ArticleNPJ genomic medicine2024
Assessing the efficacy of target adaptive sampling long-read sequencing through hereditary cancer patient genomes.
Article in NPJ genomic medicine, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 34 citations in OpenAlex.
- Sequencing approaches in hereditary cancer testing: strengths, limitations and future directions.European journal of human genetics : EJHG · 2026Review
- Length Matters: Toward the Clinical Adoption of Long-Read Sequencing.Annals of laboratory medicine · 2026Article
- Flexible and rapid validation of structural variation using adaptive sampling.European journal of human genetics : EJHG · 2026Article
- Strand-seq and the future of personalized genomics.Nature genetics · 2026Review
- MetaGLIMPSE: Meta-imputation of low-coverage sequencing data for modern and ancient genomes.American journal of human genetics · 2026Article
- Proof-of-principle: nanopore adaptive sampling enables full blood group genome analysis and resolution of hybrid alleles.Blood advances · 2026Article
- The transformative impact of ultra-rapid nanopore sequencing in precision medicine.Frontiers in immunology · 2026Review
- Circulating neuron-derived cfDNA for blood-based detection of Alzheimer's and other neurodegenerative conditions.Frontiers in neurology · 2026Article
- Targeted adaptive sampling enables clinical pharmacogenomics testing and genome-wide genotyping.Scientific reports · 2025Article
- Hidden SVA retrotransposon insertion in BRCA1 revealed by nanopore targeted sequencing causes hereditary breast and ovarian cancer.Journal of human genetics · 2025Article
- Long-read DNA and RNA sequencing for inherited polyposis and colorectal cancer: cryptic intronic variants and multiple mutational mechanisms.Journal of medical genetics · 2025Article
- MetaGLIMPSE: Meta Imputation of Low Coverage Sequencing Data for Modern and Ancient Genomes.bioRxiv : the preprint server for biology · 2025Article
- Comparison of current methods for genome-wide DNA methylation profiling.Epigenetics & chromatin · 2025Article
- Copy number and structural variant analyses of VHL gene using droplet digital PCR and targeted adaptive sampling long-read sequencing.Familial cancer · 2025Article
- Exploring Epigenetic Ageing Using Direct Methylome Sequencing.Epigenomes · 2025Article
- Establishment of a high-risk pediatric AML-derived cell line YCU-AML2 with genetic and metabolic vulnerabilities.International journal of hematology · 2025Article
- Genetics, genomics and clinical features of adenomatous polyposis.Familial cancer · 2025Review
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- Evolution of genome-wide methylation profiling technologies.Genome research · 2025Review
- Targeted Long-Read Sequencing as a Single Assay Improves the Diagnosis of Spastic-Ataxia Disorders.Annals of clinical and translational neurology · 2025Article
Corrections and comments
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Authors and funding
21 authors at 10 institutions in 2 countries.
Funding
Abstract
Innovations in sequencing technology have led to the discovery of novel mutations that cause inherited diseases. However, many patients with suspected genetic diseases remain undiagnosed. Long-read sequencing technologies are expected to significantly improve the diagnostic rate by overcoming the limitations of short-read sequencing. In addition, Oxford Nanopore Technologies (ONT) offers adaptive sampling and computationally driven target enrichment technology. This enables more affordable intensive analysis of target gene regions compared to standard non-selective long-read sequencing. In this study, we developed an efficient computational workflow for target adaptive sampling long-read sequencing (TAS-LRS) and evaluated it through application to 33 genomes collected from suspected hereditary cancer patients. Our workflow can identify single nucleotide variants with nearly the same accuracy as the short-read platform and elucidate complex forms of structural variations. We also newly identified several SINE-R/VNTR/Alu (SVA) elements affecting the APC gene in two patients with familial adenomatous polyposis, as well as their sites of origin. In addition, we demonstrated that off-target reads from adaptive sampling, which is typically discarded, can be effectively used to accurately genotype common single-nucleotide polymorphisms (SNPs) across the entire genome, enabling the calculation of a polygenic risk score. Furthermore, we identified allele-specific MLH1 promoter hypermethylation in a Lynch syndrome patient. In summary, our workflow with TAS-LRS can simultaneously capture monogenic risk variants including complex structural variations, polygenic background as well as epigenetic alterations, and will be an efficient platform for genetic disease research and diagnosis.
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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.