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Genome structural variation discovery and genotyping
Open accessAbstract
Comparisons of human genomes show that more base pairs are altered as a result of structural variation - including copy number variation - than as a result of point mutations. Here we review advances and challenges in the discovery and genotyping of structural variation. The recent application of massively parallel sequencing methods has complemented microarray-based methods and has led to an exponential increase in the discovery of smaller structural-variation events. Some global discovery biases remain, but the integration of experimental and computational approaches is proving fruitful for accurate characterization of the copy, content and structure of variable regions. We argue that the long-term goal should be routine, cost-effective and high quality de novo assembly of human genomes to comprehensively assess all classes of structural variation.
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“Determination of the length, weight and relative GC content of genome is subjected to the accuracy of the genome assembly and to the variability existing among individuals [41].”
From On the length, weight and GC content of the human genome (2019) · cites this paper as [41]
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“However, the human genetic diversity ranges from the single-nucleotide variation to large chromosomal events [41, 42].”
From On the length, weight and GC content of the human genome (2019) · cites this paper as [41]
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“Current genotyping platforms and CNV discovery algorithms enable the genotyping of ~1000 common copy number polymorphisms (CNPs) and the discovery of additional “novel” CNVs, including mutations that are rare or unique to an individual (Alkan et al., 2011).”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as Alkan et al., 2011
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Cites
Velvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,587
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877
Global variation in copy number in the human genome
Redon, R., Ishikawa, S., Fitch, K. R., Feuk, L., Perry, G. H., Andrews, T. D., Fiegler, H., Shapero, M. H., Carson, A. R., Chen, W., et al. (2006) · Nature · doi:10.1038/nature05329 · Cited by 4,377
Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
ABySS: A parallel assembler for short read sequence dataPreprint
Simpson, J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones, S. J. M., & Birol, İ. (2009) · Genome Research · doi:10.1101/gr.089532.108 · Cited by 3,658
De novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926
Detection of large-scale variation in the human genome
Iafrate, A. J., Feuk, L., Rivera, M. N., Listewnik, M. L., Donahoe, P. K., Qi, Y., Scherer, S. W., & Lee, C. (2004) · Nature Genetics · doi:10.1038/ng1416 · Cited by 2,892
Miller, D. T., Adam, M. P., Aradhya, S., Biesecker, L. G., Brothman, A. R., Carter, N. P., Church, D. M., Crolla, J. A., Eichler, E. E., Epstein, C. J., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.04.006 · Cited by 2,882
Self-citationStrong 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
Schouten, J. P. (2002) · Nucleic Acids Research · doi:10.1093/nar/gnf056 · Cited by 2,705
Cited by
Sorted by citations
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Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery
Stothard, P., Choi, J.-W., Basu, U., Thomson, J. M., Meng, Y., Liao, X., & Moore, S. S. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-559 · Cited by 184
Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits
Chakraborty, M., Emerson, J. J., Macdonald, S. J., & Long, A. D. (2019) · Nature Communications · doi:10.1038/s41467-019-12884-1 · Cited by 186
Structural variants in 3000 rice genomesPreprint
Fuentes, R. R., Chebotarov, D., Duitama, J., Smith, S., Hoz, J. D. L., Mohiyuddin, M., Wing, R. A., McNally, K. L., Tatarinova, T. V., Grigoriev, A., et al. (2019) · Genome Research · doi:10.1101/gr.241240.118 · Cited by 178
Best practices for evaluating single nucleotide variant calling methods for microbial genomics
Olson, N. D., Lund, S. P., Colman, R. E., Foster, J. T., Sahl, J. W., Schupp, J. M., Keim, P., Morrow, J. B., Salit, M., & Zook, J. M. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00235 · Cited by 177
Bioinformatics for Clinical Next Generation Sequencing
Oliver, G. R., Hart, S. N., & Klee, E. W. (2014) · Clinical Chemistry · doi:10.1373/clinchem.2014.224360 · Cited by 188
Genomic structural variation-mediated allelic suppression causes hybrid male sterility in rice
Shen, R., Wang, L., Liu, X., Wu, J., Jin, W., Zhao, X., Xie, X., Zhu, Q., Tang, H., Li, Q., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01400-y · Cited by 174
A decade of structural variants: description, history and methods to detect structural variation
Escaramís, G., Docampo, E., & Rabionet, R. (2015) · Briefings in Functional Genomics · doi:10.1093/bfgp/elv014 · Cited by 184
Evolution of genetic and genomic features unique to the human lineage
O'Bleness, M., Searles, V. B., Varki, A., Gagneux, P., & Sikela, J. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3336 · Cited by 168
Current status of structural variation studies in plants
Yuan, Y., Bayer, P. E., Batley, J., & Edwards, D. (2021) · Plant Biotechnology Journal · doi:10.1111/pbi.13646 · Cited by 163
Using ERDS to Infer Copy-Number Variants in High-Coverage Genomes
Zhu, M., Need, A. C., Han, Y., Ge, D., Maia, J. M., Zhu, Q., Heinzen, E. L., Cirulli, E. T., Pelak, K., He, M., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.07.004 · Cited by 168
High-quality genome (re)assembly using chromosomal contact data
Marie-Nelly, H., Marbouty, M., Cournac, A., Flot, J., Liti, G., Poggi-Parodi, D., Syan, S., Guillén, N., Margeot, A., Zimmer, C., et al. (2014) · Nature Communications · doi:10.1038/ncomms6695 · Cited by 174
Jasmine and Iris: population-scale structural variant comparison and analysis
Kirsche, M., Prabhu, G., Sherman, R. M., Ni, B., Battle, A. J., Aganezov, S. S., & Schatz, M. C. (2023) · Nature Methods · doi:10.1038/s41592-022-01753-3 · Cited by 167
Connecting genome structural variation with complex traits in crop plants
Gabur, I., Chawla, H. S., Snowdon, R. J., & Parkin, I. A. P. (2018) · Theoretical and Applied Genetics · doi:10.1007/s00122-018-3233-0 · Cited by 170
Plant pan-genomics and its applications
Shi, J., Tian, Z., Lai, J., & Huang, X. (2022) · Molecular Plant · doi:10.1016/j.molp.2022.12.009 · Cited by 164
Cao, H., Hastie, A., Cao, D., Lam, E. T., Sun, Y., Huang, H., Lin, L., Lin, L., Andrews, W., Chan, S., et al. (2014) · GigaScience · doi:10.1186/2047-217x-3-34 · Cited by 156
Kotini, A. G., Chang, C.-J., Boussaad, I., Delrow, J. J., Dolezal, E. K., Nagulapally, A. B., Perna, F., Fishbein, G. A., Klimek, V. M., Hawkins, R. D., et al. (2015) · Nature Biotechnology · doi:10.1038/nbt.3178 · Cited by 171
Molecular tools and analytical approaches for the characterization of farm animal genetic diversity
Lenstra, J. A., Groeneveld, L. F., Eding, H., Kantanen, J., Williams, J. L., Taberlet, P., Nicolazzi, E. L., Sölkner, J., Simianer, H., Ciani, E., et al. (2012) · Animal Genetics · doi:10.1111/j.1365-2052.2011.02309.x · Cited by 164
NGS technologies for analyzing germplasm diversity in genebanks*
Kilian, B., & Graner, A. (2012) · Briefings in Functional Genomics · doi:10.1093/bfgp/elr046 · Cited by 159
Zhang, Z., Mao, L., Chen, H., Bu, F., Li, G., Sun, J., Li, S., Sun, H., Jiao, C., Blakely, R., et al. (2015) · The Plant Cell · doi:10.1105/tpc.114.135848 · Cited by 160
Single-copy gene based 50 K SNP chip for genetic studies and molecular breeding in rice
Singh, N., Jayaswal, P. K., Panda, K., Mandal, P., Kumar, V., Singh, B., Mishra, S., Singh, Y., Singh, R., Rai, V., et al. (2015) · Scientific Reports · doi:10.1038/srep11600 · Cited by 157
Genome-wide analysis of the WRKY gene family in cotton
Dou, L., Zhang, X., Pang, C., Song, M., Wei, H., Fan, S., & Yu, S. (2014) · Molecular Genetics and Genomics · doi:10.1007/s00438-014-0872-y · Cited by 156
Copy number variation in the genomes of domestic animals
Clop, A., Vidal, O., & Amills, M. (2012) · Animal Genetics · doi:10.1111/j.1365-2052.2012.02317.x · Cited by 152
Genetic counselling and ethical issues with chromosome microarray analysis in prenatal testing
McGillivray, G., Rosenfeld, J. A., Gardner, R. J. M., & Gillam, L. H. (2012) · Prenatal Diagnosis · doi:10.1002/pd.3849 · Cited by 151
Major review: Molecular genetics of primary open-angle glaucoma
Liu, Y., & Allingham, R. R. (2017) · Experimental Eye Research · doi:10.1016/j.exer.2017.05.002 · Cited by 156
An integrated peach genome structural variation map uncovers genes associated with fruit traits
Guo, J., Cao, K., Deng, C. H., Li, Y., Zhu, G., Fang, W., Chen, C. W., Wang, X., Wu, J., Guan, L., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02169-y · Cited by 147
Somatic Mosaicism in the Human Genome
Freed, D. N., Stevens, E. L., & Pevsner, J. (2014) · Genes · doi:10.3390/genes5041064 · Cited by 156
SCALCE: boosting sequence compression algorithms using locally consistent encoding
Hach, F., Numanagić, I., Alkan, C., & Şahinalp, S. C. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts593 · Cited by 151
Self-citationGenes, economics, and happiness.
De Neve, J.-E., Christakis, N. A., Fowler, J. H., & Frey, B. S. (2012) · Journal of Neuroscience, Psychology, and Economics · doi:10.1037/a0030292 · Cited by 148
Plant pangenomes for crop improvement, biodiversity and evolution
Schreiber, M., Jayakodi, M., Stein, N., & Mascher, M. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00691-4 · Cited by 163
Accelerating read mapping with FastHASH
Xin, H., Lee, D., Hormozdiari, F., Yedkar, S., Mutlu, O., & Alkan, C. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-s1-s13 · Cited by 148
Self-citationDuitama, J., Quintero, J. C., Cruz, D. F., Quintero, C., Hubmann, G., Foulquié-Moreno, M. R., Verstrepen, K. J., Thevelein, J. M., & Tohme, J. M. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1381 · Cited by 146
Inferring synteny between genome assemblies: a systematic evaluation
Liu, D., Hunt, M., & Tsai, I. J. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2026-4 · Cited by 147
Candidate Genes and Political Behavior
Charney, E., & ENGLISH, W. (2012) · American Political Science Review · doi:10.1017/s0003055411000554 · Cited by 148
Changing local recombination patterns in Arabidopsis by CRISPR/Cas mediated chromosome engineering
Schmidt, C., Fransz, P. F., Rönspies, M., Dreißig, S., Fuchs, J., Heckmann, S., Houben, A., & Puchta, H. (2020) · Nature Communications · doi:10.1038/s41467-020-18277-z · Cited by 143
Paudel, Y., Madsen, O., Megens, H., Frantz, L., Bosse, M., Bastiaansen, J. W. M., Crooijmans, R. P. M. A., & Groenen, M. A. M. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-449 · Cited by 147
Computational Pan-Genomics: Status, Promises and ChallengesPreprint
Marschall, T., Marz, M., Abeel, T., Dijkstra, L., Dutilh, B. E., Ghaffaari, A., Kersey, P. J., Kloosterman, W. P., Mäkinen, V., Novak, A. M., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/043430 · Cited by 147
Self-citationThe challenges and importance of structural variation detection in livestock
Bickhart, D. M., & Liu, G. E. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00037 · Cited by 150
Ribosomal protein gene deletions in Diamond-Blackfan anemia
Farrar, J. E., Vlachos, A., Atsidaftos, E., Carlson-Donohoe, H., Markello, T. C., Arceci, R. J., Ellis, S. R., Lipton, J. M. M., & Bodine, D. M. (2011) · Blood · doi:10.1182/blood-2011-08-375170 · Cited by 148
Transposable element detection from whole genome sequence data
Ewing, A. D. (2015) · Mobile DNA · doi:10.1186/s13100-015-0055-3 · Cited by 155
Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes
Poole, A. C., Goodrich, J. K., Youngblut, N. D., Luque, G. G., Ruaud, A., Sutter, J. L., Waters, J. L., Shi, Q., El-Hadidi, M. S., Johnson, L. M., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.03.001 · Cited by 143
Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines
Bush, S. J., Foster, D., Eyre, D. W., Clark, E. L., Maio, N. D., Shaw, L. P., Stoesser, N. E., Peto, T., Crook, D. W., & Walker, A. S. (2020) · GigaScience · doi:10.1093/gigascience/giaa007 · Cited by 140
Genetics of Congenital Anomalies of the Kidney and Urinary Tract: The Current State of Play
Capone, V. P., Morello, W., Taroni, F., & Montini, G. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18040796 · Cited by 148
Hidden genetic variation shapes the structure of functional elements in Drosophila
Chakraborty, M., VanKuren, N. W., Zhao, R., Zhang, X., Kalsow, S., & Emerson, J. J. (2017) · Nature Genetics · doi:10.1038/s41588-017-0010-y · Cited by 138
Genomic medicine for kidney disease
Groopman, E., Rasouly, H. M., & Gharavi, A. G. (2018) · Nature Reviews Nephrology · doi:10.1038/nrneph.2017.167 · Cited by 142
Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation
Pinosio, S., Giacomello, S., Rampant, P. F., Taylor, G., Jorge, V., Paslier, M. C. L., Zaina, G., Bastien, C., Cattonaro, F., Marroni, F., et al. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw161 · Cited by 143
Discovery and population genomics of structural variation in a songbird genus
Weissensteiner, M. H., Bunikis, I., Catalán, A., Françoijs, K., Knief, U., Heim, W., Peona, V., Pophaly, S. D., Sedlazeck, F. J., Suh, A., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17195-4 · Cited by 136
Molecular genetics in glaucoma
Liu, Y., & Allingham, R. R. (2011) · Experimental Eye Research · doi:10.1016/j.exer.2011.08.007 · Cited by 136
Hommelsheim, C. M., Frantzeskakis, L., Huang, M., & Ülker, B. (2014) · Scientific Reports · doi:10.1038/srep05052 · Cited by 121
An integrative probabilistic model for identification of structural variation in sequencing data
Sindi, S., Önal, S., Peng, L., Wu, H.-T., & Raphael, B. J. (2012) · Genome biology · doi:10.1186/gb-2012-13-3-r22 · Cited by 139
Li, Y., Zheng, H., Luo, R., Wu, H., Zhu, H., Li, R., Cao, H., Wu, B., Huang, S., Shao, H., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1904 · Cited by 133
TEMP: a computational method for analyzing transposable element polymorphism in populations
Zhuang, J., Wang, J., Theurkauf, W. E., & Weng, Z. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku323 · Cited by 130
svclassify: a method to establish benchmark structural variant calls
Parikh, H. M., Mohiyuddin, M., Lam, H. Y. K., Iyer, H. K., Chen, D., Pratt, M., Bartha, G. T., Spies, N., Losert, W., Zook, J. M., et al. (2016) · BMC Genomics · doi:10.1186/s12864-016-2366-2 · Cited by 130
Eisfeldt, J., Vezzi, F., Olason, P. I., Nilsson, D., & Lindstrand, A. (2017) · F1000Research · doi:10.12688/f1000research.11168.1 · Cited by 130
Genomic landscape and evolution of metastatic chromophobe renal cell carcinoma
Casuscelli, J., Weinhold, N., Gundem, G., Wang, L., Zabor, E. C., Drill, E. N., Wang, P. I., Nanjangud, G. J., Redzematovic, A., Nargund, A. M., et al. (2017) · JCI Insight · doi:10.1172/jci.insight.92688 · Cited by 131
Tham, C. Y., Tirado-Magallanes, R., Goh, Y., Fullwood, M. J., Koh, B. T. H., Wang, W., Ng, C. H., Chng, W. J., Thiéry, A. H., Tenen, D. G., et al. (2020) · Genome biology · doi:10.1186/s13059-020-01968-7 · Cited by 129
Structural variation and genome complexity: is dispensable really dispensable?
Marroni, F., Pinosio, S., & Morgante, M. (2014) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2014.01.003 · Cited by 134
Clinical interpretation of copy number variants in the human genome
Nowakowska, B. (2017) · Journal of Applied Genetics · doi:10.1007/s13353-017-0407-4 · Cited by 141
Characteristics of de novo structural changes in the human genomePreprint
Kloosterman, W. P., Francioli, L. C., Hormozdiari, F., Marschall, T., Hehir‐Kwa, J. Y., Abdellaoui, A., Lameijer, E.-W., Moed, M. H., Koval, V., Renkens, I., et al. (2015) · Genome Research · doi:10.1101/gr.185041.114 · Cited by 127
Self-citationClinical Validation of Copy Number Variant Detection from Targeted Next-Generation Sequencing Panels
Kerkhof, J., Schenkel, L. C., Reilly, J., McRobbie, S., Aref‐Eshghi, E., Stuart, A., Rupar, C. A., Adams, P. C., Hegele, R. A., Lin, H., et al. (2017) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2017.07.004 · Cited by 130
Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes
Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., Rafajlović, M., Panova, M., Ravinet, M., Johannesson, K., et al. (2018) · Molecular Ecology · doi:10.1111/mec.14972 · Cited by 122
New insights into the performance of human whole-exome capture platforms
Meienberg, J., Žerjavic, K., Keller, I., Okoniewski, M. J., Patrignani, A., Ludin, K., Xu, Z., Steinmann, B. U., Carrel, T. P., Röthlisberger, B., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv216 · Cited by 126
The genetic basis of music ability
Tan, Y. T., McPherson, G. E., Peretz, I., Berkovic, S. F., & Wilson, S. J. (2014) · Frontiers in Psychology · doi:10.3389/fpsyg.2014.00658 · Cited by 133
Sanders, A. D., Falconer, E., Hills, M., Spierings, D. C. J., & Lansdorp, P. M. (2017) · Nature Protocols · doi:10.1038/nprot.2017.029 · Cited by 129
The genetic variability and commonality of neurodevelopmental disease
Coe, B. P., Girirajan, S., & Eichler, E. E. (2012) · American Journal of Medical Genetics Part C Seminars in Medical Genetics · doi:10.1002/ajmg.c.31327 · Cited by 132
Self-citationPrecision Editing of Large Animal Genomes
Tan, W. S., Carlson, D. F., Walton, M., Fahrenkrug, S. C., & Hackett, P. B. (2012) · Advances in genetics · doi:10.1016/b978-0-12-404742-6.00002-8 · Cited by 125
The Need for a Human Pangenome Reference Sequence
Miga, K. H., & Wang, T. (2021) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120120-081921 · Cited by 137
Computational analysis of cancer genome sequencing data
Cortés‐Ciriano, I., Gulhan, D., Lee, J. J.-K., Melloni, G. E. M., & Park, P. J. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00431-y · Cited by 118
Structural variation in 1,019 diverse humans based on long-read sequencing
Schloissnig, S., Pani, S., Ebler, J., Hain, C., Tsapalou, V., Söylev, A., Hüther, P., Ashraf, H., Prodanov, T., Asparuhova, M., et al. (2025) · Nature · doi:10.1038/s41586-025-09290-7 · Cited by 141
Wang, Q., Xia, J., Jia, P., Pao, W. J., & Zhao, Z. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbs044 · Cited by 120
novoBreak: local assembly for breakpoint detection in cancer genomes
Chong, Z., Ruan, J., Gao, M., Zhou, W., Chen, T., Fan, X., Ding, L., Lee, A. Y., Boutros, P. C., Chen, J., et al. (2016) · Nature Methods · doi:10.1038/nmeth.4084 · Cited by 117
Gardner and Sutherland's Chromosome Abnormalities and Genetic Counseling
Gardner, R. J. M., & Amor, D. J. (2018) · doi:10.1093/med/9780199329007.001.0001 · Cited by 122
Cali, D. S., Kalsi, G. S., Bingöl, Z., Fırtına, C., Subramanian, L., Kim, J. S., Ausavarungnirun, R., Alser, M., Gómez-Luna, J., Boroumand, A., et al. (2020) · IEEE/ACM International Symposium on Microarchitecture (MICRO) · doi:10.1109/micro50266.2020.00081 · Cited by 25
Self-citationBeyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy
Levy‐Sakin, M., & Ebenstein, Y. (2013) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2013.01.009 · Cited by 118
Poot, M., & Haaf, T. (2015) · Molecular Syndromology · doi:10.1159/000438812 · Cited by 116
Cooper, E., Brenton, Z. W., Flinn, B. S., Jenkins, J. W., Shu, S., Flowers, D., Luo, F., Wang, Y., Xia, P., Barry, K., et al. (2019) · BMC Genomics · doi:10.1186/s12864-019-5734-x · Cited by 114
Somatic Mutagenesis in Mammals and Its Implications for Human Disease and Aging
Zhang, L., & Vijg, J. (2018) · Annual Review of Genetics · doi:10.1146/annurev-genet-120417-031501 · Cited by 108
Human genetics and genomics a decade after the release of the draft sequence of the human genome
Naidoo, N., Yudi Pawitan, Y., Soong, R., Cooper, D. N., & Ku, C. (2011) · Human Genomics · doi:10.1186/1479-7364-5-6-577 · Cited by 117
Picky comprehensively detects high-resolution structural variants in nanopore long reads
Gong, L., Wong, C., Cheng, W., Tjong, H., Menghi, F., Ngan, C. Y., Liu, E. T., & Wei, C. (2018) · Nature Methods · doi:10.1038/s41592-018-0002-6 · Cited by 114
The structural variation landscape in 492 Atlantic salmon genomes
Bertolotti, A. C., Layer, R. M., Gundappa, M. K., Gallagher, M. D., Pehlivanoglu, E., Nome, T., Robledo, D., Kent, M., Røsæg, L. L., Holen, M. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18972-x · Cited by 112
High mutational rates of large-scale duplication and deletion in Daphnia pulexPreprint
Keith, N., Tucker, A. E., Jackson, C. E., Sung, W., Lucas‐Lledó, J. I., Schrider, D. R., Schaack, S., Dudycha, J. L., Ackerman, M. S., Younge, A., et al. (2015) · Genome Research · doi:10.1101/gr.191338.115 · Cited by 113
Hochstenbach, R., Buizer‐Voskamp, J. E., Vorstman, J. A. S., & Ophoff, R. A. (2011) · Cytogenetic and Genome Research · doi:10.1159/000332928 · Cited by 114
Centromere evolution and CpG methylation during vertebrate speciation
Ichikawa, K., Tomioka, S., Suzuki, Y., Nakamura, R., Doi, K., Yoshimura, J., Kumagai, M., Inoue, Y., Uchida, Y., Irie, N., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01982-7 · Cited by 105
Gabrielaitė, M., Torp, M. H., Rasmussen, M. S., Andreu‐Sánchez, S., Vieira, F. G., Pedersen, C. B., Kinalis, S., Madsen, M. B., Kodama, M., Demircan, G. S., et al. (2021) · Cancers · doi:10.3390/cancers13246283 · Cited by 113
Exome sequencing and whole genome sequencing for the detection of copy number variation
Hehir‐Kwa, J. Y., Pfundt, R., & Veltman, J. A. (2015) · Expert Review of Molecular Diagnostics · doi:10.1586/14737159.2015.1053467 · Cited by 117
CLEVER: clique-enumerating variant finder
Marschall, T., Costa, I. G., Canzar, S., Bauer, M. J., Klau, G. W., Schliep, A., & Schönhuth, A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts566 · Cited by 110
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Kou, Y., Liao, Y., Toivainen, T., Lv, Y., Tian, X., Emerson, J. J., Gaut, B. S., & Zhou, Y. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa185 · Cited by 105
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Quinlan, A. R., & Hall, I. M. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.10.002 · Cited by 108
PolyTB: A genomic variation map for Mycobacterium tuberculosis
Coll, F., Preston, M. D., Guerra‐Assunção, J. A., Hill-Cawthorne, G. A., Harris, D. E., Perdigão, J., Viveiros, M., Portugal, I., Drobniewski, F. A., Gagneux, S., et al. (2014) · Tuberculosis · doi:10.1016/j.tube.2014.02.005 · Cited by 109
InDel marker detection by integration of multiple softwares using machine learning techniques
Yang, J., Shi, X., Hu, L., Luo, D., Peng, J. Y., Xiong, S., Kong, F., Liu, B., & Yuan, X. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1312-2 · Cited by 106
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Coster, W. D., & Broeckhoven, C. V. (2019) · Trends in biotechnology · doi:10.1016/j.tibtech.2019.02.003 · Cited by 107
Bruno, D. L., White, S. M., Ganesamoorthy, D., Burgess, T., Butler, K., Corrie, S., Francis, D. I., Hills, L., Prabhakara, K., Ngo, C., et al. (2011) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2011-100372 · Cited by 103
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Lin, J., Wang, S., Audano, P. A., Meng, D., Flores, J. I., Kosters, W. A., Yang, X., Jia, P., Marschall, T., Beck, C. R., et al. (2022) · Nature Methods · doi:10.1038/s41592-022-01609-w · Cited by 103
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Boussaha, M., Esquerré, D., Barbieri, J., Djari, A., Pinton, A., Letaïef, R., Salin, G., Escudié, F., Roulet, A., Fritz, S., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0135931 · Cited by 106
Manel, S., Perrier, C., Pratlong, M., Abi‐Rached, L., Paganini, J., Pontarotti, P., & Aurelle, D. (2015) · Molecular Ecology · doi:10.1111/mec.13468 · Cited by 110
Gong, Y., Li, Y., Liu, X., Ma, Y., & Jiang, L. (2023) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-023-00860-1 · Cited by 112
Bryant, J., Chewapreecha, C., & Bentley, S. D. (2012) · Future Microbiology · doi:10.2217/fmb.12.108 · Cited by 98
Integrated view of genome structure and sequence of a single DNA molecule in a nanofluidic device
Marie, R., Pedersen, J. N., Bauer, D. L. V., Rasmussen, K. H., Yusuf, M., Volpi, E. V., Flyvbjerg, H., Kristensen, A., & Mir, K. U. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1214570110 · Cited by 100
Jiang, L., Jiang, J., Yang, J., Liu, X., Wang, J., Wang, H., Ding, X., Liu, J., & Zhang, Q. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-131 · Cited by 102
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Mitsuhashi, S., & Matsumoto, N. (2019) · Journal of Human Genetics · doi:10.1038/s10038-019-0671-8 · Cited by 105
Yang, H., Garcia‐Manero, G., Sasaki, K., Bravo, G. M., Tang, Z., Wei, Y., Kadia, T. M., Chien, K. S., Rush, D. M., Ha, N. H., et al. (2022) · Leukemia · doi:10.1038/s41375-022-01652-8 · Cited by 103
Metadata
- Authors
- Alkan, C., Coe, B. P., & Eichler, E. E.
- Affiliations
- University of Washington (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Eichler, Evan E.
- Venue
- Nature Reviews Genetics
- Published
- 2011-03-01
- Volume
- 12
- Issue
- 5
- Pages
- 363-376
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- PMC
- PMC4108431
- OpenAlex
- W2083870688
- Cited by
- 1,630
- References
- 121
- Citations by year
- 2026: 67 · 2025: 129 · 2024: 100 · 2023: 81 · 2022: 94 · 2021: 104 · 2020: 148 · 2019: 122 · 2018: 132 · 2017: 102 · 2016: 93 · 2015: 108 · 2014: 107 · 2013: 108 · 2012: 89
- FWCI
- 11.82
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Genetics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- Wellcome Trust
- Canadian Institutes of Health Research
- National Human Genome Research Institute (P01HG004120)
- 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 › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- structural variants, copy number variation, structural variant genotyping, structural variant calling, next-generation sequencing, de novo genome assembly, human genome, complex traits
- MeSH terms
- Genotype, Humans, Genetic Variation, Genome, Human, Sequence Analysis, DNA, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, DNA Copy Number Variations, High-Throughput Nucleotide Sequencing
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