ArticleCell genomics2023
Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq.
Article in Cell genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Article
- Sequencing approaches in hereditary cancer testing: strengths, limitations and future directions.European journal of human genetics : EJHG · 2026Review
- Personalized reference genome-based pipeline reveals comprehensive haplotype-resolved views of cancer genomes.bioRxiv : the preprint server for biology · 2026Article
- Haplotype-resolved methylomes reveal parent-of-origin DNA methylation imbalance in autism spectrum disorder.Science advances · 2026Article
- Strand-seq and the future of personalized genomics.Nature genetics · 2026Review
- The complete genome of the KOLF2.1J reference iPSC line.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking of Oxford Nanopore whole genome sequencing for germline variant and CpG methylation detection across Canada's national platform for genome sequencing and analysis.Frontiers in genetics · 2026Article
- Using long-read sequencing to detect and subtype a case with Temple syndrome.Journal of medical genetics · 2025Article
- The impact of long-read sequencing on human population-scale genomics.Genome research · 2025Review
- Review
- Diagnostic utility of single-locus DNA methylation mark in Sotos syndrome developed by nanopore sequencing-based episignature.Clinical epigenetics · 2025Article
- Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technology.Epigenetics & chromatin · 2024Review
- Expanding Upon Genomics in Rare Diseases: Epigenomic Insights.International journal of molecular sciences · 2024Review
- Prognostic importance of direct assignment of parent of origin via long-read genome and epigenome sequencing in retinoblastoma.JCI insight · 2024Article
- Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing.Genome biology · 2024Article
- Genome assembly in the telomere-to-telomere era.Nature reviews. Genetics · 2024Review
- MethPhaser: methylation-based long-read haplotype phasing of human genomes.Nature communications · 2024Article
- Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing.bioRxiv : the preprint server for biology · 2024Article
- A signal processing and deep learning framework for methylation detection using Oxford Nanopore sequencing.Nature communications · 2024Article
- Taking identity-by-descent analysis into the wild: Estimating realized relatedness in free-ranging macaques.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hundreds of loci in human genomes have alleles that are methylated differentially according to their parent of origin. These imprinted loci generally show little variation across tissues, individuals, and populations. We show that such loci can be used to distinguish the maternal and paternal homologs for all human autosomes without the need for the parental DNA. We integrate methylation-detecting nanopore sequencing with the long-range phase information in Strand-seq data to determine the parent of origin of chromosome-length haplotypes for both DNA sequence and DNA methylation in five trios with diverse genetic backgrounds. The parent of origin was correctly inferred for all autosomes with an average mismatch error rate of 0.31% for SNVs and 1.89% for insertions or deletions (indels). Because our method can determine whether an inherited disease allele originated from the mother or the father, we predict that it will improve the diagnosis and management of many genetic diseases.
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