ArticleBMC cancer2022
Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content.
Article in BMC cancer, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 23 citations in OpenAlex.
- Analysis of cell-free DNA in lymphomas: from sample collection to genotyping and minimal residual disease monitoring.Blood advances · 2026Review
- Biological basis and clinical translation prospects of circulating cell-free DNA in precision management of breast cancer (Review).Oncology letters · 2026Review
- Prenatal Whole-Genome Sequencing for Fetal Anomalies: Diagnostic Performance, Challenges, and Clinical Implications.International journal of molecular sciences · 2026Review
- Harnessing viral footprints in circulating free DNA (cfDNA) for early cancer detection: A focus on liquid-biopsy-based screening.International journal of cancer · 2026Review
- Cell-free DNA methylation and fragmentomics-based liquid biopsy for accurate esophageal cancer detection.BMC cancer · 2025Article
- Informatics at the Frontier of Cancer Research.Cancer research · 2025Review
- Application of circulating tumor DNA liquid biopsy in nasopharyngeal carcinoma: A case report and review of literature.World journal of clinical cases · 2025Article
- Multimodal cell-free DNA whole-genome TAPS is sensitive and reveals specific cancer signals.Nature communications · 2025Article
- Clonal tracking in cancer and metastasis.Cancer metastasis reviews · 2024Review
- Cell-free DNA fragmentomics and second malignant neoplasm risk in patients with PTEN hamartoma tumor syndrome.Cell reports. Medicine · 2024Article
- From haystack to high precision: advanced sequencing methods to unraveling circulating tumor DNA mutations.Frontiers in molecular biosciences · 2024Review
- Mutational spectrum of breast cancer by shallow whole-genome sequencing of cfDNA and tumor gene panel analysis.PloS one · 2024Article
- Clinical applications of circulating biomarkers in non-small cell lung cancer.Frontiers in cell and developmental biology · 2024Review
- [Research progress on circulating tumor DNA as a biomarker for minimal residual disease in solid tumors].Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics · 2023Review
- Application of PCR-based approaches for evaluation of cell-free DNA fragmentation in colorectal cancer.Frontiers in molecular biosciences · 2023Article
- The Clinical Utility of Droplet Digital PCR for Profiling Circulating Tumor DNA in Breast Cancer Patients.Diagnostics (Basel, Switzerland) · 2022Review
- Cell-Free DNA Fragmentomics: A Promising Biomarker for Diagnosis, Prognosis and Prediction of Response in Breast Cancer.International journal of molecular sciences · 2022Review
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCirculating cell-free DNA (cfDNA) in the plasma of cancer patients contains cell-free tumour DNA (ctDNA) derived from tumour cells and it has been widely recognized as a non-invasive source of tumour DNA for diagnosis and prognosis of cancer. Molecular profiling of ctDNA is often performed using targeted sequencing or low-coverage whole genome sequencing (WGS) to identify tumour specific somatic mutations or somatic copy number aberrations (sCNAs). However, these approaches cannot efficiently detect all tumour-derived genomic changes in ctDNA.
methodsWe performed WGS analysis of cfDNA from 4 breast cancer patients and 2 patients with benign tumours. We sequenced matched germline DNA for all 6 patients and tumour samples from the breast cancer patients. All samples were sequenced on Illumina HiSeqXTen sequencing platform and achieved approximately 30x, 60x and 100x coverage on germline, tumour and plasma DNA samples, respectively.
resultsThe mutational burden of the plasma samples (1.44 somatic mutations/Mb of genome) was higher than the matched tumour samples. However, 90% of high confidence somatic cfDNA variants were not detected in matched tumour samples and were found to comprise two background plasma mutational signatures. In contrast, cfDNA from the di-nucleosome fraction (300 bp-350 bp) had much higher proportion (30%) of variants shared with tumour. Despite high coverage sequencing we were unable to detect sCNAs in plasma samples.
conclusionsDeep sequencing analysis of plasma samples revealed higher fraction of unique somatic mutations in plasma samples, which were not detected in matched tumour samples. Sequencing of di-nucleosome bound cfDNA fragments may increase recovery of tumour mutations from plasma.
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