ArticleScientific reports2016
Pitfalls of haplotype phasing from amplicon-based long-read sequencing.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Long-read target enrichment sequencing for rAAV integration site analysis in engineered clones with targeted viral insertion.Molecular therapy. Nucleic acids · 2026Article
- Benchmarking of real-time, field-deployable whole-genome sequencing ofMicrobial genomics · 2026Article
- FuFiHLA: a tool for full-field HLA typing from long-read data.Bioinformatics (Oxford, England) · 2026Article
- NanoPrePro: a fully equipped, fast, and memory-efficient preprocessor for nanopore transcriptomic sequencing.Briefings in bioinformatics · 2026Article
- Analysis of clinically relevant large tandem repeats using nanopore sequencing.Scientific reports · 2025Article
- Long-range PCR and Nanopore sequencing for localisation and phasing variants: an end-to-end clinical application workflow.BMC medical genomics · 2025Article
- Beyond the Cut: Long-read sequencing reveals complex genomic and transcriptomic changes in AAV-CRISPR therapy for Duchenne Muscular Dystrophy.bioRxiv : the preprint server for biology · 2025Article
- Leveraging long-read sequencing technologies for pharmacogenomic testing: applications, analytical strategies, challenges, and future perspectives.Frontiers in genetics · 2025Review
- Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data.Briefings in bioinformatics · 2024Article
- Approach for Phased Sequence-Based Genotyping of the Critical Pharmacogene Dihydropyrimidine Dehydrogenase (International journal of molecular sciences · 2024Article
- Targeted phasing of 2-200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method.Scientific reports · 2024Article
- Characterisation of a LINE-1 Insertion in theHuman mutation · 2024Article
- Targeted haplotyping in pharmacogenomics using Oxford Nanopore Technologies' adaptive sampling.Frontiers in pharmacology · 2023Article
- Cas9 targeted nanopore sequencing with enhanced variant calling improves CYP2D6-CYP2D7 hybrid allele genotyping.PLoS genetics · 2022Article
- PacBio long-read amplicon sequencing enables scalable high-resolution population allele typing of the complex CYP2D6 locus.Communications biology · 2022Article
- What Has the Undiagnosed Diseases Network Taught Us About the Clinical Applications of Genomic Testing?Annual review of medicine · 2022Review
- Uncovering Essential Tremor Genetics: The Promise of Long-Read Sequencing.Frontiers in neurology · 2022Review
- Features and applications of haplotypes in crop breeding.Communications biology · 2021Review
- CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure.PLoS computational biology · 2021Article
- Noninvasive prenatal testing for β-thalassemia by targeted nanopore sequencing combined with relative haplotype dosage (RHDO): a feasibility study.Scientific reports · 2021Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
The long-read sequencers from Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT) offer the opportunity to phase mutations multiple kilobases apart directly from sequencing reads. In this study, we used long-range PCR with ONT and PacBio sequencing to phase two variants 9 kb apart in the RET gene. We also re-analysed data from a recent paper which had apparently successfully used ONT to phase clinically important haplotypes at the CYP2D6 and HLA loci. From these analyses, we demonstrate PCR-chimera formation during PCR amplification and reference alignment bias are pitfalls that need to be considered when attempting to phase variants using amplicon-based long-read sequencing technologies. These methodological pitfalls need to be avoided if the opportunities provided by long-read sequencers are to be fully exploited.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.