Table 2.
Genetic variants found in TP53, PIK3CA, homologous recombination (HR), and mismatch repair (MMR) genes detected in 21 inflammatory breast carcinomas assessed by tNGS *.
| Cases | TP53 | PIK3CA | HR gGenes | MMR Genes |
|---|---|---|---|---|
| IBC1 | c.3140A>G;p.His1047Arg | |||
| IBC2 | c.1633G>A; p.Glu545Lys | |||
| IBC4 |
ATM (c.3887C > G; p.Pro1296Arg) PG, Loss |
|||
| IBC5 |
BRCA2 (c.4963_4964insA; p.Tyr1655Ter) Loss |
|||
| IBC6 | ||||
| IBC7 |
BRCA2 (C.2806_2809delAAAC; p.Ala938Profs) cnLOH |
MLH1 (c.2146G > A; p.Val716Met) PG, Loss |
||
| IBC8 | c.512A > G; p.Glu171Gly PG, Loss |
|||
| IBC9 |
BRCA2 (c.5682C > G; p.Tyr1894Ter) Loss RAD51B (c.728A > G; p.Lys243Arg) cnLOH POLD1 (c.1055G > A; p.Arg352His) Gain |
|||
| IBC10 | BRCA2 (c.2T > G; p.Met1?) | |||
| IBC11 | c.309C > A; p.Tyr103Ter Gain and cnLOH |
BRCA2 (c.316+1G >T) Gain and cnLOH RAD51B (c.315+8A > G) PG, Gain and cnLOH |
MSH6 (c.3961A > G; p.Arg1321Gly) PG |
|
| IBC12 | c.659A > G; p.Tyr220Cys PG, cnLOH |
RAD51D (c.899G > A; p.Arg300Gln) PG, Loss |
PMS2 (c.2186_2187delTC; p.Leu729Glnfs) PG, Gain |
|
| IBC13 | c.712T > G; p.Cys238Gly PG |
BRCA2 (c.6988A > G; p.Ile2330Val) PG |
||
| IBC14 | c.586C > T; p.Arg196Ter PG, Loss |
BRCA2 (c.8869C > T; p.Gln2957Ter) Loss |
||
| IBC15 |
PALB2 (c.43G > T; p.Glu15Ter) cnLOH |
MSH3 (c.1567G > A; p.Glu523Lys) PG MSH3 (c.1571A > C; p.Asn524Thr) PG |
||
| IBC16 | c.856G > A; p.Glu286Lys Loss and cnLOH |
MSH3 (c.2436-5C > G Gain |
||
| IBC18 | c.626_627delGA; p.Arg209Lysfs PG, Loss |
c.3140A > T; p.His1047Leu |
BRCA2 (c.9227G > T; p.Gly3076Val) Loss |
|
| IBC20 | c.578A > T; p.His193Leu PG c.560-2A > C PG, Loss |
c.1035T > A; p.Asn345Lys |
BRCA1 (c.3858delT; p.Ser1286Argfs) PG, Loss |
MLH3 (c.2638C > G; p.Leu880Val) PG |
| IBC22 | c.731G > A; p.Gly244Asp Loss and cnLOH |
c.3140A > G; p.His1047Arg |
MUS81 (c.416G > A; p.Arg139Gln) PG |
PMS2 (c.2383G > A; p.Asp795Asn) PG |
| IBC24 | c.844C > T; p.Arg282Trp PG, Loss |
MSH6 (c.1406A > G; p.Tyr469Cys) PG |
||
| IBC25 | ||||
| IBC26 | c.542G > A; p.Arg181His PG, Loss: |
* Copy number alterations and Variant Allele Frequency (VAF) of TP53, HR and MMR genes presenting genetic variants are shown. (c.) and (p.) indicate the coding sequence and the amino acid position according to HGVS (Human Genome Variation Society), respectively. cnLOH, copy number loss of heterozygosity; PG, potentially germline variant (VAF, <0.5). Copy number loss < 2.0; Copy number gain > 2.0.