ArticleThe Journal of molecular diagnostics : JMD2024
Assay Validation of Cell-Free DNA Shallow Whole-Genome Sequencing to Determine Tumor Fraction in Advanced Cancers.
Article in The Journal of molecular diagnostics : JMD, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 16 citations in OpenAlex.
- Biological basis and clinical translation prospects of circulating cell-free DNA in precision management of breast cancer (Review).Oncology letters · 2026Review
- Crucial parameters for precise copy number variation detection in formalin-fixed paraffin-embedded solid cancer samples.Molecular oncology · 2026Article
- Liquid Biopsy in Colorectal Cancer: Future Perspectives Through the Lens of Artificial Intelligence-A Comprehensive Review of Novel Literature.International journal of molecular sciences · 2026Review
- Acute circulating tumor DNA dynamics during and after systemic therapy initiation for advanced triple-negative breast cancer.NPJ breast cancer · 2026Article
- Tumor Genomics and Liquid Biopsy in Cancer Biology: From Static Snapshots to Dynamic Measurements.Biomolecules · 2026Article
- Ultra-low-pass whole-genome sequencing of bile cfDNA in patients with biliary strictures.eGastroenterology · 2026Article
- Toward the genetic landscape of prostate cancer in India: insights from whole-exome and low-pass whole-genome sequencing of formalin-fixed paraffin-embedded tumor tissues.Frontiers in systems biology · 2026Article
- Genomics and Epigenomics Approaches for the Quantification of Circulating Tumor DNA in Liquid Biopsy: Relevance of a Multimodal Strategy.International journal of molecular sciences · 2025Review
- Integrated Multiclass Driver ctDNA Profiling Enables MPNST Detection and Monitoring in NF1 Patients.Research square · 2025Article
- A comparative study of four cell-free DNA assays for detecting circulating tumor DNA in early breast cancer.Breast cancer research : BCR · 2025Article
- The Role of ctDNA for Diagnosis and Histological Prediction in Early Stage Non-Small-Cell Lung Cancer: A Narrative Review.Diagnostics (Basel, Switzerland) · 2025Review
- Enabling sensitive and precise detection of ctDNA through somatic copy number aberrations in breast cancer.NPJ breast cancer · 2025Article
- Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2025Article
- Circulating DNA tumor fraction as a biomarker for advanced breast cancer.Frontiers in oncology · 2025Review
- SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline.Briefings in bioinformatics · 2024Article
- Optimizing ctDNA: An Updated Review of a Promising Clinical Tool for the Management of Uveal Melanoma.Cancers · 2024Review
- Binary classification of copy number alteration profiles in liquid biopsy with potential clinical impact in advanced NSCLC.Scientific reports · 2024Article
- Impact of preanalytical factors on liquid biopsy in the canine cancer model.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
14 authors at 3 institutions in 1 country.
Funding
Abstract
Blood-based liquid biopsy is increasingly used in clinical care of patients with cancer, and fraction of tumor-derived DNA in circulation (tumor fraction; TFx) has demonstrated clinical validity across multiple cancer types. To determine TFx, shallow whole-genome sequencing of cell-free DNA (cfDNA) can be performed from a single blood sample, using an established computational pipeline (ichorCNA), without prior knowledge of tumor mutations, in a highly cost-effective manner. We describe assay validation of this approach to facilitate broad clinical application, including evaluation of assay sensitivity, precision, repeatability, reproducibility, pre-analytic factors, and DNA quality/quantity. Sensitivity to detect TFx of 3% (lower limit of detection) was 97.2% to 100% at 1× and 0.1× mean sequencing depth, respectively. Precision was demonstrated on distinct sequencing instruments (HiSeqX and NovaSeq) with no observable differences. The assay achieved prespecified 95% agreement of TFx across replicates of the same specimen (repeatability) and duplicate samples in different batches (reproducibility). Comparison of samples collected in EDTA and Streck tubes from single venipuncture in 23 patients demonstrated that EDTA or Streck tubes were comparable if processed within 8 hours. On the basis of a range of DNA inputs (1 to 50 ng), 20 ng cfDNA is the preferred input, with 5 ng minimum acceptable. Overall, this shallow whole-genome sequencing of cfDNA and ichorCNA approach offers sensitive, precise, and reproducible quantitation of TFx, facilitating assay application in clinical cancer care.
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