Table 1 Data from targeted NGS for comparison of molecular profiles between tumours (note that there was not enough tissue from the primary tumour in case 1 for NGS analysis in addition to pyrosequencing)
From: Targeted sequencing may facilitate differential diagnostics of pulmonary tumours: a case series
Case no. | Tumour | Estimated tumour qty (%) | Run no. | Gene | Mutation frequency (%) | Transcript/HGVSc | Classification | Consequence | dbSNP ID |
|---|---|---|---|---|---|---|---|---|---|
2 | Breast tumour | 30 | ML00256 | PIK3CA | 36.3 | NM_006218.2: c.3140A > G | Unknown significance | Missense variant | rs121913279 |
PTEN | 6.3 | NM_000314.4: c.80-1G > C | Unknown significance | Splice acceptor variant | |||||
Lung tumour | 40 | ML00257 | PIK3CA | 24.8 | NM_006218.2: c.3140A > G | Unknown significance | Missense variant | rs121913279 | |
3 | Upper lobe tumour | 10 | ML00279 | KRAS | 12.1 | NM_033360.2: c.34G > T | Pathogenic | Missense variant | rs121913530 |
CDH1 | 50.3 | NM_004360.3: c.1774G > A | Unknown significance (probably germline variant) | Missense variant | rs35187787 | ||||
SMAD4 | 22.9 | NM_005359.5: c.1495 T > C | Unknown significance | Missense variant | |||||
3 | Lower lobe tumour | 10 | ML00280 | KRAS | 4.8 | NM_033360.2: c.34G > T | Pathogenic | Missense variant | rs121913530 |
CDH1 | 51.2 | NM_004360.3: c.1774G > A | Unknown significance (probably germline variant) | Missense variant | rs35187787 | ||||
SMAD4 | 6.3 | NM_005359.5: c.1495 T > C | Unknown significance | Missense variant | |||||
4 | Right upper lobe tumour | 25 | ML00352 | KRAS | 27.5 | NM_033360.3: c.183A > T | Pathogenic | Missense variant | rs17851045 |
4 | Left upper lobe tumour | 60 | ML00329 | EGFR | 59.9 | NM_005228.3: c.2235_2249delGGAATTAAGAGAAGC | Pathogenic | Missense variant, feature truncation | rs121913421 |
TP53 | 24.5 | NM_000546.5: c.473G > T | Presumed pathogenic | Missense variant | |||||
4 | Left lymph node metastasis | 20 | ML01103 | EGFR | 13.7 | NM_005228.3: c.2235_2249delGGAATTAAGAGAAGC | Pathogenic | Missense variant, feature truncation | rs121913421 |
TP53 | 13.7 | NM_000546.5: c.473G > T | Presumed pathogenic | Missense variant | |||||
5 | Central tumour | 15 | 366-16 | BRAF | 8.9 | NM_004333: c.1406G > T | Pathogenic | Missense variant | rs121913355 |
TP53 | 5.6 | NM_000546: c.811G > A | Pathogenic | Missense variant | |||||
5 | Subpleural tumour | 40 | 367-16 | BRAF | 37.6 | NM_004333: c.1406G > T | Pathogenic | Missense variant | rs121913355 |
6 | Right upper lobe tumour | 35 | 330-16 | EGFR | 17.1 | NM_005228: c.2573G > T | Pathogenic | Missense variant | rs121434568 |
TP53 | 17.8 | NM_000546: c.581 T > G | Pathogenic | Missense variant | |||||
6 | Right lower lobe tumour | 40 | 329-16 | (no mutations; ALK positive) | |||||
6 | Left lower lobe tumour | 30 | 279-16 | (no mutations; ALK positive) |