Table 4.

Genotyping results from BRAF-targeted amplicon sequencing

SampleaTotal reads#Alt bases%Alt basesAlt basesb per 10,000 readsZ-scorec
1:1 Ratio1,200,288551,58447.94%2,936.45.57
1:10 Ratio1,274,184105,3188.63%329.75.57
1:100 Ratio1,204,84410,4720.91%34.95.56
1:1000 Ratio1,266,0881,7930.15%7.85.39
AUSS_877 - T1,620,8123360.02%1.71.31
AUSS_877 - U1,266,6882860.02%1.10.22
BEAG_314 - U1,353,65231,1192.37%130.85.57
BEAG_927 - T1,159,4341,2930.13%7.24.99
MINP_700 - T1,206,63620,4951.83%83.65.57
MIX_022 - T1,206,4842520.02%1.00.02
MIX_022 - U1,444,6583360.02%1.00.01
MIX_038 - T1,302,4024020.03%1.30.51
MIX_366 - T1,207,8123180.03%1.20.32
MIX_366 - U1,373,1502940.02%1.10.14
MIX_707 - U1,163,15437,9847.83%289.95.57
MSNZ_415 - T1,205,01814,5541.25%69.85.57
SCOT_055 - T1,255,30613,4001.10%64.35.57
SCOT_353 - T1,180,9468260.08%4.54.86
SCOT_408 - T1,372,4406540.05%2.52.58
WEST_309 - T1,200,4743380.03%1.71.31
WEST_309 - U1,177,0482780.02%1.30.41
Mean1,268,644

NOTE: Samples in bold are statistically significant outliers and thus positive for the mutation.

  • aT = Tumor DNA; U = Urine sediment DNA.

  • bNormalized to the background T>A substitution rate at 32 other sequenced positions.

  • cStatistical outliers via Grubb test have Z-score >3.29 of 33 datapoints (P < 0.01).