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Table 3 Variants identified in DNA isolated from FFPE cell line mixes

From: Quality control material for the detection of somatic mutations in fixed clinical specimens by next-generation sequencing

     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
  1. N.A., Not Applicable; a, the MiaPaCa-2 cell line has a homozygous deletion of the CDKN2A gene