Table 1

Mutations identified by TAm-Seq in plasma samples from seven ovarian cancer patients. TAm-Seq was used to sequence DNA extracted from plasma of subjects with HGSOC (stage III/IV at diagnosis). Plasma was collected when patients presented with relapse disease, before initiation of chemotherapy. For patient 46, DNA from a formalin-fixed, paraffin-embedded (FFPE) sample was not included in the TAm-Seq set and the mutation was validated in FFPE by Sanger sequencing. CA125 was measured at time of plasma collection. Mean depth of coverage at the mutation locus in the TAm-Seq data was averaged over the repeats (RMS deviation = 850). AF, allele frequency; N, no; Y, yes.

Patient
ID
Age at
diagnosis
Time elapsed
since surgery
(months);
number of
previous
lines of
chemotherapy
CA125
(U/ml)
Plasma per
amplification
reaction
(μl)
GeneMutation
and base
change
(genome
build hg19)
Protein
change
Detected
in
FFPE
Mean
depth
(sequencing
reads)
Mean AF
using
TAm-Seq
Mean
AF
using
digital
PCR
86013; 1212250TP5317:7577120C>Tp.R273HY50000.090.10
126227; 336550TP5317:7577579G>Tp.Y234*Y50000.100.08
145850; 3260120TP5317:7578212G>Ap.R213*Y58000.150.12
25619; 1944110TP5317:7578404A>Tp.C176SY48000.040.08
276815; 1105190TP5317:7578262C>Gp.R196PY77000.060.14
EGFR7:55259437G>Ap.R832HN57000.060.05
316412; 131330TP5317:7578406C>Tp.R175HY45000.440.56
465630; 2150930TP5317:7578406C>Tp.R175HY42000.230.30

*Indicates stop codon.

†Both a TP53 and an EGFR mutation were identified in this sample (Fig. 4A).