Mapping and characterization of structural variation in 17,795 human genomes
Open accessAbstract
A key goal of whole-genome sequencing for studies of human genetics is to interrogate all forms of variation, including single-nucleotide variants, small insertion or deletion (indel) variants and structural variants. However, tools and resources for the study of structural variants have lagged behind those for smaller variants. Here we used a scalable pipeline1 to map and characterize structural variants in 17,795 deeply sequenced human genomes. We publicly release site-frequency data to create the largest, to our knowledge, whole-genome-sequencing-based structural variant resource so far. On average, individuals carry 2.9 rare structural variants that alter coding regions; these variants affect the dosage or structure of 4.2 genes and account for 4.0–11.2% of rare high-impact coding alleles. Using a computational model, we estimate that structural variants account for 17.2% of rare alleles genome-wide, with predicted deleterious effects that are equivalent to loss-of-function coding alleles; approximately 90% of such structural variants are noncoding deletions (mean 19.1 per genome). We report 158,991 ultra-rare structural variants and show that 2% of individuals carry ultra-rare megabase-scale structural variants, nearly half of which are balanced or complex rearrangements. Finally, we infer the dosage sensitivity of genes and noncoding elements, and reveal trends that relate to element class and conservation. This work will help to guide the analysis and interpretation of structural variants in the era of whole-genome sequencing. Structural variants in more than 17,000 human genomes are mapped and characterized using whole-genome sequencing, showing how this type of variation contributes to rare deleterious coding and noncoding alleles.
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Cites
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works
Self-citationRegularization Paths for Generalized Linear Models via Coordinate Descent
Friedman, J., Hastie, T., & Tibshirani, R. (2010) · Journal of Statistical Software · doi:10.18637/jss.v033.i01 · Cited by 19,927 · see citing works
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247 · see citing works
Self-citationAn integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works
The variant call format and VCFtools
Danecek, P., Auton, A., Abecasis, G. R., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G. A., Marth, G., Sherry, S. T., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr330 · Cited by 16,008 · see citing works
Minimap2: Pairwise alignment for nucleotide sequences
Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807 · see citing works
A framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,216 · see citing works
Analysis of protein-coding genetic variation in 60,706 humans
Exome Aggregation Consortium, Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., O’Donnell-Luria, A. H., Ware, J. S., Hill, A. J., et al. (2016) · Nature · doi:10.1038/nature19057 · Cited by 9,587 · see citing works
Self-citationThe Ensembl Variant Effect Predictor
McLaren, W., Gil, L., Hunt, S. E., Riat, H. S., Ritchie, G. R. S., Thormann, A., Flicek, P., & Cunningham, F. (2016) · Genome Biology · doi:10.1186/s13059-016-0974-4 · Cited by 8,099 · see citing works
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829 · see citing works
Integrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368 · see citing works
A general framework for estimating the relative pathogenicity of human genetic variants
Kircher, M., Witten, D. M., Jain, P., O'Roak, B. J., Cooper, G. M., & Shendure, J. (2014) · Nature Genetics · doi:10.1038/ng.2892 · Cited by 6,183 · see citing works
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 4,408 · see citing works
Robust relationship inference in genome-wide association studies
Manichaikul, A., Mychaleckyj, J. C., Rich, S. S., Daly, K., Sale, M., & Chen, W.-M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq559 · Cited by 3,541 · see citing works
Strong association of de novo copy number mutations with autism
Sebat, J., Lakshmi, B., Malhotra, D., Troge, J., Lese-Martin, C., Walsh, T., Yamrom, B., Yoon, S., Krasnitz, A., Kendall, J., et al. (2007) · Science · doi:10.1126/science.1138659 · Cited by 2,795 · see citing works
An integrated map of structural variation in 2,504 human genomes
Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Hsi-Yang Fritz, M., et al. (2015) · Nature · doi:10.1038/nature15394 · Cited by 2,354 · see citing works
Self-citationScaling accurate genetic variant discovery to tens of thousands of samplesPreprint
Poplin, R. E., Ruano-Rubio, V., DePristo, M. A., Fennell, T. J., Carneiro, M. O., der Auwera, G. A. V., Kling, D. E., Gauthier, L. D., Levy‐Moonshine, A., Roazen, D., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/201178 · Cited by 1,891 · see citing works
Self-citationRare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in Schizophrenia
Walsh, T., McClellan, J. M., McCarthy, S. E., Addington, A. M., Pierce, S. B., Cooper, G. M., Nord, A. S., Kusenda, M., Malhotra, D., Bhandari, A., et al. (2008) · Science · doi:10.1126/science.1155174 · Cited by 1,800 · see citing works
Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes
Stranger, B. E., Forrest, M. S., Dunning, M., Ingle, C., Beazley, C., Thorne, N., Redon, R., Bird, C., Grassi, A., Lee, C., et al. (2007) · Science · doi:10.1126/science.1136678 · Cited by 1,743 · see citing works
Ultraconserved Elements in the Human Genome
Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W. J., Mattick, J. S., & Haussler, D. (2004) · Science · doi:10.1126/science.1098119 · Cited by 1,732 · see citing works
Association between Microdeletion and Microduplication at 16p11.2 and Autism
Weiss, L. A., Shen, Y., Korn, J. M., Arking, D. E., Miller, D. T., Fossdal, R., Saemundsen, E., Stefansson, H., Ferreira, M. A. R., Green, T., et al. (2008) · New England Journal of Medicine · doi:10.1056/nejmoa075974 · Cited by 1,666 · see citing works
Abyzov, A., Urban, A. E., Snyder, M., & Gerstein, M. (2011) · Genome Research · doi:10.1101/gr.114876.110 · Cited by 1,658 · see citing works
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
McLaren, W. M., Yates, B., Ríos, D., Chen, Y., Flicek, P., & Cunningham, F. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq330 · Cited by 1,586 · see citing works
LUMPY: a probabilistic framework for structural variant discovery
Layer, R. M., Chiang, C., Quinlan, A. R., & Hall, I. M. (2014) · Genome biology · doi:10.1186/gb-2014-15-6-r84 · Cited by 1,510 · see citing works
Self-citationRare chromosomal deletions and duplications increase risk of schizophrenia
The International Schizophrenia Consortium (2008) · Nature · doi:10.1038/nature07239 · Cited by 1,475 · see citing works
Common variants at 30 loci contribute to polygenic dyslipidemia
Kathiresan, S., Willer, C. J., Peloso, G. M., Demissie, S., Musunuru, K., Schadt, E. E., Kaplan, L., Bennett, D., Li, Y., Tanaka, T., et al. (2009) · Nature Genetics · doi:10.1038/ng.291 · Cited by 1,364 · see citing works
A copy number variation morbidity map of developmental delay
Cooper, G. M., Coe, B. P., Girirajan, S., Rosenfeld, J. A., Vu, T. H., Baker, C., Williams, C., Stalker, H., Hamid, R., Hannig, V., et al. (2011) · Nature Genetics · doi:10.1038/ng.909 · Cited by 1,351 · see citing works
The Database of Genomic Variants: a curated collection of structural variation in the human genome
MacDonald, J. R., Ziman, R., Yuen, R. K. C., Feuk, L., & Scherer, S. W. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt958 · Cited by 1,346 · see citing works
GeneHancer: genome-wide integration of enhancers and target genes in GeneCards
Fishilevich, S., Nudel, R., Rappaport, N., Hadar, R., Plaschkes, I., Stein, T. I., Rosen, N., Kohn, A., Twik, M., Safran, M., et al. (2017) · Database · doi:10.1093/database/bax028 · Cited by 1,219 · see citing works
Mapping copy number variation by population-scale genome sequencing
1000 Genomes Project, Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., Abyzov, A., Yoon, S. C., Ye, K., et al. (2011) · Nature · doi:10.1038/nature09708 · Cited by 1,140 · see citing works
Myocardial Infarction Genetics Consortium (2009) · Nature Genetics · doi:10.1038/ng.327 · Cited by 1,088 · see citing works
VISTA Enhancer Browser—a database of tissue-specific human enhancers
Visel, A., Minovitsky, S., Dubchak, I., & Pennacchio, L. A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl822 · Cited by 1,080 · see citing works
Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects
Marshall, C. R., Howrigan, D. P., Merico, D., Thiruvahindrapuram, B., Wu, W., Greer, D. S., Antaki, D., Shetty, A., Holmans, P. A., Pinto, D., et al. (2017) · Nature Genetics · doi:10.1038/ng.3725 · Cited by 1,058 · see citing works
Self-citationMulti-platform discovery of haplotype-resolved structural variation in human genomes
Chaisson, M. J. P., Sanders, A. D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-08148-z · Cited by 891 · see citing works
The Wellcome Trust Case Control Consortium (2010) · Nature · doi:10.1038/nature08979 · Cited by 807 · see citing works
CrossMap: a versatile tool for coordinate conversion between genome assemblies
Zhao, H., Sun, Z., Wang, J., Huang, H., Kocher, J., & Wang, L. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt730 · Cited by 718 · see citing works
Microduplications of 16p11.2 are associated with schizophrenia
Wellcome Trust Case Control Consortium, McCarthy, S. E., Makarov, V., Kirov, G., Addington, A. M., McClellan, J., Yoon, S., Perkins, D. O., Dickel, D. E., Kusenda, M., et al. (2009) · Nature Genetics · doi:10.1038/ng.474 · Cited by 711 · see citing works
Phenotypic impact of genomic structural variation: insights from and for human disease
Weischenfeldt, J., Symmons, O., Spitz, F., & Korbel, J. O. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3373 · Cited by 674 · see citing works
Characterising and Predicting Haploinsufficiency in the Human Genome
Huang, N., Lee, I., Marcotte, E. M., & Hurles, M. E. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001154 · Cited by 659 · see citing works
Association Between Microdeletion and Microduplication at 16p11.2 and Autism
Weiss, L. A., Shen, Y., Korn, J. M., Arking, D. E., Miller, D. T., Fossdal, R., Sæmundsen, E., Stefánsson, H., Ferreira, M. A. R., Green, T. J., et al. (2008) · Obstetrical & Gynecological Survey · doi:10.1097/01.ogx.0000316305.61461.6f · Cited by 647 · see citing works
SpeedSeq: ultra-fast personal genome analysis and interpretation
Chiang, C., Layer, R. M., Faust, G. G., Lindberg, M. R., Rose, D. B., Garrison, E. P., Marth, G., Quinlan, A. R., & Hall, I. M. (2015) · Nature Methods · doi:10.1038/nmeth.3505 · Cited by 555 · see citing works
Self-citationThe impact of structural variation on human gene expression
GTEx Consortium, Chiang, C., Scott, A. J., Davis, J. R., Tsang, E. K., Li, X., Kim, Y., Hadzic, T., Damani, F. N., Ganel, L., et al. (2017) · Nature Genetics · doi:10.1038/ng.3834 · Cited by 495 · see citing works
Self-citationFast Computation and Applications of Genome Mappability
Derrien, T., Estellé, J., Marco‐Sola, S., Knowles, D. G., Raineri, E., Guigó, R., & Ribeca, P. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030377 · Cited by 476 · see citing works
Unified representation of genetic variants
Tan, A. K. S., Abecasis, G. R., & Kang, H. M. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv112 · Cited by 388 · see citing works
Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics
Khurana, E., Fu, Y., Colonna, V., Mu, X. J., Kang, H. M., Lappalainen, T., Sboner, A., Lochovsky, L., Chen, J., Harmanci, A. O., et al. (2013) · Science · doi:10.1126/science.1235587 · Cited by 359 · see citing works
Self-citationGlobal diversity, population stratification, and selection of human copy-number variation
Sudmant, P. H., Mallick, S., Nelson, B. J., Hormozdiari, F., Krumm, N., Huddleston, J., Coe, B. P., Baker, C., Nordenfelt, S., Bamshad, M., et al. (2015) · Science · doi:10.1126/science.aab3761 · Cited by 345 · see citing works
Genomic Patterns of De Novo Mutation in Simplex Autism
Turner, T. N., Coe, B. P., Dickel, D. E., Hoekzema, K., Nelson, B. J., Zody, M. C., Kronenberg, Z. N., Hormozdiari, F., Raja, A. N., Pennacchio, L. A., et al. (2017) · Cell · doi:10.1016/j.cell.2017.08.047 · Cited by 341 · see citing works
Self-citationFunSeq2: A framework for prioritizing noncoding regulatory variants in cancer
Fu, Y., Liu, Z., Lou, S., Bedford, J., Mu, X. J., Yip, K. Y.-L., Khurana, E., & Gerstein, M. (2014) · Genome biology · doi:10.1186/s13059-014-0480-5 · Cited by 334 · see citing works
Huang, Y.-F., Gulko, B., & Siepel, A. C. (2017) · Nature Genetics · doi:10.1038/ng.3810 · Cited by 329 · see citing works
dbVar and DGVa: public archives for genomic structural variation
Lappalainen, I., Lopez, J. R., Skipper, L. M., Hefferon, T. W., Spalding, D., Garner, J., Chen, C., Maguire, M., Corbett, M., Zhou, G., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1213 · Cited by 310 · see citing works
A Human Genome Structural Variation Sequencing Resource Reveals Insights into Mutational Mechanisms
Kidd, J. M., Graves, T., Newman, T. L., Fulton, R. S., Hayden, H. S., Malig, M., Kallicki, J., Kaul, R., Wilson, R. K., & Eichler, E. E. (2010) · Cell · doi:10.1016/j.cell.2010.10.027 · Cited by 297 · see citing works
Werling, D. M., Brand, H., An, J.-Y., Stone, M. R., Zhu, L., Glessner, J. T., Collins, R. L., Dong, S., Layer, R. M., Markenscoff-Papadimitriou, E., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0107-y · Cited by 293 · see citing works
Self-citationGenome-wide mapping and assembly of structural variant breakpoints in the mouse genomePreprint
Quinlan, A. R., Clark, R. A., Sokolova, S., Leibowitz, M. L., Zhang, Y., Hurles, M. E., Mell, J. C., & Hall, I. M. (2010) · Genome Research · doi:10.1101/gr.102970.109 · Cited by 282 · see citing works
Self-citationMutation spectrum revealed by breakpoint sequencing of human germline CNVs
Conrad, D. F., Bird, C., Blackburne, B. P., Lindsay, S., Mamanova, L., Lee, C., Turner, D., & Hurles, M. E. (2010) · Nature Genetics · doi:10.1038/ng.564 · Cited by 254 · see citing works
Yip, K. Y.-L., Cheng, C., Bhardwaj, N., Brown, J., Leng, J., Kundaje, A. B., Rozowsky, J. S., Birney, E., Bickel, P. J., Snyder, M. P., et al. (2012) · Genome biology · doi:10.1186/gb-2012-13-9-r48 · Cited by 248 · see citing works
A general framework for estimating the relative pathogenicity of human genetic variants
Kircher, M., Witten, D., Cooper, G. M., & Shendure, J. (2014) · F1000Research · doi:10.7490/f1000research.1095265.1 · Cited by 234 · see citing works
ORegAnno: an open-access community-driven resource for regulatory annotation
Griffith, O. L., Montgomery, S. B., Bernier, B., Chu, B., Kasaian, K., Aerts, S., Mahony, S., Sleumer, M. C., Bilenky, M., Haeussler, M., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm967 · Cited by 233 · see citing works
Bragin, E., Chatzimichali, E. A., Wright, C. F., Hurles, M. E., Firth, H. V., Bevan, A. P., & Swaminathan, G. J. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt937 · Cited by 233 · see citing works
APPRIS: annotation of principal and alternative splice isoforms
Rodriguez, J. M., Maietta, P., Ezkurdia, I., Pietrelli, A., Wesselink, J.-J., Lopez, G., Valencia, A., & Tress, M. L. (2013) · Nucleic Acids Research · doi:10.1093/nar/gks1058 · Cited by 232 · see citing works
Regier, A., Farjoun, Y., Larson, D. E., Krasheninina, O. A., Kang, H. M., Howrigan, D. P., Chen, B.-J., Kher, M., Banks, E., Ames, D. C., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06159-4 · Cited by 224 · see citing works
Self-citationPaternally inherited cis-regulatory structural variants are associated with autism
Brandler, W. M., Antaki, D., Gujral, M., Kleiber, M. L., Whitney, J., Maile, M. S., Hong, O., Chapman, T. R., Tan, S., Tandon, P., et al. (2018) · Science · doi:10.1126/science.aan2261 · Cited by 209 · see citing works
ORegAnno 3.0: a community-driven resource for curated regulatory annotation
Lesurf, R., Cotto, K. C., Wang, G., Griffith, M., Kasaian, K., Jones, S. J. M., Montgomery, S. B., Griffith, O. L., & The Open Regulatory Annotation Consortium (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1203 · Cited by 201 · see citing works
Forabosco, A., Percesepe, A., & Santucci, S. (2009) · European Journal of Human Genetics · doi:10.1038/ejhg.2008.265 · Cited by 175 · see citing works
Malhotra, A., Lindberg, M. R., Faust, G. G., Leibowitz, M. L., Clark, R. A., Layer, R. M., Quinlan, A. R., & Hall, I. M. (2013) · Genome Research · doi:10.1101/gr.143677.112 · Cited by 166 · see citing works
Self-citationPatterns of genic intolerance of rare copy number variation in 59,898 human exomes
Ruderfer, D. M., Hamamsy, T., Lek, M., Karczewski, K. J., Kavanagh, D., Samocha, K. E., Daly, M. J., MacArthur, D. G., Fromer, M., & Purcell, S. (2016) · Nature Genetics · doi:10.1038/ng.3638 · Cited by 164 · see citing works
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference
Maretty, L., Jensen, J. M., Petersen, B., Sibbesen, J. A., Liu, S. M., Villesen, P., Skov, L., Belling, K., Have, C. T., Izarzugaza, J. M. G., et al. (2017) · Nature · doi:10.1038/nature23264 · Cited by 155 · see citing works
Multi-platform discovery of haplotype-resolved structural variation in human genomesPreprint
Chaisson, M., Sanders, A. D., Zhao, X., Malhotra, A., Porubskỳ, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/193144 · Cited by 145 · see citing works
Retrotransposition of gene transcripts leads to structural variation in mammalian genomes
Ewing, A. D., Ballinger, T. J., Earl, D. A., Harris, C. C., Ding, L., Wilson, R. K., & Haussler, D. H. (2013) · Genome biology · doi:10.1186/gb-2013-14-3-r22 · Cited by 114 · see citing works
Characterizing complex structural variation in germline and somatic genomes
Quinlan, A. R., & Hall, I. M. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.10.002 · Cited by 105 · see citing works
Self-citationHehir‐Kwa, J. Y., Marschall, T., Kloosterman, W. P., Francioli, L. C., Baaijens, J. A., Dijkstra, L., Abdellaoui, A., Koval, V., Thung, D. T., Wardenaar, R., et al. (2016) · Nature Communications · doi:10.1038/ncomms12989 · Cited by 102 · see citing works
Gene Copy-Number Polymorphism Caused by Retrotransposition in Humans
Schrider, D. R., Navarro, F. C. P., Galante, P. A. F., Parmigiani, R. B., Camargo, A. A., Hahn, M. W., & SOUZA, S. J. D. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003242 · Cited by 96 · see citing works
YAHA: fast and flexible long-read alignment with optimal breakpoint detection
Faust, G. G., & Hall, I. M. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts456 · Cited by 78 · see citing works
Self-citationsvtools: population-scale analysis of structural variation
Larson, D. E., Abel, H., Chiang, C., Badve, A., Das, I., Eldred, J. M., Layer, R. M., & Hall, I. M. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz492 · Cited by 72 · see citing works
Self-citationSVScore: an impact prediction tool for structural variation
Ganel, L., Abel, H., & Hall, I. M. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw789 · Cited by 68 · see citing works
Self-citationAbyzov, A. S., Iskow, R. C., Gökçümen, Ö., Radke, D. W., Balasubramanian, S., Pei, B., Habegger, L., Lee, C., & Gerstein, M. (2013) · Genome Research · doi:10.1101/gr.154625.113 · Cited by 55 · see citing works
DENdb: database of integrated human enhancers
Ashoor, H., Kleftogiannis, D., Radovanović, A., & Bajić, V. B. (2015) · Database · doi:10.1093/database/bav085 · Cited by 50 · see citing works
The impact of structural variation on human gene expressionPreprint
Chiang, C., Scott, A. J., Davis, J. R., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/055962 · Cited by 48 · see citing works
Self-citationRegier, A., Farjoun, Y., Larson, D. E., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/269316 · Cited by 34 · see citing works
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Research works printed but not linked: 1
- [38]Hook EB & Hamerton JL in Population Cytogenetics: Studies in Humans (eds Hook EB & Porter LH) 63– 79 (Academic Press, 1977).
Cited by
Sorted by citations
A draft human pangenome reference.
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129 · see citing works
Self-citationByrska-Bishop, M., Evani, U. S., Zhao, X., Basile, A. O., Abel, H. J., Regier, A. A., Corvelo, A., Clarke, W. E., Musunuri, R., Nagulapalli, K., et al. (2022) · Cell · doi:10.1016/j.cell.2022.08.004 · Cited by 1,094 · see citing works
Self-citationHaplotype-resolved diverse human genomes and integrated analysis of structural variation
Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science · doi:10.1126/science.abf7117 · Cited by 702 · see citing works
Self-citationThe Human Pangenome Project: a global resource to map genomic diversity
Wang, T., Antonacci-Fulton, L., Howe, K., Lawson, H. A., Lucas, J. K., Phillippy, A. M., Popejoy, A. B., Asri, M., Carson, C., Chaisson, M. J. P., et al. (2022) · Nature · doi:10.1038/s41586-022-04601-8 · Cited by 494 · see citing works
Self-citationZhao, X., Collins, R. L., Lee, W.-P., Weber, A. M., Jun, Y., Zhu, Q., Weisburd, B., Huang, Y., Audano, P. A., Wang, H., et al. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.03.014 · Cited by 132 · see citing works
Comprehensive genome analysis and variant detection at scale using DRAGEN
Behera, S., Catreux, S., Rossi, M., Truong, S., Huang, Z., Ruehle, M., Visvanath, A., Parnaby, G., Roddey, C., Onuchic, V., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-024-02382-1 · Cited by 137 · see citing works
Zhou, Y., Yang, L., Han, X., Han, J., Hu, Y., Li, F., Xia, H., Peng, L., Boschiero, C., Rosen, B. D., et al. (2022) · Genome Research · doi:10.1101/gr.276550.122 · Cited by 89 · see citing works
Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus
Hickey, G., Monlong, J., Ebler, J., Novak, A., Eizenga, J. M., Gao, Y., Human Pangenome Reference Consortium, Marschall, T., Li, H., & Paten, B. (2022) · doi:10.1101/2022.10.06.511217 · Cited by 345 · see citing works
Structural variation across 138,134 samples in the TOPMed consortium
Jun, G., English, A., Metcalf, G., Yang, J., Chaisson, M., Pankratz, N., Menon, V., Salerno, W., Krasheninina, O., Smith, A., et al. (2023) · doi:10.21203/rs.3.rs-2515453/v1 · Cited by 24 · see citing works
Self-citation
- Authors
- Genomics, N. C. F. C. D., Abel, H. J., Larson, D. E., Regier, A. A., Chiang, C., Das, I., Kanchi, K. L., Layer, R. M., Neale, B. M., Salerno, W. J., Reeves, C., Buyske, S., Matise, T. C., Muzny, D. M., Zody, M. C., Lander, E. S., Dutcher, S. K., Stitziel, N. O., & Hall, I. M.
- Affiliations
- Washington University in St. Louis (US)
- University of Colorado Boulder (US)
- Broad Institute (US)
- Baylor College of Medicine (US)
- New York Genome Center (US)
- Rutgers, The State University of New Jersey (US)
- Corresponding author
- Hall, Ira M.
- ORCID
- Venue
- Nature
- Published
- 2020-05-27
- Volume
- 583
- Issue
- 7814
- Pages
- 83-89
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC7547914
- OpenAlex
- W3030556878
- Semantic Scholar
- f46ad342edc514c836f2831c96b4df3c7bcb5414
- Cited by
- 310
- References
- 78
- Citations by year
- 2026: 27 · 2025: 36 · 2024: 59 · 2023: 52 · 2022: 62 · 2021: 53 · 2020: 13 · 2019: 6 · 2017: 1
- FWCI
- 26.64
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Rutgers University Community Repository (Rutgers University) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Työväentutkimus Vuosikirja (submittedVersion, other-oa)
- Funders
- National Institutes of Health (n01hc65235-13-0-1, n01hc65234-5-0-0, n01hc65237-14-0-1, HHSN268201100004C, n01hc65236-16-0-1, n01hc65233-9-0-0, HHSN268201100001C, HHSN268201100002C, HHSN268201100003C, UL1TR001872)
- National Institute on Aging (HHSN-271-2011-00004C,, R01AG041797, P50AG008702, U24AG026395, U24AG056270, U24AG021886)
- National Heart, Lung, and Blood Institute (N01 HC065235, HHSN2682011-00001I, HHSN2682011-00002I, R01HL135156, N01 HC065237, N01 HC065234, R01HL117004, HHSN268201700001I, HHSN2682011‐00004I, HHSN268201700005C, R01HL113315, HHSN268201700003I, N01 HC065236, HHSN268201100046C, R01HL128439, HHSN268201700005I, HHSN268201700001C, N01 HC065233, HHSN2682011-00003I, HHSN268201700002I, HHSN268201700003C, HHSN268201700002C)
- National Human Genome Research Institute (UM1HG008895, UM1HG008898, U54HG003079, UM1HG008901, U01HG007416, U01HG007417, U01HG007397, U01HG007419, UM1HG008853, U01HG007376, U24HG008956)
- National Cancer Institute (R37CA054281, U01CA098758, P01CA033619, U01CA136792)
- National Institute of General Medical Sciences (R01GM059290, RL5GM118984, R35GM118335)
- National Institute of Diabetes and Digestive and Kidney Diseases (P01DK046763, P30DK020572, U01DK062413, U01DK062431, P30DK052574)
- National Institute of Environmental Health Sciences (R01ES015794, R21ES024844)
- National Center for Advancing Translational Sciences
- National Institute on Minority Health and Health Disparities (P60MD006902, R01MD010443)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- structural variants, human genome, ultra-rare variants, complex rearrangements, gene dosage, site frequency spectrum, deleterious alleles, loss-of-function alleles
- MeSH terms
- Whole Genome Sequencing, Alleles, Female, Genetics, Population, Humans, Male, Software, Genetic Variation, Genome, Human, Case-Control Studies, Gene Dosage, Quantitative Trait Loci, Epigenesis, Genetic, Racial Groups, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing
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