Circulating DNA fragmentomics and cancer screening

Thierry, Alain R.

doi:10.1016/j.xgen.2022.100242

Cited by 27 publications

(19 citation statements)

References 115 publications

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“…Fragmentomics in liquid biopsy has emerged as a promising approach for the detection and monitoring of cancer [ 165 , 166 , 167 , 168 , 169 ]. It involves analyzing the fragmentation patterns of cfDNA using NGS technologies (such as WES or WGS) without performing the DNA sonication step or using long-read sequencing [ 129 , 170 , 171 ].…”

Section: Emerging Methods For Liquid Biopsy Biomarker Discoverymentioning

confidence: 99%

Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer

Brockley¹,

Souza

Forder³

et al. 2023

Cancers

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Lung cancer detection and monitoring are hampered by a lack of sensitive biomarkers, which results in diagnosis at late stages and difficulty in tracking response to treatment. Recent developments have established liquid biopsies as promising non-invasive methods for detecting biomarkers in lung cancer patients. With concurrent advances in high-throughput sequencing technologies and bioinformatics tools, new approaches for biomarker discovery have emerged. In this article, we survey established and emerging biomarker discovery methods using nucleic acid materials derived from bodily fluids in the context of lung cancer. We introduce nucleic acid biomarkers extracted from liquid biopsies and outline biological sources and methods of isolation. We discuss next-generation sequencing (NGS) platforms commonly used to identify novel biomarkers and describe how these have been applied to liquid biopsy. We highlight emerging biomarker discovery methods, including applications of long-read sequencing, fragmentomics, whole-genome amplification methods for single-cell analysis, and whole-genome methylation assays. Finally, we discuss advanced bioinformatics tools, describing methods for processing NGS data, as well as recently developed software tailored for liquid biopsy biomarker detection, which holds promise for early diagnosis of lung cancer.

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Section: Emerging Methods For Liquid Biopsy Biomarker Discoverymentioning

confidence: 99%

Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer

Brockley¹,

Souza

Forder³

et al. 2023

Cancers

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“…Overall, cancer patient cfDNA shows subtle but reliable differences relative to healthy subjects. In individuals with cancer, cfDNA differences include a higher number of fragments below 150 bp, as well as a lower number of fragments between 151 and 218 bp; with dinucleosome-corresponding fragments peaking at 300 vs. 330 bp [20,21]. The elevated levels of total cfDNA have been demonstrated in malignant tumours among adults, including glioblastoma patients, relative to patients with non-neoplastic diseases [12].…”

Section: Of 13mentioning

confidence: 99%

Diagnostic and Prognostic Value of Circulating DNA Fragments in Glioblastoma Multiforme Patients

Jarmuzek,

Wawrzyniak-Gramacka,

Morawin

et al. 2024

IJMS

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Novel blood-circulating molecules, as potential biomarkers for glioblastoma multiforme (GBM) diagnosis and monitoring, are attracting particular attention due to limitations of imaging modalities and invasive tissue biopsy procedures. This study aims to assess the diagnostic and prognostic values of circulating cell-free DNA (cfDNA) in relation to inflammatory status in GBM patients and to determine the concentration and average size of DNA fragments typical of tumour-derived DNA fractions. Preoperative plasma samples from 40 patients (GBM 65.0 ± 11.3 years) and 40 healthy controls (HC 70.4 ± 5.4 years) were compared. The cfDNA concentrations and lengths were measured using the electrophoresis platform, and inflammatory indices (NLR, PLR, LMR, and SII) were calculated from complete blood cell analysis. More fragmented cfDNA and 4-fold higher 50–700 bp cfDNA concentrations were detected in GBM patients than in healthy controls. The average cfDNA size in the GBM group was significantly longer (median 336 bp) than in the HC group (median 271 bp). Optimal threshold values were 1265 pg/μL for 50–700 bp cfDNA (AUC = 0.857) and 290 bp for average cfDNA size (AUC = 0.814). A Kaplan–Meier survival curves analysis also demonstrated a higher mortality risk in the GBM group with a cut-off >303 bp cfDNA. This study is the first to have revealed glioblastoma association with high levels of cfDNA > 1000 pg/μL of 50–700 bp in length, which can be aggravated by immunoinflammatory reactivity.

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“…An emerging field of cfDNA analysis is fragmentomics [ 131 , 132 , 133 , 134 , 135 ]. This term refers to applications that characterize cfDNA fragmentation and topology patterns that mirror chromatin compaction, gene regulation and the epigenome [ 132 , 135 , 136 ].…”

Section: Genetic Analysis Of Circulating Cfdna In Patients With Hnsccmentioning

confidence: 99%

Circulating Tumor DNA in Head and Neck Squamous Cell Carcinoma

Brandt

Thiele

Daetwyler

et al. 2023

Cancers

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Tumors shed cell-free DNA (cfDNA) into the plasma. “Liquid biopsies” are a diagnostic test to analyze cfDNA in order to detect minimal residual cancer, profile the genomic tumor landscape, and monitor cancers non-invasively over time. This technique may be useful in patients with head and neck squamous cell carcinoma (HNSCC) due to genetic tumor heterogeneity and limitations in imaging sensitivity. However, there are technical challenges that need to be overcome for the widespread use of liquid biopsy in the clinical management of these patients. In this review, we discuss our current understanding of HNSCC genetics and the role of cfDNA genomic analyses as an emerging precision diagnostic tool.

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Circulating DNA fragmentomics and cancer screening

Cited by 27 publications

References 115 publications

Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer

Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer

Diagnostic and Prognostic Value of Circulating DNA Fragments in Glioblastoma Multiforme Patients

Circulating Tumor DNA in Head and Neck Squamous Cell Carcinoma

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