Table 1.
Mutations, identified with NGS
| Gene | Location | Mutation type | Ref - > seq | Blood [%] | EmCa [%] | OvCa [%] | Meta [%] | Coding | Amino Acid Change | PhyloP* | SIFT** | Gr*** | PPhen-2**** | COSMIC |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ARID1A | chr1: 27094447 | Insertion | A- > AT | 0 | 30 | 24 | 0 | c.3155_3156insT | p.Arg1053fs | 2.16 | ||||
| RAF1 | chr3: 12641248 | Deletion | CA- > C | 0 | 37 | 30 | 0 | c.1049_1049delT | p.Met350fs | |||||
| CTNNB1 | chr3: 41266125 | SNV | CCA - > TCA | 0 | 35 | 31 | 12 | c.122C > T | p.Thr41Ile | 2.8 0.86 2.26 | 0 | 89 | 0.996 | COSM5730; COSM5701; COSM5676; COSM29289 |
| PIK3CA | chr3: 178936095 | SNV | A- > G | 0 | 34 | 29 | 10 | c.1637A > G | p.Gln546Arg | 2.2 | 0.01 | 43 | 0.992 | COSM767; COSM12459; COSM25041 |
| ESR1 | chr6: 152419923 | SNV | A- > G | 0 | 0 | 0 | 9 | c.1610A > G | p.Tyr537Cys | 2.02 | 0 | 194 | 0.998 | COSM1074637 COSM1074639 |
| SYNE1 | chr6: 152443737 | SNV | C- > A | 0 | 41 | 38 | 6 | c.26228G > T | p.Arg8743Ile | 2.62 | 97 | |||
| PIK3CG | chr7: 106524631 | SNV | C- > G | 0 | 29 | 0 | 0 | c.2792C > G | p.Ser931Cys | 2.6 | 0 | 112 | 1 | |
| PTEN | chr10: 89692790 | SNV | T- > A | 0 | 0 | 0 | 10 | c.274G > T | p.Asp92Tyr | 2.32 | 0 | 160 | 1 | COSM86049; COSM50762; COSM3566 |
| PTEN | chr10: 89692886 | SNV | T- > A | 0 | 32 | 31 | 0 | c.370 T > A | p.Cys124Ser | 2.41 1.95 | 0.16 | 112 | 1 | COSM5224; COSM5824; COSM1577271; COSM921089 |
| PTEN | chr10: 89692892 | SNV | G- > A | 0 | 34 | 30 | 0 | c.376G > A | p.Ala126Thr | 2.41 | 0.11 | 58 | 0.999 | COSM5051; COSM5211; COSM28889 |
| PTPRT | chr20: 40710566 | SNV | C- > T | 0 | 32 | 24 | 0 | c.4285G > A | p.Val1429Met | 2.88 | 0 | 21 | 1 | |
| USP9X | chrX: 41057832 | SNV | A- > C | 0 | 0 | 30 | 0 | c.4432A > C | p.Met1478Leu | 1.78 | 0.7 | 15 | 0 |
* PhyloP score:• Positive scores -- Measure conservation, which is slower evolution than expected, at sites that are predicted to be conserved; • Negative scores -- Measure acceleration, which is faster evolution than expected, at sites that are predicted to be fast-evolving
** SIFT score: • 0.0–0.05 - deleterious; • 0.05–1.0 – tolerated
*** Grantham score: Higher Grantham scores are considered more deleterious
****PolyPhen-2 score: • 0.0–0.15 -- Variants with scores in this range are predicted to be benign; • 0.15–1.0 -- Variants with scores in this range are possibly damaging; • 0.85–1.0 -- Variants with scores in this range are more confidently predicted to be damaging