Table 1.
Validation of known SNVs and micro-indels
| Gene | Variant | True Allele Frequency | Estimated Allele Frequency |
|---|---|---|---|
|
| |||
| BRAF | V600E | 10.5% | 7.0% |
|
| |||
| cKIT | D816V | 10.0% | 11.0% |
|
| |||
| EGFR | L858R* | 3.0%* | - |
|
| |||
| EGFR | T790M* | 1.0%* | - |
|
| |||
| EGFR | G719S | 24.5% | 18.0% |
|
| |||
| KRAS | G13D | 15.0% | 16.0% |
|
| |||
| KRAS | G12D | 6.0% | 4.0% |
|
| |||
| NRAS | Q61K | 12.5% | 12.0% |
|
| |||
| PIK3CA | H1047R | 17.5% | 16.0% |
|
| |||
| PIK3CA | E545K | 9.0% | 13.0% |
|
| |||
| ALK | P1543S | 33.0% | 33.0% |
|
| |||
| APC | R2714C | 33.0% | 32.0% |
|
| |||
| ARID1A | P1562fs | 33.5% | 40.0% |
|
| |||
| BRCA2 | A1689fs | 33.0% | 35.0% |
|
| |||
| EP300 | K291fs | 8.0% | 6.0% |
|
| |||
| FBXW7 | G667fs | 33.5% | 32.0% |
|
| |||
| FGFR1 | P150L | 8.5% | 7.0% |
|
| |||
| FLT3 | S985fs | 10.5% | 8.0% |
|
| |||
| FLT3 | V197A | 11.5% | 9.0% |
|
| |||
| IDH1 | S261L | 10.0% | 8.0% |
|
| |||
| MET | V237fs | 6.5% | 5.0% |
|
| |||
| MLH1 | L323M | 8.5% | 5.0% |
|
| |||
| NF1 | L626fs | 7.5% | 5.0% |
|
| |||
| NF2 | P275fs | 8.0% | 4.0% |
|
| |||
| NOTCH1 | P668S | 31.5% | 31.0% |
|
| |||
| PDGFRA | G426D | 33.5% | 29.0% |
|
| |||
| EGFR | ΔE746 - A750 | 2.0%* | 1.0% |
| 5.0% | 2.5% | ||
| 10.0% | 8.5% | ||
| 20.0% | 14.9% | ||
| 30.0% | 21.9% | ||
| 50.0% | 42.3% | ||
|
| |||
| PMS2 | P246CfsStop3$ | N/A | 40% |
N/A: not available
*
Variants below the assay’s detection limit will not be reported
$
This variant is from a colon adenocarcinoma patient sample. All variants except this are from HorizonDx