Additional file 2: of V-J combinations of T-cell receptor predict responses to erythropoietin in end-stage renal disease patients

Overlapping read length distribution plot of end-stage renal disease patients. QC, quality control. (DOCX 260 kb

Additional file 3: of V-J combinations of T-cell receptor predict responses to erythropoietin in end-stage renal disease patients

Summary of repertoire sequencing output and overlapping proportions in end-stage renal disease samples. (DOCX 14 kb

Additional file 7: of V-J combinations of T-cell receptor predict responses to erythropoietin in end-stage renal disease patients

Quantification of T-cell repertoire diversity in end-stage renal disease (ESRD) patients. a The clonotype distribution plots of ESRD patients. The x-axis and y-axis are log10 scaled. The value of 1/D represents the T-cell receptor (TCR) β repertoire diversity. b Comparison of TCR repertoire diversity (log-scaled) between erythropoietin (EPO) responders and EPO resistants (p = 0.642) (DOCX 232 kb

Table_2_Genetic alterations in peritoneal metastatic tumors predicted the outcomes for hyperthermic intraperitoneal chemotherapy.csv

IntroductionCytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) are considered for patients with peritoneal metastasis (PM). However, patients selection that relies on conventional prognostic factors is not yet optimal. In this study, we performed whole exome sequencing (WES) to establish tumor molecular characteristics and expect to identify prognosis profiles for PM management. MethodsIn this study, blood and tumor samples were collected from patients with PM before HIPEC. Tumor molecular signatures were determined using WES. Patient cohort was divided into responders and non-responders according to 12-month progression-free survival (PFS). Genomic characteristics between the two cohorts were compared to study potential targets. ResultsIn total, 15 patients with PM were enrolled in this study. Driver genes and enriched pathways were identified from WES results. AGAP5 mutation was found in all responders. This mutation was significantly associated with better OS (p = 0.00652). ConclusionsWe identified prognostic markers that might be useful to facilitate decision-making before CRS/HIPEC.</p

Table_3_Genetic alterations in peritoneal metastatic tumors predicted the outcomes for hyperthermic intraperitoneal chemotherapy.csv

IntroductionCytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) are considered for patients with peritoneal metastasis (PM). However, patients selection that relies on conventional prognostic factors is not yet optimal. In this study, we performed whole exome sequencing (WES) to establish tumor molecular characteristics and expect to identify prognosis profiles for PM management. MethodsIn this study, blood and tumor samples were collected from patients with PM before HIPEC. Tumor molecular signatures were determined using WES. Patient cohort was divided into responders and non-responders according to 12-month progression-free survival (PFS). Genomic characteristics between the two cohorts were compared to study potential targets. ResultsIn total, 15 patients with PM were enrolled in this study. Driver genes and enriched pathways were identified from WES results. AGAP5 mutation was found in all responders. This mutation was significantly associated with better OS (p = 0.00652). ConclusionsWe identified prognostic markers that might be useful to facilitate decision-making before CRS/HIPEC.</p

Image_1_Genetic alterations in peritoneal metastatic tumors predicted the outcomes for hyperthermic intraperitoneal chemotherapy.jpeg

IntroductionCytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) are considered for patients with peritoneal metastasis (PM). However, patients selection that relies on conventional prognostic factors is not yet optimal. In this study, we performed whole exome sequencing (WES) to establish tumor molecular characteristics and expect to identify prognosis profiles for PM management. MethodsIn this study, blood and tumor samples were collected from patients with PM before HIPEC. Tumor molecular signatures were determined using WES. Patient cohort was divided into responders and non-responders according to 12-month progression-free survival (PFS). Genomic characteristics between the two cohorts were compared to study potential targets. ResultsIn total, 15 patients with PM were enrolled in this study. Driver genes and enriched pathways were identified from WES results. AGAP5 mutation was found in all responders. This mutation was significantly associated with better OS (p = 0.00652). ConclusionsWe identified prognostic markers that might be useful to facilitate decision-making before CRS/HIPEC.</p

Image_2_Genetic alterations in peritoneal metastatic tumors predicted the outcomes for hyperthermic intraperitoneal chemotherapy.jpeg

IntroductionCytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) are considered for patients with peritoneal metastasis (PM). However, patients selection that relies on conventional prognostic factors is not yet optimal. In this study, we performed whole exome sequencing (WES) to establish tumor molecular characteristics and expect to identify prognosis profiles for PM management. MethodsIn this study, blood and tumor samples were collected from patients with PM before HIPEC. Tumor molecular signatures were determined using WES. Patient cohort was divided into responders and non-responders according to 12-month progression-free survival (PFS). Genomic characteristics between the two cohorts were compared to study potential targets. ResultsIn total, 15 patients with PM were enrolled in this study. Driver genes and enriched pathways were identified from WES results. AGAP5 mutation was found in all responders. This mutation was significantly associated with better OS (p = 0.00652). ConclusionsWe identified prognostic markers that might be useful to facilitate decision-making before CRS/HIPEC.</p

Image_3_Genetic alterations in peritoneal metastatic tumors predicted the outcomes for hyperthermic intraperitoneal chemotherapy.jpeg

IntroductionCytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) are considered for patients with peritoneal metastasis (PM). However, patients selection that relies on conventional prognostic factors is not yet optimal. In this study, we performed whole exome sequencing (WES) to establish tumor molecular characteristics and expect to identify prognosis profiles for PM management. MethodsIn this study, blood and tumor samples were collected from patients with PM before HIPEC. Tumor molecular signatures were determined using WES. Patient cohort was divided into responders and non-responders according to 12-month progression-free survival (PFS). Genomic characteristics between the two cohorts were compared to study potential targets. ResultsIn total, 15 patients with PM were enrolled in this study. Driver genes and enriched pathways were identified from WES results. AGAP5 mutation was found in all responders. This mutation was significantly associated with better OS (p = 0.00652). ConclusionsWe identified prognostic markers that might be useful to facilitate decision-making before CRS/HIPEC.</p

Table_1_Genetic alterations in peritoneal metastatic tumors predicted the outcomes for hyperthermic intraperitoneal chemotherapy.csv

IntroductionCytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) are considered for patients with peritoneal metastasis (PM). However, patients selection that relies on conventional prognostic factors is not yet optimal. In this study, we performed whole exome sequencing (WES) to establish tumor molecular characteristics and expect to identify prognosis profiles for PM management. MethodsIn this study, blood and tumor samples were collected from patients with PM before HIPEC. Tumor molecular signatures were determined using WES. Patient cohort was divided into responders and non-responders according to 12-month progression-free survival (PFS). Genomic characteristics between the two cohorts were compared to study potential targets. ResultsIn total, 15 patients with PM were enrolled in this study. Driver genes and enriched pathways were identified from WES results. AGAP5 mutation was found in all responders. This mutation was significantly associated with better OS (p = 0.00652). ConclusionsWe identified prognostic markers that might be useful to facilitate decision-making before CRS/HIPEC.</p

Additional file 1 of Characterization of T-Cell receptor repertoire in immunoglobulin a nephropathy

Additional file1 : Supplementary Methods. Table S1. Baseline characteristics of all cohort subjects. Figure S1. Comparison of T-cell receptor beta-chain (TCRβ) repertoire space between IgAN, non-IgAN, and healthy group. Figure S2. Complementarity determining region (CDR3) length distribution and principal component analysis (PCA) for TRBV or TRBJ gene usage in IgAN, non-IgAN, and healthy group. Figure S3. Comparison of all TRBV or TRBJ gene usages between IgAN, non-IgAN, and healthy group