Table 1 Table listing the peptides selected for immunogenicity assessment

From: Proteogenomic approach to immunopeptidomics of ovarian tumors identifies shared peptide vaccine candidates

#

Peptide

hgnc symbol

Splicing aberration

Log2 foldchange (MAX)

Presentation patients’ HLAs (predicted affinity nM)

Presentation most frequent (1:100) HLAs in Caucasian population (predicted affinity nM)

Cum sum allele frequency

UniProt db frequency

StringTie db frequency

HEX

1

HELEKKIEL

BAIAP2L1

No

4,17

HLA-B40:01 : 31.90

HLA-B0801 : 77.17, HLA-B1302 : 91.40, HLA-B1401 : 41.98, HLA-B1402 : 41.98, HLA-B1801 : 45.84, HLA-B3701 : 32.53, HLA-B3801 : 61.82, HLA-B3901 : 67.94, HLA-B4001 : 31.90, HLA-B4002 : 31.77, HLA-B4402 : 53.47, HLA-B4403 : 50.85, HLA-B4901 : 36.05, HLA-B5001 : 43.22, HLA-C0704 : 45.65

0.517

0.091

0.091

Yes

2

TFKEKVTSL

NF1

No

3,12

HLA-B08:01 : 38.90, HLA-C01:02 : 41.52, HLA-C06:02 : 48.30, HLA-C07664 : 49.02, HLA-C07:01 : 78.12, HLA-C07:02 : 40.80

HLA-B0801 : 38.90, HLA-C0102 : 41.52, HLA-C0401 : 51.64, HLA-C0602 : 48.30, HLA-C0701 : 78.12, HLA-C0702 : 40.80, HLA-C0704 : 49.02, HLA-C1402 : 26.81, HLA-C1601 : 53.37

0.711

0.273

0.091

Yes

3

VEEDFQQKL

MECOM

No

5

HLA-B40:01 : 35.99

HLA-B3701 : 38.46, HLA-B4001 : 35.99, HLA-B4002 : 35.33, HLA-B4402 : 63.53, HLA-B4403 : 63.02, HLA-B4901 : 40.26, HLA-B5001 : 55.91

0.248

0.091

0

Yes

4

YEIDDVERL

KIF26B

No

5,93

HLA-B40:01 : 37.17

HLA-B1302 : 69.10, HLA-B1801 : 83.52, HLA-B3701 : 40.90, HLA-B3801 : 62.72, HLA-B4001 : 37.17, HLA-B4002 : 37.58, HLA-B4402 : 75.30, HLA-B4403 : 62.72, HLA-B4901 : 39.31, HLA-B5001 : 51.92, HLA-C0704 : 87.87

0.353

0.182

0.182

No

5

LPLHKVKSL

PPP2R5D, PPP2R5C

No

1,09

HLA-B07:02 : 36.29, HLA-B08:01 : 40.68

HLA-B0702 : 36.29, HLA-B0801 : 40.68, HLA-B1401 : 94.99, HLA-B1402 : 94.99, HLA-B3503 : 56.60, HLA-B5501 : 51.67

0.319

0.455

0.455

Yes

6

KVAELLEKY

FAM83H, MIR4664

No

4,8

HLA-A03:01 : 64.65, HLA-B15:01 : 37.21

HLA-A0301 : 64.65, HLA-A1101 : 51.55, HLA-A2501 : 62.16, HLA-A2601 : 71.50, HLA-A2902 : 27.18, HLA-A3201 : 26.47, HLA-B1501 : 37.21, HLA-B5701 : 73.69, HLA-C0202 : 33.17, HLA-C1203 : 42.10, HLA-C1601 : 45.00

0.546

0.182

0.091

Yes

7

DRYLLVSQF

DDX42

Yes

0,8

HLA-C0701 : 99.20, HLA-C0702 : 78.47

HLA-B1401 : 61.09, HLA-B1402 : 61.09, HLA-C0701 : 99.20, HLA-C0702 : 78.47

0.34

0

0.182

No

8

VVHLIKNAY

ITGB2

No

2,32

HLA-B15:01 : 60.34, HLA-B35:01 : 77.65

HLA-A2902 : 75.75, HLA-B1501 : 60.34, HLA-B3501 : 77.65, HLA-C0202 : 83.24, HLA-C1203 : 68.44, HLA-C1601 : 71.47

0.278

0

0.455

Yes

9

TYSEKTTLF

MUC16

No

8,04

HLA-A24:02 : 22.63

HLA-A2301 : 24.50, HLA-A2402 : 22.63, HLA-C0401 : 83.52, HLA-C0602 : 74.83, HLA-C0701 : 80.69, HLA-C0702 : 32.51, HLA-C0704 : 61.39, HLA-C1402 : 27.55, HLA-C1601 : 70.40

0.667

0.091

0

Yes

10

ALKARTVTF

CCR5

No

4,64

HLA-A32:01 : 61.19, HLA-B08:01 : 52.67, HLA-B15:01 : 32.83

HLA-A3201 : 61.19, HLA-B0801 : 52.67, HLA-B1501 : 32.83, HLA-C0202 : 87.59, HLA-C1203 : 82.87, HLA-C1601 : 75.30

0.336

0.455

0

Yes

11

KLFTSTGLK

AKAP12

No

−2,4

HLA-A03:01 : 24.94

HLA-A0301 : 24.94, HLA-A1101 : 30.37, HLA-A3001 : 32.59, HLA-A3101 : 97.42

0.241

0.364

0.182

Yes

12

KYLTIYLQK

TRMT10B

Yes

−1

HLA-A3101 : 50.27

HLA-A3001 : 66.08, HLA-A3101 : 50.27

0.04

0

0.364

Yes

13

TPHPSELKVM

SCRIB

No

−1,13

HLA-B07:02 : 57.26

HLA-B0702 : 57.26, HLA-B5501 : 83.88

0.149

0.455

0.455

Yes

  1. Log2 foldchange (MAX) indicates the highest log2 fold-change in expression of the associated HGSC gene, as observed in the tumor vs. healthy tissue. “Presentation patients’ HLAs (predicted affinity nM)” represents the predicted binding affinity for HLAs expressed in our patients cohort. “Presentation most frequent (1:100) HLAs in Caucasian population (predicted affinity nM)” represents the predicted binding affinity for HLAs highly frequent in the “USA NMDP European Caucasian” population (allelefrequency.net). “Cum sum allele frequency” indicates the cumulative sum of the frequencies of all the HLA alleles able to bind given peptide. Uniprot db frequency and StringTie db frequency correspond to the frequency a given peptide was empirically observed in the datasets generated matching the peptides spectra using the Uniprot database or the StringTie dataset respectively. The column called HEX shows whether a given peptide was a hit using the HEX pathogen-similarity software and met the inclusion criteria.
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