Dataset Information

TNER: a novel background error suppression method for mutation detection in circulating tumor DNA.

ABSTRACT:

Background

Ultra-deep next-generation sequencing of circulating tumor DNA (ctDNA) holds great promise as a tool for the early detection of cancer and for monitoring disease progression and therapeutic responses. However, the low abundance of ctDNA in the bloodstream coupled with technical errors introduced during library construction and sequencing complicates mutation detection.

Results

To achieve high accuracy of variant calling via better distinguishing low-frequency ctDNA mutations from background errors, we introduce TNER (Tri-Nucleotide Error Reducer), a novel background error suppression method that provides a robust estimation of background noise to reduce sequencing errors. The results on both simulated data and real data from healthy subjects demonstrate that the proposed algorithm consistently outperforms a current, state-of-the-art, position-specific error polishing model, particularly when the sample size of healthy subjects is small.

Conclusions

TNER significantly enhances the specificity of downstream ctDNA mutation detection without sacrificing sensitivity. The tool is publicly available at https://github.com/ctDNA/TNER .

SUBMITTER: Deng S

PROVIDER: S-EPMC6195972 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Publications

TNER: a novel background error suppression method for mutation detection in circulating tumor DNA.

Deng Shibing S Lira Maruja M Huang Donghui D Wang Kai K Valdez Crystal C Kinong Jennifer J Rejto Paul A PA Bienkowska Jadwiga J Hardwick James J Xie Tao T

BMC bioinformatics 20181020 1

<h4>Background</h4>Ultra-deep next-generation sequencing of circulating tumor DNA (ctDNA) holds great promise as a tool for the early detection of cancer and for monitoring disease progression and therapeutic responses. However, the low abundance of ctDNA in the bloodstream coupled with technical errors introduced during library construction and sequencing complicates mutation detection.<h4>Results</h4>To achieve high accuracy of variant calling via better distinguishing low-frequency ctDNA muta ...[more]

PMID: 30342468

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Project description:BackgroundEsophageal cancer (ECa) is one of the most deadly cancers, with increasing incidence worldwide and poor prognosis. While endoscopy is recommended for the detection of ECa in high-risk individuals, it is not suitable for large-scale screening due to its invasiveness and inconvenience.MethodsIn this study, a novel gene methylation panel was developed for a blood-based test, and its diagnostic efficacy was evaluated using a cohort of 304 participants (203 cases, 101 controls). The assessment focused on the DNA methylation levels of SEPTIN9, tissue factor pathway inhibitor 2 (TFPI2), and the fragile histidine triad gene (FHIT) in patients with ECa, benign esophageal disease, and healthy controls. The receiver operating characteristic (ROC) curve was generated for the panel to calculate the area under the curve (AUC), sensitivity, specificity, and 95% confidence intervals (CIs), along with a comparison to the gold standard of pathological examination. The consistency between biomarker and pathological diagnosis was evaluated with kappa analysis conducted with IBM SPSS Statistics. The Chi-square test or Fisher's exact test was utilized to assess the association of test positivity with demographic characteristics.ResultsIn patients with ECa, SEPTIN9, TFPI2, and FHIT DNA methylation levels were significantly higher compared to those with benign esophageal disease or healthy controls. The panel demonstrated promising potential as a noninvasive tool for distinguishing malignant tumors from both healthy controls and benign esophageal diseases, achieving an area under the ROC curve of 0.925 (95% CI: 0.889-0.952), with a sensitivity of 79.8% [95% CI 73.6-85.1%] and specificity of 95.0% [95% CI 88.8-98.4%]. In particular, the panel showed exceptional diagnostic efficiency for stage 0, I, and II cancer patients with sensitivity at 69.0, 75.5%, and 78.9%, respectively. The comparison revealed a Kappa value of 0.725 between RT-PCR testing and the established gold standard of pathological examination, indicating a high level of consistency. Additionally, there was no bias in diagnostic efficiency based on age, gender, or the presence of other malignancies (non-esophageal cancers).ConclusionsThe study's findings suggested that the DNA methylation biomarkers panel holds promise as a non-invasive and convenient diagnostic test for ECa. The panel's ability to distinguish malignant tumors from benign esophageal diseases, coupled with its high sensitivity and specificity, presented opportunities to enhance the over-all diagnosis of high-risk population when in conjunction with existing detection methods.

Dataset Information

TNER: a novel background error suppression method for mutation detection in circulating tumor DNA.

Background

Results

Conclusions

Publications

TNER: a novel background error suppression method for mutation detection in circulating tumor DNA.

Similar Datasets

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