Table 3. NGS analysis from LBC samples for breast cancer FNA.
| case | Intrinsic subtype | Storage time | QC score | Mean read depth | Variant call | VAF(%) | CNV (fold) | |
|---|---|---|---|---|---|---|---|---|
| 1 | Luminal | 12 months | 0.004 | 466 | GATA3pLeu397fs | 36.6 | none | |
| 2 | Luminal | 8 months | 0.002 | 435 | PMS2 amp | (4.0) | ||
| ESR1pVal422del | 12.1 | CCND1 amp | (5.4) | |||||
| PTENpTyr176* | 38.5 | MDM2 amp | (6.0) | |||||
| 3 | TNBC | 7 months | 0.018 | 501 | RETpPro140Arg | 28.1 | NBN amp | (4.2) |
| CDKN2A loss | (0.98) | |||||||
| CBFB loss | (1.0) | |||||||
| CDH1 loss | (1.0) | |||||||
| TP53 loss | (1.0) | |||||||
| 4 | Her2(+) DCIS | 5 months | 0.002 | 529 | TP53pHis214Arg | 21.2 | PMS2 amp | (4.6) |
| FN11 amp | (6.7) | |||||||
| ERBB2 amp | (6.9) | |||||||
| CHEK2 amp | (4.0) | |||||||
| 5 | ER(+) SpCC | 4 months | 0.005 | 392 | AKT1pGlu17Lys | 44.9 | none | |
| TP53pArg280Lys | 23.0 | |||||||
| 6 | TNBC | 1 month | 0.001 | 418 | PTGFR loss | (0.7) | ||
| NEK2 amp | (5.2) | |||||||
| FBXO32 amp | (4.3) | |||||||
| MYC amp | (5.2) | |||||||
| PIK3CApGlu542Lys | 60.5 | CDKN2A amp | (6.2) | |||||
| TP53pPro278His | 74.7 | GATA3 amp | (11.5) | |||||
| AKT1 amp | (4.5) | |||||||
| RAD51 amp | (4.7) | |||||||
| CBFB amp | (6.6) | |||||||
TNBC, Triple negative breast cancer; Her2, Human epidermal grwoth factor receptor 2; DCIS, Ductal carcinoma in situ; ER, Estrogen receptor; ER(+)SpCC, ER positive spindle cell carcinoma; VAF, Variant allele fraction; CNV, Copy number variation
* indicated a generation of stop codon.