ArticleBMC medical genomics2025
Long-range PCR and Nanopore sequencing for localisation and phasing variants: an end-to-end clinical application workflow.
Article in BMC medical genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
1 citing paper in PubMed.
- Resolving haplotypes of the glucose-6-phosphate dehydrogenase gene using long-range polymerase chain reaction and Oxford Nanopore sequencing.Biology methods & protocols · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
backgroundNext-Generation short-read sequencing has limited diagnostic utility in phasing distantly separated variants and analysing genomic regions with high homology. Determining the phase of variants from parental chromosomes is critical for accurate identification of compound heterozygosity. Long-read sequencing technology is able to overcome these limitations through the analysis of long haplotypes of separated variants. This study has developed and validated a robust, end-to-end workflow for phasing and localising variants using long-range PCR (LR-PCR) and targeted Nanopore sequencing for clinical implementation.
methodsNA24385 (HG002) reference DNA was used for all tests. Four PCR kits were tested to optimise LR-PCR for targets between 1 and 20 kb. Amplicons were barcoded and sequenced on Flongle flow cells, with up to eight amplicons on each flow cell. An in-house bioinformatic pipeline was developed to analyse the amplicons. This pipeline is capable of detecting chimeric reads (a known PCR artefact), and incorporating Clair3 for variant calling, and WhatsHap and HapCUT2 for phasing.
resultsThe UltraRun LongRange PCR Kit performed with a 90% success rate for DNA amplification up to 22 kb. All 15 tested heterozygous Single Nucleotide Variant (SNV) pairs, and 10 small InDels, with inter-variant distances from 5.8 to 21.4 kb, were phased with 100% concordance to known phase. Furthermore, SNV calling within six low-mappability genes demonstrated precision and sensitivity of 1 against benchmark data. The median proportion of chimeric reads was maintained at 2.80% (range 1.79-16.12%) under optimised conditions.
conclusionsThis study establishes a reliable and affordable clinical diagnostic workflow for accurate phasing of variants separated by up to ~ 20 kb and for variant localisation in genomic regions not able to be sequenced by short-read sequencing. This integrated approach enables implementation in diagnostic settings to resolve complex genetic findings and improve variant interpretation. The bioinformatic pipeline and documentation are available at https://github.com/j-jamshidi/ONT_amp_phase .
Indexed as
Identifiers
What OpenQuestion holds
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.