ArticleNature methods2023
Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.
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Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 126 papers.
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126citing papers in PubMed
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126 citing papers in PubMed.
- Optimized Amplicon Strategy for Long-Read Sequencing of the Chikungunya Virus Genome.Methods in molecular biology (Clifton, N.J.) · 2027Article
- An Icelandic pangenome reference.Nature · 2026Article
- Comparison of nanopore sequencing, MethylationEPIC array, and EM-Seq for DNA methylation detection.Computational biology and chemistry · 2026Article
- Nanopore Ultra-Long Sequencing for FSHD: From Molecular Diagnosis to Preimplantation Genetic Testing.Genes · 2026Review
- Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic.Nature biotechnology · 2026Article
- Leveraging long read RNA-seq to decipher neuronal regulation of alternative polyadenylation.Nature communications · 2026Article
- A Personalized Haplotype-Resolved Near-Gapless Genome Framework for Somatic Variant Discovery in Hepatocellular Carcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Long-read sequencing of single cell-derived melanoma sublines reveals divergent and parallel genomic and epigenomic evolutionary trajectories.Nature communications · 2026Article
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- iSCORE-PD: an isogenic stem cell collection to research Parkinson's disease.Nature communications · 2026Article
- Structural variants are enriched in deleterious visible phenotypes inGenome research · 2026Article
- Using combined RNA/DNA short read sequencing to investigate allele-specific expression from the inactive X chromosome in human cells.bioRxiv : the preprint server for biology · 2026Article
- Determinants of haplotype phasing accuracy in long-read human genome sequencing.bioRxiv : the preprint server for biology · 2026Article
- Manual validation finds ultra-long-read sequencing best enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin with nanopore.G3 (Bethesda, Md.) · 2026Article
- Long-Read Haplotype Phasing Resolves Allelic Configuration as a Missing Layer of Precision Oncology.medRxiv : the preprint server for health sciences · 2026Article
- From variants to answers: The evolution of genetic counseling in IEI.Journal of human immunity · 2026Review
- SVScope improves somatic structural variations detection via graph-genome optimization.Genome biology · 2026Article
- ModelingbioRxiv : the preprint server for biology · 2026Article
- cuteHap: Haplotype-Aware Structural Variant Detection in Phased Long-Read Sequencing Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
66 more citing papers are in PubMed but not listed here.
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Authors and funding
30 authors.
Mikhail Kolmogorov *Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA. mikhail.kolmogorov@nih.gov.ORCID http://orcid.org/0000-0002-5489-9045
Kimberley J Billingsley *Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA. kimberley.billingsley@nih.gov.ORCID http://orcid.org/0000-0002-8003-4029
Mira MastorasUC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.ORCID http://orcid.org/0000-0001-6897-0116
Melissa MeredithUC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.ORCID http://orcid.org/0000-0001-5736-3193
Jean MonlongUC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
Ryan Lorig-RoachUC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
Mobin AsriUC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
Pilar Alvarez JerezCenter for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
Laksh MalikCenter for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
Ramita DewanLaboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-7611-7032
Xylena ReedCenter for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
Rylee M GennerCenter for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
Kensuke DaidaCenter for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-9177-9587
Sairam BeheraHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.ORCID http://orcid.org/0000-0002-9047-0203
Kishwar ShafinGoogle LLC, Mountain View, CA, USA.ORCID http://orcid.org/0000-0001-5252-3434
Trevor PesoutUC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.
Jeshuwin PrabakaranCenter for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-0409-9760
Paolo CarnevaliChan Zuckerberg Initiative, Redwood City, CA, USA.
Jianzhi YangDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
Arang RhieGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-9809-8127
Sonja W ScholzNeurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-6623-0429
Bryan J TraynorLaboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0003-0527-2446
Karen H MigaUC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.ORCID http://orcid.org/0000-0002-3670-4507
Miten JainDepartment of Bioengineering, Northeastern University, Boston, MA, USA.ORCID http://orcid.org/0000-0002-4571-3982
Winston TimpDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.ORCID http://orcid.org/0000-0003-2083-6027
Adam M PhillippyGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0003-2983-8934
Mark ChaissonDepartment of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0001-5395-1457
Fritz J SedlazeckHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.ORCID http://orcid.org/0000-0001-6040-2691
Cornelis BlauwendraatCenter for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA. cornelis.blauwendraat@nih.gov.ORCID http://orcid.org/0000-0001-9358-8111
Benedict PatenUC Santa Cruz Genomics Institute, Santa Cruz, CA, USA. bpaten@ucsc.edu.ORCID http://orcid.org/0000-0001-8863-3539
Funding
The AnVIL Data Ecosystem DACReS SupplementU24HG010262 · NHGRI · BROAD INSTITUTE, INC. · PI Robert J Carroll, Jonathan Lawson · 2018 to 2026
$40.5MLong-read DNA sequencing of Alzheimers Disease and Related Dementias casesZIAAG000538 · NIA · NATIONAL INSTITUTE ON AGING · PI COOKSON, MARK · 2020 to 2025
$39.6MResearch Education ComponentP30AG019610 · NIA · SUN HEALTH RESEARCH INSTITUTE · PI GONZALEZ HERNANDEZ, GRACIELA · 2001 to 2020
$32.5MThe Integration of Trans-omics for Precision Medicine (TOPMED) and Other Heart, Lung, Blood and Sleep (HLBS) Data Sets with the Data CommonsOT3HL142481 · NHLBI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI GROSSMAN, ROBERT L., PATEN, BENEDICT · 2017 to 2020
$24.9MResearch Education ComponentP30AG072980 · NIA · BANNER HEALTH · PI HEATHER Allyson BIMONTE-NELSON · 2021 to 2026
$24.9MTISSUE REPOSITORY COREP01AG000538 · NIA · UNIVERSITY OF CALIFORNIA-IRVINE · PI CRIBBS, DAVID HASTINGS · 1985 to 2018
$24.8MGENCODE: comprehensive reference genome annotation for human and mouseU24HG007234 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI Fergal James Martin · 2021 to 2026
$16.1MGenetic characterization of atypical parkinsonismZIANS003154 · NINDS · NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKE · PI SCHOLZ, SONJA · 2016 to 2025
$15.4MNational Brain and Tissue Resource for Parkinson's Disease and Related DisordersU24NS072026 · NINDS · BANNER SUN HEALTH RESEARCH INSTITUTE · PI BEACH, THOMAS G · 2011 to 2015
$7.8MDockstore: The Community Platform for Reproducible Biomedical Workflows and ApplicationsU24HG011853 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Jonathan Lawson, Benedict Paten · 2021 to 2026
$5.7MNanopore based profiling of epigenetic stateR01HG009190 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI TIMP, WINSTON GEORGE · 2017 to 2024
$4.8MComputational tools for uniform processing and integration of human reference atlas data [2 of 5]OT2OD033761 · OD · CARNEGIE-MELLON UNIVERSITY · PI PATEN, BENEDICT, RUFFALO, MATTHEW · 2022 to 2025
$4.2MIntramural NIH HHS ZIA AG000538Intramural NIH HHS ZIA NS003154NHGRI NIH HHS R01 HG009190NHGRI NIH HHS R01 HG010485NHGRI NIH HHS T32 HG012344NHGRI NIH HHS U01 HG010961NHGRI NIH HHS U24 HG007234NHGRI NIH HHS U24 HG010262NHGRI NIH HHS U24 HG011853NHLBI NIH HHS OT3 HL142481NIA NIH HHS P01 AG000538NIA NIH HHS P30 AG019610NIA NIH HHS P30 AG072980NIH HHS OT2 OD026682NIH HHS OT2 OD033761NINDS NIH HHS U24 NS072026
Abstract
Long-read sequencing technologies substantially overcome the limitations of short-reads but have not been considered as a feasible replacement for population-scale projects, being a combination of too expensive, not scalable enough or too error-prone. Here we develop an efficient and scalable wet lab and computational protocol, Napu, for Oxford Nanopore Technologies long-read sequencing that seeks to address those limitations. We applied our protocol to cell lines and brain tissue samples as part of a pilot project for the National Institutes of Health Center for Alzheimer's and Related Dementias. Using a single PromethION flow cell, we can detect single nucleotide polymorphisms with F1-score comparable to Illumina short-read sequencing. Small indel calling remains difficult within homopolymers and tandem repeats, but achieves good concordance to Illumina indel calls elsewhere. Further, we can discover structural variants with F1-score on par with state-of-the-art de novo assembly methods. Our protocol phases small and structural variants at megabase scales and produces highly accurate, haplotype-specific methylation calls.
Indexed as
Genome, HumanNanopore SequencingHaplotypesHigh-Throughput Nucleotide SequencingHumansMethylationPilot ProjectsSequence Analysis, DNA
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