Table 1.
Mutation frequency of cMNR and FSP sequences
| Gene | cMNR | Intestinal Expression | Mutation Frequency | WT FSP Sequence | SYFPEITHI Score | netMHC | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Type | Monomorphic | Normal | Tumor | Total | FS-Specific | Db | Kb | % rank | ||||
|
| ||||||||||||
| Nacad | C14 | yes | yes | yes | 75% | FS(−1) | 56.25% | VIYAPPPPAEGRWPCWLLRAH* | 15 | s0 | s0 | 3 |
| w0 | w0 | |||||||||||
| FS(−2) | 37.5% | DVIYAPPPQQRGGGRAGYSERIDGQRDRETGVSAGTRPGHARGGCGR* | 14 | s0 | s0 | 6 | ||||||
| w0 | w0 | |||||||||||
|
| ||||||||||||
| Xirp1 | C9 | yes | yes | yes | 37.5% | FS(−1) | 31.25% | GKGPGGPPLSSPKRVMYRLSVGCLRPTL* | 19 | s0 | s1 | 0.4 |
| w2 | w4 | |||||||||||
| FS(−2) | 6.25% | GKGPGGPP* | - | - | - | - | ||||||
|
| ||||||||||||
| 5730596B20Rik | C12 | yes | yes | yes | 37.5% | FS(−1) | 37.5% | GTLPPPPPTQH* | 6 | s0 | s0 | 39 |
| w0 | w0 | |||||||||||
| FS(−2) | 0.00% | LGTLPPPPQPSTEQSGWKHHQ* | 7 | s0 | s0 | 55 | ||||||
| w0 | w0 | |||||||||||
|
| ||||||||||||
| Rif1 | A12 | yes | yes | yes | 33.3% | FS(−1) | 20.00% | AHTDKKKK* | - | - | - | - |
| FS(−2) | 13.33% | AHTKDKKKSETVGQTETRIFISKNKEW* | 15 | s0 | s0 | 4.5 | ||||||
| w0 | w0 | |||||||||||
|
| ||||||||||||
| Maz | C8 | yes | yes | yes | 33.3% | FS(−1) | 20.00% | PCTLLAPPSPCWAWTPGGWAAS* | 7 | s0 | s0 | 9.5 |
| w0 | w0 | |||||||||||
| FS(−2) | 13.33% | FPCTLLAPLPRAGPGLPGGGRPHELLPATSGSRPEPPAGRG* | 17 | s0 | s0 | 3.5 | ||||||
| w0 | w0 | |||||||||||
|
| ||||||||||||
| Hic1 | C10 | yes | yes | yes | 31.25% | FS(−1) | 18.75% | DRTFPSPPRIGAI* | 14 | s0 | s0 | 5 |
| w0 | w0 | |||||||||||
| FS(−2) | 12.5% | DRTFPSPPELARYNI* | 18 | s0 | s0 | 4.5 | ||||||
| w0 | w0 | |||||||||||
|
| ||||||||||||
| Sdccag1 | A11 | yes | yes | yes | 25% | FS(−1) | 25.00% | EAPKGKKKSKRTSSCRSRRRTSRCL* | 12 | s0 | s0 | 8 |
| w0 | w0 | |||||||||||
| FS(−2) | 6.25% | EAPKGKKKAKEQAAAEAAEEQAAACRCGSQPVSLCQCQKIL* | 16 | s0 | s0 | 2.5 | ||||||
| w0 | w0 | |||||||||||
|
| ||||||||||||
| Tmem107 | G9 | yes | yes | yes | 25% | FS(−1) | 25.00% | TQYFGMGGVVENRSQI* | 24 | s2 | s0 | 0.5 |
| w1 | w0 | |||||||||||
| FS(−2) | 6.25% | TQYFGMGGWWKIDPKSEGFPHLDLSCTCEIGRVLKSHTHPNPPAYKVWRFKCLGWKGL* | 21 | s0 | s1 | 0.25 | ||||||
| w0 | w2 | |||||||||||
|
| ||||||||||||
| Srcin1 | C9 | yes | yes | yes | 25% | FS(−1) | 25.00% | DEGMWPPPTTS* | 6 | s0 | s0 | 31 |
| w0 | w0 | |||||||||||
| FS(−2) | 0.00% | VDEGMWPPQQPPEPVPQEGGS* | 12 | s0 | s0 | 22 | ||||||
| w0 | w0 | |||||||||||
|
| ||||||||||||
| Marcks | A11 | yes | yes | yes | 20% | FS(−1) | 20.00% | SSETPKKKRSAFPSRSPSS* | 12 | s0 | s0 | 5.5 |
| w0 | w0 | |||||||||||
| FS(−2) | 0.00% | SSETPKKKEALFLQEVLQAERLLLQEEQEGVGRGR* | 16 | s0 | s0 | 0.8 | ||||||
| w3 | w0 | |||||||||||
|
| ||||||||||||
| Senp6 | A11 | yes | yes | yes | 18.75% | FS(−1) | 18.75% | VKCSMKKKIMLSMKMKNQVTENLRARTFVIEPKVRMASGMNASVLYIIQMP* | 27 | s10 | s0 | 0.03 |
| w12 | w2 | |||||||||||
| FS(−2) | 0.00% | VKCSMKKKSCYQ* | 1 | s0 | s0 | 20 | ||||||
| w0 | w0 | |||||||||||
|
| ||||||||||||
| Phactr4 | A10 | yes | yes | yes | 18.75% | FS(−1) | 18.75% | PWKWRKKKAVISSKRHQKF* | 12 | s0 | s0 | 3.5 |
| w0 | w0 | |||||||||||
| FS(−2) | 0.00% | PWKWRKKKQ* | 2 | s0 | s0 | 75 | ||||||
| w0 | w0 | |||||||||||
|
| ||||||||||||
| Chrnb2 | C10 | yes | yes | yes | 18.75% | FS(−1) | 12.5% | VRTRPSPPHLSPASWVLKPFAINAKGIFLILCGNWQQGCLCHLGMHLRHRQVGL* | 21 | s1 | s0 | 0.5 |
| w3 | w1 | |||||||||||
| FS(−2) | 6.25% | VRTRPSPPISLQPHGS* | 16 | s0 | s0 | 11 | ||||||
| w0 | w0 | |||||||||||
Genes affected by coding mononucleotide (cMNR) frameshift (FS) mutations and derived frameshift peptides (FSPs). Predicted immunoscores for FSPs (bold letters) including an 8 amino acid wild type (WT) sequence are indicated for C57BL/6 alleles H2-Db and H2-Kb (SYFPEITHI 1.0 and netMHC4.0). The numbers of strong (s) and weak (w) binders are shown. Low numbers of percent rank (% rank) as well as SYFPEITHI scores >12 predict strong MHC binding. FSPs used for further analysis are indicated by grey boxes.