ArticleGenome research2024
High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation.
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Article in Genome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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92citing papers in PubMed
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Who cites it
92 citing papers in PubMed.
- Resolving missing human polymorphic inversions and other complex variants from ultralong read data.Genome research · 2026Article
- An Icelandic pangenome reference.Nature · 2026Article
- Predictive models of the genetic bases underlying budding yeast fitness in multiple environments.NAR genomics and bioinformatics · 2026Article
- Toward the clinical application of long-read sequencing in repeat-expansion disorders.Nature genetics · 2026Review
- Nano-RAPID: Integrated Diagnosis for Sarcoma Using a Nanopore Sequencer.Genes, chromosomes & cancer · 2026Article
- ONT-only genome assembly of a Korean male individual using a semen sample.Genes & genomics · 2026Article
- Accurate imputation of inversions in human genomes using different algorithms and data sources.NAR genomics and bioinformatics · 2026Article
- Population-scale disease-associated tandem repeat analysis reveals locus and ancestry-specific insights.Nature communications · 2026Article
- Dissecting the relationship between haplotypes around ATXN2 CAG repeats and the number of CAA interruptions by long-read sequencing.medRxiv : the preprint server for health sciences · 2026Article
- Uniparental Disomy Reveals Hidden Genetic Causes of Congenital Heart Disease.Research square · 2026Article
- Targeted long-read sequencing enables comprehensive analysis of the genetic and epigenetic landscape of inherited myopathies.Nature communications · 2026Article
- needLR: long-read structural variant annotation with population-scale frequency estimation.Bioinformatics (Oxford, England) · 2026Article
- How variant discovery redefines genetic prevalence: the case of cystine stone disease.European journal of human genetics : EJHG · 2026Article
- Complementarity of Long-Reads and Optical Mapping in Parkinson's Disease for Structural Variants.Annals of clinical and translational neurology · 2026Article
- Structural variant discovery and diagnostic impact in rare diseases from short-read and long-read sequencing.medRxiv : the preprint server for health sciences · 2026Article
- Ensilication preserves high-molecular weight native DNA for clinical long-read sequencing.Genome biology · 2026Article
- Germline sequence variation within the ribosomal DNA is associated with human complex traits.Cell genomics · 2026Article
- Tandem repeats in human brain evolution and disease susceptibility.Molecules and cells · 2026Review
- Whole genome sequencing of pre-treatment and post-treatment locally advanced rectal cancer using long and short read technologies.Scientific reports · 2026Article
- Sensitivity of HiFi long-read genome sequencing for difficult-to-detect pathogenic variants when applied to real-world clinical laboratory samples.American journal of human genetics · 2026Article
32 more citing papers are in PubMed but not listed here.
Corrections and comments
- Update of
Authors and funding
50 authors.
Jonas A Gustafson *Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA.ORCID 0000-0002-5748-905X
Sophia B Gibson *Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA.ORCID 0000-0001-9839-9045
Nikhita Damaraju *Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA.ORCID 0000-0001-5054-037X
Miranda P G ZaluskyDivision of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA.ORCID 0000-0002-4721-7499
Kendra HoekzemaDepartment of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.ORCID 0000-0002-8058-0177
David TwesigomweSydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa.ORCID 0000-0002-5421-5512
Lei YangPacific Northwest Research Institute, Seattle, Washington 98122, USA.ORCID 0000-0001-9284-1744
Anthony A SneadDepartment of Biology, New York University, New York, New York 10003, USA.ORCID 0000-0002-5020-8729
Phillip A RichmondAlamya Health, Baton Rouge, Louisiana 70806, USA.ORCID 0000-0003-1882-6014
Wouter De CosterApplied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp 2650, Belgium.ORCID 0000-0002-5248-8197
Nathan D OlsonMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.ORCID 0000-0003-2585-3037
Andrea GuarracinoDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA.ORCID 0000-0001-9744-131X
Qiuhui LiDepartment of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA.ORCID 0009-0004-6740-8040
Angela L MillerDivision of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA.ORCID 0000-0002-9200-1873
Joy GoffenaDivision of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA.ORCID 0000-0002-2346-2879
Zachary B AndersonDivision of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA.ORCID 0009-0005-7292-2535
Sophie H R StorzDivision of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA.ORCID 0009-0001-3099-9738
Sydney A WardDivision of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA.ORCID 0009-0009-3206-1725
Maisha SinhaDivision of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA.ORCID 0009-0001-7224-0244
Claudia Gonzaga-JaureguiInternational Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Mexico City 76230, Mexico.ORCID 0000-0002-4667-3679
Wayne E ClarkeNew York Genome Center, New York, New York 10013, USA.ORCID 0000-0003-2471-0712
Anna O BasileNew York Genome Center, New York, New York 10013, USA.ORCID 0000-0001-5112-5880
André CorveloNew York Genome Center, New York, New York 10013, USA.ORCID 0000-0003-0989-7806
Catherine ReevesNew York Genome Center, New York, New York 10013, USA.ORCID 0000-0002-9942-8909
Adrienne HellandNew York Genome Center, New York, New York 10013, USA.ORCID 0009-0006-2552-7791
Rajeeva Lochan MusunuriNew York Genome Center, New York, New York 10013, USA.ORCID 0000-0001-5671-1766
Mahler RevsineDepartment of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA.ORCID 0000-0002-3638-9762
Karynne E PattersonDepartment of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.ORCID 0000-0002-0853-1231
Cate R PaschalDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington 98195, USA.
Christina ZakarianDepartment of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.ORCID 0009-0003-7619-6433
Sara GoodwinCold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.ORCID 0000-0002-6110-7296
Tanner D JensenDepartment of Genetics, Stanford University, Stanford, California 94305, USA.ORCID 0000-0002-1873-8607
Esther RobbDepartment of Computer Science, Stanford University, Stanford, California 94305, USA.ORCID 0009-0009-4103-7639
1000 Genomes ONT Sequencing Consortium
University of Washington Center for Rare Disease Research (UW-CRDR)
Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium
William Richard McCombieCold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.ORCID 0000-0003-1899-0682
Fritz J SedlazeckHuman Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.ORCID 0000-0001-6040-2691
Justin M ZookMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.ORCID 0000-0003-2309-8402
Stephen B MontgomeryDepartment of Genetics, Stanford University, Stanford, California 94305, USA.ORCID 0000-0002-5200-3903
Erik GarrisonDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA.ORCID 0000-0003-3821-631X
Mikhail KolmogorovCancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA.ORCID 0000-0002-5489-9045
Michael C SchatzHuman Technopole, Milan 20157, Italy.ORCID 0000-0002-4118-4446
Richard N McLaughlinMolecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA.ORCID 0000-0003-0950-2253
Harriet DashnowDepartment of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA.ORCID 0000-0001-8433-6270
Michael C ZodyInternational Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Mexico City 76230, Mexico.ORCID 0000-0001-6594-7199
Matt LooseDeep Seq, School of Life Sciences, University of Nottingham, Nottingham NG7 2TQ, UK.ORCID 0000-0002-5264-0929
Miten JainDepartment of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA.ORCID 0000-0002-4571-3982
Evan E EichlerDepartment of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.ORCID 0000-0002-8246-4014
Danny E MillerDivision of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA; dm1@uw.edu.ORCID 0000-0001-6096-8601
Funding
Single-Cell Biology Shared ResourceP30CA045508 · NCI · COLD SPRING HARBOR LABORATORY · PI David A Tuveson · 1987 to 2026
$118.9MINSTITUTIONAL TRAINING GRANT IN GENOME SCIENCET32HG000044 · NHGRI · STANFORD UNIVERSITY · PI MICHAEL P. SNYDER · 1995 to 2026
$32.2MINTERDISCIPLINARY TRAINING IN GENOMIC SCIENCEST32HG000035 · NHGRI · UNIVERSITY OF WASHINGTON · PI Bruce Colston Trapnell · 1995 to 2026
$24.2MImplementing the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)U24HG010263 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI Enis Afgan, VINCENT JAMES CAREY · 2018 to 2026
$23.8MStanford Mendelian Genomics Research CenterU01HG011762 · NHGRI · STANFORD UNIVERSITY · PI Jonathan Adam Bernstein, Stephen Montgomery · 2021 to 2026
$16.7MUniversity of Washington Mendelian Genomics Research Center (UW-MGRC)U01HG011744 · NHGRI · UNIVERSITY OF WASHINGTON · PI MICHAEL Joseph BAMSHAD, Evan Eichler · 2021 to 2026
$15.8MUniversity of Washington (UW) Mendelian Genomics Data Coordinating CenterU24HG011746 · NHGRI · UNIVERSITY OF WASHINGTON · PI Susanne May, ALI SHOJAIE · 2021 to 2026
$14.8MBroad Institute Mendelian Genomic Research CenterU01HG011755 · NHGRI · BROAD INSTITUTE, INC. · PI Anne O'Donnell-Luria, MICHAEL E TALKOWSKI · 2021 to 2026
$14.6MFrequency of variants of unknown significance by ancestry groups in the All of Us Research Program cohortU01HG011758 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI RICHARD A GIBBS, JAMES R. LUPSKI · 2021 to 2026
$13.8MPediatric Mendelian Genomics Research CenterU01HG011745 · NHGRI · UNIVERSITY OF CALIFORNIA-IRVINE · PI Eric J. Vilain · 2021 to 2026
$13.3MTherapeutic target discovery in ADSP data via comprehensive whole-genome analysis incorporating ethnic diversity and systems approachesU01AG058589 · NIA · BOSTON UNIVERSITY MEDICAL CAMPUS · PI BOERWINKLE, ERIC A., DE JAGER, PHILIP L · 2018 to 2022
$11.1MSequence-resolved structural variation of human genomesR01HG010169 · NHGRI · UNIVERSITY OF WASHINGTON · PI Evan Eichler · 2018 to 2026
$4.5MNCI NIH HHS P30 CA045508NCI NIH HHS R03 CA272952NCI NIH HHS R50 CA243890NCI NIH HHS U01 CA253481NHGRI NIH HHS R00 HG012796NHGRI NIH HHS R01 HG010169NHGRI NIH HHS R01 HG013017NHGRI NIH HHS T32 HG000035NHGRI NIH HHS T32 HG000044NHGRI NIH HHS U01 HG011744NHGRI NIH HHS U01 HG011745NHGRI NIH HHS U01 HG011755NHGRI NIH HHS U01 HG011758NHGRI NIH HHS U01 HG011762NHGRI NIH HHS U24 HG010263NHGRI NIH HHS U24 HG011746NIAID NIH HHS R21 AI174130NIA NIH HHS U01 AG058589NIDA NIH HHS U01 DA057530NIGMS NIH HHS R35 GM142773NIH HHS DP5 OD033357NINDS NIH HHS UG3 NS132105
Abstract
Fewer than half of individuals with a suspected Mendelian or monogenic condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control data sets for variant filtering and prioritization has made tertiary analysis of LRS data challenging. To address this, the 1000 Genomes Project (1KGP) Oxford Nanopore Technologies Sequencing Consortium aims to generate LRS data from at least 800 of the 1KGP samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal patterns of human variation. Here, we present data from analysis of the first 100 samples, representing all 5 superpopulations and 19 subpopulations. These samples, sequenced to an average depth of coverage of 37× and sequence read N50 of 54 kbp, have high concordance with previous studies for identifying single nucleotide and indel variants outside of homopolymer regions. Using multiple structural variant (SV) callers, we identify an average of 24,543 high-confidence SVs per genome, including shared and private SVs likely to disrupt gene function as well as pathogenic expansions within disease-associated repeats that were not detected using short reads. Evaluation of methylation signatures revealed expected patterns at known imprinted loci, samples with skewed X-inactivation patterns, and novel differentially methylated regions. All raw sequencing data, processed data, and summary statistics are publicly available, providing a valuable resource for the clinical genetics community to discover pathogenic SVs.
Indexed as
Genetic VariationGenome, HumanNanopore SequencingHigh-Throughput Nucleotide SequencingHuman Genome ProjectHumansPolymorphism, Single NucleotideSequence Analysis, DNA
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