Search

Additional file 3: Table S1. Baseline clinicopathologic characteristics of the 36 patients in the DYNAMIC cohort. Table S2. Summary of data in related studies on ctDNA-based MRD detection in early-stage lung cancer. Table S3. Analytical performance of timMRD model at various cutoff levels (percentile of chi-square distribution for timMRD scores) and tumor-informed ctDNA mutation status for the 155 patients with tumor-informed ctDNA mutation data at the last follow-up. Of the 155 patients, 11 patients had follow-up data at 120 days before relapse and 52 patients had follow-up data at the same time-point.

Additional file 1. Supplementary Methods.

Additional file 2: Figure S1. Detailed workflow of the methylation-based analysis and timMRD model. Figure S2. Quality control of bisulfite sequencing for all patient tissue and blood samples. Figure S3. Distinct methylation profile of tumor tissues. Figure S4. Somatic mutation profile of baseline blood samples for 155 patients with paired tissue-based mutation data. Figure S5. Spike-in dilution experiments and numerical simulation trials demonstrate accuracy and robustness of the timMRD model. Figure S6. Relationship between tumor-informed ctDNA mutation, methylation status, and clinical features. Figure S7. Perioperative dynamics of timMRD scores, MethylMean, and tumor-informed ctDNA somatic mutation status. Figure S8. Perioperative management does not affect timMRD scores. Figure S9. TimMRD scores are positively correlated with somatic mutations (maxAF) in all ctDNA-positive samples. Figure S10. Plasma B and Plasma C reflect disease relapse using timMRD scores and tumor-informed ctDNA somatic mutations at postoperative time-points, but not MethylMean. Figure S11. Prognostication using ctDNA mutation status or timMRD score evaluated at postoperative follow-up time-points for either Plasma B or Plasma C in MEDAL cohort. Figure S12. Two-year prognostication using timMRD score evaluated at postoperative follow-up time-points using Plasma B or Plasma C in MEDAL cohort. Figure S13. Dynamics of ctDNA mutation and timMRD score in two relapsed patients of the MEDAL cohort.

Afatinib has improved the prognosis of epidermal growth factor receptor-positive advanced non-small cell lung cancer and has been explored in the treatment of human epidermal growth factor receptor 2 (HER2)-amplified breast cancer. However, its clinical efficacy in HER2-amplified endometrial cancer has not been reported. Herein, we present the clinical benefit of afatinib in a case of stage IIIC endometrioid adenocarcinoma refractory to multiple lines of chemotherapy and eventually developed pulmonary, abdominal and pelvic metastasis. Upon referral to our clinic, capture-based targeted sequencing was performed on both blood and tumor samples and revealed HER2 amplification. The patient was administered with afatinib and achieved partial response (PR) after two months of treatment, reflected by a significant reduction in pulmonary lesions and serum levels of tumor markers including carcinoembryonic antigen (CEA), cancer antigen (CA) 19-9, 125, 15-3 and cytokeratin 19 fragment antigen 21-1 (CY211). The patient passed away after 3 months of afatinib treatment due to suspected complications of severe intestinal obstruction. Our report demonstrates the efficacy of afatinib in a heavily pre-treated HER2-amplified endometrial cancer patient with multi-organ metastasis. This case also highlights the need to include comprehensive mutational profiling in the standard management of endometrial cancer patients for treatment guidance.

Additional file 1:. Figure S1. Kaplan Meier curves comparing the progression-free survival (expressed in months) of patients with (A) single CD74-ROS1 and various single non-CD74 ROS1 fusions; and (B) single ROS1 fusions and non-reciprocal/reciprocal ROS1 translocations. The risk table below summarizes the number of patients included per time point

Additional file 2: Figure S1. Baseline mutational profile of Training cohort A. The patients were grouped according to the treatment received; A+T, EGFR-TKI with bevacizumab; T, single-agent EGFR-TKI. Figure S2. Heat map illustrating the association between gene mutation or pathway (y-axis) and clinical characteristics, progression-free survival (PFS), and overall survival (OS) (x-axis) for single-agent EGFR-TKI group (A) and EGFR-TKI plus bevacizumab group (B). Blue indicates no statistical difference. The intensity of red color indicates the level of statistical significance with corresponding p-values indicated. Figure S3. Patients in cohort A with brain, liver, or pleural metastasis had significantly shorter progression-free survival (PFS) and overall survival (OS) with single-agent EGFR-TKI (A) but not on EGFR-TKI plus bevacizumab combination (B). Figure S4. Patients with concomitant TP53 mutation had significantly longer progression-free survival (PFS) and overall survival (OS) with EGFR-TKI plus bevacizumab combination. Kaplan-Meier curves for PFS (A) and OS (B) of patients with EGFR-mutant advanced NSCLC with concurrent TP53 mutations (TP53+, red color) or wild-type TP53 (TP53-, blue color) treated with either EGFR-TKI with bevacizumab (A+T, solid lines) or EGFR-TKI monotherapy (T-single, dashed lines). The table below summarizes the p-values. Figure S5. Patients with concomitant TP53 mutations located in exons 5-8 had significantly longer progression-free survival (PFS) and overall survival (OS) with EGFR-TKI plus bevacizumab combination. Kaplan-Meier curves for PFS (A, C) and OS (B, D) of patients with EGFR-mutant advanced NSCLC with or without concurrent TP53 mutations located between exon 5-8 (TP53_hot; A-B) or mutations that result in loss-of-function (TP53_LOF; C-D) and were treated with either EGFR-TKI with bevacizumab (A+T) or EGFR-TKI monotherapy (T-single). Kaplan-Meier curves for PFS (E, G) and OS (F, H) of patients with concomitant TP53 and RB1 mutations who were treated with either T-only (E, F) or A+T (G, H). Figure S6. Nomograms were constructed for predicting the risk of 12-month and 24-month overall survival (OS) (A). Survival analysis of the training cohort A was performed using Kaplan-Meier curves to compare the OS of patients in the T group (B) or A+T (C) group, which were further subgrouped according to the median score into low-risk (< median score) and high-risk (≥ median score). Figure S7. Tabulated summary of the hazard ratios for each molecular and clinical features calculated for the patients treated with EGFR-TKI with bevacizumab (A+T) using Cox multivariable analysis for progression-free survival (A) and overall survival (B).

Additional file 1: Table S1. The 168 panel genes list.

Additional file 2:. Table S1. List of genes included in the 168-gene panel (Lung Plasma, Burning Rock Biotech). Table S2. Distribution of ROS1 fusions among the 220 patients with single ROS1 fusion and 15 patients with non-reciprocal/reciprocal ROS1 translocations. Table S3. Detailed breakpoint information for the non-reciprocal/reciprocal ROS1 translocations detected in the cohort. Table S4. Response to crizotinib of ROS1-rearranged lung cancers. Table S5. Clinicopathologic characteristics of the patients with single ROS1 fusions and non-reciprocal/reciprocal ROS1 translocations. Table S6. Treatment outcomes on first-line crizotinib therapy of the 159 patients with single ROS1 fusion grouped according to ROS1 fusion partners. Table S7. Detailed clinicopathologic characteristics and clinical outcomes of the 13 patients with uncommon non-CD74 ROS1 fusions. Table S8. Detailed clinicopathologic characteristics and clinical outcomes of the patients with non-reciprocal/reciprocal ROS1 translocations. Table S9. Comparison of concurrent mutation according to ROS1 mutation. Table S10. Cox regression analysis for progression-free survival (n=168). Table S11. Detailed clinicopathological characteristics and clinical outcomes of the 9 patients with concomitant driver mutations. Table S12. Detailed clinicopathological characteristics and clinical outcomes of the 8 patients with concomitant brain and non-brain progression on first-line crizotinib therapy. Table S13. Clinicopathological characteristics of the patients with brain progression and non-brain progression on first-line crizotinib therapy