Table 2

Mutations identified by TAm-Seq in a set of 62 plasma samples from ovarian cancer patients. Forty mutations were identified by TAm-Seq using stringent parameters for mutation calling. Plasma samples described in this table are distinct from those in Table 1, but patients included overlap. Additional data on patients and mutations are provided in table S6.

Sample
number
Plasma volume per
amplification reaction (μl)
DNA amount per
amplification reaction (ng)
GeneProtein
change
Mean depth
(sequencing reads)
Mean AF using
TAm-Seq
Mean AF using
digital PCR
1700.9TP53p.R273C6400.2600.167
21604.2TP53p.R248Q3400.2440.150
31605.7TP53p.R248Q6400.5070.410
41209.9TP53p.R213X8100.0590.035
51201.4TP53p.C141Y6800.0210.013
61202.1TP53p.C141Y7200.0440.038
719017.9TP53p.I195N8000.0910.081
816014.8TP53p.R175H5100.6080.627
916010.7TP53p.R175H5500.5260.604
101606.1TP53p.R175H5300.6510.682
111604.9TP53p.R175H4900.5260.581
131602.8TP53p.C135R4800.0390.045
141602.5TP53p.C135R6100.0460.120
151603.0TP53p.C135R4700.0910.068
161303.7TP53p.R196P10700.0880.135
EGFRp.R832H6140.0480.050
171604.2TP53p.C176S5800.1130.432
181604.4TP53p.C176S6200.0290.108
201405.2TP53p.R175H6500.2010.226
211403.6TP53p.R175H6500.0850.074
221404.1TP53p.R175H6300.0810.125
231403.7TP53p.R175H7100.0740.106
241407.1TP53p.R175H7600.2690.286
251303.9TP53p.R273H7500.0940.099
261605.7TP53p.R282W6400.0480.061
271503.6TP53p.C141Y4800.3210.364
291509.5TP53p.E258K1900.5480.253
311603.6TP53p.C135Y6200.0400.034
321402.4TP53p.E56X14800.1370.122
3316013.2TP53p.K132N7400.2160.206
34605.3TP53p.K132N5700.1510.201
361605.8TP53p.K132N6200.1910.275
371609.4TP53p.K132N5300.2870.362
3816010.1TP53p.K132N5900.2750.331
3916016.4TP53p.K132N7000.3150.323
4016019.7TP53p.K132N8300.4350.482
4116015.0TP53p.K132N7300.4520.445
421608.5TP53p.K132N5600.1850.245
431503.6TP53Splicing6800.1430.121
441705.2TP53p.C238R15430.0710.073

†Both a TP53 and an EGFR mutation were identified in this sample, collected from patient 27 (Table 1), 25 months after initial surgery (Fig. 4A).

‡The amplicon containing the mutation failed amplification in this sample in the initial experiment and was identified successfully in repeat analysis.