Table I.
Genetic variants found in the cSCC patient by IT-PGM sequencing.
| Genea | Mutationb | AFc (%) | Relevanced | Prediction testj | (Refs.) |
|---|---|---|---|---|---|
| FGFR3 | c.1138G>A p.Gly380Arg (COSM24842) | 28.7 | Pathogenice,f | (23,24) | |
| c.1953G>A p.Thr651=(rs7688609) | 100.0 | Benigne,g | |||
| EGFR | c.1498+22 A>T (rs1558544) | 100.0 | NCg,i | NNSPLICE: Unchanged | |
| c.2361G>A p.Gln787=(rs1050171) | 100.0 | Benigne,g | |||
| MET | c.534C>T p.Ser178Ser (rs35775721) | 67.2 | Benigng | ||
| MAP2K1 | c.174G>C p.Gln58His | 15.8 | Likely pathogenici | PROVEAN: Deleterius; | |
| SIFT: Damaging; | |||||
| PolyPhen: Possibly damaging; | |||||
| CRAVAT: High pathogenicity cancer driver impact | |||||
| TP53 | c.743G>A p. Arg248Gln (COSM10662) | 21.1 | Pathogenice,f,h | (25–27) | |
| c.836_861del27 | 31.1 | Likely pathogenici | PROVEAN: Deleterius | ||
| p.Gly279_Asn288delinsAsp | CRAVAT: High pathogenicity cancer driver impact | ||||
| c.215 C>G p.Pro72Arg, (rs1042522, COSM250061) | 60.2 | Uncertain significancee,f,i | (30) | ||
| c.1-46C>T | 21.2 | NA | NNSPLICE: Unchanged |
The following 22 genes were analyzed: DDR2, NRAS, ALK, ERBB4, CTNNB1, PIK3CA, FBXW7, FGFR3, BRAF, EGFR, MET, FGFR1, NOTCH1, FGFR2, PTEN, KRAS, AKT1, MAP2K1, ERBB2, TP53, SMAD4, STK11.
Sequence variant nomenclature according to HGVS recommendations (http://varnomen.hgvs.org/); (COSMIC and/or dbSNP ID numbers).
AF: Variant allele frequency in the tumor sample.
Biological impact of the variant according to:
ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/)
COSMIC (http://cancer.sanger.ac.uk/cosmic)
IARC database (http://p53.iarc.fr/)
In silico prediction tests (see next column).
In silico prediction on the biological impact of the variant according to multiple software (PolyPhen-2, http://genetics.bwh.harvard.edu/pph2/; SIFT, http://sift.jcvi.org/; PROVEAN, http://provean.jcvi.org/index.php; CRAVAT, https://www.cravat.us/CRAVAT/; NNSPLICE, http://www.fruitfly.org/seq_tools/splice.html.