ArticleNature communications2019
Multi-platform discovery of haplotype-resolved structural variation in human genomes.
Registry-linked trialAbstract read
In one paragraph
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT05295277 (Validation of Optical Genome Mapping for the Identification of Constitutional Genomic Variants in a Postnatal Cohort), which is not on this map. Cited by 555 papers.
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555citing papers in PubMed
–field-weighted citation impact
What it found
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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.
Validation of Optical Genome Mapping for the Identification of Constitutional Genomic Variants in a Postnatal Cohort
Who cites it
555 citing papers in PubMed.
- Article
- Genome-wide analysis of common structural variants in Alzheimer's disease identifies a risk-associated regulatory CCG repeat in FAM193B.Nature neuroscience · 2026Article
- Resolving missing human polymorphic inversions and other complex variants from ultralong read data.Genome research · 2026Article
- Point mutations and complex variants impact gene expression and addiction-related behaviors in Heterogeneous Stock rats.bioRxiv : the preprint server for biology · 2026Article
- Accurate imputation of inversions in human genomes using different algorithms and data sources.NAR genomics and bioinformatics · 2026Article
- Lineage-associated small inversions disruptMicrobiology spectrum · 2026Article
- Comprehensive evaluation of structural variation detection for germline and somatic analysis with long-read sequencing data.Briefings in bioinformatics · 2026Article
- Long-Read Sequencing in CKD Diagnostics: Breaking Genomic Barriers and Expanding Global Inclusion.Kidney international reports · 2026Review
- Diagnostic evaluation and clinical utility of C-MoKa for prenatal genetic testing.Journal of translational medicine · 2026Article
- Benchmarking long-read variant sensitivity across ONT and PacBio platforms using known clinically reported variants in a cohort of critically ill newborns.medRxiv : the preprint server for health sciences · 2026Article
- De Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools for read mapping.Briefings in bioinformatics · 2026Article
- needLR: long-read structural variant annotation with population-scale frequency estimation.Bioinformatics (Oxford, England) · 2026Article
- DNA Replication Errors Drive Genome-Wide Small Inverted Triplication Dynamics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genomic Variability of the HCT116 Cell Line Identified Using Oxford Nanopore Sequencing.International journal of molecular sciences · 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
- From fragments to full pictures: how long-read sequencing platforms are revolutionizing oncology research.Molecular biology reports · 2026Review
- Article
- Long-read genome sequencing improves detection and functional interpretation of structural and repeat variants in autism.Cell genomics · 2026Article
- Strand-seq and the future of personalized genomics.Nature genetics · 2026Review
- Neoantigen Targeting as a Novel Approach for Therapy-Resistant Tumors.Molecular diagnosis & therapy · 2026Review
495 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
97 authors.
Mark J P ChaissonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
Ashley D SandersEuropean Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.
Xuefang ZhaoDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.ORCID http://orcid.org/0000-0003-4036-9577
Ankit MalhotraThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
David PorubskyEuropean Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, AV, NL-9713, The Netherlands.
Tobias RauschEuropean Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.ORCID http://orcid.org/0000-0001-5773-5620
Eugene J GardnerInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.ORCID http://orcid.org/0000-0001-9671-1533
Oscar L RodriguezDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
Li GuoThe School of Life Science and Technology of Xi'an Jiaotong University, 710049, Xi'an, China.
Ryan L CollinsCenter for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA, 02114, USA.
Xian FanDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
Jia WenDepartment of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
Robert E HandsakerDepartment of Genetics, Harvard Medical School, Boston, MA, 02115, USA.ORCID http://orcid.org/0000-0002-3128-3547
Susan FairleyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
Zev N KronenbergDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
Xiangmeng KongYale University Medical School, Computational Biology and Bioinformatics Program, New Haven, CT, 06520, USA.
Fereydoun HormozdiariBiochemistry and Molecular Medicine, University of California Davis, Davis, CA, 95616, USA.
Dillon LeeUSTAR Center for Genetic Discovery and Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
Aaron M WengerPacific Biosciences, Menlo Park, CA, 94025, USA.ORCID http://orcid.org/0000-0003-1183-0432
Alex R HastieBionano Genomics, San Diego, CA, 92121, USA.
Danny AntakiBeyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego, La Jolla, CA, 92093, USA.ORCID http://orcid.org/0000-0003-0381-7801
Thomas AnantharamanBionano Genomics, San Diego, CA, 92121, USA.
Peter A AudanoDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.ORCID http://orcid.org/0000-0002-5187-0415
Harrison BrandCenter for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA, 02114, USA.
Stuart CantsilierisDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
Han CaoBionano Genomics, San Diego, CA, 92121, USA.
Eliza CerveiraThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
Chong ChenDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
Xintong ChenInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.ORCID http://orcid.org/0000-0002-2536-165X
Chen-Shan ChinPacific Biosciences, Menlo Park, CA, 94025, USA.ORCID http://orcid.org/0000-0003-4394-2455
Zechen ChongDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.ORCID http://orcid.org/0000-0001-5750-1808
Nelson T ChuangInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
Christine C LambertPacific Biosciences, Menlo Park, CA, 94025, USA.
Deanna M Church10X Genomics, Pleasanton, CA, 94566, USA.ORCID http://orcid.org/0000-0003-4264-1853
Laura ClarkeEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.ORCID http://orcid.org/0000-0002-5989-6898
Andrew FarrellUSTAR Center for Genetic Discovery and Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
Joey FloresIllumina Clinical Services Laboratory, Illumina, Inc., 5200 Illumina Way, San Diego, CA, 92122, USA.
Timur GaleevYale University Medical School, Computational Biology and Bioinformatics Program, New Haven, CT, 06520, USA.
David U GorkinDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA.ORCID http://orcid.org/0000-0003-4944-4107
Madhusudan GujralBeyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego, La Jolla, CA, 92093, USA.
Victor GuryevEuropean Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, AV, NL-9713, The Netherlands.
William Haynes Heaton10X Genomics, Pleasanton, CA, 94566, USA.
Jonas KorlachPacific Biosciences, Menlo Park, CA, 94025, USA.ORCID http://orcid.org/0000-0003-3047-4250
Sushant KumarYale University Medical School, Computational Biology and Bioinformatics Program, New Haven, CT, 06520, USA.
Jee Young KwonThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
Ernest T LamBionano Genomics, San Diego, CA, 92121, USA.
Jong Eun LeeDNA Link, Seodaemun-gu, Seoul, South Korea.
Joyce LeeBionano Genomics, San Diego, CA, 92121, USA.ORCID http://orcid.org/0000-0002-3492-1102
Wan-Ping LeeThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
Sau Peng LeeTreeCode Sdn Bhd, Bandar Botanic, 41200, Klang, Malaysia.
Shantao LiYale University Medical School, Computational Biology and Bioinformatics Program, New Haven, CT, 06520, USA.
Patrick Marks10X Genomics, Pleasanton, CA, 94566, USA.
Karine Viaud-MartinezIllumina Clinical Services Laboratory, Illumina, Inc., 5200 Illumina Way, San Diego, CA, 92122, USA.
Sascha MeiersEuropean Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.
Katherine M MunsonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.ORCID http://orcid.org/0000-0001-8413-6498
Fabio C P NavarroYale University Medical School, Computational Biology and Bioinformatics Program, New Haven, CT, 06520, USA.ORCID http://orcid.org/0000-0002-5640-9070
Bradley J NelsonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
Conor NodzakDepartment of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
Amina NoorBeyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego, La Jolla, CA, 92093, USA.
Sofia Kyriazopoulou-Panagiotopoulou10X Genomics, Pleasanton, CA, 94566, USA.
Andy W C PangBionano Genomics, San Diego, CA, 92121, USA.
Yunjiang QiuLudwig Institute for Cancer Research, La Jolla, CA, 92093, USA.ORCID http://orcid.org/0000-0002-0539-9714
Gabriel RosanioBeyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego, La Jolla, CA, 92093, USA.
Mallory RyanThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
Adrian StützEuropean Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.
Diana C J SpieringsEuropean Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, AV, NL-9713, The Netherlands.
Alistair WardUSTAR Center for Genetic Discovery and Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
AnneMarie E WelchDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
Ming XiaoSchool of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA.
Wei Xu10X Genomics, Pleasanton, CA, 94566, USA.
Chengsheng ZhangThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
Qihui ZhuThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
Xiangqun Zheng-BradleyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
Ernesto LowyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.ORCID http://orcid.org/0000-0001-9312-1159
Sergei YakneenEuropean Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.ORCID http://orcid.org/0000-0001-7827-9839
Steven McCarrollDepartment of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
Goo JunHuman Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77225, USA.
Li DingDepartment of Medicine, McDonnell Genome Institute, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MI, 63108, USA.
Chong Lek KohHigh Impact Research, University of Malaya, 50603, Kuala Lumpur, Malaysia.
Bing RenDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA.ORCID http://orcid.org/0000-0002-5435-1127
Paul FlicekEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.ORCID http://orcid.org/0000-0002-3897-7955
Ken ChenDepartment of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.ORCID http://orcid.org/0000-0003-4013-5279
Mark B GersteinYale University Medical School, Computational Biology and Bioinformatics Program, New Haven, CT, 06520, USA.
Pui-Yan KwokInstitute for Human Genetics, University of California-San Francisco, San Francisco, CA, 94143, USA.
Peter M LansdorpEuropean Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, AV, NL-9713, The Netherlands.
Gabor T MarthUSTAR Center for Genetic Discovery and Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
Jonathan SebatBeyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry University of California San Diego, La Jolla, CA, 92093, USA.ORCID http://orcid.org/0000-0002-9087-526X
Xinghua ShiDepartment of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.ORCID http://orcid.org/0000-0003-4662-3177
Ali BashirDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
Kai YeMOE Key Lab for Intelligent Networks & Networks Security, School of Electronics and Information Engineering, Xi'an Jiaotong University, 710049, Xi'an, China.
Scott E DevineInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
Michael E TalkowskiCenter for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA, 02114, USA.
Ryan E MillsDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
Tobias MarschallCenter for Bioinformatics, Saarland University and the Max Planck Institute for Informatics, 66123, Saarbrücken, Germany.ORCID http://orcid.org/0000-0002-9376-1030
Jan O KorbelEuropean Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany. jan.korbel@embl.de.ORCID http://orcid.org/0000-0002-2798-3794
Evan E EichlerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA. eee@gs.washington.edu.ORCID http://orcid.org/0000-0002-8246-4014
Charles LeeThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA. charles.lee@jax.org.
Funding
Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Scott Kopetz · 1985 to 2026
$290.8MShared Resource ManagementP30CA034196 · NCI · JACKSON LABORATORY · PI William Carl Skarnes · 1985 to 2026
$61.9MSequence and Assembly of Segmental DuplicationsR01HG002385 · NHGRI · UNIVERSITY OF WASHINGTON · PI Evan Eichler · 2001 to 2026
$13.3MAn Integrative Analysis of Structural Variation for the 1000 Genomes ProjectU41HG007497 · NHGRI · JACKSON LABORATORY · PI LEE, CHARLES · 2013 to 2017
$13.0MClinical Diagnostic Sequencing of Structural VariationR01HD081256 · NICHD · MASSACHUSETTS GENERAL HOSPITAL · PI TALKOWSKI, MICHAEL E · 2015 to 2025
$7.2MSingle molecule DNA mapping for genome and CNV analysisR01HG005946 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KWOK, PUI-YAN, XIAO, MING · 2010 to 2021
$6.5MScalable tool and comprehensive maps to interpret structural variation across the neuropsychiatric spectrumR01MH115957 · NIMH · BROAD INSTITUTE, INC. · PI TALKOWSKI, MICHAEL E · 2019 to 2025
$5.4MRobust Software Tools for Variant Identification and Functional AssessmentU01HG006513 · NHGRI · UNIVERSITY OF UTAH · PI ABECASIS, GONCALO, MARTH, GABOR T · 2012 to 2015
$4.2MNatural Genetic Variation in the Human GenomeR01HG002898 · NHGRI · UNIVERSITY OF MARYLAND BALTIMORE · PI DEVINE, SCOTT E · 2004 to 2019
$3.7MDiversity Action Plan: UW GenOM ProjectR25HG007153 · NHGRI · UNIVERSITY OF WASHINGTON · PI EICHLER, EVAN · 2013 to 2020
$2.3MA Community Driven Framework for Genome Based Clinical DiagnosticsR01HG008628 · NHGRI · UNIVERSITY OF UTAH · PI EILBECK, KAREN LOUISE, MARTH, GABOR T · 2015 to 2017
$1.8MNatural mutagenesis of human genomes by endogenous retrotransposonsR01CA166661 · NCI · UNIVERSITY OF MARYLAND BALTIMORE · PI DEVINE, SCOTT E · 2012 to 2016
$1.6MNCI NIH HHS R01 CA166661NHGRI NIH HHS F31 HG009223NHGRI NIH HHS R01 HG002385NHGRI NIH HHS R01 HG002898NHGRI NIH HHS R01 HG005946NHGRI NIH HHS R01 HG007068NHGRI NIH HHS R01 HG008628NHGRI NIH HHS R15 HG009565NHGRI NIH HHS U01 HG006513NHGRI NIH HHS U41 HG007497NIAID NIH HHS R21 AI117407NICHD NIH HHS R01 HD081256NIMH NIH HHS R01 MH115957NIMH NIH HHS R56 MH115957Wellcome Trust
Abstract
The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (<50 bp) and 27,622 SVs (≥50 bp) per genome. We also discover 156 inversions per genome and 58 of the inversions intersect with the critical regions of recurrent microdeletion and microduplication syndromes. Taken together, our SV callsets represent a three to sevenfold increase in SV detection compared to most standard high-throughput sequencing studies, including those from the 1000 Genomes Project. The methods and the dataset presented serve as a gold standard for the scientific community allowing us to make recommendations for maximizing structural variation sensitivity for future genome sequencing studies.
Indexed as
Genomic Structural VariationAlgorithmsChromosome MappingDatabases, GeneticGenome, HumanGenomicsHaplotypesHigh-Throughput Nucleotide SequencingHumansINDEL MutationWhole Genome Sequencing
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Read underepoch 390
Registered trials
NCT05295277ClinicalTrials.gov
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.