Background
Materials and methods
Cell lines
Tissue specimens
Single gene mutation assays
Amplicon Name | Primer Sequence (5'-3') | Amplicon Size (bp) |
---|---|---|
BRAF_conserved | BRAF-F1: TGCTTGCTCTGATAGGA | 241 |
BRAF_R: CTAGTAACTCAGCAGCA | ||
BRAF_V600E | BRAF-F2: TGGTCTAGCTACAGA | 141 |
BRAF_R: CTAGTAACTCAGCAGCA | ||
SMAD4_conserved | SMAD4_F1: TTGTCTTTTCTTTAGGGC | 286 |
SMAD4_R: AAGATAGTTCTTTTCTTTTGG | ||
SMAD4_48586344_C > T | SMD4_F2: ATTTAGTGGTGATTGAAAT | 181 |
SMAD4_R: AAGATAGTTCTTTTCTTTTGG | ||
RET_conserved | RET_F1: GTGCTATTTTTCCTCACA | 268 |
RET_R: AGGGCTATAAAAAGCTTAG | ||
RET_43615612_A > G | RET_F2: GCTTGTCCCGG | 176 |
RET_R: AGGGCTATAAAAAGCTTAG |
DNA isolation
Library preparation
Determining the Limit of Detection (LoD)
Analytical performance evaluation
Data analysis pipeline
Variant calling
Quality Control (QC) material
Results
Analytical performance characteristics
Cell Line / Sample Name | HCT116 | MiaPaCa-2 | H1975 | SK-MEL-28 | 4-Cell Line Mix | Human Placenta | 4-Cell Line Mix (Dil 1:2) | 4-Cell Line Mix (Dil 1:3) | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene Symbol | hg19 Coordinates | Variant Type | Variant | Freq. (%) | Found | Found | Found | Found | Expected | Found | Found | Expected | Found | Expected | Found |
ABL1
| 133738370 | SNV | G | 52.4 | N.A. | N.A. | N.A. | 13.1 | 12.6 ± 0.5 | N.A. | 6.1 | 6.3 ± 0.2 | 4.1 | 4.4 ± 0.5 | |
APC
| 112175770 | SNV | A | 98.1 | 74.4 | 51.7 | 88.5 | 78.1 | 80.0 ± 0.9 | 2.1 | 40.7 | 40.8 ± 0.9 | 27.8 | 29.4 ± 0.8 | |
ATM
| 108138003 | SNV | C | N.A. | N.A. | N.A. | N.A. | N.A. | N.A. | 55.8 | 27.9 | 32.1 ± 0.2 | 37.2 | 40.6 ± 0.4 | |
BRAF
| 140453136 | SNV | A | N.A. | N.A. | N.A. | 99.3 | 24.8 | 21.7 ± 4.0 | N.A. | 12.3 | 13.7 ± 0.2 | 8.2 | 9.6 ± 0.2 | |
CDKN2A
| 21971153 | SNV | T | N.A. | N.A. | 96.4 | N.A. | 24.1 | 35.7 ± 2.6 | N.A. | 16.9 | 10.4 ± 1.1 | 11.3 | 8.4 ± 0.9 | |
CSF1R
| 149433596 | SNV | C | 99.6 | 99.3 | 100.0 | N.A. | 74.7 | 58.6 ± 4.5 | 90.5 | 72.9 | 68.8 ± 0.6 | 78.8 | 80.5 ± 1.2 | |
CSF1R
| 149433597 | SNV | T | 99.6 | 99.1 | 100.0 | N.A. | 74.7 | 62.3 ± 9.8 | 93.2 | 74.3 | 76.9 ± 0.7 | 80.6 | 85.7 ± 0.8 | |
CTNNB1
| 41266134 | DEL | CTT | 50.2 | N.A. | N.A. | N.A. | 12.5 | 10.7 ± 1.8 | N.A. | 4.7 | 4.8 ± 0.6 | 3.2 | 3.1a ± 0.1 | |
EGFR
| 55242487 | SNV | T | N.A. | N.A. | N.A. | 99.3 | 24.8 | 22.8 ± 2.6 | N.A. | 12.3 | 13.4 ± 0.1 | 8.2 | 8.0 ± 0.6 | |
EGFR
| 55249063 | SNV | A | 100.0 | 23.2 | 70.6 | 100.0 | 73.4 | 75.3 ± 1.7 | 97.6 | 85.9 | 84.4 ± 0.7 | 89.8 | 90.1 ± 0.3 | |
EGFR
| 55249071 | SNV | T | N.A. | N.A. | 70.7 | N.A. | 17.7 | 27.1 ± 2.5 | N.A. | 12.7 | 13.6 ± 1.1 | 8.4 | 8.9 ± 1.2 | |
EGFR
| 55259515 | SNV | G | N.A. | N.A. | 56.7 | N.A. | 14.2 | 17.8 ± 0.7 | N.A. | 9.2 | 8.8 ± 1.3 | 6.1 | 6.4 ± 0.5 | |
ERBB4
| 212812097 | SNV | G | 100.0 | N.A. | 75.9 | N.A. | 44.0 | 54.0 ± 0.2 | 62.9 | 58.4 | 46.8 ± 1.6 | 59.9 | 59.0 ± 2.3 | |
FGFR3
| 1807894 | SNV | A | 100.0 | 100.0 | 99.6 | 100.0 | 99.9 | 99.6 ± 0.2 | 100.0 | 99.9 | 99.9 ± 0.1 | 99.9 | 99.8 ± 0.1 | |
FLT3
| 28602367 | SNV | A | 46.9 | N.A. | N.A. | N.A. | 11.7 | 15.4 ± 3.2 | N.A. | 8.8 | 7.0 ± 0.3 | 5.9 | 6.4 ± 0.8 | |
FLT3
| 28610183 | SNV | C | 100.0 | 66.5 | 99.6 | 69.2 | 83.8 | 80.9 ± 1.1 | 100.0 | 90.9 | 90.8 ± 0.1 | 93.9 | 93.4 ± 0.5 | |
HRAS
| 534242 | SNV | C | 99.5 | 61.9 | 40.4 | 46.9 | 62.2 | 67.6 ± 1.1 | 2.6 | 34.7 | 32.0 ± 0.2 | 24.0 | 21.5 ± 1.2 | |
KDR
| 55946354 | SNV | A | 48.5 | N.A. | N.A. | N.A. | 12.1 | 15.9 ± 1.0 | 51.3 | 33.3 | 34.5 ± 1.1 | 39.3 | 41.0 ± 1.1 | |
KDR
| 55972974 | SNV | T | 52.6 | N.A. | N.A. | N.A. | 13.1 | 13.2 ± 4.3 | N.A. | 8.1 | 7.3 ± 0.5 | 5.4 | 5.1 ± 0.1 | |
KRAS
| 25398281 | SNV | A | 46.4 | N.A. | N.A. | N.A. | 11.6 | 11.3 ± 0.7 | N.A. | 5.9 | 6.2 ± 0.4 | 3.9 | 4.2 ± 0.1 | |
KRAS
| 25398285 | SNV | T | N.A. | 99.9 | N.A. | N.A. | 25.0 | 24.7 ± 1.2 | N.A. | 12.8 | 13.7 ± 0.5 | 8.5 | 9.5 ± 0.1 | |
MET
| 116339672 | SNV | T | N.A. | 72.9 | N.A. | N.A. | 18.2 | 15.3 ± 2.0 | N.A. | 6.9 | 7.9 ± 0.0 | 4.6 | 4.8 ± 0.1 | |
NOTCH1
| 139390822 | SNV | G | N.A. | 100.0 | N.A. | N.A. | 25.0 | 22.5 ± 0.3 | N.A. | 11.1 | 9.3 ± 0.2 | 7.4 | 7.1 ± 0.1 | |
PDGFRA
| 55141055 | SNV | G | 99.7 | 100.0 | 99.7 | 100.0 | 99.8 | 99.9 ± 0.2 | 99.9 | 99.8 | 99.9 ± 0.1 | 99.8 | 100.0 ± 0.1 | |
PDGFRA
| 55152040 | SNV | T | N.A. | N.A. | 50.8 | N.A. | 12.7 | 11.8 ± 2.8 | 3.8 | 8.8 | 7.5 ± 0.1 | 7.1 | 6.0 ± 0.7 | |
PIK3CA
| 178917005 | SNV | G | N.A. | N.A. | 100.0 | N.A. | 25.0 | 28.6 ± 7.6 | N.A. | 11.6 | 13.9 ± 0.1 | 7.8 | 10.2 ± 0.6 | |
PIK3CA
| 178927410 | SNV | G | N.A. | N.A. | 45.1 | N.A. | 11.3 | 10.7 ± 1.2 | N.A. | 5.8 | 5.9 ± 0.2 | 3.9 | 4.0 ± 0.2 | |
PIK3CA
| 178952085 | SNV | G | 47.7 | N.A. | N.A. | N.A. | 11.9 | 11.3 ± 2.3 | N.A. | 4.9 | 6.4 ± 0.4 | 3.2 | 3.9a ± 0.1 | |
PTEN
| 89711881 | SNV | G | N.A. | N.A. | N.A. | 99.3 | 24.8 | 24.3 ± 1.0 | N.A. | 11.8 | 9.5 ± 0.8 | 7.9 | 8.4 ± 0.6 | |
RET
| 43613843 | SNV | T | 100.0 | 65.8 | 100.0 | N.A. | 66.4 | 70.8 ± 2.1 | 100.0 | 86.1 | 86.8 ± 0.6 | 90.7 | 91.3 ± 0.5 | |
RET
| 43615612 | SNV | G | 45.2 | N.A. | N.A. | N.A. | 11.3 | 15.1 ± 0.3 | N.A. | 7.4 | 7.2 ± 0.3 | 5.0 | 2.9 ± 0.5 | |
RET
| 43615633 | SNV | G | N.A. | 64.5 | N.A. | N.A. | 16.1 | 14.1 ± 0.0 | N.A. | 7.1 | 7.6 ± 0.5 | 4.7 | 3.7 ± 1.1 | |
SMAD4
| 48586344 | SNV | T | 47.6 | N.A. | N.A. | N.A. | 11.9 | 17.2 ± 1.4 | N.A. | 8.1 | 6.5 ± 0.2 | 5.4 | 4.9 ± 0.2 | |
SMARCB1
| 24176287 | SNV | A | 50.7 | N.A. | 40.8 | N.A. | 22.9 | 22.0 ± 2.3 | N.A. | 11.8 | 14.6 ± 0.1 | 7.9 | 10.7 ± 0.4 | |
SMO
| 128846374 | SNV | A | 52.6 | N.A. | N.A. | N.A. | 13.1 | 10.5 ± 1.5 | N.A. | 5.8 | 7.8 ± 2.0 | 3.9 | 4.4 ± 0.2 | |
TP53
| 7577025 | SNV | T | N.A. | N.A. | N.A. | N.A. | N.A. | N.A. | 79.0 | 39.5 | 29.1 ± 1.5 | 52.6 | 41.4 ± 1.1 | |
TP53
| 7577120 | SNV | A | N.A. | N.A. | 99.9 | N.A. | 25.0 | 31.6 ± 2.6 | N.A. | 16.7 | 20.8 ± 0.8 | 11.1 | 16.0 ± 0.1 | |
TP53
| 7577539 | SNV | T | N.A. | 99.5 | N.A. | N.A. | 24.9 | 18.8 ± 0.7 | N.A. | 9.6 | 11.3 ± 0.1 | 6.4 | 9.1 ± 0.1 | |
TP53
| 7579472 | SNV | G | 94.2 | N.A. | 94.2 | N.A. | 47.1 | 63.6 ± 8.9 | 20.4 | 45.1 | 54.3 ± 2.3 | 36.9 | 42.7 ± 1.7 |
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 |
Effect of formalin fixation and Laser Capture Microdissection (LCM)
VariantCaller plugin parameters
Mean | S.D. | Confidence Level | z | Cutoff (at z-score) | |
---|---|---|---|---|---|
Coverage | 1231 | 526 | 95 % | 199 | 200 |
Number of ≥ Q20 bases | 2.5E + 07 | 2.4E + 06 | 95 % | 2.0E + 07 | 2.0E + 07 |
Quality (log10) | 3.65 | 0.45 | 99 % | 2.48 | 300a
|
Strand Bias | 0.7 | 0.04 | 99 % | 0.79 | 0.79 |
Clinical specimens
KRAS or EGFR or BRAF Mutation Status | ||
---|---|---|
Sample_ID | Single-Gene Assay | CHP2 Assay |
DNA_01 |
EGFR c.2369C > T (p.Thr790Met) |
EGFR c.2369C > T (p.Thr790Met) |
DNA_02 |
EGFR c.2156G > C p.Gly719Ala |
EGFR c.2156G > C p.Gly719Ala |
DNA_03 | Negative | Negative |
DNA_04 | Negative | Negative |
DNA_05 |
EGFR Exon 20 INS |
EGFR c.2307_2308ins9 (p.V769_D770insASV) |
DNA_06 | Negative | Negative |
DNA_07 | Negative | Negative |
DNA_08 |
EGFR c.2369C > T (p.Thr790Met) |
EGFR c.2369C > T (p.Thr790Met) |
DNA_09 |
EGFR c.2369C > T (p.Thr790Met) |
EGFR c.2369C > T (p.Thr790Met) |
DNA_10 |
EGFR Exon 19 DEL |
EGFR c.2236_2250del15 (p.E746_A750delELREA) |
DNA_11 | Negative | Negative |
DNA_12 | Negative | Negative |
DNA_13 | Negative | Negative |
DNA_14 | Negative | Negative |
DNA_15 | Negative | Negative |
DNA_16 | Negative | Negative |
DNA_17 | Negative | Negative |
DNA_18 | Negative | Negative |
DNA_19 | Negative | Negative |
DNA_20 | Negative | Negative |
DNA_21 |
KRAS c.35G > T (p.Gly12Val) |
KRAS c.35G > T (p.Gly12Val) |
DNA_22 | Negative | Negative |
DNA_23 |
EGFR c.2582 T > A (p.Leu861Gln) |
EGFR c.2582 T > A (p.Leu861Gln) |
DNA_24 |
EGFR c.2582 T > A (p.Leu861Gln) |
EGFR c.2582 T > A (p.Leu861Gln) |
DNA_25 | Negative | Negative |
DNA_26 |
BRAF c.1799 T > A (p.Val600Glu) |
BRAF c.1799 T > A (p.Val600Glu) |
DNA_27 |
KRAS c.34G > A (p.Gly12Ser) | c.34G > A (p.Gly12Ser) |
DNA_28 | Negative | Negative |
DNA_29 |
EGFR c.2155G > A (p.Gly719Ser) |
EGFR c.2155G > A (p.Gly719Ser) |
DNA_30 | Negative | Negative |
DNA_31 | Negative | Negative |
DNA_32 |
KRAS c.34G > T (p.Gly12Cys) | c.34G > T (p.Gly12Cys) |
DNA_33 |
BRAF c.1798_1799delGTinsAA (p.Val600Lys) |
BRAF c.1798_1799delGTinsAA (p.Val600Lys) |
DNA_34 |
BRAF c.1798_1799delGTinsAA (p.Val600Lys) |
BRAF c.1798_1799delGTinsAA (p.Val600Lys) |
DNA_35 |
EGFR Exon 19 DEL |
EGFR c.2235_2246del12 (p.Glu746_Glu749del) |
DNA_36 | Negative | Negative |
DNA_37 |
EGFR c.2573 T > G (p.Leu858Arg) |
EGFR c.2573 T > G (p.Leu858Arg) |
DNA_38 |
EGFR c.2573 T > G (p.Leu858Arg) |
EGFR c.2573 T > G (p.Leu858Arg) |
DNA_39 |
KRAS c.34G > T (p.Gly12Cys) | c.34G > T (p.Gly12Cys) |
DNA_40 | Negative | Negative |
DNA_41 |
KRAS c.38G > A (p.Gly13Asp) | c.38G > A (p.Gly13Asp) |
DNA_42 |
KRAS c.38G > A (p.Gly13Asp) | c.38G > A (p.Gly13Asp) |
DNA_43 |
EGFR c.2573 T > G (p.Leu858Arg) | Negative |
DNA_44 |
EGFR Exon 20 INS | c.2312_2314dupACC (p.Pro772delinsHisPro) |
DNA_45 | Negative | Negative |
DNA_46 | Negative | Negative |
DNA_47 |
KRAS c.35G > T (p.Gly12Val) | c.35G > T (p.Gly12Val) |
DNA_48 | Negative | Negative |
DNA_49 | Negative | Negative |
DNA_50 |
BRAF c.1799 T > A (p.V600Glu) | c.1799 T > A (p.V600Glu) |
DNA_51 |
KRAS c.35G > A (p.Gly12Asp) | c.35G > A (p.Gly12Asp) |
DNA_52 |
BRAF c.1799 T > A (p.Val600Glu) |
BRAF c.1799 T > A (p.Val600Glu) |
DNA_53 |
KRAS c.35G > T (p.Gly12Val) |
KRAS c.35G > T (p.Gly12Val) |
DNA_54 |
EGFR c.2573 T > G (p.Leu858Arg) |
EGFR c.2573 T > G (p.Leu858Arg) |
DNA_55 |
BRAF c.1799 T > A (p.Val600Glu) |
BRAF c.1799 T > A (p.Val600Glu) |
Common variants and artifacts
Gene_Position_Variant | Class |
---|---|
EGFR_55249063_G > A | High Allele Frequency SNP |
FGFR3_1807894_G > A | High Allele Frequency SNP |
FLT3_28610183_T > C | High Allele Frequency SNP |
PDGFRA_55141055_A > G | High Allele Frequency SNP |
CSF1R_149433596_A > C | End of Amplicon |
CSF1R_149433597_C > T | End of Amplicon |
STK11_1220321_T > C | Homopolymer |
PTEN_89711834_INS > T | Homopolymer |
RB1_48953805_DEL > A | Homopolymer |
Performance of the Quality Control (QC) Material
Gene Symbol | hg19 Coordinates | Variant Type | Variant | Mean Frequency (%) | Standard Deviation | %CV |
---|---|---|---|---|---|---|
BRAF
| 140453136 | SNV | A | 18.5 | 1.5 | 7.9 % |
EGFR
| 55242487 | SNV | T | 17.1 | 1.4 | 7.9 % |
EGFR
| 55249071 | SNV | T | 28.6 | 1.7 | 6.1 % |
EGFR
| 55259515 | SNV | G | 23.4 | 1.5 | 6.5 % |
KRAS
| 25398281 | SNV | A | 9.6 | 0.7 | 7.0 % |
KRAS
| 25398285 | SNV | T | 37.9 | 1.1 | 2.8 % |
PIK3CA
| 178952085 | SNV | G | 9.1 | 1.0 | 11.1 % |
CTNNB1
| 41266134 | DEL | CTT | 11.5 | 2.0 | 17.8 % |