BACKGROUND: Molecular subtyping is an essential complementarity after pathological analyses for targeted therapy. This study aimed to investigate the consistency of next-generation sequencing (NGS) results between circulating tumor DNA (ctDNA)-based and tissue-based in non-small cell lung cancer (NSCLC) and identify the patient characteristics that favor ctDNA testing. METHODS: Patients who diagnosed with NSCLC and received both ctDNA- and cancer tissue-based NGS before surgery or systemic treatment in Lung Cancer Center, Sichuan University West China Hospital between December 2017 and August 2022 were enrolled. A 425-cancer panel with a HiSeq 4000 NGS platform was used for NGS. The unweighted Cohen's kappa coefficient was employed to discriminate the high-concordance group from the low-concordance group with a cutoff value of 0.6. Six machine learning models were used to identify patient characteristics that relate to high concordance between ctDNA-based and tissue-based NGS. RESULTS: A total of 85 patients were enrolled, of which 22.4% (19/85) had stage III disease and 56.5% (48/85) had stage IV disease. Forty-four patients (51.8%) showed consistent gene mutation types between ctDNA-based and tissue-based NGS, while one patient (1.2%) tested negative in both approaches. Patients with advanced diseases and metastases to other organs would be suitable for the ctDNA-based NGS, and the generalized linear model showed that T stage, M stage, and tumor mutation burden were the critical discriminators to predict the consistency of results between ctDNA-based and tissue-based NGS. CONCLUSION ctDNA-based NGS showed comparable detection performance in the targeted gene mutations compared with tissue-based NGS, and it could be considered in advanced or metastatic NSCLC.
Humans ; Carcinoma, Non-Small-Cell Lung/pathology* ; Circulating Tumor DNA/blood* ; High-Throughput Nucleotide Sequencing/methods* ; Female ; Male ; Lung Neoplasms/pathology* ; Middle Aged ; Mutation/genetics* ; Aged ; Adult ; Aged, 80 and over

OBJECTIVE: To explore the clinical significance of 26 circulating tumor DNA (ctDNA) associated with multiple myeloma (MM) in peripheral blood of new diagnosed patients. METHODS: We conducted a study to detect 26 ctDNA mutations in the peripheral blood of 31 newly diagnosed multiple myeloma (NDMM) patients. RESULTS: Among the 31 NDMM patients, the ctDNA detection rate was 93.55%, significantly higher than that of FISH and chromosome screening methods. The most frequently mutated genes in NDMM were ACTG1 and GNAS. Notably, ACTG1 mutations were exclusive to NDMM patients, furthermore, resulted from the missense mutation of the exon 4. ACTG1 was the gene most frequently co-mutated with others. All patients with ACTG1 mutations were surviving, and there was a positive correlation between ACTG1 mutation and the survival of patients. GNAS mutations were confined to exon 1. CONCLUSION The detection rate of ctDNA sequencing in peripheral blood of NDMM patients was higher than that in bone marrow. ACTG1 and GNAS genes have a guiding role in the prognosis of newly diagnosed patients.
Humans ; Multiple Myeloma/blood* ; Circulating Tumor DNA/genetics* ; Mutation ; Prognosis ; GTP-Binding Protein alpha Subunits, Gs/genetics* ; Chromogranins ; Male ; Female ; Middle Aged

OBJECTIVE: To explore the clinical significance of circulating tumor DNA (ctDNA) in response evaluation and relapse monitoring for patients with primary mediastinal large B-cell lymphoma (PMBCL). METHODS: The clinical characteristics, efficacy and survival of 38 PMBCL patients in our hospital from January 2010 to April 2020 were retrospectively analyzed. The ctDNA monitoring was conducted by targeted next-generation sequencing (NGS). RESULTS: Among the 38 patients, 26 cases were female, and 32 cases were diagnosed with Ann Arbor stage I-II. The 5-year overall survival (OS) rate and progression-free survival (PFS) rate were 74.7% and 61.7%, respectively. Males and those with high aaIPI scores (3 points) had a relatively poor prognosis. The NGS results of 23 patients showed that STAT6 (65.2%), SOCS1 (56.5%), and TNFAIP3 (56.5%) were the most common mutated genes. Patients with stable disease (SD)/progressive disease (PD) exhibited enrichment in cell cycle, FoxO, and TNF signaling pathways. A total of 29 patients underwent end-of-treatment PET/CT (EOT PET/CT), and 16 of them received ctDNA monitoring with 12 negative. Among 6 patients with EOT PET/CT positive (Deauville 4), 4 underwent ctDNA monitoring, and 3 of them were negative, being still in continuous remission without any subsequent anti-tumor therapy. CONCLUSION CtDNA may be combined with PET/CT to assess efficacy, monitor relapse, and guide treatment of PMBCL.
Humans ; Circulating Tumor DNA/blood* ; Female ; Mediastinal Neoplasms ; Male ; Retrospective Studies ; High-Throughput Nucleotide Sequencing ; Prognosis ; Lymphoma, Large B-Cell, Diffuse/genetics* ; Middle Aged ; Adult ; Aged ; Neoplasm Recurrence, Local ; Mutation

Non-small-cell lung cancer (NSCLC), the most common type of lung cancer accounting for 85% of the cases, is often diagnosed at advanced stages owing to the lack of efficient early diagnostic tools. 5-Hydroxymethylcytosine (5hmC) signatures in circulating cell-free DNA (cfDNA) that carries the cancer-specific epigenetic patterns may represent the valuable biomarkers for discriminating tumor and healthy individuals, and thus could be potentially useful for NSCLC diagnosis. Here, we employed a sensitive and reliable method to map genome-wide 5hmC in the cfDNA of Chinese NSCLC patients and detected a significant 5hmC gain in both the gene bodies and promoter regions in the blood samples from tumor patients compared with healthy controls. Specifically, we identified six potential biomarkers from 66 patients and 67 healthy controls (mean decrease accuracy >3.2, P < 3.68E-19) using machine-learning-based tumor classifiers with high accuracy. Thus, the unique signature of 5hmC in tumor patient's cfDNA identified in our study may provide valuable information in facilitating the development of new diagnostic and therapeutic modalities for NSCLC.
5-Methylcytosine ; analogs & derivatives ; blood ; Biomarkers, Tumor ; blood ; genetics ; Carcinoma, Non-Small-Cell Lung ; blood ; diagnosis ; genetics ; Case-Control Studies ; Circulating Tumor DNA ; blood ; DNA Methylation ; Epigenomics ; Female ; Humans ; Lung Neoplasms ; blood ; diagnosis ; genetics ; Male ; Middle Aged

Prostate cancer is characterized by bone metastases and difficulty of objectively measuring disease burden. In this context, cell-free circulating tumor DNA (ctDNA) and circulating tumor cell (CTC) quantitation and genomic profiling afford the ability to noninvasively and serially monitor the tumor. Recent data suggest that ctDNA and CTC quantitation are prognostic for survival. Indeed, CTC enumeration using the CellSearch^® platform is validated as a prognostic factor and warrants consideration as a stratification factor in randomized trials. Changes in quantities of CTCs using CellSearch also are prognostic and may be employed to detect a signal of activity of new agents. Molecular profiling of both CTCs and ctDNA for androgen receptor (AR) variants has been associated with outcomes in the setting of novel androgen inhibitors. Serial profiling to detect the evolution of new alterations may inform drug development and help develop precision medicine. The costs of these assays and the small quantities in which they are detectable in blood are a limitation, and novel platforms are required to address this challenge. The presence of multiple platforms to assay CTCs and ctDNA also warrants the consideration of a mechanism to allow comparison of data across platforms. Further validation and the continued development and standardization of these promising modalities will facilitate their adoption in the clinic.
Biomarkers, Tumor/blood* ; DNA, Neoplasm/blood* ; Humans ; Male ; Neoplastic Cells, Circulating/immunology* ; Prognosis ; Prostatic Neoplasms/pathology* ; Transcriptome

PURPOSE: Enhancer of zeste homolog 2 (EZH2), a kind of transcriptional repressor, is reportedly over-expressed in metastatic prostate cancer. In this study, we analyzed EZH2 mRNA in circulating tumor cells (CTCs) in peripheral blood as a biomarker in patients with metastatic prostate cancer. PATIENTS AND METHODS: Ber-EP4 coated immunomagnetic beads were used to harvest CTCs, and mRNA was isolated by oligo- dT conjugated immunomagnetic beads. Reverse transcriptase- polymerase chain reaction for EZH2 mRNA was performed and the expression density was measured. The sensitivity of this test for detection of EZH2 mRNA was determined by serial dilutions of a human prostate cancer cell line. Blood samples were collected from 20 patients each with metastatic or localized prostate cancer and 10 healthy volunteers. RESULTS: Sensitivity experiments showed that the test was highly sensitive as it could detect 10 tumor cells per 5mL. EZH2 mRNA expression was obtained from peripheral blood samples of patients and control subjects. EZH2 mRNA expression density in the metastatic prostate cancer group was significantly higher than in the control (p=0.023) and localized prostate cancer groups (p=0.019). There was no difference between the control and localized prostate cancer groups (p > 0.05). CONCLUSION: EZH2 mRNA expression in circulating epithelial cells represents a promising marker for detecting early metastasis in prostate cancer. However, more specific and sensitive techniques for detection of CTCs are needed to avoid mononuclear cell contamination.
Aged ; DNA-Binding Proteins/*genetics ; Humans ; Male ; Middle Aged ; Neoplasm Metastasis ; Neoplastic Cells, Circulating/*metabolism ; Prostatic Neoplasms/*blood/genetics/pathology ; RNA, Messenger/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription Factors/*genetics ; Tumor Cells, Cultured