Journal: BioMed Research International

Article Title: Optimization of Preanalytical Variables for cfDNA Processing and Detection of ctDNA in Archival Plasma Samples

doi: 10.1155/2021/5585148

Figure Lengend Snippet: Workflow and experimental design for evaluating cfDNA yields affected by blood collection tubes (BCTs), storage times, and centrifugation regimes. RT: room temperature. Fresh purified samples are framed by green color while samples stored for 1 h, 4 h, and 24 h before plasma separation and freezing are framed with red color. ∗ The storage at RT refers to EDTA BCTs, which were at 4°C for 24 h before plasma separation. Each step is performed in technical duplicates obtained from the same BCT for corresponding storage time and centrifugation regime.

Article Snippet: To examine the impact of purification kits on the yield of cfDNA, three DNA purification kits were compared: DNeasy Blood & Tissue Kit (Qiagen), QIAamp Circulating Nucleic Acid Kit (Qiagen), and Quick-cfDNA Serum & Plasma Kit (Zymo Research). cfDNA was purified from blood samples collected from healthy volunteers ( n = 3).

Techniques: Centrifugation, Purification

Journal: BioMed Research International

Article Title: Optimization of Preanalytical Variables for cfDNA Processing and Detection of ctDNA in Archival Plasma Samples

doi: 10.1155/2021/5585148

Figure Lengend Snippet: Comparison of cfDNA purification kits. (a) The mean of cfDNA yield of duplicate purification for each volunteer and each kit with a standard deviation. (b) The mean yield of cfDNA from all three volunteers with standard deviation. P value obtained by one-way ANOVA test. Bars represent the total yield of cfDNA purified from 1 ml of plasma in technical duplicates.

Article Snippet: To examine the impact of purification kits on the yield of cfDNA, three DNA purification kits were compared: DNeasy Blood & Tissue Kit (Qiagen), QIAamp Circulating Nucleic Acid Kit (Qiagen), and Quick-cfDNA Serum & Plasma Kit (Zymo Research). cfDNA was purified from blood samples collected from healthy volunteers ( n = 3).

Techniques: Purification, Standard Deviation

Journal: Oncology Reports

Article Title: Genome-wide copy number analysis of circulating tumor cells in breast cancer patients with liver metastasis

doi: 10.3892/or.2020.7650

Figure Lengend Snippet: Flow chart of the schematic overview of the current study design for the genome-wide copy number analysis of CTCs of BCLM. CTCs, circulating tumor cells; BCLM, breast cancer liver metastasis; MLBACs, multiple annealing and looping based amplification cycles; CNVs, copy number variations; PET/CT, positron emission tomography/computed tomography.

Article Snippet: CTCs from 7.5 ml blood sample were captured with the CellSearch Circulating Tumor Cell Kit (cat. no. K062013; Veridex, LLC) for 1 h at room temperature.

Techniques: Genome Wide, Multiple Annealing and Looping–Based Amplification Cycles, Positron Emission Tomography-Computed Tomography, Positron Emission Tomography, Computed Tomography

Journal: Oncology Reports

Article Title: Genome-wide copy number analysis of circulating tumor cells in breast cancer patients with liver metastasis

doi: 10.3892/or.2020.7650

Figure Lengend Snippet: Analysis of CTCs in different patient samples. (A) Comparison of the CTC count between newly diagnosed liver metastases (n=23) and recurrent liver metastases (n=20) in a 7.5 ml blood sample of BCLM patients (n=43). In general, higher percentages of CTCs were observed in newly diagnosed BCLM patients (mean CTCs in newly diagnosed metastases 38.30 vs. 25.50 in recurrent metastases). (B) Linear logistic regression of CTC detection. Average (black line) CTC recovery was calculated by using the linear logistic regression from 43 BCLM patients. The cut-off levels (10 CTCs for expected and 5 CTCs for CellSearch per sample) are indicated by the dashed lines. *P<0.05. CTCs, circulating tumor cells; BCLM, breast cancer liver metastasis.

Article Snippet: CTCs from 7.5 ml blood sample were captured with the CellSearch Circulating Tumor Cell Kit (cat. no. K062013; Veridex, LLC) for 1 h at room temperature.

Techniques: Comparison

Journal: Oncology Reports

Article Title: Genome-wide copy number analysis of circulating tumor cells in breast cancer patients with liver metastasis

doi: 10.3892/or.2020.7650

Figure Lengend Snippet: Gallery of fluorescent immunostaining of CTCs, EPCs and leukocytes (WBCs) from patients with BCLM. Cells were stained by anti-CD45-APC antibody, 4′,6-diamidino-2-phenylindole (DAPI, nuclear staining; pink color), anti-CK8-PE (green color). The CTC sample is characterized by a CD45 − /Nucleus + /CK8 + of a diameter <8 µm, while CD45 + /Nucleus + /CK8 − are identified as WBCs. Cells that stain CD45 − /Nucleus + /CK8 + are identified as EPCs with a diameter <8 µm (magnification 200 µm). BCLM, breast cancer liver metastasis; CTCs, circulating tumor cells; CK, cytokeratin; EPCs, epithelial cells; WBCs, white blood cells.

Article Snippet: CTCs from 7.5 ml blood sample were captured with the CellSearch Circulating Tumor Cell Kit (cat. no. K062013; Veridex, LLC) for 1 h at room temperature.

Techniques: Immunostaining, Staining

Journal: Oncology Reports

Article Title: Genome-wide copy number analysis of circulating tumor cells in breast cancer patients with liver metastasis

doi: 10.3892/or.2020.7650

Figure Lengend Snippet: Visualization of 10× genome-wide gene copy number analysis between newly diagnosed liver metastases (A) CTCs from newly diagnosed liver metastases (B) recurrent liver metastases (C) and CTCs from recurrent liver metastases (D) The histogram shows the frequency of genomic gains (blue) and losses (red) of CTCs. Most significant CNVs in each group are shown with star symbol (*). CTCs, circulating tumor cells; CNVs, copy number variations.

Article Snippet: CTCs from 7.5 ml blood sample were captured with the CellSearch Circulating Tumor Cell Kit (cat. no. K062013; Veridex, LLC) for 1 h at room temperature.

Techniques: Genome Wide

Journal: Oncology Reports

Article Title: Genome-wide copy number analysis of circulating tumor cells in breast cancer patients with liver metastasis

doi: 10.3892/or.2020.7650

Figure Lengend Snippet: Heat map representation of CTC-shared CNVs in newly diagnosed liver metastases (A) CTCs of newly diagnosed liver metastases (B) recurrent liver metastases (C) and CTCs of recurrent liver metastases (D) Heat map representation of frequently deregulated genes in different groups. CTCs, circulating tumor cells; CNVs, copy number variations.

Article Snippet: CTCs from 7.5 ml blood sample were captured with the CellSearch Circulating Tumor Cell Kit (cat. no. K062013; Veridex, LLC) for 1 h at room temperature.

Techniques:

Journal: Oncology Reports

Article Title: Genome-wide copy number analysis of circulating tumor cells in breast cancer patients with liver metastasis

doi: 10.3892/or.2020.7650

Figure Lengend Snippet: GSEA of different groups in newly diagnosed liver metastases (A) CTCs of newly diagnosed liver metastases (B) recurrent liver metastases (C) and CTCs of recurrent liver metastases (D) The size and color intensity of a circle represents the numbers of genes and ∓log10 (P-value) for each group, respectively. GSEA, gene set enrichment analysis, CTCs, circulating tumor cells.

Article Snippet: CTCs from 7.5 ml blood sample were captured with the CellSearch Circulating Tumor Cell Kit (cat. no. K062013; Veridex, LLC) for 1 h at room temperature.

Techniques:

Journal: Oncology Reports

Article Title: Genome-wide copy number analysis of circulating tumor cells in breast cancer patients with liver metastasis

doi: 10.3892/or.2020.7650

Figure Lengend Snippet: PPI network of commonly deregulated targeted genes and pathways in newly diagnosed liver metastases (A), CTCs of newly diagnosed liver metastases (B), recurrent liver metastases (C) and CTCs of recurrent liver metastases (D). Filled color represents the -log2 (fold change) of each gene, and border orange color represents the module to which each gene belongs. CTCs, circulating tumor cells; PPI, protein-protein interaction.

Article Snippet: CTCs from 7.5 ml blood sample were captured with the CellSearch Circulating Tumor Cell Kit (cat. no. K062013; Veridex, LLC) for 1 h at room temperature.

Techniques:

Journal: Thoracic Cancer

Article Title: Prognostic and predictive impact of molecular tumor burden index in non‐small cell lung cancer patients

doi: 10.1111/1759-7714.15098

Figure Lengend Snippet: ctDNA level of pretreatment samples. (a) Kaplan–Meier survival analysis of overall survival (OS) stratified by ctDNA status of baseline. (b) Kaplan–Meier survival analysis of progression‐free survival (PFS) stratified by ctDNA status of baseline. (c) Sum of longest axial diameters (SLD) in patients with ctDNA‐positive versus those with ctDNA‐negative. (d) Correlation between baseline molecular tumor burden index (mTBI) and variant allele frequency (VAF). ctDNA, circulating tumor DNA.

Article Snippet: Circulating cell‐free DNA was isolated from plasma using the QIAsymphony circulating DNA kit (Qiagen).

Techniques: Variant Assay