Article Figures & Data
Figures
- Figure 1.
Overview of the clinical setting. A, Diagram comparing radiographic response assessment and the potential use of cfDNA to assess molecular response. B, Timing of imaging and blood collections for patients in the study.
- Figure 2.
Serial assessment of ctDNA to determine MP. A, The genome-wide plots of CNAs detected for 1 patient. The T0 baseline blood draw was collected 13 days before the start of treatment, and T1 was collected 21 days after the start of treatment. B, Normalized fragment length exhibits the reverse pattern compared with CNAs. C, Overall, there was a strong negative correlation between the normalized fragment length at each genomic position and the inferred copy number (Spearman rho = −0.57; P < 10−10). D, This case showed an increase in TFR at follow-up time points T1 and T2, detectable in advance of imaging that indicated PD. E, Another case showed a marked decrease in TFR at T1 and T2, concordant with later imaging that showed PR.
- Figure 3.
ctDNA assessments following first or second cycle of therapy predicted progression. A, Comparison of imaging results at FFUI, sum of longest diameters assessed by RECIST 1.1, with ctDNA assessment of MP indicated by a confident increase in TFR for either posttreatment sample (n = 91, sensitivity = 54%, specificity = 100%). Cases of clinical progression are indicated by plus signs. B, TFR at T1 (left, n = 85) and T2 (right, n = 66) compared with radiographic or clinical assessment of PD or nonPD, showing predictive performance at each timepoint. Diamonds indicate no change. C, For patients with MP (n = 13), detection of MP was observed to precede the detection of progression by standard-of-care imaging by a median of 39 days. Two cases showed MP after FFUI, by 1 day and 21 days. PFS (D) and OS (E) for all patients grouped by MP. Patients with MP had significantly shorter PFS (P = 4.2 × 10−10) and OS (P = 3.6 × 10−5). HR with 95% CIs for cancer type subsets (F) and treatment modality subsets (G).
- Figure 4.
MMR was associated with a favorable outcome. PFS (A) and OS (B) for patients with MP or MMR. Patients with MMR had significantly longer PFS (P = 0.028) and OS (P = 0.0036). Survival analysis of the subset of patients with nonPD assessed radiographically at FFUI (N = 66), stratified by response status at FFUI (C and D) or MMR (E and F).
- Figure 5.
Methylation may provide an orthogonal signal to CNAs for response monitoring. Distribution of average methylation levels in genome-wide 1 megabase bins for a patient with nonPD (A) and a patient with PD (B). Distributions are plotted at baseline and during treatment.
Tables
- Table 1.
Patient and sample characteristics.
Median (min–max) N = 91 (%) Age 70 (30–89) Sex Female 50 (55) Male 41 (45) Cancer type Lung 40 (44) Breast 24 (26) Melanoma 6 (7) Pancreas 4 (4) Colon 3 (3) Rectum 3 (3) Renal 3 (3) Biliary 2 (2) Stomach 2 (2) Bladder 2 (2) Prostate 1 (1) Sarcoma 1 (1) Treatment types Chemotherapy 32 (35) Chemotherapy, antibody 10 (11) Immunotherapy 24 (26) Immunotherapy, chemotherapy 9 (10) Immunotherapy, HDACi 1 (1) Endocrine 4 (4) Endocrine, CDK4/6i 6 (7) Targeted alone 5 (5) Lines of therapy 1 48 (53) 2 23 (25) 3+ 20 (22) Timing (days since treatment start) T1 21 (14–40) 85 (93) T2 42 (37–84) 66a (72) First follow-up 69 (26–208) Last follow-up 384 (60–754) Protocol WGS 53 (58) WGBS 38b (42)
Supplementary Data
- Supplementary tables 1-3, 5-11 and Figures 1-10 - Supplementary Table S1. Clinical sites and cancer type. Participants from four of the five sites were included in the study, and those from one site were held for future studies. Supplementary Table S2. Longitudinal samples from a cohort of healthy participants. 4 healthy participants were processed with both WGS and WGBS. Supplementary Table S3. Smoking status. Supplementary Table S5. Clinical covariates and imaging. Analysis of clinical covariates and PD at FFUI, using Fisher’s exact test. Significant p-values (p<0.05) are indicated with *. Supplementary Table S6. Molecular progression and radiographic assessment at FFUI by sequencing protocol. Supplementary Table S7. Clinical covariates and survival. Univariate cox analysis of clinical covariates and PFS or OS. Significant p-values (p<0.05) are indicated with *. Supplementary Table S8. Multivariate analysis of MP and survival. Significant p-values (p<0.05) are indicated with *. Supplementary Table S9. Molecular progression and assessment at FFUI for cancer, treatment type, and prior treatment subsets. Supplementary Table S10. Analysis of MP, MMR, and survival. Significant p-values (p<0.05) are indicated with *. Supplementary Table S11. Multivariate analysis of MMR and survival. Significant p-values (p<0.05) are indicated with *. Supplementary Figure S1. Longitudinal WGS data for a healthy individual. Supplementary Figure S2. Participant flow diagram. Supplementary Figure S3. Comparison of Tumor Fraction Ratio (TFR) across sequencing protocols. Supplementary Figure S4. Sample timing and sensitivity. Supplementary Figure S5. PFS and OS for all patients in the study. Supplementary Figure S6. PFS and OS by MP for cancer type subgroups. Supplementary Figure S7. PFS and OS by MP for treatment type subgroups. Supplementary Figure S8. PFS and OS by MP for prior treatment subgroups. Supplementary Figure S9. OS and MP for patients with PD at FFUI (n=24). Supplementary Figure S10. PFS and OS by MMR for patients with nonPD at FFUI.
- Supplementary Table S4 - List of on-study therapies.
Supplementary Data
- Supplementary tables 1-3, 5-11 and Figures 1-10 -
Supplementary Table S1. Clinical sites and cancer type. Participants from four of the five sites were included in the study, and those from one site were held for future studies. Supplementary Table S2. Longitudinal samples from a cohort of healthy participants. 4 healthy participants were processed with both WGS and WGBS. Supplementary Table S3. Smoking status. Supplementary Table S5. Clinical covariates and imaging. Analysis of clinical covariates and PD at FFUI, using Fisher's exact test. Significant p-values (p<0.05) are indicated with *. Supplementary Table S6. Molecular progression and radiographic assessment at FFUI by sequencing protocol. Supplementary Table S7. Clinical covariates and survival. Univariate cox analysis of clinical covariates and PFS or OS. Significant p-values (p<0.05) are indicated with *. Supplementary Table S8. Multivariate analysis of MP and survival. Significant p-values (p<0.05) are indicated with *. Supplementary Table S9. Molecular progression and assessment at FFUI for cancer, treatment type, and prior treatment subsets. Supplementary Table S10. Analysis of MP, MMR, and survival. Significant p-values (p<0.05) are indicated with *. Supplementary Table S11. Multivariate analysis of MMR and survival. Significant p-values (p<0.05) are indicated with *. Supplementary Figure S1. Longitudinal WGS data for a healthy individual. Supplementary Figure S2. Participant flow diagram. Supplementary Figure S3. Comparison of Tumor Fraction Ratio (TFR) across sequencing protocols. Supplementary Figure S4. Sample timing and sensitivity. Supplementary Figure S5. PFS and OS for all patients in the study. Supplementary Figure S6. PFS and OS by MP for cancer type subgroups. Supplementary Figure S7. PFS and OS by MP for treatment type subgroups. Supplementary Figure S8. PFS and OS by MP for prior treatment subgroups. Supplementary Figure S9. OS and MP for patients with PD at FFUI (n=24). Supplementary Figure S10. PFS and OS by MMR for patients with nonPD at FFUI.
- Supplementary Table S4 - List of on-study therapies.
- Supplementary tables 1-3, 5-11 and Figures 1-10 -
Volume 19, Issue 7
