Table 1.
EGFR and KRAS mutational status comparison between Sanger Sequencing and NGS (Next-Generation Sequencing) Variant Caller software. This table reports the EGFR or KRAS mutational status, previously defined by Sanger Sequencing from the 12 patients compared to the Variant Caller NGS results. The EGFR or KRAS mutation nomenclature is based on the convention recommended by the Human Genome Variation Society [10,11].
| Patient | Tumor Type | EGFR and KRAS Status by Sanger Sequencing | EGFR and KRAS Status Confirmed by VC Software | Allele Name |
|---|---|---|---|---|
| 1 | SF | NM_033360.3 (KRAS): c.34G>C | Confirmed KRAS mutation | COSM518 |
| (p.Gly12Arg) | AF: 29.8% | |||
| 1 | FFPE | NM_033360.3 (KRAS): c.34G>C | Confirmed KRAS mutation | COSM518 |
| (p.Gly12Arg) | AF: 58.6% | |||
| 2 | SF | NM_033360.3 (KRAS): c.34G>T | Confirmed KRAS mutation | COSM516 |
| (p.Gly12Cys) | AF: 24.1% | |||
| 2 | FFPE | NM_033360.3 (KRAS): c.34G>T | Confirmed KRAS mutation | COSM516 |
| (p.Gly12Cys) | AF: 6.4% | |||
| 3 | SF | NM_005228.3 (EGFR): c.2239_2240TT>CC | Confirmed EGFR mutation | COSM24267 |
| (p.Lys747Pro) | AF: 37.8% | |||
| 3 | FFPE | NM_005228.3 (EGFR): c.2239_2240TT>CC | Confirmed EGFR mutation | COSM24267 |
| (p.Lys747Pro) | AF: 45.6% | |||
| 4 | SF | NM_033360.3 (KRAS): c.35G>T | Confirmed KRAS mutation | COSM520 |
| (p.Gly12Val) | AF: 24.0% | |||
| 4 | FFPE | NM_033360.3 (KRAS): c.35G>T | Confirmed KRAS mutation | COSM520 |
| (p.Gly12Val) | AF: 23.2% | |||
| 5 | SF | NM_005228.3 (EGFR): c.2237_2255delinsT | Confirmed EGFR mutation | COSM12384 |
| (p.Glu746_Ser752delinsVal) | AF: 5.6% | |||
| 5 | FFPE | NM_005228.3 (EGFR): c.2237_2255delinsT | Confirmed EGFR mutation | COSM12384 |
| (p.Glu746_Ser752delinsVal) | AF: 10.5% | |||
| 6 | SF | NM_005228.3 (EGFR): c.2236_2250del | Confirmed EGFR mutation | COSM6225 |
| (p.Glu746_Ala750del) | AF: 7.8% | |||
| 6 | FFPE | NM_005228.3 (EGFR): c.2236_2250del | Confirmed EGFR mutation | COSM6225 |
| (p.Glu746_Ala750del) | AF: 45.8% | |||
| 7 | SF | NM_033360.3 (KRAS): c.35G>A | Confirmed KRAS mutation | COSM521 |
| (p.Gly12Asp) | AF: 38.6% | |||
| 7 | FFPE | NM_033360.3 (KRAS): c.35G>A | Confirmed KRAS mutation | COSM521 |
| (p.Gly12Asp) | AF: 26.3% | |||
| 8 | SF | NM_033360.3 (KRAS): c.34G>T | Confirmed KRAS mutation | COSM516 |
| (p.Gly12Cys) | AF: 50.5% | |||
| 8 | FFPE | NM_033360.3 (KRAS): c.34G>T | Confirmed KRAS mutation | COSM516 |
| (p.Gly12Cys) | AF: 24.5% | |||
| 9 | SF | NM_033360.3 (KRAS): c.34G>T | Confirmed KRAS mutation | COSM516 |
| (p.Gly12Cys) | AF: 42.0% | |||
| 9 | FFPE | NM_033360.3 (KRAS): c.34G>T | Confirmed KRAS mutation | COSM516 |
| (p.Gly12Cys) | AF: 41.7% | |||
| 10 | SF | NM_005228.3 (EGFR): c.2573T>G | Confirmed EGFR mutation | COSM6224 |
| (p.Leu858Arg) | AF: 45.3% | |||
| 10 | FFPE | NM_005228.3 (EGFR): c.2573T>G | Confirmed EGFR mutation | COSM6224 |
| (p.Leu858Arg) | AF: 40.2% | |||
| 11 | SF | NM_033360.3 (KRAS): c.37G>T | Confirmed KRAS mutation | COSM527 |
| (p.Gly13Cys) | AF: 32.0% | |||
| 11 | FFPE | NM_033360.3 (KRAS): c.37G>T | Confirmed KRAS mutation | COSM527 |
| (p.Gly13Cys) | AF: 24.2% | |||
| 12 | SF | NM_033360.3 (KRAS): c.34G>T | Confirmed KRAS mutation | COSM516 |
| (p.Gly12Cys) | AF: 31.0% | |||
| 12 | FFPE | NM_033360.3 (KRAS): c.34G>T | Confirmed KRAS mutation | COSM516 |
| (p.Gly12Cys) | AF: 42.6% |
Abbreviations: SF: Snap Frozen; FFPE: Formalin-Fixed Paraffin-Embedded; VC: Variant Caller; AF: Allele Frequency.