ArticlePloS one2018
ERASE-Seq: Leveraging replicate measurements to enhance ultralow frequency variant detection in NGS data.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis.Nature communications · 2021Trial
- Article
- Review
- Nucleotide-based genetic networks: Methods and applications.Journal of biosciences · 2022Article
- The economic value of liquid biopsy for genomic profiling in advanced non-small cell lung cancer.Therapeutic advances in medical oncology · 2022Article
- Review
- CRISPAltRations: a validated cloud-based approach for interrogation of double-strand break repair mediated by CRISPR genome editing.Molecular therapy. Methods & clinical development · 2021Article
- Sensitivity, specificity, and accuracy of a liquid biopsy approach utilizing molecular amplification pools.Scientific reports · 2021Article
- Fusion genes as biomarkers in pediatric cancers: A review of the current state and applicability in diagnostics and personalized therapy.Cancer letters · 2021Review
- Comparing cell-free circulating tumor DNA mutational profiles of disease-free and nonresponders patients with oropharyngeal squamous cell carcinoma.Laryngoscope investigative otolaryngology · 2020Article
- A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA.BMC bioinformatics · 2020Article
- Empirical design of a variant quality control pipeline for whole genome sequencing data using replicate discordance.Scientific reports · 2019Article
- Development and Application of Duplex Sequencing Strategy for Cell-Free DNA-Based Longitudinal Monitoring of Stage IV Colorectal Cancer.The Journal of molecular diagnostics : JMD · 2019Article
- Review
- Considerations and quality controls when analyzing cell-free tumor DNA.Biomolecular detection and quantification · 2019Article
- Clinical relevance of circulating molecules in cancer: focus on gastrointestinal stromal tumors.Therapeutic advances in medical oncology · 2019Review
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The accurate detection of ultralow allele frequency variants in DNA samples is of interest in both research and medical settings, particularly in liquid biopsies where cancer mutational status is monitored from circulating DNA. Next-generation sequencing (NGS) technologies employing molecular barcoding have shown promise but significant sensitivity and specificity improvements are still needed to detect mutations in a majority of patients before the metastatic stage. To address this we present analytical validation data for ERASE-Seq (Elimination of Recurrent Artifacts and Stochastic Errors), a method for accurate and sensitive detection of ultralow frequency DNA variants in NGS data. ERASE-Seq differs from previous methods by creating a robust statistical framework to utilize technical replicates in conjunction with background error modeling, providing a 10 to 100-fold reduction in false positive rates compared to published molecular barcoding methods. ERASE-Seq was tested using spiked human DNA mixtures with clinically realistic DNA input quantities to detect SNVs and indels between 0.05% and 1% allele frequency, the range commonly found in liquid biopsy samples. Variants were detected with greater than 90% sensitivity and a false positive rate below 0.1 calls per 10,000 possible variants. The approach represents a significant performance improvement compared to molecular barcoding methods and does not require changing molecular reagents.
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