ArticleBMC genomics2016
Improving alignment accuracy on homopolymer regions for semiconductor-based sequencing technologies.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Ion Torrent Genexus as a Fast and Reliable Solution for HIV-1 Drug Resistance Testing: Comparison with the GeneStudio S5 Workflow.International journal of molecular sciences · 2026Article
- Next-generation Sequencing and Other Second Tier Tests in Newborn Screening for (X-linked) Agammaglobulinemia.Journal of clinical immunology · 2025Article
- Genomic landscape of hepatocellular carcinoma in Egyptian patients by whole exome sequencing.BMC medical genomics · 2024Article
- The performance of homopolymer detection using dichromatic and tetrachromatic fluorogenic next-generation sequencing platforms.BMC genomics · 2024Article
- Advanced variant classification framework reduces the false positive rate of predicted loss-of-function variants in population sequencing data.American journal of human genetics · 2023Article
- Prevalence of BRCA homopolymeric indels in an ION Torrent-based tumour-to-germline testing workflow in high-grade ovarian carcinoma.Scientific reports · 2023Article
- Article
- Advanced variant classification framework reduces the false positive rate of predicted loss of function (pLoF) variants in population sequencing data.medRxiv : the preprint server for health sciences · 2023Article
- Optimizing Insertion and Deletion Detection Using Next-Generation Sequencing in the Clinical Laboratory.The Journal of molecular diagnostics : JMD · 2022Article
- Tatajuba: exploring the distribution of homopolymer tracts.NAR genomics and bioinformatics · 2022Article
- Update on Molecular Diagnosis in Extranodal NK/T-Cell Lymphoma and Its Role in the Era of Personalized Medicine.Diagnostics (Basel, Switzerland) · 2022Review
- Article
- VLSI Structures for DNA Sequencing-A Survey.Bioengineering (Basel, Switzerland) · 2020Review
- Nanopore sequencing: An enrichment-free alternative to mitochondrial DNA sequencing.Electrophoresis · 2019Article
- NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform.GigaScience · 2018Article
- Discriminating a common somatic ASXL1 mutation (c.1934dup; p.G646Wfs*12) from artifact in myeloid malignancies using NGS.Leukemia · 2018Article
- Variable-order sequence modeling improves bacterial strain discrimination for Ion Torrent DNA reads.BMC bioinformatics · 2017Article
- Sequencing the CYP2D6 gene: from variant allele discovery to clinical pharmacogenetic testing.Pharmacogenomics · 2017Review
- Intelligent biology and medicine in 2015: advancing interdisciplinary education, collaboration, and data science.BMC genomics · 2016Article
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Authors and funding
10 authors.
Funding
Abstract
backgroundIon Torrent and Ion Proton are semiconductor-based sequencing technologies that feature rapid sequencing speed and low upfront and operating costs, thanks to the avoidance of modified nucleotides and optical measurements. Despite of these advantages, however, Ion semiconductor sequencing technologies suffer much reduced sequencing accuracy at the genomic loci with homopolymer repeats of the same nucleotide. Such limitation significantly reduces its efficiency for the biological applications aiming at accurately identifying various genetic variants.
resultsIn this study, we propose a Bayesian inference-based method that takes the advantage of the signal distributions of the electrical voltages that are measured for all the homopolymers of a fixed length. By cross-referencing the length of homopolymers in the reference genome and the voltage signal distribution derived from the experiment, the proposed integrated model significantly improves the alignment accuracy around the homopolymer regions.
conclusionsBesides improving alignment accuracy on homopolymer regions for semiconductor-based sequencing technologies with the proposed model, similar strategies can also be used on other high-throughput sequencing technologies that share similar limitations.
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