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Table 2 Variants identified in DNA isolated from frozen 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 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
  1. Freq. Frequency; N.A., Not Applicable; a, these variants were called 90 % of the time