ArticleBMC genomics2017
Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- TCR Analyses of Two Vast and Shared Melanoma Antigen-Specific T Cell Repertoires: Common and Specific Features.Frontiers in immunology · 2018Trial
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- Long-term prognostic value of ctDNA in early breast cancer: insights from the neoadjuvant ABCSG-34 Trial.NPJ breast cancer · 2026Article
- Circulating tumour DNA in mCRPC: bridging tumour biology and real-time treatment monitoring.Frontiers in molecular medicine · 2026Review
- Emerging role of low-frequency somatic mutations in cancer relapse: from early detection to precision oncology.Frontiers in oncology · 2026Review
- Benchmarking UMI clustering tools for accurate detection of low-frequency variants from deep sequencing.Scientific reports · 2025Article
- Deciphering Autoimmune Diseases: Unveiling the Diagnostic, Therapeutic, and Prognostic Potential of Immune Repertoire Sequencing.Inflammation · 2025Review
- Utilizing TP53 hotspot mutations as effective predictors of gemcitabine treatment outcome in non-small-cell lung cancer.Cell death discovery · 2025Article
- Molecular characterization of ovarian squamous cell carcinoma originating from mature teratoma.Journal of molecular medicine (Berlin, Germany) · 2025Article
- Evaluating Bioinformatics Processing of Somatic Variant Detection in cfDNA Using Targeted Sequencing with UMIs.International journal of molecular sciences · 2024Article
- Persistent Low-Level Variants in a Subset of Viral Genes Are Highly Predictive of Poor Outcome in Immunocompromised Patients With Cytomegalovirus Infection.The Journal of infectious diseases · 2024Article
- Cell-Free DNA in Plasma Reveals Genomic Similarity Between Biliary Tract Inflammatory Lesion and Biliary Tract Cancer.Phenomics (Cham, Switzerland) · 2024Article
- The performance of homopolymer detection using dichromatic and tetrachromatic fluorogenic next-generation sequencing platforms.BMC genomics · 2024Article
- Rare subclonal sequencing of breast cancers indicates putative metastatic driver mutations are predominately acquired after dissemination.Genome medicine · 2024Article
- Evaluating the performance of low-frequency variant calling tools for the detection of variants from short-read deep sequencing data.Scientific reports · 2023Article
- Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data.Nature methods · 2023Article
- Article
- Systematic detection of mosaicism by using digital NGS reveals three new MEN1 mosaicisms.Endocrine connections · 2022Article
- Effect of Antigen Retrieval on Genomic DNA From Immunodissected Samples.The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society · 2022Article
- Cytoplasmic p53 aggregates accumulated in p53-mutated cancer correlate with poor prognosis.PNAS nexus · 2022Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDetection of DNA mutations at very low allele fractions with high accuracy will significantly improve the effectiveness of precision medicine for cancer patients. To achieve this goal through next generation sequencing, researchers need a detection method that 1) captures rare mutation-containing DNA fragments efficiently in the mix of abundant wild-type DNA; 2) sequences the DNA library extensively to deep coverage; and 3) distinguishes low level true variants from amplification and sequencing errors with high accuracy. Targeted enrichment using PCR primers provides researchers with a convenient way to achieve deep sequencing for a small, yet most relevant region using benchtop sequencers. Molecular barcoding (or indexing) provides a unique solution for reducing sequencing artifacts analytically. Although different molecular barcoding schemes have been reported in recent literature, most variant calling has been done on limited targets, using simple custom scripts. The analytical performance of barcode-aware variant calling can be significantly improved by incorporating advanced statistical models.
resultsWe present here a highly efficient, simple and scalable enrichment protocol that integrates molecular barcodes in multiplex PCR amplification. In addition, we developed smCounter, an open source, generic, barcode-aware variant caller based on a Bayesian probabilistic model. smCounter was optimized and benchmarked on two independent read sets with SNVs and indels at 5 and 1% allele fractions. Variants were called with very good sensitivity and specificity within coding regions.
conclusionsWe demonstrated that we can accurately detect somatic mutations with allele fractions as low as 1% in coding regions using our enrichment protocol and variant caller.
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