Nature Genetics: doi: /ng Supplementary Figure 1. Workflow of CDR3 sequence assembly from RNA-seq data.

Transcription

1 Supplementary Figure 1 Workflow of CDR3 sequence assembly from RNA-seq data. Paired-end short-read RNA-seq data were mapped to human reference genome hg19, and unmapped reads in the TCR regions were extracted for pairwise comparison. CDR3 sequences were assembled from disjoint read sets and annotated using IMGT nomenclatures.

2 Supplementary Figure 2 Number of reads/contigs at each step of the CDR3 assembly method. For a selected sample, we demonstrate the number of reads or contigs kept at each step of our method. The numbers are included at the bottom of each text box. The selected sample represents the median library size of TCGA tumors with the median number of assembled CDR3 sequences.

3 Supplementary Figure 3 Method evaluation using TCGA tumors profiled with both TCR sequencing and RNA-seq. Left, relationship between CDR3 transcripts called from TCR-seq and RNA-seq data. Middle, distribution of clonal frequencies of RNAseq assemblies and TCR-seq transcripts. Right, another visualization of the clonal frequency distribution: the x axis shows the quantiles of clonal frequencies from immunoseq data, and the y axis shows the fraction of above-quantile TCR transcripts called from RNA-seq data.

4 Supplementary Figure 4 Schematics of two simulation approaches used to validate the method developed in this work. Descriptions for each approach can be found in the Online Methods.

5 Supplementary Figure 5 Performance evaluation of the CDR3 assembly algorithm using an in silico mixture experiment. Our method was applied to data sets produced by the second simulation approach (Online Methods), and the CDR3 calls were compared to the gold standard TCR sequencing reads. (a) At different levels of T cell infiltration, our method recovered 4 6% of the infiltrating T cell repertoire, with 94 98% accuracy. (b) The called CDR3 sequences (infiltration level of 60%) were enriched for T cells with high clonal frequency. (c) Quantile quantile plot showing that the clonal frequency for called CDR3 sequences is skewed to the higher end in comparison to the background distribution.

6 Supplementary Figure 6 Evaluation of the CDR3 assembly algorithm at high coverage and comparison with issake. Both methods were applied to analyze the data sets produced from the first simulation approach (Online Methods). Called CDR3 sequences were compared to the 100 simulated transcripts, and true or false positive rates were calculated. False positive calls were defined as contigs that did not contain the CDR3 region. Standard deviation was estimated using 100 simulations at each given level of coverage. The true positive rate was the number of unique correct calls divided by 100, and the false positive rate was the number of unique incorrect calls divided by the total number of CDR3 calls. (a,b) These results were visualized as box plots for our method (a) and issake (b). We did not include a precision recall curve at each coverage setting because there was not a continuous threshold that would affect the performance in our algorithm.

7 Supplementary Figure 7 Differential usage of TRAV and TRBV genes in lower-grade glioma and kidney clear cell cancer. (a c) Bar plots of TRAV and TRBV gene usage in glioma (a,b) and kidney tumors (c) are presented. TRAV and TRBV genes are in the same order as in Figure 1a,b, and the fractions were calculated in the same way.

8 Supplementary Figure 8 Distribution of read counts for assembled CDR3 contigs. Read counts for each CDR3 contig were obtained from the assembly algorithm. When shared across multiple contigs, the count for a read was evenly split between each contig.

9 Supplementary Figure 9 Association of CPK with genes involved in cytolysis. The expression levels of previously defined cytolytic genes 19,27 were associated with CPK. The heat map displays values from partial Spearman s correlation corrected for tumor purity. Cancers with fewer than ten samples were excluded. Statistical significance was evaluated using partial Spearman s correlation test.

10 Supplementary Figure 10 Scatterplot between CPK and mutation load. Each point on the plot represents a cancer sample, with color referring to the corresponding disease type. The statistical significance of the association was evaluated using Spearman s correlation. This represents a complementary analysis to Figure 4b.

11 Supplementary Figure 11 Fraction of public -CDR3 sequences across cancer types. For each cancer type, the fraction was calculated as the number -CDR3 sequences in the final public sequence set divided by the number of total distinct -CDR3 sequences. All fractions were then mean centered, with the mean being the number of total public - CDR3 sequences divided by the number of total distinct -CDR3 sequences. Significance was evaluated using the binomial test, with the mean being the expected frequency and counts for public and total -CDR3 sequences for each cancer as observations.

12 Supplementary Figure 12 MHC I binding predictions for SPAG5 and TSSK6 protein sequences. Complete amino acid sequences for SPAG5 and TSSK6 were obtained from the NCBI protein database. All tiling nine-amino-acid sequences were analyzed by NetMHC4.0 for MHC I binding predictions. The peptides with strong binding (rank <0.5%) to an MHC I allele are underlined, and the corresponding MHC I allele is labeled by color. Only common MHC I alleles (HLA-A01:01, HLA-A02:01, HLA-A03:01, HLA-A07:02 and HLA-B08:01) with high population frequencies are displayed in the plot for visualization purposes.

13 Supplementary Figure 13 MHC II binding predictions for peptides produced from PRAMEF4 F300V. MHC II binding was predicted by NetMHC-II 2.2. Fifteen-amino-acid sequences are the standard input for the webserver, and one mutated peptide was predicted to bind to three MHC II alleles with high affinity.

14 Supplementary Figure 14 Box plot of PRAMEF4 expression levels in multiple cancer types and paired normal tissues. Testicular cancer (TGCT) is highlighted by the blue box. Numbers of outliers are included in red along the top of the plot.

15 Cancer Survival Age Gender Race *:$FDR<0.1 HR Correlation FC4(M/F) FC4(A/W) FC4(B/W) HR:$Hazard$Ratio$from$Cox$proportional$hazard$model BLCA 5.60E:07 : * 0.96 M/F:$Male/Female BRCA 1.90E:22 :0.1286* NA A/W:$Asian/White CESC 9.20E: NA NA 1.1 B/W:$Black/White COAD 1.10E: NA 0.85 GBM 1.90E+20 : NA NA NA HNSC 5.80E:50 : NA 1 KIRC 2.50E:31 : * NA 0.97 LGG 3.2e+153* NA NA LIHC 5.10E: NA LUAD 2.20E:42 : * NA 1.09 LUSC 1.20E NA 0.94 MESO 5.90E:05 NA NA NA NA PAAD 8.70E * NA NA SARC 4.40E:77 : NA NA SKCM 1.70E:06 : NA NA KIRP NA : NA 1.06 PCPG NA : NA NA PRAD NA NA NA NA TGCT NA : NA NA NA THCA NA : UCEC NA : NA NA 1.17

16 HLA$A0101 HLA$A0201 HLA$A0301 HLA$A2402 HLA$A2601 HLA$A3001 Pos Peptide ID nm Rank Core nm Rank Core nm Rank Core nm Rank Core nm Rank Core nm Rank Core 0 SCLKTSLKV PRAMEF SCLKTSLKV SCLKTSLKV SCLKTSLKV SCLKTSLKV SCLKTSLKV SCLKTSLKV 1 CLKTSLKVL PRAMEF CLKTSLKVL CLKTSLKVL CLKTSLKVL CLKTSLKVL CLKTSLKVL CLKTSLKVL 2 LKTSLKVLT PRAMEF LKTSLKVLT LKTSLKVLT LKTSLKVLT LKTSLKVLT LKTSLKVLT LKTSLKVLT 3 KTSLKVLTI PRAMEF KTSLKVLTI KTSLKVLTI KTSLKVLTI KTSLKVLTI KTSLKVLTI KTSLKVLTI 4 TSLKVLTIT PRAMEF TSLKVLTIT TSLKVLTIT TSLKVLTIT TSLKVLTIT TSLKVLTIT TSLKVLTIT 5 SLKVLTITN PRAMEF SLKVLTITN SLKVLTITN SLKVLTITN SLKVLTITN SLKVLTITN SLKVLTITN 6 LKVLTITNC PRAMEF LKVLTITNC LKVLTITNC LKVLTITNC LKVLTITNC LKVLTITNC LKVLTITNC 7 KVLTITNCV PRAMEF KVLTITNCV KVLTITNCV KVLTITNCV KVLTITNCV KVLTITNCV KVLTITNCV 8 VLTITNCVL PRAMEF VLTITNCVL VLTITNCVL VLTITNCVL VLTITNCVL VLTITNCVL VLTITNCVL 0 SCLKTSLKF PRAMEF4$WT SCLKTSLKF SCLKTSLKF SCLKTSLKF SCLKTSLKF SCLKTSLKF SCLKTSLKF 1 CLKTSLKFL PRAMEF4$WT CLKTSLKFL CLKTSLKFL CLKTSLKFL CLKTSLKFL CLKTSLKFL CLKTSLKFL 2 LKTSLKFLT PRAMEF4$WT LKTSLKFLT LKTSLKFLT LKTSLKFLT LKTSLKFLT LKTSLKFLT LKTSLKFLT 3 KTSLKFLTI PRAMEF4$WT KTSLKFLTI KTSLKFLTI KTSLKFLTI KTSLKFLTI KTSLKFLTI KTSLKFLTI 4 TSLKFLTIT PRAMEF4$WT TSLKFLTIT TSLKFLTIT TSLKFLTIT TSLKFLTIT TSLKFLTIT TSLKFLTIT 5 SLKFLTITN PRAMEF4$WT SLKFLTITN SLKFLTITN SLKFLTITN SLKFLTITN SLKFLTITN SLKFLTITN 6 LKFLTITNC PRAMEF4$WT LKFLTITNC LKFLTITNC LKFLTITNC LKFLTITNC LKFLTITNC LKFLTITNC 7 KFLTITNCV PRAMEF4$WT KFLTITNCV KFLTITNCV KFLTITNCV KFLTITNCV KFLTITNCV KFLTITNCV 8 FLTITNCVL PRAMEF4$WT FLTITNCVL FLTITNCVL FLTITNCVL FLTITNCVL FLTITNCVL FLTITNCVL 0 TGDTTPLPD MUC TGDTTPLPD TGDTTPLPD TGDTTPLPD TGDTTPLPD TGDTTPLPD TGDTTPLPD 1 GDTTPLPDT MUC GDTTPLPDT GDTTPLPDT GDTTPLPDT GDTTPLPDT GDTTPLPDT GDTTPLPDT 2 DTTPLPDTD MUC DTTPLPDTD DTTPLPDTD DTTPLPDTD DTTPLPDTD DTTPLPDTD DTTPLPDTD 3 TTPLPDTDT MUC TTPLPDTDT TTPLPDTDT TTPLPDTDT TTPLPDTDT TTPLPDTDT TTPLPDTDT 4 TPLPDTDTS MUC TPLPDTDTS TPLPDTDTS TPLPDTDTS TPLPDTDTS TPLPDTDTS TPLPDTDTS 5 PLPDTDTSS MUC PLPDTDTSS PLPDTDTSS PLPDTDTSS PLPDTDTSS PLPDTDTSS PLPDTDTSS 6 LPDTDTSSA MUC LPDTDTSSA LPDTDTSSA LPDTDTSSA LPDTDTSSA LPDTDTSSA LPDTDTSSA 7 PDTDTSSAS MUC PDTDTSSAS PDTDTSSAS PDTDTSSAS PDTDTSSAS PDTDTSSAS PDTDTSSAS 8 DTDTSSAST MUC DTDTSSAST DTDTSSAST DTDTSSAST DTDTSSAST DTDTSSAST DTDTSSAST 0 TGDTTPLPV MUC4$WT TGDTTPLPV TGDTTPLPV TGDTTPLPV TGDTTPLPV TGDTTPLPV TGDTTPLPV 1 GDTTPLPVT MUC4$WT GDTTPLPVT GDTTPLPVT GDTTPLPVT GDTTPLPVT GDTTPLPVT GDTTPLPVT 2 DTTPLPVTD MUC4$WT DTTPLPVTD DTTPLPVTD DTTPLPVTD DTTPLPVTD DTTPLPVTD DTTPLPVTD 3 TTPLPVTDT MUC4$WT TTPLPVTDT TTPLPVTDT TTPLPVTDT TTPLPVTDT TTPLPVTDT TTPLPVTDT 4 TPLPVTDTS MUC4$WT TPLPVTDTS TPLPVTDTS TPLPVTDTS TPLPVTDTS TPLPVTDTS TPLPVTDTS 5 PLPVTDTSS MUC4$WT PLPVTDTSS PLPVTDTSS PLPVTDTSS PLPVTDTSS PLPVTDTSS PLPVTDTSS 6 LPVTDTSSA MUC4$WT LPVTDTSSA LPVTDTSSA LPVTDTSSA LPVTDTSSA LPVTDTSSA LPVTDTSSA 7 PVTDTSSAS MUC4$WT PVTDTSSAS PVTDTSSAS PVTDTSSAS PVTDTSSAS PVTDTSSAS PVTDTSSAS 8 VTDTSSAST MUC4$WT VTDTSSAST VTDTSSAST VTDTSSAST VTDTSSAST VTDTSSAST VTDTSSAST 0 THITEPSTG MUC5B THITEPSTG THITEPSTG THITEPSTG THITEPSTG THITEPSTG THITEPSTG 1 HITEPSTGT MUC5B HITEPSTGT HITEPSTGT HITEPSTGT HITEPSTGT HITEPSTGT HITEPSTGT 2 ITEPSTGTS MUC5B ITEPSTGTS ITEPSTGTS ITEPSTGTS ITEPSTGTS ITEPSTGTS ITEPSTGTS 3 TEPSTGTSH MUC5B TEPSTGTSH TEPSTGTSH TEPSTGTSH TEPSTGTSH TEPSTGTSH TEPSTGTSH 4 EPSTGTSHT MUC5B EPSTGTSHT EPSTGTSHT EPSTGTSHT EPSTGTSHT EPSTGTSHT EPSTGTSHT 5 PSTGTSHTP MUC5B PSTGTSHTP PSTGTSHTP PSTGTSHTP PSTGTSHTP PSTGTSHTP PSTGTSHTP 6 STGTSHTPA MUC5B STGTSHTPA STGTSHTPA STGTSHTPA STGTSHTPA STGTSHTPA STGTSHTPA 7 TGTSHTPAA MUC5B TGTSHTPAA TGTSHTPAA TGTSHTPAA TGTSHTPAA TGTSHTPAA TGTSHTPAA 8 GTSHTPAAT MUC5B GTSHTPAAT GTSHTPAAT GTSHTPAAT GTSHTPAAT GTSHTPAAT GTSHTPAAT 0 THITEPSTV MUC5B$WT THITEPSTV THITEPSTV THITEPSTV THITEPSTV THITEPSTV THITEPSTV 1 HITEPSTVT MUC5B$WT HITEPSTVT HITEPSTVT HITEPSTVT HITEPSTVT HITEPSTVT HITEPSTVT 2 ITEPSTVTS MUC5B$WT ITEPSTVTS ITEPSTVTS ITEPSTVTS ITEPSTVTS ITEPSTVTS ITEPSTVTS 3 TEPSTVTSH MUC5B$WT TEPSTVTSH TEPSTVTSH TEPSTVTSH TEPSTVTSH TEPSTVTSH TEPSTVTSH 4 EPSTVTSHT MUC5B$WT EPSTVTSHT EPSTVTSHT EPSTVTSHT EPSTVTSHT EPSTVTSHT EPSTVTSHT 5 PSTVTSHTP MUC5B$WT PSTVTSHTP PSTVTSHTP PSTVTSHTP PSTVTSHTP PSTVTSHTP PSTVTSHTP 6 STVTSHTPA MUC5B$WT STVTSHTPA STVTSHTPA STVTSHTPA STVTSHTPA STVTSHTPA STVTSHTPA 7 TVTSHTPAA MUC5B$WT TVTSHTPAA TVTSHTPAA TVTSHTPAA TVTSHTPAA TVTSHTPAA TVTSHTPAA 8 VTSHTPAAT MUC5B$WT VTSHTPAAT VTSHTPAAT VTSHTPAAT VTSHTPAAT VTSHTPAAT VTSHTPAAT

17 HLA$B0702 HLA$B0801 HLA$B1501 HLA$B2705 HLA$B3901 HLA$B4001 HLA$B5801 nm Rank Core nm Rank Core nm Rank Core nm Rank Core nm Rank Core nm Rank Core nm Rank Core SCLKTSLKV SCLKTSLKV SCLKTSLKV SCLKTSLKV SCLKTSLKV SCLKTSLKV SCLKTSLKV CLKTSLKVL CLKTSLKVL CLKTSLKVL CLKTSLKVL CLKTSLKVL CLKTSLKVL CLKTSLKVL LKTSLKVLT LKTSLKVLT LKTSLKVLT LKTSLKVLT LKTSLKVLT LKTSLKVLT LKTSLKVLT KTSLKVLTI KTSLKVLTI KTSLKVLTI KTSLKVLTI KTSLKVLTI KTSLKVLTI KTSLKVLTI TSLKVLTIT TSLKVLTIT TSLKVLTIT TSLKVLTIT TSLKVLTIT TSLKVLTIT TSLKVLTIT SLKVLTITN SLKVLTITN SLKVLTITN SLKVLTITN SLKVLTITN SLKVLTITN SLKVLTITN LKVLTITNC LKVLTITNC LKVLTITNC LKVLTITNC LKVLTITNC LKVLTITNC LKVLTITNC KVLTITNCV KVLTITNCV KVLTITNCV KVLTITNCV KVLTITNCV KVLTITNCV KVLTITNCV VLTITNCVL VLTITNCVL VLTITNCVL VLTITNCVL VLTITNCVL VLTITNCVL VLTITNCVL SCLKTSLKF SCLKTSLKF SCLKTSLKF SCLKTSLKF SCLKTSLKF SCLKTSLKF SCLKTSLKF CLKTSLKFL CLKTSLKFL CLKTSLKFL CLKTSLKFL CLKTSLKFL CLKTSLKFL CLKTSLKFL LKTSLKFLT LKTSLKFLT LKTSLKFLT LKTSLKFLT LKTSLKFLT LKTSLKFLT LKTSLKFLT KTSLKFLTI KTSLKFLTI KTSLKFLTI KTSLKFLTI KTSLKFLTI KTSLKFLTI KTSLKFLTI TSLKFLTIT TSLKFLTIT TSLKFLTIT TSLKFLTIT TSLKFLTIT TSLKFLTIT TSLKFLTIT SLKFLTITN SLKFLTITN SLKFLTITN SLKFLTITN SLKFLTITN SLKFLTITN SLKFLTITN LKFLTITNC LKFLTITNC LKFLTITNC LKFLTITNC LKFLTITNC LKFLTITNC LKFLTITNC KFLTITNCV KFLTITNCV KFLTITNCV KFLTITNCV KFLTITNCV KFLTITNCV KFLTITNCV FLTITNCVL FLTITNCVL FLTITNCVL FLTITNCVL FLTITNCVL FLTITNCVL FLTITNCVL TGDTTPLPD TGDTTPLPD TGDTTPLPD TGDTTPLPD TGDTTPLPD TGDTTPLPD TGDTTPLPD GDTTPLPDT GDTTPLPDT GDTTPLPDT GDTTPLPDT GDTTPLPDT GDTTPLPDT GDTTPLPDT DTTPLPDTD DTTPLPDTD DTTPLPDTD DTTPLPDTD DTTPLPDTD DTTPLPDTD DTTPLPDTD TTPLPDTDT TTPLPDTDT TTPLPDTDT TTPLPDTDT TTPLPDTDT TTPLPDTDT TTPLPDTDT TPLPDTDTS TPLPDTDTS TPLPDTDTS TPLPDTDTS TPLPDTDTS TPLPDTDTS TPLPDTDTS PLPDTDTSS PLPDTDTSS PLPDTDTSS PLPDTDTSS PLPDTDTSS PLPDTDTSS PLPDTDTSS LPDTDTSSA LPDTDTSSA LPDTDTSSA LPDTDTSSA LPDTDTSSA LPDTDTSSA LPDTDTSSA PDTDTSSAS PDTDTSSAS PDTDTSSAS PDTDTSSAS PDTDTSSAS PDTDTSSAS PDTDTSSAS DTDTSSAST DTDTSSAST DTDTSSAST DTDTSSAST DTDTSSAST DTDTSSAST DTDTSSAST TGDTTPLPV TGDTTPLPV TGDTTPLPV TGDTTPLPV TGDTTPLPV TGDTTPLPV TGDTTPLPV GDTTPLPVT GDTTPLPVT GDTTPLPVT GDTTPLPVT GDTTPLPVT GDTTPLPVT GDTTPLPVT DTTPLPVTD DTTPLPVTD DTTPLPVTD DTTPLPVTD DTTPLPVTD DTTPLPVTD DTTPLPVTD TTPLPVTDT TTPLPVTDT TTPLPVTDT TTPLPVTDT TTPLPVTDT TTPLPVTDT TTPLPVTDT TPLPVTDTS TPLPVTDTS TPLPVTDTS TPLPVTDTS TPLPVTDTS TPLPVTDTS TPLPVTDTS PLPVTDTSS PLPVTDTSS PLPVTDTSS PLPVTDTSS PLPVTDTSS PLPVTDTSS PLPVTDTSS LPVTDTSSA LPVTDTSSA LPVTDTSSA LPVTDTSSA LPVTDTSSA LPVTDTSSA LPVTDTSSA PVTDTSSAS PVTDTSSAS PVTDTSSAS PVTDTSSAS PVTDTSSAS PVTDTSSAS PVTDTSSAS VTDTSSAST VTDTSSAST VTDTSSAST VTDTSSAST VTDTSSAST VTDTSSAST VTDTSSAST THITEPSTG THITEPSTG THITEPSTG THITEPSTG THITEPSTG THITEPSTG THITEPSTG HITEPSTGT HITEPSTGT HITEPSTGT HITEPSTGT HITEPSTGT HITEPSTGT HITEPSTGT ITEPSTGTS ITEPSTGTS ITEPSTGTS ITEPSTGTS ITEPSTGTS ITEPSTGTS ITEPSTGTS TEPSTGTSH TEPSTGTSH TEPSTGTSH TEPSTGTSH TEPSTGTSH TEPSTGTSH TEPSTGTSH EPSTGTSHT EPSTGTSHT EPSTGTSHT EPSTGTSHT EPSTGTSHT EPSTGTSHT EPSTGTSHT PSTGTSHTP PSTGTSHTP PSTGTSHTP PSTGTSHTP PSTGTSHTP PSTGTSHTP PSTGTSHTP STGTSHTPA STGTSHTPA STGTSHTPA STGTSHTPA STGTSHTPA STGTSHTPA STGTSHTPA TGTSHTPAA TGTSHTPAA TGTSHTPAA TGTSHTPAA TGTSHTPAA TGTSHTPAA TGTSHTPAA GTSHTPAAT GTSHTPAAT GTSHTPAAT GTSHTPAAT GTSHTPAAT GTSHTPAAT GTSHTPAAT THITEPSTV THITEPSTV THITEPSTV THITEPSTV THITEPSTV THITEPSTV THITEPSTV HITEPSTVT HITEPSTVT HITEPSTVT HITEPSTVT HITEPSTVT HITEPSTVT HITEPSTVT ITEPSTVTS ITEPSTVTS ITEPSTVTS ITEPSTVTS ITEPSTVTS ITEPSTVTS ITEPSTVTS TEPSTVTSH TEPSTVTSH TEPSTVTSH TEPSTVTSH TEPSTVTSH TEPSTVTSH TEPSTVTSH EPSTVTSHT EPSTVTSHT EPSTVTSHT EPSTVTSHT EPSTVTSHT EPSTVTSHT EPSTVTSHT PSTVTSHTP PSTVTSHTP PSTVTSHTP PSTVTSHTP PSTVTSHTP PSTVTSHTP PSTVTSHTP STVTSHTPA STVTSHTPA STVTSHTPA STVTSHTPA STVTSHTPA STVTSHTPA STVTSHTPA TVTSHTPAA TVTSHTPAA TVTSHTPAA TVTSHTPAA TVTSHTPAA TVTSHTPAA TVTSHTPAA VTSHTPAAT VTSHTPAAT VTSHTPAAT VTSHTPAAT VTSHTPAAT VTSHTPAAT VTSHTPAAT

18 HLA$C0401 HLA$C0602 HLA$C0702 nm Rank Core nm Rank Core nm Rank Core H_Avg_RanksN_binders SCLKTSLKV SCLKTSLKV SCLKTSLKV CLKTSLKVL CLKTSLKVL CLKTSLKVL LKTSLKVLT LKTSLKVLT LKTSLKVLT KTSLKVLTI KTSLKVLTI KTSLKVLTI TSLKVLTIT TSLKVLTIT TSLKVLTIT SLKVLTITN SLKVLTITN SLKVLTITN LKVLTITNC LKVLTITNC LKVLTITNC KVLTITNCV KVLTITNCV KVLTITNCV VLTITNCVL VLTITNCVL VLTITNCVL SCLKTSLKF SCLKTSLKF SCLKTSLKF CLKTSLKFL CLKTSLKFL CLKTSLKFL LKTSLKFLT LKTSLKFLT LKTSLKFLT KTSLKFLTI KTSLKFLTI KTSLKFLTI TSLKFLTIT TSLKFLTIT TSLKFLTIT SLKFLTITN SLKFLTITN SLKFLTITN LKFLTITNC LKFLTITNC LKFLTITNC KFLTITNCV KFLTITNCV KFLTITNCV FLTITNCVL FLTITNCVL FLTITNCVL TGDTTPLPD TGDTTPLPD TGDTTPLPD GDTTPLPDT GDTTPLPDT GDTTPLPDT DTTPLPDTD DTTPLPDTD DTTPLPDTD TTPLPDTDT TTPLPDTDT TTPLPDTDT TPLPDTDTS TPLPDTDTS TPLPDTDTS PLPDTDTSS PLPDTDTSS PLPDTDTSS LPDTDTSSA LPDTDTSSA LPDTDTSSA PDTDTSSAS PDTDTSSAS PDTDTSSAS DTDTSSAST DTDTSSAST DTDTSSAST TGDTTPLPV TGDTTPLPV TGDTTPLPV GDTTPLPVT GDTTPLPVT GDTTPLPVT DTTPLPVTD DTTPLPVTD DTTPLPVTD TTPLPVTDT TTPLPVTDT TTPLPVTDT TPLPVTDTS TPLPVTDTS TPLPVTDTS PLPVTDTSS PLPVTDTSS PLPVTDTSS LPVTDTSSA LPVTDTSSA LPVTDTSSA PVTDTSSAS PVTDTSSAS PVTDTSSAS VTDTSSAST VTDTSSAST VTDTSSAST THITEPSTG THITEPSTG THITEPSTG HITEPSTGT HITEPSTGT HITEPSTGT ITEPSTGTS ITEPSTGTS ITEPSTGTS TEPSTGTSH TEPSTGTSH TEPSTGTSH EPSTGTSHT EPSTGTSHT EPSTGTSHT PSTGTSHTP PSTGTSHTP PSTGTSHTP STGTSHTPA STGTSHTPA STGTSHTPA TGTSHTPAA TGTSHTPAA TGTSHTPAA GTSHTPAAT GTSHTPAAT GTSHTPAAT THITEPSTV THITEPSTV THITEPSTV HITEPSTVT HITEPSTVT HITEPSTVT ITEPSTVTS ITEPSTVTS ITEPSTVTS TEPSTVTSH TEPSTVTSH TEPSTVTSH EPSTVTSHT EPSTVTSHT EPSTVTSHT PSTVTSHTP PSTVTSHTP PSTVTSHTP STVTSHTPA STVTSHTPA STVTSHTPA TVTSHTPAA TVTSHTPAA TVTSHTPAA VTSHTPAAT VTSHTPAAT VTSHTPAAT

19 Sample ID Cancer HLA-A genotype HLA-B genotype HLA-C genotype CDR3 motif Mutation TCGA-4K-AA1I TGCT A*01:01 A*30:01 B*13:02 B*13:02 C*06:02 C*06:02 GESEQY PRAMEF4 F300V TCGA-2G-AAGE TGCT A*01:01 A*01:01 B*08:01 B*57:01 C*07:01 C*07:01 GESEQY PRAMEF4 F300V TCGA-2G-AAKO TGCT A*01:01 A*02:01 B*08:01 B*18:01 C*07:01 C*12:03 GESEQY PRAMEF4 F300V TCGA-B KIRC A*68:02 A*74:01 B*53:01 B*53:01 C*04:01 C*04:01 GLAEQY MUC4 V4195D TCGA-G DLBC A*02:02 A*68:02 B*35:01 B*58:01 C*04:01 C*07:18 GLAEQY MUC4 V4195D TCGA-FF-8041 DLBC A*01:01 A*02:07 B*15:02 B*15:17 C*07:01 C*08:01 GLAEQY MUC4 V4195D TCGA-BH-A0HA BRCA A*03:01 A*31:01 B*07:02 B*07:02 C*07:02 C*07:02 RDNSYEQYMUC5B V3490G TCGA-G DLBC A*01:01 A*33:03 B*08:01 B*50:01 C*06:02 C*07:01 RDNSYEQYMUC5B V3490G TCGA-FF-A7CR DLBC A*24:07 A*24:10 B*15:02 B*27:06 C*03:04 C*07:02 RDNSYEQYMUC5B V3490G