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. 2022 Feb 10;28(9):1841–1853. doi: 10.1158/1078-0432.CCR-21-1242

Figure 2.

Figure 2. Settings to generate in silico spike-in simulation data. The simulation data are generated using WES data taken from (i) 12 patients with MBC and 6 patients with CRPC and (ii) 8 patients with NSCLC. Each patient has an early plasma sample (Blood T1), a WBC sample (WBC), and a late plasma sample (Blood T2). The three WES datasets from a patient are used directly or mixed to generate the simulation samples. To simulate the scenario of monitoring a patient for MRD or cancer recurrence, each case contains three simulation samples: a pretreatment plasma sample, a pretreatment WBC sample, and a posttreatment plasma sample. The raw data from Blood T1 are used directly as the pretreatment plasma sample for all cases. WBC and Blood T2 are mixed at specified dilutions to simulate the posttreatment plasma sample. To simulate remission cases, we generate two independent random samplings from the raw WBC data to use as the pretreatment WBC sample and the posttreatment plasma sample. To simulate the emergence of second primary cancers, each case contains two simulation samples: a pretreatment WBC sample and a posttreatment plasma sample. The generation of simulation samples for second primary cancer monitoring is the same as for MRD/recurrence monitoring, except that the pretreatment plasma sample (Blood T1) is not used.

Settings to generate in silico spike-in simulation data. The simulation data are generated using WES data taken from (i) 12 patients with MBC and 6 patients with CRPC and (ii) 8 patients with NSCLC. Each patient has an early plasma sample (Blood T1), a WBC sample (WBC), and a late plasma sample (Blood T2). The three WES datasets from a patient are used directly or mixed to generate the simulation samples. To simulate the scenario of monitoring a patient for MRD or cancer recurrence, each case contains three simulation samples: a pretreatment plasma sample, a pretreatment WBC sample, and a posttreatment plasma sample. The raw data from Blood T1 are used directly as the pretreatment plasma sample for all cases. WBC and Blood T2 are mixed at specified dilutions to simulate the posttreatment plasma sample. To simulate remission cases, we generate two independent random samplings from the raw WBC data to use as the pretreatment WBC sample and the posttreatment plasma sample. To simulate the emergence of second primary cancers, each case contains two simulation samples: a pretreatment WBC sample and a posttreatment plasma sample. The generation of simulation samples for second primary cancer monitoring is the same as for MRD/recurrence monitoring, except that the pretreatment plasma sample (Blood T1) is not used.