Targeted sequencing of some of the clone-specific variants identified in run D1111.
Amplicon sequencing of the target sites was performed on the MiSeq platform. 3 out of the 14 targets appeared to have a high noise levels in the blood sample (highlighted in orange) and were therefore deemed inconclusive. Of the remaining 11 mutations only one did not seem to have any evidence in the bulk DNA sample of the PT2R tumor (highlighted in blue). VAWF: Variant Allele Well Fraction.
Application of DigiPico sequencing and MutLX analysis to a diverse set of clinical samples.
Run ID
Patient ID
Sample type
Collection site
Sequencing platform
Total UTD
Passed UTDs
Validation rate*
AUC
D1110
#11152
Recurrence
PT2R
NextSeq
1634
4b
NA
0.95
D1111
#11152
Recurrence
PT2R
NextSeq
1325
266
240/266c
0.85
D1112*
#11152
Recurrence
PT2R
HiSeq 4000
1219
210
189/210c
0.85
D1511
#11152
Recurrence
PALNR
HiSeq X
1786
9
NA
0.94
D1210
#11152
Pre-chemo
OM
NextSeq
3139
28
16/28c
0.94
D1211
#11152
Pre-chemo
OM
HiSeq 4000
5521
69
17/69c
0.91
D1212
#11152
Pre-chemo
OM
HiSeq 4000
5015
24
16/24c
0.94
D1213
#11152
Pre-chemo
OM
HiSeq 4000
5090
46
25/46c
0.93
D1214
#11152
Pre-chemo
OM
HiSeq 4000
3415
37
27/37c
0.93
DE011
#11513
Normal
Blood
HiSeq X
1759
7b
NA
0.95
DE111
#11513
Pre-chemo
Ascites
HiSeq X
3685
4b
NA
0.97
D6311
OP1036
Pre-chemo
RPCG
HiSeq X
3185
12
NA
0.96
DA111
#11502
Pre-chemo
LPrt
NextSeq
12511
10
NA
0.97
GM12885
-
Cell line
-
NextSeq
2970
3b
NA
0.96
* Run D1112 is a technical replicate of run D1111. b Runs where true UTDs are not expected to be present.c Validation through comparison with independent high-depth WGS data from the bulk of the tumor. * Validation rate is an under-estimation for the positive predictive value of clone-specific variants. PT2R: Pelvic Tumor Recurrence; PALNR: Para-Aortic Lymph Node Recurrence; OM: Omental Mass; RPCG: Right Paracolic Gutter; LPrt: Left Peritoneum; NA: Not Available; AUC: Area Under the Curve of receiver operating characteristic plot.
The study of active mutational processes using DigiPico/MutLX.
Table 2
Summary of patient samples and associated sequencing experiments.