Feasibility Analysis of Cell-Free DNA Derived from Plasma of Lung Cancer Patients for Next-Generation Sequencing

Jiang, Xiaoxing; Li, Hui; Liu, Jingjing; Sun, Heping; Zhang, Linna; Li, Wenxiu; Yao, Jie; Cheng, Ying

doi:10.1089/bio.2019.0115

Cited by 4 publications

(2 citation statements)

References 17 publications

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“…Several manufacturers, such as Qiagen, Norgen, Thermo, and Promega, produce specialized commercial kits for extracting blood-derived cfDNA ( Diefenbach et al, 2018 ; van Dessel et al, 2019 ; Huebner et al, 2021 ; Wang et al, 2021 ). Among these, Qiagen’s systematic kits are the most commonly used ( Vermeulen et al, 2017 ; Jain et al, 2019 ; Jiang et al, 2020 ; Kallionpaa et al, 2021 ), However, comparing the performance of these kits is challenging due to variations in sample collection, processing, and analysis procedures ( Table 5 ). For example, when PCR is used to quantify specific genes, the sensitivity may decrease or even vanish as cfDNA fragments become shorter ( Ungerer et al, 2020 ).…”

Section: Preanalytical Variables Affecting Cfdna Analysismentioning

confidence: 99%

The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples

Peng,

Pan,

Zhou

et al. 2024

Front. Cell Dev. Biol.

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Cell-free DNA (cfDNA), a burgeoning class of molecular biomarkers, has been extensively studied across a variety of biomedical fields. As a key component of liquid biopsy, cfDNA testing is gaining prominence in disease detection and management due to the convenience of sample collection and the abundant wealth of genetic information it provides. However, the broader clinical application of cfDNA is currently impeded by a lack of standardization in the preanalytical procedures for cfDNA analysis. A number of fundamental challenges, including the selection of appropriate preanalytical procedures, prevention of short cfDNA fragment loss, and the validation of various cfDNA measurement methods, remain unaddressed. These existing hurdles lead to difficulties in comparing results and ensuring repeatability, thereby undermining the reliability of cfDNA analysis in clinical settings. This review discusses the crucial preanalytical factors that influence cfDNA analysis outcomes, including sample collection, transportation, temporary storage, processing, extraction, quality control, and long-term storage. The review provides clarification on achievable consensus and offers an analysis of the current issues with the goal of standardizing preanalytical procedures for cfDNA analysis.

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Section: Preanalytical Variables Affecting Cfdna Analysismentioning

confidence: 99%

The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples

Peng,

Pan,

Zhou

et al. 2024

Front. Cell Dev. Biol.

View full text Add to dashboard Cite

show abstract

“…It becomes more popular and widely used in clinical oncology due to its high accuracy and sensitivity for mutation detection (14,15). Furthermore, it systematically provides genomic profiles from both tumor tissue and ctDNA samples (16,17). Applications of NGS in cancer genomics mainly focuses on whole-exome sequencing (WES) and whole-genome sequencing (WGS) (18).…”

Section: Background and Motivationmentioning

confidence: 99%

Comparative analysis of mutational landscapes identified from exome sequencing of tumor tissues and circulating tumor DNA

Leenanitikul

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Next-generation sequencing of circulating tumor DNA (ctDNA) has been used as a noninvasive alternative for cancer diagnosis and characterization of tumor mutational landscape. However, low ctDNA fraction and other factors can limit the ability of ctDNA analysis to capture tumor-specific and actionable variants. In this study, whole-exome sequencings (WES) were performed on paired ctDNA and tumor biopsy in 15 cancer patients to assess the extent of concordance between mutational profiles derived from the two source materials. We found that up to 16.4% ctDNA fraction can still be insufficient for detecting tumor-specific variants and that high concordance with tumor biopsy is achieved when ctDNA fraction is 30% or higher. Most importantly, ctDNA analysis can consistently capture tumor heterogeneity and detect key cancer-related genes even in a patient with both primary and metastatic tumors.�

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Liquid Biopsies Based on Cell-Free DNA Integrity as a Biomarker for Cancer Diagnosis: A Meta-Analysis

Rodríguez-Ces,

Rapado-González,

Salgado-Barreira

et al. 2024

Diagnostics

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Liquid biopsies have been identified as a viable source of cancer biomarkers. We aim to evaluate the diagnostic accuracy of cell-free DNA integrity (cfDI) in liquid biopsies for cancer. A comprehensive literature search was conducted through PubMed, Embase, Web of Science, and Cochrane Library up to June 2024. Seventy-two study units from forty-six studies, comprising 4286 cancer patients, were identified and evaluated. The Quality Assessment for Studies of Diagnostic Accuracy-2 (QUADAS-2) was used to assess study quality. Meta-regression analysis was employed to investigate the underlying factors contributing to heterogeneity, alongside an evaluation of publication bias. The bivariate random-effect model was utilized to compute the primary diagnostic outcomes and their corresponding 95% confidence intervals (CIs). The pooled sensitivity, specificity, and positive and negative likelihood ratios of cfDI in cancer diagnosis were 0.70 and 0.77, 3.26 and 0.34, respectively. The overall area under the curve was 0.84, with a diagnostic odds ratio of 10.63. This meta-analysis suggested that the cfDI index has a promising potential as a non-invasive and accurate diagnostic tool for cancer. Study registration: The study was registered at PROSPERO (reference No. CRD42021276290).

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Feasibility Analysis of Cell-Free DNA Derived from Plasma of Lung Cancer Patients for Next-Generation Sequencing

Cited by 4 publications

References 17 publications

The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples

The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples

Comparative analysis of mutational landscapes identified from exome sequencing of tumor tissues and circulating tumor DNA

Liquid Biopsies Based on Cell-Free DNA Integrity as a Biomarker for Cancer Diagnosis: A Meta-Analysis

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