIVGSPLARVADADPASAP 15 ENSG00000076604 CPEDQLPLDYAKLPHPYPQIYPDPE 16 MLLT6 CCVCSDERGWAETPLVYCDGHACSV PP5 1 KRT10 GGSSGGGYGGGSSSGGHGGGSSSGG 2 ADAMTSL5 QTPTLAPDPCPPSPDTRGRAHRLLH 3 ZBTB45 FSHRALLERHLAVHPAP 4 THNSL2 FMPEELPQLDRGPLCQWSTLSYPGL 5 ENSG00000144115 MELPQLDRGPLCQWSTLSYPGL 6 JPH2 PASPASDGPALPLPAIPRGGFALSL 7 ENSG00000179253 YDFDHLLSPALPSSTSVAREGPSLI 8 PCDHB15 YEALQAFEFRVGTTDRGFPALSSEA 9 MAK IFKICQVLGTPKNSDWPEGYQLASS 10 RIMS1 RDMAKPAACKTPGNAENQPHQPSPR 11 NEFM RSNEKEQLQGLNNRFAGYIEKVHYL 12 PREX2 QWVYNSIESAQEYLQKSHSKPPGDE 13 ACTL7B RPTYFISSTVGKCCPEAADAGDTRK 14 ADAMTS13 VRRILYCARAHGKDDGEEILLDTQC 15 ZNF658 CNECGRSFAHISDLKAHQRIHTGEK 16 IDNK KDGVALKCEESGNEAKQAEMQLLVV PP6 1 GABRA3 DSPTETKTYNSVRKVDKISRIIFPV 2 PLXNB3 PGISSQHFTYQGGVGGSWPVCSGLG 3 DCAF8L2 NTTVKGVNFYGPMSEFVVSGSDCGH 4 NYX VLEHLLLNDNLLSELPADAFRGLRR 5 ZNF157 KIFSMKKSLCQHLRTHTGEKPYECS 6 KDM5C AERHGSRARGRARERRRRRKVDRGG 7 ENSG00000268674-1 RAGTGASREEGTFGQNVWDKSDGSS 8 ENSG00000268674-2 GTFGQNVWDKSDGSSIQVPQKMRVR 9 ENSG00000268674-3 SDGSSIQVPQKMRVRKMRAQT 10 AGAP6-1 EVGEDLHMHHVRDGRCLKLWSLTFL 11 AGAP6-2 VRDGRCLKLWSLTFLPIQSQAQYSR 12 AGAP6-3 SLTFLPIQSQAQYSRGTLKQKLWSL 13 AGAP6-4 AQYSRGTLKQKLWSLTLLPIQRQAQ 14 AGAP6-5 KLWSLTLLPIQRQAQYSRGTLKQML 15 Ex_ENSG00000204149-1 EVGEDLHMHHVRDGRCLKLWSLTLL 16 Ex_ENSG00000204149-2 VRDGRCLKLWSLTLLPIQRQAQYSR 17 Ex_ENSG00000204149-3 SLTLLPIQRQAQYSRGTLKQML PP7 1 FAIM2(1) GMKAGAFPPAPTVVPLHPSWAYVDP 2 IQSEC1 GHHTQYCHMQNPAPYHHHHHHHPPQ 3 ENSG000000148926(1) MGSQVAFVPPPPARSSPDAA 4 KRTAP9-7 PTCCRTTCWKPTIVTTCSSTPCCQP 5 FBXL8 RVCRAWAAAATCSVWHDTKISCECE 6 GPR182 QPKSRRHCLLLCTYVAVFVMCWLPY 7 NEK11 LLSKLDHPAIVKLHASFVEQDNFCI 8 ARIH2 NHMQCSKCKHDFRWMCLGDWKTHGS 9 VPS41 WKDNVTLIIGWGNSVKVCSVKERHA

NCI- PP1 1 KLF5 ATYFPPSPPSSEAGSPDRQAEMLQN 4095 2 ZC3H3 HGPRKPSASQRPPRQTPSSAALTAA 3 WRNIP1 MEVSGPEDDPFISQLHQVQCPVCQ 4 SENP2 LMVGNHALIQGLNKEKFDLLLVDPN 5 UGT8 ATRIQIALKYDENNKQFAILIIQLS 6 WWC1 SDQGENVAEINREVGQKLGLSNGGQ 7 PEX1 MTEYKLVVVGADGVGKSALTIQLI 8 KRAS GDPSYPWLADSWTATSLPVNNSNSG 9 ROBO2 KGLVLRQHGIRLMEAQIATGGIIDP 10 PGBD1 YKRRPEVDPLPFLGPFPAGPLAVAG 11 PLEC QMKQSRGADLKNWALVVYEMVPSNS 12 ESRRA EEDPVLPPVPDGTGEPTVPEGAIWE PP2 1 LIX1L LLEELANSDPKLSLTGVPIVQWPKR 2 TACC2 VFTPYSAAFLLKDTEEGPPATECGY 2 KDM2A QMKQSRGADLKNWALVVYEMVPSNS 3 KCNH2 EEDPVLPPVPDGTGEPTVPEGAIWE 4 PCSK5 LLEELANSDPKLSLTGVPIVQWPKR 5 KCNN3 VFTPYSAAFLLKDTEEGPPATECGY 6 DNAJB6 FFFLLRSKGECHHSCPDHYYVEQST 7 FAM109A SVAVGTTHTPISYSPIGVSSTSFPT 8 DDX60 DALAEERMRRGQTALPAQPAGLRPP 9 DUOX2 QSHPCLLPQPRSPPCPCPAGPVPSR 10 COL17A1 DAEYAYFNFPELISLRTALILHLQK 11 WISP1 YWFENTRNGLFSNKEIEDIRNTTLR 12 COL17A1 GAGGGPWGPAPAGCPCGSCCSWWKW 13 WISP1 VLATALSPAPTTKDFTPAPLEDTSS PP3 1 AGAP3 SSSPKLDPPPSPPSNRKKHRRKKST 2 ZC3H3 ALRGKSSPVLKKPPNKGLVQVTTHR 3 C8orf82 RLYHPAPERAGGGGLVRSALAFELS 4 LINC00115 VFHRPHPRPSWPHRAALGFGRRQSS 5 TRIM11 CAACERSGEHWALRVRPLQDAAEDL 6 CPEB3 DPRKTIFVGGVPLPLRAVELAMIMD 7 PRB1 PQGPPPQGGNRPLGPPPPGKPQGPP 8 PRG4 AGGAEGETPHMLFRPHVFMPEVTPD 9 HLA-DQB1 TVEWRAQSESAQRKMLSGVGGFVLG 10 ZNF717 GICHRSLVELQEL 11 MUC4 VSTGHTTPLPVTYTSSASTGHATSL 12 MCHR2 PLCTIITSLDTCTQFACSAIMTVMS 13 OBSCN WHKGMERIQPGGWFEVVSQGRQQML PP4 1 DSPP SNSSDSSDSSNSRDSSDSSDSSDGS 2 ADAMTSL2 EQAGGGACEGPPWGKGFRDRNVTGT 3 RSAD2 QIKALNPVRWKVLQCLLIEGENCGE 4 AEBP1 EEWTPTEKVKCPRIGMESHRIEDNQ 5 AKAP6 EALKKGGVLLPNYLLEKVDSINEKW 6 TMEM132D SSSMGLMEGRGTMTDRSILQKKKGQ 7 DPY19L2 FEKVIFGILTVMPIQGYANLRNQWS 8 ARL14EPL DFNPETRQQKKKSRMSKMNEYFSTK 9 SPTB MRETWLSENQRLMAQDNFGYDLAAV 10 PPM1K NCAWSAALDLEPMDTICGASVEREI 11 TTN SWFKDGKEIAASERYRIAFVEGTAS 12 IL17F GIINENQRVSMSHNIESRSTSPWNY PP5 1 FRMPD1 SVKLLARQCTALMAAVFCLTQKFRA 2 LRFN5 GCIQFTTEQDYVHCHFMQSQFLGGT 3 ANKRD18B NEEMITKKVAQYLQQLNDLKAENAR 4 NPC1L1 GSGIQPLNEGVACCNESQGDDVATC 5 PCDHB3 NFEAINSYEVDIKAKDGGGLSGKST 6 LRRC4 LTVIPSGAFEYLYKLRELWLRNNPI 7 MAGI2 ELQQIIRDNLYLCTVPCTTRPHKEG 8 LMOD1 PKPSPQPSPKPSTKNSPKKGGAPAA 9 ZNF853 ELMVLPAVAAPAMVAIPGPAGSAAL 10 TENM3 APDPGNLAALGSFPHGHSEGAPRQE 11 MYO1G GTITDRIFLQTLVMHHRHHLHYTSR 12 SYT7 TTSQSLGQLQAHLASAPGPNPRAYG

NCI- PP1 1 DNAH1 DKRRKGVFGPPLRRNFIFFIDDLNM 4110 2 PCDH10 KALGHSDRCWMPYFVPSDGRQAADY 3 TRIM2 FTLSLRLYDQHIQGSPFKLKVIRSA 4 FSTL5 IHTQPVGKQFDRLDDFFIPTTTLII 5 C4orf22 KILNVDPKAQPGGNSTRITILTELY 6 PDHA2 DEICLTLYGDGAVNQGQIAEAFNMA 7 42069 LVWLREQIVHGGEPIWLEHAAPPFN 8 SLC6A3 PAKEPNAVGPKELELILVKEQNGVQ 9 SLC34A1 SSTSTSIIVSMVPSGLLEVSSAIPI 10 MCTP1 GPGAHLCHQKSSFLPGTACLEQLLE 11 KIF25 RASQGALAPQLVLGNPAGHAEQVQA 12 TRERF1 PRVLGDHLLLDPPHELPPYTPPPML 13 ZAN ISPEKPTISTEKHTIPTEKPTIPTE 14 MUC12 TTLSPASMTSLGIGEESTTSRSQPG 15 MUC17 SPEASTLSTTPVNSNSPVITSTEVS PP2 1 CNTNAP2 RVTAERNVKQASQQVDRLPQQIRKA 2 NFE2L3 LDINIFDEINLMLLATEDNFDPIDV 3 CARD11 METLKDEEDALWDNVECNRHMLSRY 4 IKZF1 MGCHGFRDPFECSMCGYHSQDRYEF 5 STEAP4 FVLIMPCVDNTLKRIRQGWERNSKH 6 RP1L1-2 GVEAPEAEGDAQPESEDVEAPEAEG 7 OXR1-1 QGDLGCGSPPHRSPAPSSPEGPDTG 8 OXR1-2 QGDLGCGSPPHRSPAPSSPEGPDYY 9 KIFC2 AVLHAPVPTTARVRLSRPQRACPSS 10 KCTD9 TPTKSELRCQGLKFSGADLSRLDLR 11 AKNA SFTIPQPRSAEWGPGPAEDPQASAA 12 BARX1 PFHSHLAVLKAELAAVFKFPLAPLG 13 RBMXL3 GRDRVGRPDRGLSLPMETGSPPLHD 14 GLUD2 DCDILIPAATEKKLTKSNAPRVKAK 15 FAM47C TGVSHLRPEPPKTRVSSLRPEPLET PP3 1 SLC7A3 MPWQAFRIFGQKLVRRRTLE 2 TGIF2LX LPLWPLPKGQMSIEKQPDPESAPSQ 3 PRDM13 RSAFKPAGLARAGAAAHGDPYREES 4 GRID2IP RAPRCGRGLALGCELLRLAGRKRPD 5 RTKN CSPASVAPAPDWAHPLPWGRPRTFS 6 KIFC2 GAGQVCACRSPPPRARPPAPLARRS 7 RTKN SPASVAPAPDWTPPLPWGRPRTFSL 8 DBF4B PCLPVSQPWSQPPPQPQPHAGRELL 9 ETV3L GELPGVASFTPPHPPPLPSNWTCLS 10 SELP-1 RFRQKDDGKCPLIPHSHLGTYGVFT 11 SELP-2 VPTCQDDGKCPLIPHSHLGTYGVFT 12 EXOC8 GASRLRRQLESGSFEARLYVKQLSQ 13 CSMD2 SEELLCLSGERRNWDRPLPTCVAEC 14 KANK4 REQRIRELEFTVDQLEGQFHQENAK 15 CLCA1 MFAQHVDSIVEFYTEQNHNKEAPNK PP4 1 CNNM1-1 FEPGLGLRQMLAVPL 2 STK32C WSVGVMAYELLRRWRPYDIHSSNAV 3 ADAM8 PSRGPQELVPTTPPGQPARHPASSV 4 SSRP1 TTGKNEVTLEFHRNDDAEVSLMEVR 5 OR52E8 ILSYVRILYAVFSLPSWEARLKALN 6 CDHR5 TSTSHQPATPSGVTAQTPEPGTSQP 7 TCIRG1 ATLVVLALAMVPVLLLGTPLHLLHR 8 DDX47-1 LDIPHVDVVVNFHIPTHSKDYIHRV 9 DDX47-2 LDIPHVDVVVNFHIPTHSKVSPIAN 10 BICD1 KSKIGSPKVSGESSVTVPTIDTYLL 11 KRT84 EIATYRRLLEGEKSRLCEGVGPVNI 12 ZIC5 GTPVGAPLSPVLEPARSHSSTLSPQ 13 IL25 EELLRWSTVPVPLLEPARPNRHPES 14 SIPA1L1 PKNIRSHFQHVFAIVRVHNPCSDSV PP5 1 CYP11A1 TLQRYLVNDLVLQDYMIPAKTLVQV 2 ACAN VPSPGEEEGGTPSSPSGVEEWIVTQ 3 ZNF768 AQSSKFQEGAEMVLNPEEKSPLNIS 4 PIGQ MWWALGPPGILPPGMVLK 5 HYDIN-1 DQEHIPFGPVVYETQATRRILMMNT 6 RBFOX1-1 LVLSSLQASIYRRGYNRFAPY 7 RBFOX1-2 TYGVGAMASIYRRGYNRFAPY 8 HS3ST3B1 PALATAPDGTPPSLPFRAPPATPLA 9 FAM64A LPLRAVNLNLRAEPSWKRLETPEPG 10 SIRT7-1 MRLLMAELGLEILAYSRWQDPIFSL 11 SIRT7-2 AGISTAASIPDYQGPNGVWTLLQKG 12 SIGLEC15 RPEHLDTPDTPPQSQAQESNYENLS 13 DCC VPTLESAQYPGIFPSPTCGYPHPQF 14 SOGA2 QEEVELGGTRWNSLDSKPILWHWDR PP6 1 SOGA2 WNSLDSKPILWHWDRQVCAGACGEL 2 DCAF15 FCQILYDHSTCPQAPASPPEPQSPE 3 DNAJB1 ERIPQTSRTVLERVLPI 4 MYO9B LPRWAPGAREAAVPVRRREPPARRP 5 UBA2-3 NLSAKRSRIEQKKELDDVIALD 6 LAIR1-1 PSISAEPGTVIPPGEPCDFRVPGPG 7 LAIR1-2 IPPGEPCDFRVPGPGWGSNIPPGEGE 8 BRSK1 FRDRERLHRELRIEEENQEKMIYYL 9 FBLN7 RPCRHLPKTISFNYLSLPSNLKTPI 10 DCAF17 QQKLDLGCACRWDGTTGTVGEAPFG 11 TTN PPIVETLKNAEVMLECELSGTPPFE 12 EFR3B SVAVEEQERERRQQVVEKFQKAPFE 13 THADA TGQEQSFPSLGSFNSRGALGALMAC 14 SIRPD MPIPASLLHPPLPSLLLYL PP7 1 LCE1D CGSNSGGCCSSGRGGCCLSHHRRHR 2 NUP210L KTYLTNTLNSTVLKLFITTGRNGVN 3 FCRL3 AAAALLHYARARKKPGGLSATGTSS 4 KIAA0754 AASVPTSEEPASQAAAVSNPEEPTS 5 ANKRD13C AHYPVHECVFKGNVRRLSSLIRTHN 6 SSX2IP RILKSHVEKLDNHVSKVHLEGFNDE 7 CDC7 DLTALAQIMTIRRSRETIQAAKTFG 8 CNNM1-2 RTFAVSRGDSLARSPVNRSPSRCSG 9 C10orf2 PLISRRDAEVVLASRELDSLALNQS 10 SMC3 EGDQVSHRGALTEGYYDTRKSRLEL 11 USP6NL DRTPFTLNLRIWVIYIFEGERVLTA 12 EIF3A-1 EDDRGPWRNMDDMDDNRLSRRADDD PP8 1 EIF3A-2 DDMDDNRLSRRADDDRFP 2 GJD4 PTEKSLLMLFLWSVSALSFLLGLAD 3 ZCCHC24 CSWQFSRTSSTCSCQSSRTSSTSCS 4 OR52A1 IAAVVRSFFICCLFIFLVYRLTYCG 5 DCHS1 KVMAVSGSKAELRQQTGTATVRVSI 6 TMTC1 ADVLACLLFLLAILSYNRSLDQGCV 7 SLC38A4 LVILVPTIKYIFRFIGASSATMLIF 8 POTEG GSSKSNVGTSGDNDDSAMKTLRSKM 9 ESR2 SRKLAHLLNAVTYALVWVIAKSGIS 10 HERC2 KMIVDPADSSYMRSLVVVSGGNSLN 11 ATP8B4 CEVPNNKLDKFMVILSWKDSKHSLN 12 ACSBG1 ELIITAGGENVPSVPIEEAVKMELP PP9 1 ZKSCAN2 DSDDDEIGIEFICKSEIHGAPVLFQ 2 HYDIN TQATRRILMMNTVDVGARFKWDIKK 3 CTU2 GEDYGEPAPEEPTPAPRPSREQKCV 4 SLFN5 AIKVEKFCCAVFIKVPSSWQVKDNR 5 KRTAP4-7 ETTCCHPRCCISTCCRPSCCMSSCC 6 ACLY DIGALNGIFVLGWSMGFIGHYLDQK 7 RND2 ERSVRDVFHVATLASLGRGHRQLRR 8 SCN4A NLFLALLLSSFSATVWQPRMRMAR 9 FADS6 SLFALPAGFLCLHWENALVFASGIT 10 TP53 NSFEVRVCACPGSDRRTEEENLRKK 11 ODF4 QNSPLPFQWRITQSFRWMAQVLASE 12 KIAA1328 PQRGTVTGVRKDESTSPMPTGSLKD PP10 1 MTCL1-1 CPGRGPEGTWQEEVELGGTRWNSLD 2 MTCL1-4 WHWDRQVCAGACGELLCSSDRGTAH 3 MTCL1-5a ACGELLCSSDRGTAHCRHCPPPVSA 4 MTCL1-5b RGTAHCRHCPPPVSADREHLEV 5 ZNF98 FAQDLWPKQGKKKYFQKVILRTYKK 6 ZNF99 TVHKVIHTAEKPFKCEECGKAFKRF 7 UBA2-1a AQPSTSTAQEQDNVLIVDSNEEDSS 8 UBA2-1b QDNVLIVDSNEEDSSNNADVSE 9 UBA2 DSSNNADVSEEEKSRKRKLDEKENL 10 SRRM5 ARDCSRSRSPYKERDRSRSRSPNKA 11 OPA3 CSCLMLEYWRHQSQQRRKEKERRVA 12 ZNF628 VCGKSFTQSTNLLQHQRVHTGERPF PP11 1 PNPLA6 NMRSWCSGHLHLCCPRRLFSRRSPA 2 GMEB2 TLKDWKRAIRMNSIMLRKIMDSGEL 3 SON ASNTMDSQMLASTTMDSQMLATSSM 4 ATP11B FLSKLLFVHGHFHYIRIATLVQYFF 5 ACAA1 GIRPSTTMEGLAELKPAFKKDGSTT 6 OR5H6 IGTILISYTIILLTILEKKSIKGIR 7 LPHN3-1 EDNRPFIKSWVICAIALLCLLGLTW 8 LPHN3-2 SGCLDNIKSWVICAIALLCLLGLTW 9 DDX41 SLLDQHQHLKEKPEARKESAKEKQL 10 IRX1 PYGQFQYGDPGRHKNATRESTSTLK 11 SREK1IP1 VRAGCKKCGYPGYLTFECRNFLRVD 12 BVES RFLCWSRERLTYVLESEPFLYEIFR PP12 1 TAAR5 NGSCPRTVHTLGSQLVIYLACAAGM 2 OLIG3 SPDMDEMYLRDHPHRHHHHQESRLN 3 ARID1B MMVPDQRINHESKWPSHVSQRQPYM 4 DPCR1 APPTSEENSSNQRKDPMIRNQRSVD 5 MDGA1 KNGKPARMSKRLRVTRNDPELPAVT 6 PKHD1 DLTSGTEPFCGRLSLRQPRHLVLTP 7 TES EHDVLLSNEEDRNVGKLFEDTKYTT 8 TTC26 GACVGIFQMIIAEREPKETLREVLH 9 GPC2 CLNVVRGCLSSRRLEPDWGNYLDGL 10 RP1L1-1 QEAEEAAQEAEGESQPESEVIESQE 11 GML FALLLAMELPLVSASATMRAQWTYS 12 PCMTD1-1a AMKPEEPPQNLLTEKIMKLTLPESL 13 PCMTD1-1b LLTEKIMKLTLPESLKAYLTYF PP13 1 RXRA CEGCKGFFKRTVHKDLTYTCRDNKD 2 PRSS3-1a TRIQVRLGEHNIEVLEGNEQFIYAV 3 PRSS3-1b NIEVLEGNEQFIYAVKIIRHPKYNR 4 ALG13 NLKPVTQVMSVPPWNAMPSRKGRGY 5 SMARCA1 SQMTRLLDILEDDCMWRGYEYCRLD 6 SASH3 TQKKKLSLQRSSIFKDFAKSKPSSP 7 MAGED2 MPATETKKVSHVSDTKVNTKAQETE 8 AWAT2 RGGRRFTCVRHWHLWKHYSDYFPLK 9 AQP7 TDQENNPALPGTHALVIGILVVIIG 10 IGFN1 SKAGFRDGLGSSEEMGSVNEAGYRK 11 FAM186A PLNPQQAQTLGITLTPKQAQALGIP 12 NPIPL2 KPKRRRADEVEQPPKPKRQREAEAQ 13 IGFN1 SVNKAGYRKDLGDPKGMGSGSKASF

NCI- PP1 1 MSTO1 PYHRGEAQRNIYCLLNTAFGLVHLT 4114 2 NUF2 LVTHLDSFLPICWVNDFETADILCP 3 GPAM LLGPLLEAYSSAVIFVHNFSGPVPE 4 CORO1B RMSERQLALWDPKNLEEPMALQELD 5 PIWIL4 VGCVASVNPRITSWFSRCILQRTMT 6 SVOP TSVVFVGMMSSSMLWGNISDQYGRK 7 WDR66 SIVNWYSHLKLGTIRTLSFSKTPAT 8 SKP1P2 MLCHATVVASSSAFLF 9 ENSG00000185958 PGISLTTQQAQKIGIPLTPQQAQAL 10 ZMYND15-1 KPAQGSGARPAPGPPPPTPIPNSLC 11 ZMYND15-2 PGPPPPTPIPNSLCSSCPHPKAPRR 12 ZMYND15-3 LCSSCPHPKAPRRKETWAGGPPAEM 13 TP53-1 TCTYSPALNKMFRQLAKTCPVQLWV 14 TP53-2 NVLYSPALNKMFRQLAKTCPVQLWV 15 TP53-3 SGTAKSVTCTMFRQLAKTCPVQLWV PP2 1 DHAH17 LGSLDGTLESMEKIPSSLDNLLLHA 2 NTN1 TWARRLRKFQQREKGKCKKA 3 ZNF486 KAYTTSSNLTEHMTTHTGEKPYKCK 4 ZNF626 AFKYSSTLTTHKIIHTGEKPYKCEE 5 ZNF91 LTKHKIIHSGEKPYKCEECGKAFNR 6 ZNF681-1 KPYKCEECGKAFSQSSHLTTHKIIH 7 ZNF681-2 PYKCEECGKAFNKSSHLTRHKIIHT 8 ZNF254 CEECGKSFSQSSNLTTHKIIHTGEK 9 ZNF57 QFKANGSVSLQDIYGQEKSKEQTIP 10 ZNF304 SHLVQHKKVHTGERPKECSECGKFF 11 MUC16 LVFSQSSENSETPALVDSSAGLERA 12 ZNF121 FRASSHLQKHVRNHTGEKPYICNEC 13 WNT10A RPHNRNGGQLEPCPAGAPSPAPGAP 14 ADRA2B FLVSLAAADILVTTLIIPFSLANEL 15 SEZ6L IPALSPLLPEEACPKHALPPKKKLP PP3 1 SCN10A GVTDDGVFPGDHKSHRGSLLLGGGA 2 YIPF5 YDYSQQGRFVPPNMMQPQQPYTGQI 3 TTC26 AVYLQQIPDSTITLNLKACNHFRLY 4 ZNF853 QVLQQQEQLQQQLQEQQLLQQQQEQ 5 TFPI2 CEGNANNFYTWETCDDACWRIEKVP 6 CSMD3 WEPGKRRCAKCGHLDFILMKKMGIK 7 VPS37A LMDKQGVYVTSPSVNNFTMHSDLGK 8 DENND1A TAWSGSTLPSRPPTPNVATPFTPQF 9 NOTCH1 GLCVDAGNTHHCCCQAGYTGSYCED 10 HIATL2 LSDVWGRKPFLLSTVFFTCFPIPLM 11 KIAA1210 MRAGWTPQGFSAFHASLLPG 12 KCND1 LAEDEEAEQAGDSPALPAGSSLRQR 13 HUWE1 PDIFTEVANCCIHIALPAPRGSGTA

NCI- PP1 1 AMBP TPPDNIQVQENFSISRIYGKWYNLA 4166 2 GOLGA8J PPAVPSEVELQHVRKELERVAGELQ 3 PPFIBP1 KMMSDASDMLAASLEQMDGIIAGSK 4 HLA-DQA2 IVVGTVFIIQGLCSVGASRHQGLL 5 ZNF727 GKAFGLCSIFTEQKKIFSREKCYKC 6 ING5 SGGRGLKSKSVNYFFFILLLL 7 SCN9A ACFTDGCVRRFSYCQVNIESGKGKI 8 PDE4DIP LPGAKPGPSMTDELVPVSLTGL 9 DNAH1 EFRVIFDSLEPHQEPLPGIWDQYLD 10 RNF133 SKYSETWLALIEWGGCTFTQKIKVA 11 CXorf22 SVRLQKKQAEREHMYSYDDTDIGLE 12 GBA3 HYRFSLSWSRLLRDGTTGFINQKGI 13 MAP3K5 GGSLSALLRSKWAPLKDNEQTIGFY 14 ENPP6 LQDRLNVIIFSDQGMTDIFWMDKVI 15 ATAD3A ADIIREQIRLKASEHRQTVLESIRT PP2 1 SCN9A ACFTDGCVWRFSYCQVNIESGKGKI 2 SLAIN1 MVVVGLCLRLLLFFR 3 GBA3 HYRFSLSWSRLLRDGTTGFINQKAI 4 MDH1B LFDNKQAEEHLKRLVVETQDLASPV 5 ZKSCAN3 QFLTILPGNLQSCVREQHPESGEEV 6 FRMPD1 PDRACLASNPGLYNVSQGDTLELQL 7 VWF AFVLEGSDKIGETDFNRSKEFMEEV 8 CD19 YENEDEELTQPVTRTMDFLSPHGSA 9 ANKRD30A HIHEQIMEYIRKSSKNHQNTNPEGT 10 TP53 YMCNSSCMGGMNWRPILTIITLEDS 11 STARD9 ATVPRPPCRSKLMSCSSLSPQRLCS 12 ARHGAP11A YESVGWRLANQQTLKNRIESVKTGL 13 FAT4 ASPRGSEAPVEYFIVSVRCEEKTVG 14 MST1 QCQRWSAETPHKLQFTFTSEPHAQL 15 FANCM DIKAVQQVITNLPIGQIELRSEDSP PP3 1 PPFIBP1 MMSDASDMLAASLEQMDGIIAGSK 2 FANCM YCQAVQQVITNLPIGQIELRSEDSP 3 ANHX HYRLVMRRLGVAVLTPVQKFRCRKR 4 NTMT1 GMLGGYGHISSIGINSSRKFLQRFL 5 SUN1 AIQGNGDVGAAATTAHNGFSCSNCS 6 TTN GGSMITGYIVEKHDLPDGRWMKASF 7 TP53 YMCNSSCMGGMNW 8 CCDC64 SMQVHALREDFRDKNSSTNQHIIRL 9 SLC26A1 FANLIYFLMGTSWHVSVGIFSLLCL 10 RUFY3 LDVEKELEMQISIRQEMELAMKMLE 11 GATA2 HSGHILPTPTPIPPSSSLSFGHPHP 12 C2CD5 TNCQSSCTEGEVAT 13 MFSD8 VVRSYTAGATSLLERTSSMANISMC 14 UBE3C GRIGPLQSTLDVSLESPPLSVSEER 15 NOD1 EMEIIPSESHPHLQLLKSNRELLVT PP4 1 CNTN5 IVVICSAEGEPSDAPTDVKATSVSV 2 NYAP2 SGRSLLRKSSSGQRSKEPAEKSTEE 3 MST1 SASAGPLRRRTSCSSRLPPNRMHNW 4 PRLHR SLQLVHQLKGLIMLLYSVVVVVGLV 5 UBE3C SELIKVLKCVLVSLESPPLSVSEER 6 EBF1 CRVLLTHEIMCSHCCDKKSCGNRNE 7 ATR TQDIASDLCQLSAQTVFSMLDHLTQ 8 KANK1 INDPKALTSKDMSFCLNTLQHEWFR 9 TNFSF13B IYGQVLYTDKTYTMGHLIQRKKVHV 10 NPLOC4 VYTFSISQNPFPVENRDVLGETQDF 11 WNK3 CDNIFITGPTGSLKIGDLGLATLMR 12 PLEKHH1 RSETGQYATYCQWAVERTLRTGERE 13 MCAT AVEPLTQALKAVNIKKPLVSVYSNV 14 NPAS1 SSSSSSSLADTPKIEASLTKVPPSS PP5 1 HIST2H2BF GPRALAAAAPRYGRRLQYAHAATVW 2 WNT8B ERALQLSSHGGLHSANRETAFVHAI 3 OR10K2 TLVLAIPLLLILLSYVHILSAILQF 4 KIF7 LEVGTASRDIQLWEDERGNVVLCGV 5 SUN1 GDVGAAATTAHNGFSCSNCS 6 SIGLEC11 VAALLAFCSCLVIFRVKICRKEARK 7 NPAS1 SSSSSSSLADTPKIESATTWTWGPQ 8 AKAP6 GDAVNVLKQKFTNEGESIKLPNSSQ 9 OR9K2 LRNKDVQEALKKILEKKNIIL 10 RYR2 PNIFLGVSEGSAHYKKWYYELMVDH 11 USP24 SSIRVEEIIPAAQVAIQTMEVSDFT 12 GP1BA DRCELTKLQVDGMLPVLGTLDLSHN 13 WNK1 EMYEEKYDESVDIYAFGMCMLEMAT 14 KANK1 TLREADAGGSHESFCLNTLQHEWFR 15 PSD2 YHLEGFQRCDVAWQLGKNNEFSRLV

NCI- PP1/TMG1 1 KDM6A-1 KSCSNTSALAARSKYLQNTSDNWSG 4177 2 ZNF233 LLTTSSATSLAQYPRIHRPGLLQQL 3 OR5W2 AVFLAVYIINFSENLGMIVLIRMDY 4 MMP14 KAFRVWESATPLCFREVPYAYIREG 5 USP51 PSLCLVCEMSSLCHAMYSGSRTPHI 6 TRIM42 HLVNHLNCPMCSQLRLHSFMLPCNH 7 NLRP8 KRCQYLHEVELTITLNFMNVWKLSS 8 ETV6 TNMTYEKMSRALRHYYTTTN 9 DCHS1 RAPGSGTATSGGEGRTRREAPRELR 10 ZNF880 QRIHTGEKPYKCNECGKVFTQNSHL 11 PAQR5 FDYIGHSHQLFHMCVILATHMQMEA 12 ANKRD36C GANIEECSEDEYSPLFLAVSQRKVK 13 TP53 SQKTYQGSYGFRQGFLHSGTAKSVT 14 OR7D4 MDTFLLAVMAYDWFVAICHPLHYTV 15 UBE3D-1 ICKRCKVMLGETLSSGKNFITRSQN 16 PXDN RGINPHRLYNGHTLPMPRLVSTTLI PP2/TMG2 1 PLA2G4B PHLCLLDVGYLISTSCLPLLQPTRD 2 MC5R SSPCEDMGIAVELFLTLGVISLLEN 3 UBE3D-2 ICKRCKVMLGETLSSETTKFYMTEI 4 NDUFA4L2 TRASPGLVAMTTTLSQRWDRKNNPE 5 RHPN2 DFFQKLGPLSVFLANKRWTPPRSIR 6 PASK NLKELFFSDQTDRTSSNCSCATSEL 7 KDM6A-2 KSCSNTSALAARSKYLQACKPHHPN 8 MAGEC1 FEGFPQSPLQIPLSSSSSSSTLLSL 9 TRIM17 VEEEQRLLQALEKEEEETASRLRES 10 SPATA31A6 QAKGKPSPWQSSMSTGESSKEAQKV 11 ZNF91 CGKAFSRSSTLTNHKTIHTGEKPYK 12 SHANK1 AGLGSQEKSLPARPPAARRSLLHRL 13 KMT2D ASRLSPPPEDSPLSPPPEESPMSPP 14 PRAMEF4 STLEELPTELFPQLFMEAFSRRRCE 15 HCN3 DSPATLLARSAWCSAGSPASPLVPV 16 MYT1L EDGCHERDDDTTPVNSDRSEEVFDM PP3/TMG3 1 SNX17 GQQLREGSFRVTCMRCWRVTSSVPL 2 CNTNAP2 PWGVFLENMGKEGFIKLELKSATEV 3 KDM6A-3 KSCSNTSALAARSKYLQAQLCNLPQ 4 WDR5B TENLIASAALENYKTIKLWMSNH 5 KRAS MTEYKLVVVGAVGVGKSALTIQLI 6 ZNF710 HQNVRPFVCTECSMEFSQIHHLKQH 7 HPSE2 HCYIDGRVVKVMVFLKTRLLDTLSD 8 EIF2B1 TLLFTDLGVLTPSMSSSSSIC 9 EMR1 NIFSVLDKVCENNTTVVSLKNTTES 10 MYT1L RNPDMEVDENGTPDLSMNKQRPRDS 11 NAALAD2 GYPAKEYTFRLDGEEGVGIPRIPVH 12 POTEG SGDHDDSAMKTLSSKMGKWCRHCFP 13 ZNF555 KPYECKQCGKAFRLSACFREHVRMH 14 PDGFC PQHERIITVSTNESIHSPRFPHTYP 15 ZNF287 KAYRQGANLTQHHRIHTGEKPYKCN 16 PCDHB4 ENNSPALHIGSVRATDRDSGTNAQV PP4/TMG4 1 SLITRK2 CENKGFTTVSLLQPPPVSNLSAFSQ LLQPPPVSNLSAFSQWKPLDKTVSK SAFSQWKPLDKTVSKRICQLLQRGD KTVSKRICQLLQRGDSSPR 2 TTC9C STSPAHSLLLPGRGGGGSNRKAEAS PGRGGGGSNRKAEASVPGVLTPATI KAEASVPGVLTPATIPE 3 ZMYND15 KPAQGSGARPAPGPPPPHPHPQLPL APGPPPPHPHPQLPLLLLPPPEGAE PQLPLLLLPPPEGAEEKRNLGGGPA PEGAEEKRNLGGGPAGGN 4 PIEZO1 EEEEDSRDEGLGGATPHQATQVPEG 5 ZNF81 KTIGHGQVFTQNASYSHHENTHTGV

NCI- No PP 1 MM DSPP DSSDSSDSSDSSESSDSSDSSESSD 2 FAM155B VPCKQYCLEVQTQCPFILPDNEEMV 3 FAM71F1 SFPHRKTWRKSKTTVKVTRSYPTFP 4 FANCM TKIVSLKKKVSKDIKKDQLKKENNH 5 FOLH1 TPGYPANEYAYRHGIAEAVGLPSIP 6 IVL EGQLKHLEQQEGSLEHLEHQEGQLG 7 JAKMIP1 VLRDGAADKVKTVLLTEAREEARRA 8 KIRREL GATIGASILLIFHFIALVFFLYRRR 9 KRAS MTEYKLVVVGADGVGKSALTIQLI 10 MUC4 LHVTDASSASTGHATPLPVTSLSSV 11 NRG1 AQEPVKKLANSRQAKRTKPNGHIAN 12 OR5H14 LYPAIMTNGLCIWLLILSYVGGLLH 13 PAPD5 QAVGKMQSTQTTSTSNSTNKSQHGS 14 PHLDB3 TESSRDAPEATPLIAMAATPPASTS 15 PLAC4 PSLLTLDTLTHPRYPHSSPWTLSLT 16 POM121 ATTEALSPPKTPNLLPPLGLSQSGP 17 SCN4B NEKSDPKVTLKDNDRITLVGSTKEK 18 TAS2R31 VKRQKISFADQIVTALAVSRVGLLW 19 TEX14 QTALFVAALLGLGKFVDVLVDYGSD 20 UPK3BL GPYRVKFLVMNDKGPVAETKWSSDT 21 VCPIP1 GAAFATRSKAQRENSVEELEEMDSQ 22 ZNF587 KNLDDTAYLHQHRKQHIGEKFYRKS 23 USP17L11 ALGAEDTDRRAKIGRLKRDHPCLQAPE 24 USP17L18 ALGAEDTDRRATIGRLKRDHPCLQAPE 25 ZP3 DCGTPSHSRRQPRVMSQWSRSASRN 26 FAM194A EEEEVEEEEEEVEEEELVGEEQELE 27 PRR21 ALRPCLFTHGPSPMPLHPRPFVHAS 28 TARP VVYFAIITCCLLGRTAFCCNGEKS 29 TAS2R30 CAIYFLSMIISVWNFGRLEKQPVFM 30 NOTCH2NL VPCAPSPCVNGGSCRQTGDFTFECN 31 TAS2R30 YEGNVTWKIKLRRAMYHSNMTLTML 32 PRR21 PPCLFTHGPSSMALHPRPFVHASSP Pos. = Position Supplemental Table 7. HLA-I restriction elements from the patients included in the study Patient HLA-I ID A A B B C C

4078 23:01 30:01 07:02 44:03 04:01 07:02 4095 02:01 03:01 14:01 44:03 08:02 16:01 4110 02:01 03:01 14:02 44:02 07:04 08:02 4114 01:01 02:01 51:01 44:03 07:04 08:02 4166 02:01 03:01 07:02 55:01 03:03 07:02 4177 02:01 15:18 40:02 03:04 08:01 HLA was determined from next generation sequencing data using the algorithm PHLAT, as described in (35).