Size distribution of cell-free DNA in oncology

Udomruk, Sasimol; Orrapin, Santhasiri; Pruksakorn, Dumnoensun; Chaiyawat, Parunya

doi:10.1016/j.critrevonc.2021.103455

Cited by 22 publications

(33 citation statements)

References 117 publications

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“… 2 , 13 , 17 Biomarker research centered on liquid biopsies (LBs) has promised to solve the problems of tissue biopsies and high tumor heterogeneity. 18 , 19 …”

Section: Introductionmentioning

confidence: 99%

“… 23 , 25 , 26 Circulating tumor DNA (ctDNA) are tumor-specific DNA fragments detectable in body fluids. 18 , 21 Since cancer patients have an increased amount of cfDNA, specific analytical methods enable the detection of ctDNA in the larger cfDNA fraction, 13 , 27 namely, analysis of tumor-specific somatic mutations, structural variations, and changes in epigenetic patterns. 13 , 18 , 23 , 27 Of these, the most promise as cancer biomarkers has been shown by cfDNA methylation and mutation analysis.…”

Section: Introductionmentioning

confidence: 99%

“… 18 , 21 Since cancer patients have an increased amount of cfDNA, specific analytical methods enable the detection of ctDNA in the larger cfDNA fraction, 13 , 27 namely, analysis of tumor-specific somatic mutations, structural variations, and changes in epigenetic patterns. 13 , 18 , 23 , 27 Of these, the most promise as cancer biomarkers has been shown by cfDNA methylation and mutation analysis. 21 , 28 , 29 cfDNA’s non-genetic properties also vary between different biological states.…”

Section: Introductionmentioning

confidence: 99%

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The utility of cfDNA in TGCT patient management: a systematic review

et al. 2022

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Background: Testicular germ cell tumors (TGCTs) are the most common young male malignancy with a steadily rising incidence. Standard clinical practice is radical orchidectomy of suspicious lumps followed by histopathological diagnosis and tumor subtyping. This practice can lead to complications and quality of life issues for the patients. Liquid biopsies, especially cell-free DNA (cfDNA), promised to be true surrogates for tissue biopsies, which are considered dangerous to perform in cases of testicular tumors. In this study, we have performed a systematic review on the potential of cfDNA in TGCT patient management, its potential challenges in translation to clinical application and possible approaches in further research. Materials & Methods: The review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines on EuropePMC and PUBMED electronic databases, with the last update being on October 21, 2021. Due to the high heterogeneity in identified research articles, we have performed an overview of their efficacy. Results: Eight original articles have been identified on cfDNA in TGCT patients published from 2004 to 2021, of which six had more than one TGCT patient enrolled and were included in the final analysis. Three studies investigated cfDNA methylation, one has investigated mutations in cfDNA, two have investigated cfDNA amount, and one has investigated cfDNA integrity in TGCT. The sensitivity of cfDNA for TGCT was found to be higher than in serum tumor markers and lower than miR-371a-3p, with comparable specificity. cfDNA methylation analysis has managed to accurately detect teratoma in TGCT patients. Conclusion: Potential challenges in cfDNA application to TGCT patient management were identified. The challenges relating to the biology of TGCT with its low mutational burden and low cfDNA amounts in blood plasma make next-generation sequencing (NGS) methods especially challenging. We have also proposed possible approaches to help find clinical application, including a focus on cfDNA methylation analysis, and potentially solving the challenge of teratoma detection.

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“… 2 , 13 , 17 Biomarker research centered on liquid biopsies (LBs) has promised to solve the problems of tissue biopsies and high tumor heterogeneity. 18 , 19 …”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The utility of cfDNA in TGCT patient management: a systematic review

et al. 2022

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“…As DNA in liquid biopsies mostly originates from apoptotic and necrotic cells and in this case has to be bisulfite converted, it is highly fragmented with an estimated maximum of ~ 160 bp. However, depending on sample type, cell-free DNA in liquid biopsies can be as small as < 100 bp which should be taken into account when designing an assay [ 65 – 69 ].…”

Section: Resultsmentioning

confidence: 99%

“…Last, liquid biopsies mostly carry highly fragmented cell-free DNA of maximum ~ 160 bp (length of DNA wrapped around one nucleosome), and DNA is additionally fragmented by bisulfite conversion. Therefore, amplicon size was evaluated, with the preferred amplicon size being a maximum of 120 bp [ 65 – 69 ]. All primers and probes were scored according to these criteria (defined in Table 2 ).…”

Section: Methodsmentioning

confidence: 99%

Technical considerations in PCR-based assay design for diagnostic DNA methylation cancer biomarkers

et al. 2022

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BackgroundDNA methylation biomarkers for early detection, risk stratification and treatment response in cancer have been of great interest over the past decades. Nevertheless, clinical implementation of these biomarkers is limited, as only < 1% of the identified biomarkers is translated into a clinical or commercial setting. Technical factors such as a suboptimal genomic location of the assay and inefficient primer or probe design have been emphasized as important pitfalls in biomarker research. Here, we use eleven diagnostic DNA methylation biomarkers for colorectal cancer (ALX4,APC,CDKN2A,MGMT,MLH1,NDRG4,SDC2,SFRP1,SFRP2,TFPI1andVIM), previously described in a systematic literature search, to evaluate these pitfalls.ResultsTo assess the genomic assay location, the optimal genomic locations according to TCGA data were extracted and compared to the genomic locations used in the published assays for all eleven biomarkers. In addition, all primers and probes were technically evaluated according to several criteria, based on literature and expert opinion. Both assay location and assay design quality varied widely among studies.ConclusionsLarge variation in both assay location and design hinders the development of future DNA methylation biomarkers as well as inter-study comparability.

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Clinical applications of next‐generation sequencing‐based ctDNA analyses in breast cancer: defining treatment targets and dynamic changes during disease progression

Klocker,

Hasenleithner,

Bartsch

et al. 2024

Molecular Oncology

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The advancements in the detection and characterization of circulating tumor DNA (ctDNA) have revolutionized precision medicine and are likely to transform standard clinical practice. The non‐invasive nature of this approach allows for molecular profiling of the entire tumor entity, while also enabling real‐time monitoring of the effectiveness of cancer therapies as well as the identification of resistance mechanisms to guide targeted therapy. Although the field of ctDNA studies offers a wide range of applications, including in early disease, in this review we mainly focus on the role of ctDNA in the dynamic molecular characterization of unresectable locally advanced and metastatic BC (mBC). Here, we provide clinical practice guidance for the rapidly evolving field of molecular profiling of mBC, outlining the current landscape of liquid biopsy applications and how to choose the right ctDNA assay. Additionally, we underline the importance of exploring the clinical relevance of novel molecular alterations that potentially represent therapeutic targets in mBC, along with mutations where targeted therapy is already approved. Finally, we present a potential roadmap for integrating ctDNA analysis into clinical practice.

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Size distribution of cell-free DNA in oncology

Cited by 22 publications

References 117 publications

The utility of cfDNA in TGCT patient management: a systematic review

The utility of cfDNA in TGCT patient management: a systematic review

Technical considerations in PCR-based assay design for diagnostic DNA methylation cancer biomarkers

Clinical applications of next‐generation sequencing‐based ctDNA analyses in breast cancer: defining treatment targets and dynamic changes during disease progression

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