{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T20:27:13Z","timestamp":1770755233559,"version":"3.50.0"},"reference-count":77,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,10,16]],"date-time":"2022-10-16T00:00:00Z","timestamp":1665878400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Basic Science Center Program","award":["32288101"],"award-info":[{"award-number":["32288101"]}]},{"name":"Strategic Priority Research Program"},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32030020"],"award-info":[{"award-number":["32030020"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31961130380"],"award-info":[{"award-number":["31961130380"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UK Royal Society-Newton Advanced Fellowship","award":["NAF\\R1\\191094"],"award-info":[{"award-number":["NAF\\R1\\191094"]}]},{"name":"Shanghai Municipal Science and Technology","award":["2017SHZDZX01"],"award-info":[{"award-number":["2017SHZDZX01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Structural variations (SVs) play important roles in human evolution and diseases, but there is a lack of data resources concerning representative samples, especially for East Asians. Taking advantage of both next-generation sequencing and third-generation sequencing data at the whole-genome level, we developed the database PGG.SV to provide a practical platform for both regionally and globally representative structural variants. In its current version, PGG.SV archives 584 277 SVs obtained from whole-genome sequencing data of 6048 samples, including 1030 long-read sequencing genomes representing 177 global populations. PGG.SV provides (i) high-quality SVs with fine-scale and precise genomic locations in both GRCh37 and GRCh38, covering underrepresented SVs in existing sequencing and microarray data; (ii) hierarchical estimation of SV prevalence in geographical populations; (iii) informative annotations of SV-related genes, potential functions and clinical effects; (iv) an analysis platform to facilitate SV-based case-control association studies and (v) various visualization tools for understanding the SV structures in the human genome. Taken together, PGG.SV provides a user-friendly online interface, easy-to-use analysis tools and a detailed presentation of results. PGG.SV is freely accessible via https:\/\/www.biosino.org\/pggsv.<\/jats:p>","DOI":"10.1093\/nar\/gkac905","type":"journal-article","created":{"date-parts":[[2022,10,16]],"date-time":"2022-10-16T10:07:26Z","timestamp":1665914846000},"page":"D1109-D1116","source":"Crossref","is-referenced-by-count":10,"title":["PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform"],"prefix":"10.1093","volume":"51","author":[{"given":"Yimin","family":"Wang","sequence":"first","affiliation":[{"name":"Key Laboratory of Computational Biology, National Genomics Data Center\u00a0& Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunchao","family":"Ling","sequence":"additional","affiliation":[{"name":"Key Laboratory of Computational Biology, National Genomics Data Center\u00a0& Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiao","family":"Gong","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai 200438 , China"},{"name":"Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University , Shanghai 201203 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaohan","family":"Zhao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai 200438 , China"},{"name":"Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University , Shanghai 201203 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hanwen","family":"Zhou","sequence":"additional","affiliation":[{"name":"Key Laboratory of Computational Biology, National Genomics Data Center\u00a0& Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bo","family":"Xie","sequence":"additional","affiliation":[{"name":"Key Laboratory of Computational Biology, National Genomics Data Center\u00a0& Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haiyi","family":"Lou","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai 200438 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinhao","family":"Zhuang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Computational Biology, National Genomics Data Center\u00a0& Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li","family":"Jin","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai 200438 , China"},{"name":"Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University , Shanghai 201203 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"The Han100K Initiative","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0610-9106","authenticated-orcid":false,"given":"Shaohua","family":"Fan","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai 200438 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guoqing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Computational Biology, National Genomics Data Center\u00a0& Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1975-1002","authenticated-orcid":false,"given":"Shuhua","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai 200438 , China"},{"name":"Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University , Shanghai 201203 , China"},{"name":"Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University , Shanghai 200032 , China"},{"name":"School of Life Science and Technology, ShanghaiTech University , Shanghai 201210 , China"},{"name":"Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming 650223 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,10,16]]},"reference":[{"key":"2023010804331665600_B1","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/j.cell.2020.08.006","article-title":"Distinct classes of complex structural variation uncovered across thousands of cancer genome graphs","volume":"183","author":"Hadi","year":"2020","journal-title":"Cell"},{"key":"2023010804331665600_B2","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1016\/j.cell.2018.06.039","article-title":"Genomic hallmarks and structural variation in metastatic prostate cancer","volume":"174","author":"Quigley","year":"2018","journal-title":"Cell"},{"key":"2023010804331665600_B3","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1038\/s41586-020-03078-7","article-title":"Patterns of de novo tandem repeat mutations and their role in autism","volume":"589","author":"Mitra","year":"2021","journal-title":"Nature"},{"key":"2023010804331665600_B4","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1038\/s41586-020-2579-z","article-title":"Genome-wide detection of tandem DNA repeats that are expanded in autism","volume":"586","author":"Trost","year":"2020","journal-title":"Nature"},{"key":"2023010804331665600_B5","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/s13059-017-1158-6","article-title":"Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome","volume":"18","author":"Collins","year":"2017","journal-title":"Genome Biol."},{"key":"2023010804331665600_B6","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1016\/j.ajhg.2016.06.036","article-title":"Rare inherited and de novo CNVs reveal complex contributions to ASD risk in multiplex families","volume":"99","author":"Leppa","year":"2016","journal-title":"Am. J. Hum. Genet."},{"key":"2023010804331665600_B7","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1038\/s41593-022-01031-7","article-title":"Integrating whole-genome sequencing with multi-omic data reveals the impact of structural variants on gene regulation in the human brain","volume":"25","author":"Vialle","year":"2022","journal-title":"Nat. Neurosci."},{"key":"2023010804331665600_B8","doi-asserted-by":"crossref","first-page":"5637","DOI":"10.1093\/hmg\/ddv277","article-title":"Heterozygote carriers for CNVs in PARK2 are at increased risk of Parkinson's disease","volume":"24","author":"Huttenlocher","year":"2015","journal-title":"Hum. Mol. Genet."},{"key":"2023010804331665600_B9","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1016\/j.ajhg.2020.07.004","article-title":"Evolution of a human-specific tandem repeat associated with ALS","volume":"107","author":"Course","year":"2020","journal-title":"Am. J. Hum. Genet."},{"key":"2023010804331665600_B10","doi-asserted-by":"crossref","first-page":"107","DOI":"10.15252\/emmm.201707838","article-title":"Genomic structural variations lead to dysregulation of important coding and non-coding RNA species in dilated cardiomyopathy","volume":"10","author":"Haas","year":"2018","journal-title":"EMBO Mol. Med."},{"key":"2023010804331665600_B11","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1038\/s41588-020-0646-x","article-title":"Recurrent inversion toggling and great ape genome evolution","volume":"52","author":"Porubsky","year":"2020","journal-title":"Nat. Genet."},{"key":"2023010804331665600_B12","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/s41467-019-13624-1","article-title":"Rare copy number variants in over 100,000 european ancestry subjects reveal multiple disease associations","volume":"11","author":"Li","year":"2020","journal-title":"Nat. Commun."},{"key":"2023010804331665600_B13","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1038\/s41436-020-0759-8","article-title":"Copy-number variation contributes 9% of pathogenicity in the inherited retinal degenerations","volume":"22","author":"Zampaglione","year":"2020","journal-title":"Genet. Med."},{"key":"2023010804331665600_B14","doi-asserted-by":"crossref","first-page":"eaam6393","DOI":"10.1126\/science.aam6393","article-title":"Resistance to malaria through structural variation of red blood cell invasion receptors","volume":"356","author":"Leffler","year":"2017","journal-title":"Science"},{"key":"2023010804331665600_B15","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1186\/s13059-022-02636-8","article-title":"Towards accurate and reliable resolution of structural variants for clinical diagnosis","volume":"23","author":"Liu","year":"2022","journal-title":"Genome Biol."},{"key":"2023010804331665600_B16","doi-asserted-by":"crossref","first-page":"2990","DOI":"10.1038\/s41467-020-16736-1","article-title":"Functional annotation of rare structural variation in the human brain","volume":"11","author":"Han","year":"2020","journal-title":"Nat. Commun."},{"key":"2023010804331665600_B17","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/s13073-019-0692-0","article-title":"Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants","volume":"11","author":"Middelkamp","year":"2019","journal-title":"Genome Med."},{"key":"2023010804331665600_B18","doi-asserted-by":"crossref","first-page":"eaax2083","DOI":"10.1126\/science.aax2083","article-title":"Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes","volume":"366","author":"Hsieh","year":"2019","journal-title":"Science"},{"key":"2023010804331665600_B19","doi-asserted-by":"crossref","first-page":"aab3761","DOI":"10.1126\/science.aab3761","article-title":"Global diversity, population stratification, and selection of human copy-number variation","volume":"349","author":"Sudmant","year":"2015","journal-title":"Science"},{"key":"2023010804331665600_B20","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1016\/j.ajhg.2021.03.008","article-title":"Association of structural variation with cardiometabolic traits in finns","volume":"108","author":"Chen","year":"2021","journal-title":"Am. J. Hum. Genet."},{"key":"2023010804331665600_B21","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1038\/nature18964","article-title":"The simons genome diversity project: 300 genomes from 142 diverse populations","volume":"538","author":"Mallick","year":"2016","journal-title":"Nature"},{"key":"2023010804331665600_B22","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1016\/j.cell.2020.05.024","article-title":"Population structure, stratification, and introgression of human structural variation","volume":"182","author":"Almarri","year":"2020","journal-title":"Cell"},{"key":"2023010804331665600_B23","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nature15394","article-title":"An integrated map of structural variation in 2,504 human genomes","volume":"526","author":"Sudmant","year":"2015","journal-title":"Nature"},{"key":"2023010804331665600_B24","doi-asserted-by":"crossref","first-page":"D936","DOI":"10.1093\/nar\/gks1213","article-title":"DbVar and DGVa: public archives for genomic structural variation","volume":"41","author":"Lappalainen","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023010804331665600_B25","doi-asserted-by":"crossref","first-page":"D986","DOI":"10.1093\/nar\/gkt958","article-title":"The database of genomic variants: a curated collection of structural variation in the human genome","volume":"42","author":"MacDonald","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023010804331665600_B26","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1038\/s41586-020-2287-8","article-title":"A structural variation reference for medical and population genetics","volume":"581","author":"Collins","year":"2020","journal-title":"Nature"},{"key":"2023010804331665600_B27","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1016\/j.cell.2018.12.019","article-title":"Characterizing the major structural variant alleles of the human genome","volume":"176","author":"Audano","year":"2019","journal-title":"Cell"},{"key":"2023010804331665600_B28","doi-asserted-by":"crossref","first-page":"eabf7117","DOI":"10.1126\/science.abf7117","article-title":"Haplotype-resolved diverse human genomes and integrated analysis of structural variation","volume":"372","author":"Ebert","year":"2021","journal-title":"Science"},{"key":"2023010804331665600_B29","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1038\/s41576-020-0236-x","article-title":"Long-read human genome sequencing and its applications","volume":"21","author":"Logsdon","year":"2020","journal-title":"Nat. Rev. Genet."},{"key":"2023010804331665600_B30","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1016\/j.ajhg.2021.03.014","article-title":"Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies","volume":"108","author":"Zhao","year":"2021","journal-title":"Am. J. Hum. Genet."},{"key":"2023010804331665600_B31","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1101\/gr.214007.116","article-title":"Discovery and genotyping of structural variation from long-read haploid genome sequence data","volume":"27","author":"Huddleston","year":"2017","journal-title":"Genome Res."},{"key":"2023010804331665600_B32","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/s41576-019-0180-9","article-title":"Structural variation in the sequencing era","volume":"21","author":"Ho","year":"2020","journal-title":"Nat. Rev. Genet."},{"key":"2023010804331665600_B33","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1186\/s13059-019-1720-5","article-title":"Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing","volume":"20","author":"Kosugi","year":"2019","journal-title":"Genome Biol."},{"key":"2023010804331665600_B34","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with burrows-wheeler transform","volume":"26","author":"Li","year":"2010","journal-title":"Bioinformatics"},{"key":"2023010804331665600_B35","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"2023010804331665600_B36","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1038\/nmeth.1363","article-title":"BreakDancer: an algorithm for high-resolution mapping of genomic structural variation","volume":"6","author":"Chen","year":"2009","journal-title":"Nat. Methods"},{"key":"2023010804331665600_B37","doi-asserted-by":"crossref","first-page":"7256","DOI":"10.1038\/ncomms8256","article-title":"Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms","volume":"6","author":"Abyzov","year":"2015","journal-title":"Nat. Commun."},{"key":"2023010804331665600_B38","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1101\/gr.114876.110","article-title":"CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing","volume":"21","author":"Abyzov","year":"2011","journal-title":"Genome Res."},{"key":"2023010804331665600_B39","doi-asserted-by":"crossref","first-page":"2865","DOI":"10.1093\/bioinformatics\/btp394","article-title":"Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads","volume":"25","author":"Ye","year":"2009","journal-title":"Bioinformatics"},{"key":"2023010804331665600_B40","doi-asserted-by":"crossref","first-page":"R84","DOI":"10.1186\/gb-2014-15-6-r84","article-title":"LUMPY: a probabilistic framework for structural variant discovery","volume":"15","author":"Layer","year":"2014","journal-title":"Genome Biol."},{"key":"2023010804331665600_B41","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1093\/bioinformatics\/btv710","article-title":"Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications","volume":"32","author":"Chen","year":"2016","journal-title":"Bioinformatics"},{"key":"2023010804331665600_B42","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/nrg2958","article-title":"Genome structural variation discovery and genotyping","volume":"12","author":"Alkan","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"2023010804331665600_B43","doi-asserted-by":"crossref","first-page":"2741","DOI":"10.1093\/bioinformatics\/btv204","article-title":"MetaSV: an accurate and integrative structural-variant caller for next generation sequencing","volume":"31","author":"Mohiyuddin","year":"2015","journal-title":"Bioinformatics"},{"key":"2023010804331665600_B44","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1038\/s41592-018-0001-7","article-title":"Accurate detection of complex structural variations using single-molecule sequencing","volume":"15","author":"Sedlazeck","year":"2018","journal-title":"Nat. Methods"},{"key":"2023010804331665600_B45","doi-asserted-by":"crossref","first-page":"1784","DOI":"10.1038\/s41467-018-08148-z","article-title":"Multi-platform discovery of haplotype-resolved structural variation in human genomes","volume":"10","author":"Chaisson","year":"2019","journal-title":"Nat. Commun."},{"key":"2023010804331665600_B46","doi-asserted-by":"crossref","first-page":"abg8871","DOI":"10.1126\/science.abg8871","article-title":"Pangenomics enables genotyping of known structural variants in 5202 diverse genomes","volume":"374","author":"Sir\u00e9n","year":"2021","journal-title":"Science"},{"key":"2023010804331665600_B47","doi-asserted-by":"crossref","first-page":"e67615","DOI":"10.7554\/eLife.67615","article-title":"Local adaptation and archaic introgression shape global diversity at human structural variant loci","volume":"10","author":"Yan","year":"2021","journal-title":"Elife"},{"key":"2023010804331665600_B48","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"2023010804331665600_B49","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1186\/s13059-019-1909-7","article-title":"Paragraph: a graph-based structural variant genotyper for short-read sequence data","volume":"20","author":"Chen","year":"2019","journal-title":"Genome Biol."},{"key":"2023010804331665600_B50","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1038\/nmeth.3505","article-title":"SpeedSeq: ultra-fast personal genome analysis and interpretation","volume":"12","author":"Chiang","year":"2015","journal-title":"Nat. Methods"},{"key":"2023010804331665600_B51","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1093\/bioinformatics\/btt730","article-title":"CrossMap: a versatile tool for coordinate conversion between genome assemblies","volume":"30","author":"Zhao","year":"2014","journal-title":"Bioinformatics"},{"key":"2023010804331665600_B52","doi-asserted-by":"crossref","first-page":"692","DOI":"10.1038\/ng.3834","article-title":"The impact of structural variation on human gene expression","volume":"49","author":"Chiang","year":"2017","journal-title":"Nat. Genet."},{"key":"2023010804331665600_B53","doi-asserted-by":"crossref","first-page":"1652","DOI":"10.1038\/s41588-019-0521-9","article-title":"The impact of short tandem repeat variation on gene expression","volume":"51","author":"Fotsing","year":"2019","journal-title":"Nat. Genet."},{"key":"2023010804331665600_B54","doi-asserted-by":"crossref","first-page":"2927","DOI":"10.1038\/s41467-020-16482-4","article-title":"Properties of structural variants and short tandem repeats associated with gene expression and complex traits","volume":"11","author":"Jakubosky","year":"2020","journal-title":"Nat. Commun."},{"key":"2023010804331665600_B55","doi-asserted-by":"crossref","first-page":"1076","DOI":"10.1038\/s41588-020-0680-8","article-title":"Alteration of genome folding via contact domain boundary insertion","volume":"52","author":"Zhang","year":"2020","journal-title":"Nat. Genet."},{"key":"2023010804331665600_B56","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1126\/science.aad8411","article-title":"Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals","volume":"352","author":"Lan","year":"2016","journal-title":"Science"},{"key":"2023010804331665600_B57","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1016\/j.tree.2020.03.002","article-title":"A roadmap for understanding the evolutionary significance of structural genomic variation","volume":"35","author":"M\u00e9rot","year":"2020","journal-title":"Trends Ecol. Evol."},{"key":"2023010804331665600_B58","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.tig.2021.06.015","article-title":"Genome structural variation in human evolution","volume":"38","author":"Hollox","year":"2022","journal-title":"Trends Genet."},{"key":"2023010804331665600_B59","doi-asserted-by":"crossref","first-page":"5118","DOI":"10.1038\/s41467-021-25435-4","article-title":"Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in neanderthals and humans","volume":"12","author":"Hsieh","year":"2021","journal-title":"Nat. Commun."},{"key":"2023010804331665600_B60","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1016\/j.ajhg.2022.02.010","article-title":"The individual and global impact of copy-number variants on complex human traits","volume":"109","author":"Auwerx","year":"2022","journal-title":"Am. J. Hum. Genet."},{"key":"2023010804331665600_B61","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets","volume":"4","author":"Chang","year":"2015","journal-title":"Gigascience"},{"key":"2023010804331665600_B62","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1038\/ng.3461","article-title":"Abundant contribution of short tandem repeats to gene expression variation in humans","volume":"48","author":"Gymrek","year":"2016","journal-title":"Nat. Genet."},{"key":"2023010804331665600_B63","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1186\/s13059-019-1838-5","article-title":"PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations","volume":"20","author":"Zhang","year":"2019","journal-title":"Genome Biol."},{"key":"2023010804331665600_B64","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1038\/nrg3373","article-title":"Phenotypic impact of genomic structural variation: insights from and for human disease","volume":"14","author":"Weischenfeldt","year":"2013","journal-title":"Nat. Rev. Genet."},{"key":"2023010804331665600_B65","doi-asserted-by":"crossref","first-page":"1499","DOI":"10.1126\/science.abg8289","article-title":"Protein-coding repeat polymorphisms strongly shape diverse human phenotypes","volume":"373","author":"Mukamel","year":"2021","journal-title":"Science"},{"key":"2023010804331665600_B66","doi-asserted-by":"crossref","first-page":"2249","DOI":"10.1101\/gr.275488.121","article-title":"Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes","volume":"31","author":"Scott","year":"2021","journal-title":"Genome Res."},{"key":"2023010804331665600_B67","doi-asserted-by":"crossref","first-page":"14366","DOI":"10.1038\/ncomms14366","article-title":"Dosage sensitivity is a major determinant of human copy number variant pathogenicity","volume":"8","author":"Rice","year":"2017","journal-title":"Nat. Commun."},{"key":"2023010804331665600_B68","doi-asserted-by":"crossref","first-page":"bax028","DOI":"10.1093\/database\/bax028","article-title":"GeneHancer: genome-wide integration of enhancers and target genes in genecards","volume":"2017","author":"Fishilevich","year":"2017","journal-title":"Database (Oxford)"},{"key":"2023010804331665600_B69","doi-asserted-by":"crossref","first-page":"D235","DOI":"10.1093\/nar\/gky1025","article-title":"SEdb: a comprehensive human super-enhancer database","volume":"47","author":"Jiang","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2023010804331665600_B70","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The gene ontology consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"2023010804331665600_B71","doi-asserted-by":"crossref","first-page":"D325","DOI":"10.1093\/nar\/gkaa1113","article-title":"The gene ontology resource: enriching a GOld mine","volume":"49","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023010804331665600_B72","doi-asserted-by":"crossref","first-page":"D1005","DOI":"10.1093\/nar\/gky1120","article-title":"The NHGRI-EBI GWAS catalog of published genome-wide association studies, targeted arrays and summary statistics 2019","volume":"47","author":"Buniello","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2023010804331665600_B73","doi-asserted-by":"crossref","first-page":"2235","DOI":"10.1056\/NEJMsr1406261","article-title":"ClinGen\u2013the clinical genome resource","volume":"372","author":"Rehm","year":"2015","journal-title":"N. Engl. J. Med."},{"key":"2023010804331665600_B74","doi-asserted-by":"crossref","first-page":"1732","DOI":"10.1016\/j.gim.2022.04.017","article-title":"The gene curation coalition: a global effort to harmonize gene-disease evidence resources","volume":"24","author":"DiStefano","year":"2022","journal-title":"Genet. Med."},{"key":"2023010804331665600_B75","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023010804331665600_B76","first-page":"615","article-title":"Miropeats: graphical DNA sequence comparisons","volume":"11","author":"Parsons","year":"1995","journal-title":"Comput. Appl. Biosci."},{"key":"2023010804331665600_B77","doi-asserted-by":"crossref","first-page":"e1005944","DOI":"10.1371\/journal.pcbi.1005944","article-title":"MUMmer4: a fast and versatile genome alignment system","volume":"14","author":"Mar\u00e7ais","year":"2018","journal-title":"PLoS Comput. Biol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/D1\/D1109\/48441527\/gkac905.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/D1\/D1109\/48441527\/gkac905.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,8]],"date-time":"2023-01-08T04:37:48Z","timestamp":1673152668000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/51\/D1\/D1109\/6761741"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,16]]},"references-count":77,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2022,10,16]]},"published-print":{"date-parts":[[2023,1,6]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkac905","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,6]]},"published":{"date-parts":[[2022,10,16]]}}}