Table 1.
Applied molecular assays and detected alterations. Detected molecular alterations with NGS. Of note, the nomenclature of MET point mutations depends on the applied transcript number.
| Date | April 2020 | January 2021 | December 2021 | January 2022 | May 2022 | May 2022 | |||
|---|---|---|---|---|---|---|---|---|---|
| Assay | NEO- Plus |
NEO- Select |
NEO- Liquid |
HS2- Lung |
HS2- Lung |
HS- Liquid |
|||
| Sample Type | FFPE | FFPE | Eff. | FFPE | FFPE | Cf | |||
| Point Mutations detected with HC-NGS | |||||||||
| Gen | Transcript. | DNA-change | Protein change | Variant Allelic Frequency | |||||
| EGFR | NM_005228.4 | c.2236_2250del | p.E746_A750del | 17% | 56% | 7% | 27% | 39% | 60% |
| TP53 | NM_001126112.2 | c.559 + 1G > A | p.? | 12% | 61% | 7% | 15% | 31% | 41% |
| MET | NM_00112750.3 (NM_000245.4) | c.3736G > A (c.3682G > A) | p.D1246N (p.D1228N) | - | - | 0.1% | - | - | 0.7% |
| MET | NM_00112750.3 (NM_000245.4) | c.3736G > C (c.3682G > C) | p.D1246H (p.D1228H) | - | - | - | - | - | 0.4% |
| MET | NM_00112750.3 (NM_000245.4) | c.3637C > G (c.3583C > G) | p.L1213V (p.L1195V) | - | - | - | - | - | 0.5% |
| Amplifications detected with HC-NGS | |||||||||
| Gen | Transcript | Level 1 | |||||||
| EGFR | NM_005228.4 | - | + | - | + | + | n.a. | ||
| MET | NM_00112750.3 | - | ++ | ++ | ++ | ++ | n.a. | ||
| Additional alterations detected with HC-NGS | |||||||||
| Tumor Mutational Burden (Muts/mB) | 17.42 | - | - | - | - | - | |||
| Microsatellite Instability | MSI-L | - | - | - | - | - | |||
| TP53, NRAS, BRCA2, and ARAF | - | DEL | - | - | - | - | |||
1 +: low-level amplified, ++: focally amplified, -: not detected, n.a.: not included in the assay, DEL: gen deletion, MSI-L: microsatellite-low, FFPE: formalin-fixed, paraffin-embedded tissue material, Eff.: pleural effusion, Cf.: cf-DNA.