Table 3 Variants identified in DNA isolated from FFPE cell line mixes
Cell Line/Sample Name | HCT116 | MiaPaCa-2 | H1975 | SK-MEL-28 | 4-Cell Line Mix | H1975 Dil in MiaPaCa-2 (1:14) | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene Symbol | hg19 Coordinates | Variant Type | Variant | Frequency (%) | Found | Found | Found | Found | Expected | Found | Expected | Found |
ABL1 | 133738370 | SNV | G | 37.0 | N.A. | N.A. | N.A. | 9.3 | 12.4 ± 2.6 | 0.0 | N.A. | |
APC | 112175770 | SNV | A | 98.0 | 72.7 | 36.5 | 91.3 | 74.6 | 78.4 ± 1.2 | 70.2 | 65.4 ± 1.4 | |
BRAF | 140453136 | SNV | A | N.A. | N.A. | N.A. | 100.0 | 25.0 | 21.1 ± 2.5 | 0.0 | N.A. | |
CDKN2A | 21971153 | SNV | T | N.A. | N.A. | 98.8 | N.A. | 24.7 | 17.9 ± 0.6 | 100.0a | 98.6 ± 0.9 | |
CSF1R | 149433596 | SNV | C | 100.0 | 100.0 | 100.0 | N.A. | 75.0 | 61.4 ± 2.6 | 100.0 | 99.9 ± 0.2 | |
CSF1R | 149433597 | SNV | T | 95.7 | 96.1 | 97.2 | N.A. | 72.3 | 58.0 ± 3.7 | 96.2 | 97.2 ± 0.9 | |
CTNNB1 | 41266134 | DEL | CTT | 44.9 | N.A. | N.A. | N.A. | 11.2 | 12.9 ± 1.6 | 0.0 | N.A. | |
EGFR | 55242487 | SNV | T | N.A. | N.A. | N.A. | 100.0 | 25.0 | 20.9 ± 0.1 | 0.0 | N.A. | |
EGFR | 55249063 | SNV | A | 100.0 | 35.6 | 75.3 | 100.0 | 77.7 | 74.0 ± 3.2 | 38.4 | 48.1 ± 0.6 | |
EGFR | 55249071 | SNV | T | N.A. | N.A. | 74.8 | N.A. | 18.7 | 17.9 ± 0.9 | 5.2 | 30.4 ± 1.3 | |
EGFR | 55259515 | SNV | G | N.A. | N.A. | 71.7 | N.A. | 17.9 | 13.1 ± 2.3 | 5.0 | 21.8 ± 0.8 | |
ERBB4 | 212812097 | SNV | G | 100.0 | N.A. | 72.3 | N.A. | 43.1 | 45.2 ± 3.7 | 5.1 | 26.8 ± 1.1 | |
FGFR3 | 1807894 | SNV | A | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 ± 0.0 | 100.0 | 100.0 ± 0.0 | |
FLT3 | 28602367 | SNV | A | 49.5 | N.A. | N.A. | N.A. | 12.4 | 17.8 ± 0.8 | 0.0 | N.A. | |
FLT3 | 28610183 | SNV | C | 100.0 | 64.3 | 100.0 | 65.2 | 82.4 | 81.1 ± 0.8 | 66.8 | 69.0 ± 0.9 | |
HRAS | 534242 | SNV | C | 98.9 | 47.8 | 38.9 | 48.5 | 58.5 | 60.6 ± 2.5 | 47.2 | 48.2 ± 2.9 | |
KDR | 55946354 | SNV | A | 47.9 | N.A. | N.A. | N.A. | 12.0 | 17.9 ± 1.2 | 0.0 | N.A. | |
KDR | 55972974 | SNV | T | 47.1 | N.A. | N.A. | N.A. | 11.8 | 16.8 ± 1.1 | 0.0 | N.A. | |
KRAS | 25398281 | SNV | A | 47.7 | N.A. | N.A. | N.A. | 11.9 | 12.1 ± 1.8 | 0.0 | N.A. | |
KRAS | 25398285 | SNV | T | N.A. | 100.0 | N.A. | N.A. | 25.0 | 36.6 ± 1.2 | 93.0 | 80.3 ± 1.4 | |
MET | 116339672 | SNV | T | N.A. | 70.3 | N.A. | N.A. | 17.6 | 19.2 ± 0.8 | 65.4 | 43.2 ± 1.1 | |
NOTCH1 | 139390822 | SNV | G | N.A. | 100.0 | N.A. | N.A. | 25.0 | 33.4 ± 1.1 | 93.0 | 70.6 ± 1.5 | |
PDGFRA | 55141055 | SNV | G | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 ± 0.0 | 100.0 | 100.0 ± 0.0 | |
PDGFRA | 55152040 | SNV | T | N.A. | N.A. | 51.3 | N.A. | 12.8 | 8.7 ± 0.2 | 3.6 | 18.1 ± 1.4 | |
PIK3CA | 178917005 | SNV | G | N.A. | N.A. | 100.0 | N.A. | 25.0 | 14.7 ± 0.9 | 7.0 | 28.0 ± 0.8 | |
PIK3CA | 178927410 | SNV | G | N.A. | N.A. | 47.1 | N.A. | 11.8 | 8.8 ± 0.0 | 3.3 | 13.5 ± 1.0 | |
PIK3CA | 178952085 | SNV | G | 47.7 | N.A. | N.A. | N.A. | 11.9 | 12.3 ± 1.0 | 0.0 | N.A. | |
PTEN | 89711881 | SNV | G | N.A. | N.A. | N.A. | 100.0 | 25.0 | 18.8 ± 1.9 | 0.0 | N.A. | |
RET | 43613843 | SNV | T | 100.0 | 67.5 | 100.0 | N.A. | 66.9 | 70.6 ± 2.8 | 69.8 | 76.2 ± 1.5 | |
RET | 43615612 | SNV | G | 49.1 | N.A. | N.A. | N.A. | 12.3 | 14.6 ± 2.4 | 0.0 | N.A. | |
RET | 43615633 | SNV | G | N.A. | 65.1 | N.A. | N.A. | 16.3 | 22.8 ± 0.1 | 60.5 | 44.9 ± 1.5 | |
SMAD4 | 48586344 | SNV | T | 50.6 | N.A. | N.A. | N.A. | 12.7 | 15.9 ± 1.6 | 0.0 | N.A. | |
SMARCB1 | 24176287 | SNV | A | 52.1 | N.A. | 46.3 | N.A. | 24.6 | 20.2 ± 0.6 | 3.2 | 15.6 ± 1.0 | |
SMO | 128846374 | SNV | A | 51.0 | N.A. | N.A. | N.A. | 12.8 | 12.7 ± 1.8 | 0.0 | N.A. | |
TP53 | 7577120 | SNV | A | N.A. | N.A. | 100.0 | N.A. | 25.0 | 20.7 ± 0.8 | 7.0 | 32.8 ± 1.6 | |
TP53 | 7577539 | SNV | T | N.A. | 99.9 | N.A. | N.A. | 25.0 | 27.6 ± 1.1 | 92.9 | 67.8 ± 1.4 | |
TP53 | 7579472 | SNV | G | 84.2 | N.A. | 90.8 | N.A. | 43.8 | 57.6 ± 8.3 | 6.4 | 37.9 ± 5.2 | |