One mRNA sequence encodes 24 selected antigen regions — read the methods used to design it , and suggest changes .
This lead design uses matched-normal white-blood-cell DNA alongside Yash’s tumour DNA and RNA. All 12 mutation regions meeting our eligibility criteria are included.
The RNA, from 5′ to 3′
724-amino-acid protein
5′ → 3′ · schematic widths
· follow the numbered path
5′ UTR RNA 1–63 nt
A noncoding leader and Kozak sequence before the protein-coding region, the same as those used in PVX-001 , our COVID vaccine candidate.
View recorded sequence
AGAAUCCUUU
SEC RNA 64–141 nt
The N-terminal 26 amino acids of Yash’s HLA-C*01:02 protein: its 24-amino-acid signal peptide plus the following two native residues. His tumour DNA and RNA support this sequence.
View recorded sequence
AUGCGGGUGA
24 antigen regions + linkers RNA 142–2,070 nt
Each selected region contributes 25 amino acids. The order of the
regions and the joining sequences were chosen jointly, taking the
SEC and MITD boundaries into account. Explore the regions below.
MITD RNA 2,071–2,235 nt
The C-terminal 55 amino acids of Yash’s HLA-B*15:08 protein, including its membrane anchor and trafficking tail. His tumour DNA and RNA support this sequence.
View recorded sequence
AUCGUCGGAA
Read the allele sequence evidence
Stop RNA 2,236–2,244 nt
Three consecutive stop codons, UAA–UAG–UGA, terminate the protein-coding sequence. This is the same stop block used in PVX-001 , our COVID vaccine candidate.
View recorded sequence
UAAUAGUGA
3′ UTR RNA 2,245–2,315 nt
A noncoding region after the stop codons, the same as what was used in PVX-001 , our COVID vaccine candidate.
View recorded sequence
GCUGGAGCCU
PolyA
The polyadenosine tail at the 3′ end of the RNA.
Sequence sketch AAAAA…AAAAA
The encoded regions
In their actual order · select to explore
12 5 5 2 Short linkers
CTA / self protein · region 1 of 24
SPATA31A6 CTA / self protein
←
→
A reference protein region from a cancer–testis antigen (CTA)
gene with positive supplied expression.
Encoded 25-aa region Protein 27–51
S L S A S Q P P E P S L P L E H P S P E P P A L F
Reference sequence; no mutation
Predicted HLA-I binding
33.6 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 127.7 A*33:03 2,064.4 B*08:01 123.4 B*15:08 56.1 C*01:02 33.6 C*07:02 66.4
ASQPPEPSL9 aa · HLA-C*01:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
13.61 transformed TPM
How expression is used in selection
Supplied gene expression.
The supplied gene value is used directly as the expression
proxy.
Region score = affinity contribution sum × √expression
proxy.
DNA mutation · region 2 of 24
PPIC P187S
←
→
Paired tumour–normal Mutect2 calling retained this protein-changing variant. Isovar reconstructed the altered sequence from tumour RNA.
Encoded 25-aa region Protein 52–76
S I E L Q A T D G H D R S L T S C S I I N S G K I
Predicted HLA-I binding
36.5 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 231.4 A*33:03 10,022.6 B*08:01 2,406.7 B*15:08 3,030.4 C*01:02 36.5 C*07:02 157
ATDGHDRSL9 aa · HLA-C*01:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
72.92 transformed TPM
Paired tumour–normal DNA and RNA support
Tumour DNA: 49 alternate reads / 124 depth. Normal DNA: 47 reference-supporting fragments and 0 alternate-supporting fragments. RNA: 9 mutant-supporting fragments / 41 eligible fragments. The RNA-derived region also retains the reviewed N190S background difference.
DNA mutation · region 3 of 24
TGFBR2 N515fs
←
→
Paired tumour–normal Mutect2 calling retained this protein-changing variant. Isovar reconstructed the altered sequence from tumour RNA.
Encoded 25-aa region Protein 77–101
E P P F G S K V R E H P C V E S M K D K R V E R S
Predicted HLA-I binding
38 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 27,552.9 A*33:03 38 B*08:01 3,937.3 B*15:08 18,878.4 C*01:02 15,716.5 C*07:02 8,061.7
ESMKDKRVER10 aa · HLA-A*33:03
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
55.74 transformed TPM
Paired tumour–normal DNA and RNA support
Tumour DNA: 144 alternate reads / 365 depth. Normal DNA: 40 reference-supporting fragments and 0 alternate-supporting fragments. RNA: 85 mutant-supporting fragments / 206 eligible fragments.
DNA mutation · region 4 of 24
PLEC R2171W
←
→
Paired tumour–normal Mutect2 calling retained this protein-changing variant. Isovar reconstructed the altered sequence from tumour RNA.
Encoded 25-aa region Protein 103–127
R R L R E R A E Q E S A W Q L Q L A Q E A A Q K R
Predicted HLA-I binding
413.3 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 19,538.2 A*33:03 6,536.9 B*08:01 14,646.4 B*15:08 19,784.6 C*01:02 3,630.5 C*07:02 413.3
ERAEQESAWQL11 aa · HLA-C*07:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
92.29 transformed TPM
Paired tumour–normal DNA and RNA support
Tumour DNA: 59 alternate reads / 228 depth. Normal DNA: 26 reference-supporting fragments and 0 alternate-supporting fragments. RNA: 8 mutant-supporting fragments / 16 eligible fragments.
Splice event · region 5 of 24
HLA-B Splice event
←
→
This region is reconstructed from Yash’s RNA around a LENS-identified join, using an annotated upstream coding frame.
Encoded 25-aa region Protein 132–156
I T Q R K W E A A R E A E Q R S L P G G H V R G V
The teal marker locates the RNA join.
Compared with the annotated protein Reference I T Q R K W E A A R E A E Q R R A Y L E G E C V E
Candidate I T Q R K W E A A R E A E Q R S L P G G H V R G V
This shows the annotated protein context from the upstream coding anchor. The observed RNA path differs from that annotated path; this is not a single-residue edit map.
Reference sequence and transcript ENST00000412585.7. GENCODE 37 annotated protein context.
Predicted HLA-I binding
66.2 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 17,064.1 A*33:03 66.2 B*08:01 3,407.9 B*15:08 6,133.3 C*01:02 100.1 C*07:02 626.3
EQRSLPGGHVR11 aa · HLA-A*33:03
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
185.96 transformed TPM
How expression is used in selection
Supplied expression of the assigned gene; no splice-fraction
multiplier.
The supplied gene value is used directly as the expression proxy.
Region score = affinity contribution sum × √expression
proxy.
RNA-supported splice region
The complete 25-aa sequence has 2 supporting RNA fragment names. The junction was not detected in either searched normal-reference catalog.
Splice event · region 6 of 24
MUC5B Splice event
←
→
This region is reconstructed from Yash’s RNA around a LENS-identified join, using an annotated upstream coding frame.
Encoded 25-aa region Protein 159–183
L T T T A T T P A A T I S T V T P S S A L G T T H
The teal marker locates the RNA join.
Compared with the annotated protein Reference L T T T A T T P [−700 aa] A A T S S T V T P S S A L G T T H
Candidate L T T T A T T P joined A A T I S T V T P S S A L G T T H
The observed RNA path omits 700 reference amino acids in this comparison. Shading marks amino-acid differences; teal marks the RNA join separately.
Reference sequence and transcript Omitted reference segment (700 aa):
AATSSTVTPSSALGTTHTPPVPNTTATTHGRSLSPSSPHTVRTAWTSATSGTLGTTHITEPSTGTSHTPAATTGTTQHSTPALSSPHPSSRTTESPPSPGTTTPGHTRATSRTTATATPSKTRTSTLLPSSPTSAPITTVVTMGCEPQCAWSEWLDYSYPMPGPSGGDFDTYSNIRAAGGAVCEQPLGLECRAQAQPGVPLRELGQVVECSLDFGLVCRNREQVGKFKMCFNYEIRVFCCNYGHCPSTPATSSTATPSSTPGTTWILTEQTTAATTTATTGSTAIPSSTPGTAPPPKVLTSTATTPTATSSKATSSSSPRTATTLPVLTSTATKSTATSFTPIPSFTLGTTGTLPEQTTTPMATMSTIHPSSTPETTHTSTVLTTKATTTRATSSMSTPSSTPGTTWILTELTTAATTTAATGPTATPSSTPGTTWILTEPSTTATVTVPTGSTATASSTRATAGTLKVLTSTATTPTVISSRATPSSSPGTATALPALRSTATTPTATSVTAIPSSSLGTAWTRLSQTTTPTATMSTATPSSTPETVHTSTVLTTTTTTTRATGSVATPSSTPGTAHTTKVPTTTTTGFTATPSSSPGTALTPPVWISTTTTPTTRGSTVTPSSIPGTTHTATVLTTTTTTVATGSMATPSSSTQTSGTPPSLTTTATTITATGSTTNPSSTPGTTPIPPVLTTTATTPENST00000529681.5. GENCODE 37 annotated protein context.
Predicted HLA-I binding
44.9 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 3,961.1 A*33:03 4,040 B*08:01 1,680.9 B*15:08 291.8 C*01:02 44.9 C*07:02 1,150
TATTPAATI9 aa · HLA-C*01:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
284.04 transformed TPM
How expression is used in selection
Supplied expression of the assigned gene; no splice-fraction
multiplier.
The supplied gene value is used directly as the expression proxy.
Region score = affinity contribution sum × √expression
proxy.
RNA-supported splice region
The complete 25-aa sequence has 2 supporting RNA fragment names. The junction was not detected in either searched normal-reference catalog.
DNA mutation · region 7 of 24
KLF5 D418N
←
→
Paired tumour–normal Mutect2 calling retained this protein-changing variant. Isovar reconstructed the altered sequence from tumour RNA.
Encoded 25-aa region Protein 185–209
T W E G C D W R F A R S N E L T R H Y R K H T G A
Predicted HLA-I binding
37 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 531.5 A*33:03 47.4 B*08:01 216.9 B*15:08 507.4 C*01:02 1,897.7 C*07:02 37
WRFARSNEL9 aa · HLA-C*07:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
1,297.24 transformed TPM
Paired tumour–normal DNA and RNA support
Tumour DNA: 213 alternate reads / 725 depth. Normal DNA: 50 reference-supporting fragments and 0 alternate-supporting fragments. RNA: 30 mutant-supporting fragments / 116 eligible fragments.
DNA mutation · region 8 of 24
SYT12 P391L
←
→
Paired tumour–normal Mutect2 calling retained this protein-changing variant. Isovar reconstructed the altered sequence from tumour RNA.
Encoded 25-aa region Protein 212–236
G R G D N V G H V I I G L S A S G M G T T H W N Q
Predicted HLA-I binding
243.7 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 8,478.8 A*33:03 1,768.9 B*08:01 9,241.8 B*15:08 3,010.5 C*01:02 243.7 C*07:02 3,207.4
NVGHVIIGL9 aa · HLA-C*01:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
7.92 transformed TPM
Paired tumour–normal DNA and RNA support
Tumour DNA: 290 alternate reads / 845 depth. Normal DNA: 56 reference-supporting fragments and 0 alternate-supporting fragments. RNA: 2 mutant-supporting fragments / 8 eligible fragments.
DNA mutation · region 9 of 24
VPS11 D151A
←
→
Paired tumour–normal Mutect2 calling retained this protein-changing variant. Isovar reconstructed the altered sequence from tumour RNA.
Encoded 25-aa region Protein 241–265
H E N L N F M A I G F T A G S V T L N K G D I T R
Predicted HLA-I binding
115.6 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 9,193.1 A*33:03 288.1 B*08:01 9,007.5 B*15:08 2,075.5 C*01:02 115.6 C*07:02 466.7
FTAGSVTL8 aa · HLA-C*01:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
15.71 transformed TPM
Paired tumour–normal DNA and RNA support
Tumour DNA: 78 alternate reads / 205 depth. Normal DNA: 32 reference-supporting fragments and 0 alternate-supporting fragments. RNA: 7 mutant-supporting fragments / 23 eligible fragments.
CTA / self protein · region 10 of 24
PRAME CTA / self protein
←
→
A reference protein region from a cancer–testis antigen (CTA)
gene with positive supplied expression.
Encoded 25-aa region Protein 267–291
S Y E D I H G T L H L E R L A Y L H A R L R E L L
Reference sequence; no mutation
Predicted HLA-I binding
15.3 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 386.9 A*33:03 46.3 B*08:01 15.3 B*15:08 59.5 C*01:02 52.9 C*07:02 26.9
YLHARLREL9 aa · HLA-B*08:01
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
17.01 transformed TPM
How expression is used in selection
Supplied gene expression.
The supplied gene value is used directly as the expression
proxy.
Region score = affinity contribution sum × √expression
proxy.
DNA mutation · region 11 of 24
RXRA A241S
←
→
Paired tumour–normal Mutect2 calling retained this protein-changing variant. Isovar reconstructed the altered sequence from tumour RNA.
Encoded 25-aa region Protein 295–319
D M P V E R I L E A E L S V E P K T E T Y V E A N
Predicted HLA-I binding
58.1 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 61 A*33:03 564.3 B*08:01 3,042.8 B*15:08 58.1 C*01:02 394.4 C*07:02 170.7
SVEPKTETY9 aa · HLA-B*15:08
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
23.01 transformed TPM
Paired tumour–normal DNA and RNA support
Tumour DNA: 230 alternate reads / 658 depth. Normal DNA: 42 reference-supporting fragments and 0 alternate-supporting fragments. RNA: 23 mutant-supporting fragments / 42 eligible fragments.
DNA mutation · region 12 of 24
SF1 R218Q
←
→
Paired tumour–normal Mutect2 calling retained this protein-changing variant. Isovar reconstructed the altered sequence from tumour RNA.
Encoded 25-aa region Protein 322–346
P S P E P I Y N S E G K Q L N T R E F R T R K K L
Predicted HLA-I binding
41.5 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 7,415.8 A*33:03 54.1 B*08:01 2,488.9 B*15:08 8,873.6 C*01:02 311.3 C*07:02 41.5
IYNSEGKQL9 aa · HLA-C*07:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
157.41 transformed TPM
Paired tumour–normal DNA and RNA support
Tumour DNA: 129 alternate reads / 377 depth. Normal DNA: 57 reference-supporting fragments and 0 alternate-supporting fragments. RNA: 21 mutant-supporting fragments / 66 eligible fragments.
Gene fusion · region 13 of 24
CDH1::NRG1 In-frame junction
←
→
The in-frame CDH1::NRG1 junction is explicitly included alongside the predicted alternative fusion tail.
Encoded 25-aa region Protein 347–371
S T Y T A L I I A T D N A T S T S T T G T S H L V
Predicted HLA-I binding
509 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 509 A*33:03 14,117.1 B*08:01 23,992.8 B*15:08 10,767.5 C*01:02 1,489.4 C*07:02 15,889.1
ATDNATSTST10 aa · HLA-A*01:01
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
68.66 transformed TPM
CDH1, the left fusion partner.
In-frame fusion junction
The source call reports 200 junction reads and one spanning fragment. This region is included explicitly; its best eligible prediction is 508.95 nM.
CTA / self protein · region 14 of 24
TEKT5 CTA / self protein
←
→
A reference protein region from a cancer–testis antigen (CTA)
gene with positive supplied expression.
Encoded 25-aa region Protein 373–397
F T I D D T L Q T L K L R L R E T Q D T L Q L L V
Reference sequence; no mutation
Predicted HLA-I binding
23.7 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 55.6 A*33:03 24.9 B*08:01 85.6 B*15:08 246.3 C*01:02 23.7 C*07:02 38.9
TIDDTLQTL9 aa · HLA-C*01:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
4.84 transformed TPM
How expression is used in selection
Supplied gene expression.
The supplied gene value is used directly as the expression
proxy.
Region score = affinity contribution sum × √expression
proxy.
DNA mutation · region 15 of 24
HSPG2 R3952L
←
→
Paired tumour–normal Mutect2 calling retained this protein-changing variant. Isovar reconstructed the altered sequence from tumour RNA.
Encoded 25-aa region Protein 398–422
L P A L T N T H H E L L L D V E F K P L A P D G V
Predicted HLA-I binding
81.1 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 892.1 A*33:03 547 B*08:01 754.6 B*15:08 4,120.5 C*01:02 81.1 C*07:02 750.3
LTNTHHELL9 aa · HLA-C*01:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
167.61 transformed TPM
Paired tumour–normal DNA and RNA support
Tumour DNA: 217 alternate reads / 390 depth. Normal DNA: 46 reference-supporting fragments and 0 alternate-supporting fragments. RNA: 5 mutant-supporting fragments / 9 eligible fragments.
Splice event · region 16 of 24
MUC3A Splice event
←
→
This region is reconstructed from Yash’s RNA around a LENS-identified join, using an annotated upstream coding frame.
Encoded 25-aa region Protein 425–449
T S Q P T T I T P S S V G F S G S L P M M T D L T
The teal marker locates the RNA join.
Compared with the annotated protein Reference T S Q P T T I T P S S V G I S G S L P [−753 aa] M M T D L T
Candidate T S Q P T T I T P S S V G F S G S L P joined M M T D L T
The observed RNA path omits 753 reference amino acids in this comparison. Shading marks amino-acid differences; teal marks the RNA join separately.
Reference sequence and transcript Omitted reference segment (753 aa):
MMTDLTSVYTVSNMSARPTTVIPSSPTVQNTEISISVSMTSATTPSGGPTFTSTENTPTRSLLTSFPMTHSFSSSMSESSAGTTHTESISSPRGTTSTLHTTVESTPSPTTTTSFTTSTMMEPPSSTVSTTGRGQTTFPSSTATFPETTTLTPTTDISTVSLTTAMTSPPPVSSSITPTNTMTSMRTTTYWPTATNTLSPLTSSILSSTPVPSTEMITSHTTNTTPLSTLVTTLLTTITRSTPTSETTYPTSPTSIVSDSTTEITYSTSITGTLSTATTLPPTSSSLPTTETATMTPTTTLITTTPNTTSLSTPSFTSSTIYSTVSTSTTAISSASPTSGTMVTSTTMTPSSLSTDTPSTTPTTITYPSVGSTGFLTTATDLTSTFTVSSSSAMSTSVIPSSPSIQNTETSSLVSMTSATTPSLRPTITSTDSTLTSSLLTTFPSTYSFSSSMSASSAGTTHTETISSLPASTNTIHTTAESALAPTTTTSFTTSPTMEPPSTTVATTGTGQTTFPSSTATFLETTTLTPTTDFSTESLTTAMTSTPPITSSITPTDTMTSMRTTTSWPTATNTLSPLTSSILSSTPVPSTEVTTSHTTNTNPVSTLVTTLPITITRSTLTSETAYPSSPTSTVTESTTEITYPTTMTETSSTATSLPPTSSLVSTAETAKTPTTNLVTTTTKTTSHSTTSFTSSTIYSTASTPTTAITSVPTTLGTMVTSTSMIPSTVSTGIPTSQPTTITPSSVGISGSLPENST00000379458.9. GENCODE 37 annotated protein context.
Predicted HLA-I binding
260.8 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 13,566.9 A*33:03 7,655.4 B*08:01 10,926.2 B*15:08 353.3 C*01:02 260.8 C*07:02 669.1
VGFSGSLPM9 aa · HLA-C*01:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
656.58 transformed TPM
How expression is used in selection
Supplied expression of the assigned gene; no splice-fraction
multiplier.
The supplied gene value is used directly as the expression proxy.
Region score = affinity contribution sum × √expression
proxy.
RNA-supported splice region
The complete 25-aa sequence has 3 supporting RNA fragment names. The junction was not detected in either searched normal-reference catalog.
Gene fusion · region 17 of 24
CDH1::NRG1 Alternative fusion tail
←
→
This region comes from the predicted alternative CDH1::NRG1 fusion tail.
Encoded 25-aa region Protein 454–478
E P D T F M E Q K I T Y I Y I H H W D K P S C K M
Predicted HLA-I binding
70.2 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 120.6 A*33:03 81.5 B*08:01 70.2 B*15:08 1,823.6 C*01:02 84.1 C*07:02 126.4
FMEQKITYI9 aa · HLA-B*08:01
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
68.66 transformed TPM
CDH1, the left fusion partner.
How expression is used in selection
Supplied CDH1 expression × bounded fusion fraction.
Fusion proxy: 68.66 × 11.59% = 7.96.
Region score = affinity contribution sum × √expression
proxy.
RNA-supported fusion hypothesis
The event is supported at its exact breakpoints; this
selected frameshift-tail sequence is a predicted product.
DNA mutation · region 18 of 24
ARHGAP40 R438W
←
→
Paired tumour–normal Mutect2 calling retained this protein-changing variant. Isovar reconstructed the altered sequence from tumour RNA.
Encoded 25-aa region Protein 482–506
T V M A P N L F L H Q G W P P K L P K G K E K Q L
Predicted HLA-I binding
138.2 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 18,273.7 A*33:03 287 B*08:01 5,650.4 B*15:08 10,818.7 C*01:02 140.9 C*07:02 138.2
LHQGWPPKL9 aa · HLA-C*07:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
6.27 transformed TPM
Paired tumour–normal DNA and RNA support
Tumour DNA: 196 alternate reads / 596 depth. Normal DNA: 49 reference-supporting fragments and 0 alternate-supporting fragments. RNA: 9 mutant-supporting fragments / 20 eligible fragments.
CTA / self protein · region 19 of 24
LRRC36 CTA / self protein
←
→
A reference protein region from a cancer–testis antigen (CTA)
gene with positive supplied expression.
Encoded 25-aa region Protein 507–531
G S Y A G K I H S I G D A F R N F K N L R S L D L
Reference sequence; no mutation
Predicted HLA-I binding
21 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 2,498.4 A*33:03 26.1 B*08:01 151.1 B*15:08 190.2 C*01:02 48.7 C*07:02 21
SYAGKIHSI9 aa · HLA-C*07:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
9.15 transformed TPM
How expression is used in selection
Supplied gene expression.
The supplied gene value is used directly as the expression
proxy.
Region score = affinity contribution sum × √expression
proxy.
DNA mutation · region 20 of 24
AQP3 C11Y
←
→
Paired tumour–normal Mutect2 calling retained this protein-changing variant. Isovar reconstructed the altered sequence from tumour RNA.
Encoded 25-aa region Protein 534–558
M G R Q K E L V S R Y G E M L H I R Y R L L R Q A
Predicted HLA-I binding
29.4 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 107.1 A*33:03 55.1 B*08:01 143.3 B*15:08 203.7 C*01:02 863.3 C*07:02 29.4
SRYGEMLHI9 aa · HLA-C*07:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
19.64 transformed TPM
Paired tumour–normal DNA and RNA support
Tumour DNA: 106 alternate reads / 314 depth. Normal DNA: 46 reference-supporting fragments and 0 alternate-supporting fragments. RNA: 2 mutant-supporting fragments / 4 eligible fragments.
CTA / self protein · region 21 of 24
YBX2 CTA / self protein
←
→
A reference protein region from a cancer–testis antigen (CTA)
gene with positive supplied expression.
Encoded 25-aa region Protein 560–584
P N R R K S R R F I P R P P S V A P P P M V A E I
Reference sequence; no mutation
Predicted HLA-I binding
29.8 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 1,826.4 A*33:03 593.1 B*08:01 265.5 B*15:08 252.1 C*01:02 29.8 C*07:02 38.7
VAPPPMVAEI10 aa · HLA-C*01:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
15.48 transformed TPM
How expression is used in selection
Supplied gene expression.
The supplied gene value is used directly as the expression
proxy.
Region score = affinity contribution sum × √expression
proxy.
Splice event · region 22 of 24
F5 Splice event
←
→
This region is reconstructed from Yash’s RNA around a LENS-identified join, using an annotated upstream coding frame.
Encoded 25-aa region Protein 586–610
A L G Q M P I F P D L S H T T L S L D F S Q T N L
The teal marker locates the RNA join.
Compared with the annotated protein Reference A L G Q M P I S P D [−45 aa] L S H T T L S L D F S Q T N [−45 aa] L
Candidate A L G Q M P I F P D joined L S H T T L S L D F S Q T N joined L
The observed RNA path omits 90 reference amino acids in this comparison. Shading marks amino-acid differences; teal marks the RNA join separately.
Reference sequence and transcript Omitted reference segment (45 aa):
LSHTTLSPDLSHTTLSLDLSQTNLSPELSQTNLSPALGQMPLSPDOmitted reference segment (45 aa):
LSPELSHMTLSPELSQTNLSPALGQMPISPDLSHTTLSLDFSQTNENST00000367796.3. GENCODE 37 annotated protein context.
Predicted HLA-I binding
24.2 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 57.3 A*33:03 2,640.8 B*08:01 58.4 B*15:08 50.4 C*01:02 24.2 C*07:02 36.5
IFPDLSHTTL10 aa · HLA-C*01:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
470.6 transformed TPM
How expression is used in selection
Supplied expression of the assigned gene; no splice-fraction
multiplier.
The supplied gene value is used directly as the expression proxy.
Region score = affinity contribution sum × √expression
proxy.
RNA-supported splice region
The complete 25-aa sequence has 2 supporting RNA fragment names. The junction was not detected in either searched normal-reference catalog.
DNA mutation · region 23 of 24
KCTD19 G920R
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→
Paired tumour–normal Mutect2 calling retained this protein-changing variant. Isovar reconstructed the altered sequence from tumour RNA.
Encoded 25-aa region Protein 614–638
M D L L I Q R G L S R S V S Y S I L R K Y L Q E D
Predicted HLA-I binding
36.9 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 919.3 A*33:03 36.9 B*08:01 255.2 B*15:08 579.3 C*01:02 486.7 C*07:02 104.2
RSVSYSILR9 aa · HLA-A*33:03
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
9.91 transformed TPM
Paired tumour–normal DNA and RNA support
Tumour DNA: 134 alternate reads / 419 depth. Normal DNA: 49 reference-supporting fragments and 0 alternate-supporting fragments. RNA: 2 mutant-supporting fragments / 7 eligible fragments.
Splice event · region 24 of 24
MUC6 Splice event
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→
This region is reconstructed from Yash’s RNA around a LENS-identified join, using an annotated upstream coding frame.
Encoded 25-aa region Protein 643–667
P S S F S M A K T S T S L P Y H T S S T H H P E V
The teal marker locates the RNA join.
Compared with the annotated protein Reference R S S F S T A K T [−169 aa] S T S L P Y H T S S T H H P E V
Candidate P S S F S M A K T joined S T S L P Y H T S S T H H P E V
The observed RNA path omits 169 reference amino acids in this comparison. Shading marks amino-acid differences; teal marks the RNA join separately.
Reference sequence and transcript Omitted reference segment (169 aa):
STSLHSHTSSTHHPEVTSTSTTSITPNHTSTGTRTPVAHTTSATSSRLPTPFTTHSPPTGTTPISSTGPVTATSFQTTTTYPTPSHPHTTLPTHVPSFSTSLVTPSTHTVIIPTHTQMATSASIHSMPTGTIPPPTTIKATGSTHTAPPMTPTTSGTSQSPSSFSTAKTENST00000421673.7. GENCODE 37 annotated protein context.
Predicted HLA-I binding
24.2 nM at best
Best eligible short peptide for each allele. Lower values
indicate stronger binding. Select a row to see the peptide in
context.
A*01:01 2,049.5 A*33:03 3,233.8 B*08:01 47.4 B*15:08 80.9 C*01:02 24.2 C*07:02 129
SMAKTSTSL9 aa · HLA-C*01:02
Bars show affinity on a logarithmic scale. All six allele
values are in nM.
Gene expression
65.81 transformed TPM
How expression is used in selection
Supplied expression of the assigned gene; no splice-fraction
multiplier.
The supplied gene value is used directly as the expression proxy.
Region score = affinity contribution sum × √expression
proxy.
RNA-supported splice region
The complete 25-aa sequence has 3 supporting RNA fragment names. The junction was not detected in either searched normal-reference catalog.
