The DOI matches its Crossref record.
Recent Segmental Duplications in the Human Genome
Abstract
Primate-specific segmental duplications are considered important in human disease and evolution. The inability to distinguish between allelic and duplication sequence overlap has hampered their characterization as well as assembly and annotation of our genome. We developed a method whereby each public sequence is analyzed at the clone level for overrepresentation within a whole-genome shotgun sequence. This test has the ability to detect duplications larger than 15 kilobases irrespective of copy number, location, or high sequence similarity. We mapped 169 large regions flanked by highly similar duplications. Twenty-four of these hot spots of genomic instability have been associated with genetic disease. Our analysis indicates a highly nonrandom chromosomal and genic distribution of recent segmental duplications, with a likely role in expanding protein diversity.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cited by
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
A haplotype map of the human genome
The International HapMap Consortium (2005) · Nature · doi:10.1038/nature04226 · Cited by 5,858
Finishing the euchromatic sequence of the human genome
International Human Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03001 · Cited by 4,971
A draft sequence of the Neandertal genome
Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science · doi:10.1126/science.1188021 · Cited by 4,318
Self-citationDetection 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
International Chicken Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03154 · Cited by 2,750
Large-scale copy number polymorphism in the human genome
Sebat, J., Lakshmi, B., Troge, J., Alexander, J., Young, J., Lundin, P., Månér, S., Massa, H., Walker, M., Chi, M., et al. (2004) · Science · doi:10.1126/science.1098918 · Cited by 2,557
GMAP: A genomic mapping and alignment program for mRNA and EST sequences
Wu, T. D., & Watanabe, C. K. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti310 · Cited by 2,354
Evolution by gene duplication: An update
Zhang, J. (2003) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(03)00033-8 · Cited by 2,201
A high-coverage genome sequence from an archaic denisovan individual
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science · doi:10.1126/science.1224344 · Cited by 1,967
Self-citationThe Diploid Genome Sequence of an Individual Human
Levy, S., Sutton, G., Ng, P. C., Feuk, L., Halpern, A. L., Walenz, B. P., Axelrod, N., Huang, J., Kirkness, E. F., Denisov, G., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050254 · Cited by 1,778
Genome structural variation discovery and genotyping
Alkan, C., Coe, B. P., & Eichler, E. E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2958 · Cited by 1,630
Self-citationEvolutionary and biomedical insights from the rhesus macaque genome.
Gibbs, R. A., Rogers, J., Katze, M. G., Bumgarner, R., Weinstock, G. M., Mardis, E. R., Remington, K. A., Strausberg, R. L., Venter, J. C., Wilson, R. K., et al. (2007) · Science · doi:10.1126/science.1139247 · Cited by 1,403
Self-citationThe Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution
The Bovine Genome Sequencing and Analysis Consortium, Elsik, C. G., Tellam, R. L., Worley, K. C., Gibbs, R. A., Muzny, D. M., Weinstock, G. M., Adelson, D. L., Eichler, E. E., Elnitski, L., et al. (2009) · Science · doi:10.1126/science.1169588 · Cited by 1,287
Self-citationExome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations
O'Roak, B. J., Deriziotis, P., Lee, C., Vives, L., Schwartz, J. J., Girirajan, S., Karakoc, E., MacKenzie, A. P., Ng, S. B., Baker, C., et al. (2011) · Nature Genetics · doi:10.1038/ng.835 · Cited by 1,203
Self-citationMapping 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
Copy number variation in human health, disease, and evolution
Zhang, F., Gu, W., Hurles, M. E., & Lupski, J. R. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.9.081307.164217 · Cited by 1,207
Human genetic variation and its contribution to complex traits
Frazer, K. A., Murray, S. S., Schork, N. J., & Topol, E. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2554 · Cited by 1,073
The origin of new genes: Glimpses from the young and old
Long, M., Betrán, E., Thornton, K., & Wang, W. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1204 · Cited by 933
A copy number variation map of the human genome
Zarrei, M., MacDonald, J. R., Merico, D., & Scherer, S. W. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3871 · Cited by 921
The UCSC genome browser and associated tools
Kuhn, R. M., Haussler, D., & Kent, W. J. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs038 · Cited by 883
Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
Kent, W. J., Baertsch, R., Hinrichs, A., Miller, W., & Haussler, D. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1932072100 · Cited by 850
Direct determination of diploid genome sequences
Weisenfeld, N. I., Kumar, V., Shah, P., Church, D. M., & Jaffe, D. B. (2017) · Genome Research · doi:10.1101/gr.214874.116 · Cited by 803
Mechanisms underlying structural variant formation in genomic disorders
Carvalho, C. M. B., & Lupski, J. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2015.25 · Cited by 774
Personalized copy number and segmental duplication maps using next-generation sequencing
Alkan, C., Kidd, J. M., Marques-Bonet, T., Aksay, G., Antonacci, F., Hormozdiari, F., Kitzman, J. O., Baker, C., Malig, M., Mutlu, O., et al. (2009) · Nature Genetics · doi:10.1038/ng.437 · Cited by 748
Self-citationThe genome of melon ( Cucumis melo L.)
Garcia-Mas, J., Benjak, A., Sanseverino, W., Bourgeois, M., Mir, G., González, V. M., Hénaff, E., Câmara, F., Cozzuto, L., Lowy, E., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1205415109 · Cited by 744
Chromosome 21 and Down syndrome: from genomics to pathophysiology
Antonarakis, S. E., Lyle, R., Dermitzakis, E. T., Reymond, A., & Deutsch, S. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1448 · Cited by 703
An initial map of insertion and deletion (INDEL) variation in the human genome
Mills, R. E., Luttig, C. T., Larkins, C. E., Beauchamp, A., Tsui, C., Pittard, W. S., & Devine, S. E. (2006) · Genome Research · doi:10.1101/gr.4565806 · Cited by 673
Common deletion polymorphisms in the human genome
McCarroll, S. A., Hadnott, T. N., Perry, G. H., Sabeti, P. C., Zody, M. C., Barrett, J. C., Dallaire, S., Gabriel, S. B., Lee, C., Daly, M. J., et al. (2006) · Nature Genetics · doi:10.1038/ng1696 · Cited by 701
Diversity of Human Copy Number Variation and Multicopy Genes
Sudmant, P. H., Kitzman, J. O., Antonacci, F., Alkan, C., Malig, M., Tsalenko, A., Sampas, N., Bruhn, L., Shendure, J., 1000 Genomes Project, et al. (2010) · Science · doi:10.1126/science.1197005 · Cited by 667
Self-citationSharp, A. J., Hansen, S., Selzer, R. R., Cheng, Z., Regan, R., Hurst, J. A., Stewart, H., Price, S. M., Blair, E., Hennekam, R. C., et al. (2006) · Nature Genetics · doi:10.1038/ng1862 · Cited by 658
Self-citationPopulation analysis of large copy number variants and hotspots of human genetic disease
Itsara, A., Cooper, G. M., Baker, C., Girirajan, S., Li, J., Absher, D., Krauss, R. M., Myers, R. M., Ridker, P. M., Chasman, D. I., et al. (2009) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.12.014 · Cited by 591
Self-citationResurrecting Surviving Neandertal Lineages from Modern Human Genomes
Vernot, B., & Akey, J. M. (2014) · Science · doi:10.1126/science.1245938 · Cited by 562
Inhibition of SRGAP2 function by its human-specific paralogs induces neoteny during spine maturation
Charrier, C., Joshi, K., Coutinho-Budd, J., Kim, J.-E., Lambert, N., de Marchena, J., Jin, W.-L., Vanderhaeghen, P., Ghosh, A., Sassa, T., et al. (2012) · Cell · doi:10.1016/j.cell.2012.03.034 · Cited by 454
Mefford, H. C., Muhle, H., Ostertag, P., von Spiczak, S., Buysse, K., Baker, C., Franke, A., Malafosse, A., Genton, P., Thomas, P., et al. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000962 · Cited by 474
Self-citationExcavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals
Vernot, B., Tucci, S., Kelso, J., Schraiber, J. G., Wolf, A. B., Gittelman, R. M., Dannemann, M., Grote, S., McCoy, R. C., Norton, H., et al. (2016) · Science · doi:10.1126/science.aad9416 · Cited by 459
Transcription Elongation Can Affect Genome 3D Structure
Heinz, S., Texari, L., Hayes, M. G. B., Urbanowski, M., Chang, M. W., Givarkes, N., Rialdi, A., White, K. M., Albrecht, R. A., Pache, L., et al. (2018) · Cell · doi:10.1016/j.cell.2018.07.047 · Cited by 453
Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication
Dennis, M. Y., Nuttle, X., Sudmant, P. H., Antonacci, F., Graves, T. A., Nefedov, M., Rosenfeld, J. A., Sajjadian, S., Malig, M., Kotkiewicz, H., et al. (2012) · Cell · doi:10.1016/j.cell.2012.03.033 · Cited by 407
Self-citationA complete reference genome improves analysis of human genetic variation
Aganezov, S., Yan, S. M., Soto, D. C., Kirsche, M., Zarate, S., Avdeyev, P., Taylor, D. J., Shafin, K., Shumate, A., Xiao, C., et al. (2022) · Science · doi:10.1126/science.abl3533 · Cited by 441
Mouradov, D., Sloggett, C., Jorissen, R. N., Love, C. G., Li, S., Burgess, A. W., Arango, D., Strausberg, R. L., Buchanan, D., Wormald, S., et al. (2014) · Cancer Research · doi:10.1158/0008-5472.can-14-0013 · Cited by 375
A genome-wide comparison of recent chimpanzee and human segmental duplications
Cheng, Z., Ventura, M., She, X., Khaitovich, P., Graves, T., Osoegawa, K., Church, D., DeJong, P., Wilson, R. K., Pääbo, S., et al. (2005) · Nature · doi:10.1038/nature04000 · Cited by 398
Self-citationLyons, J. J., Yu, X., Hughes, J. D., Le, Q. T., Jamil, A., Bai, Y., Ho, N., Zhao, M., Liu, Y., O'Connell, M. P., et al. (2016) · Nature Genetics · doi:10.1038/ng.3696 · Cited by 394
Common deletions and SNPs are in linkage disequilibrium in the human genome
Hinds, D. A., Kloek, A. P., Jen, M., Chen, X., & Frazer, K. A. (2006) · Nature Genetics · doi:10.1038/ng1695 · Cited by 372
Segmental duplications and their variation in a complete human genome
Vollger, M. R., Guitart, X., Dishuck, P. C., Mercuri, L., Harvey, W. T., Gershman, A., Diekhans, M., Sulovari, A., Munson, K. M., Lewis, A. P., et al. (2022) · Science · doi:10.1126/science.abj6965 · Cited by 350
Self-citationLong-read sequence assembly of the gorilla genome
Gordon, D., Huddleston, J., Chaisson, M. J. P., Hill, C. M., Kronenberg, Z. N., Munson, K. M., Malig, M., Raja, A., Fiddes, I., Hillier, L. W., et al. (2016) · Science · doi:10.1126/science.aae0344 · Cited by 333
Self-citationContribution of Global Rare Copy-Number Variants to the Risk of Sporadic Congenital Heart Disease
Soemedi, R., Wilson, I. J., Bentham, J., Darlay, R., Töpf, A., Zelenika, D., Cosgrove, C., Setchfield, K., Thornborough, C., Granados-Riveron, J., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.08.003 · Cited by 315
Woolston, A., Khan, K., Spain, G., Barber, L. J., Griffiths, B., Gonzalez-Exposito, R., Hornsteiner, L., Punta, M., Patil, Y., Newey, A., et al. (2019) · Cancer Cell · doi:10.1016/j.ccell.2019.05.013 · Cited by 254
Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals
Chen, L., Wolf, A. B., Fu, W., Li, L., & Akey, J. M. (2020) · Cell · doi:10.1016/j.cell.2020.01.012 · Cited by 254
Hardison, R. C. (2003) · PLoS Biology · doi:10.1371/journal.pbio.0000058 · Cited by 252
Rare copy number variants are an important cause of epileptic encephalopathies
Mefford, H. C., Yendle, S. C., Hsu, C., Cook, J., Geraghty, E., McMahon, J. M., Eeg‐Olofsson, O., Sadleir, L. G., Gill, D., Ben‐Zeev, B., et al. (2011) · Annals of Neurology · doi:10.1002/ana.22645 · Cited by 247
Self-citationEvolutionary toggling of the MAPT 17q21.31 inversion region
Zody, M. C., Jiang, Z., Fung, H.-C., Antonacci, F., Hillier, L. W., Cardone, M. F., Graves, T. A., Kidd, J. M., Cheng, Z., Abouelleil, A., et al. (2008) · Nature Genetics · doi:10.1038/ng.193 · Cited by 227
Self-citationStrategies and tools for whole-genome alignments
Couronne, O., Poliakov, A., Bray, N., Ishkhanov, T., Ryaboy, D., Rubin, E., Pachter, L., & Dubchak, I. (2003) · Genome Research · doi:10.1101/gr.762503 · Cited by 224
Olson, N. D., Wagner, J., McDaniel, J., Stephens, S. H., Westreich, S. T., Prasanna, A. G., Johanson, E., Boja, E., Maier, E. J., Serang, O., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100129 · Cited by 202
Copy number variation and evolution in humans and chimpanzees
Perry, G. H., Yang, F., Marques-Bonet, T., Murphy, C., Fitzgerald, T., Lee, A. S., Hyland, C., Stone, A. C., Hurles, M. E., Tyler-Smith, C., et al. (2008) · Genome Research · doi:10.1101/gr.082016.108 · Cited by 202
Self-citationRole of selection in fixation of gene duplications
Kondrashov, F. A., & Kondrashov, A. S. (2006) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2005.08.033 · Cited by 195
Berg, J. S., Brunetti-Pierri, N., Peters, S. U., Kang, S.-H. L., Fong, C.-T., Salamone, J., Freedenberg, D., Hannig, V. L., Prock, L. A., Miller, D. T., et al. (2007) · Genetics in Medicine · doi:10.1097/gim.0b013e3180986192 · Cited by 193
Long-Read DNA Sequencing: Recent Advances and Remaining Challenges
Warburton, P. E., & Sebra, R. P. (2023) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-101722-103045 · Cited by 163
The evolution and population diversity of human-specific segmental duplications
Dennis, M. Y., Harshman, L., Nelson, B. J., Penn, O., Cantsilieris, S., Huddleston, J., Antonacci, F., Penewit, K., Denman, L., Raja, A., et al. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-016-0069 · Cited by 159
Self-citationEvolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
Gentles, A. J., Wakefield, M. J., Kohany, O., Gu, W., Batzer, M. A., Pollock, D. D., & Jurka, J. (2007) · Genome Research · doi:10.1101/gr.6070707 · Cited by 156
Recurrent de novo mutations in neurodevelopmental disorders: properties and clinical implications
Wilfert, A. B., Sulovari, A., Turner, T. N., Coe, B. P., & Eichler, E. E. (2017) · Genome Medicine · doi:10.1186/s13073-017-0498-x · Cited by 144
Self-citationMefford, H. C., Cooper, G. M., Zerr, T., Smith, J. D., Baker, C., Shafer, N., Thorland, E. C., Skinner, C., Schwartz, C. E., Nickerson, D. A., et al. (2009) · Genome Research · doi:10.1101/gr.094987.109 · Cited by 132
Self-citationGain‐of‐function ADCY5 mutations in familial dyskinesia with facial myokymia
Chen, Y., Friedman, J. R., Chen, D., Chan, G. C. ‐., Bloss, C. S., Hisama, F. M., Topol, S. E., Carson, A. R., Pham, P. H., Bonkowski, E. S., et al. (2014) · Annals of Neurology · doi:10.1002/ana.24119 · Cited by 126
Quantifying the mechanisms of domain gain in animal proteins
Buljan, M., Frankish, A., & Bateman, A. (2010) · Genome Biology · doi:10.1186/gb-2010-11-7-r74 · Cited by 112
Increased mutation and gene conversion within human segmental duplications
Vollger, M. R., Dishuck, P. C., Harvey, W. T., DeWitt, W. S., Guitart, X., Goldberg, M. E., Rozanski, A. N., Lucas, J., Asri, M., Human Pangenome Reference Consortium, et al. (2023) · Nature · doi:10.1038/s41586-023-05895-y · Cited by 104
Self-citationEvolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia
Tucci, S., Vohr, S. H., McCoy, R. C., Vernot, B., Robinson, M. R., Barbieri, C., Nelson, B. J., Fu, W., Purnomo, G. A., Sudoyo, H., et al. (2018) · Science · doi:10.1126/science.aar8486 · Cited by 97
Self-citationEpi4K: Gene discovery in 4,000 genomes
The Epi4K Consortium (2012) · Epilepsia · doi:10.1111/j.1528-1167.2012.03511.x · Cited by 85
Study, D. (. D. I. S. A. C., Liu, J., Zhou, Y., Liu, S., Song, X., Yang, X.-Z., Fan, Y., Chen, W., Akdemir, Z. C., Yan, Z., et al. (2018) · Human Genetics · doi:10.1007/s00439-018-1910-3 · Cited by 77
Murthy, S. K., Nygren, A. O. H., El Shakankiry, H. M., Schouten, J. P., Al Khayat, A. I., Ridha, A., & Al Ali, M. T. (2007) · Cytogenetic and Genome Research · doi:10.1159/000097433 · Cited by 79
Recurrent inversion toggling and great ape genome evolution
Porubsky, D., Sanders, A. D., Höps, W., Hsieh, P., Sulovari, A., Li, R., Mercuri, L., Sorensen, M., Murali, S. C., Gordon, D., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0646-x · Cited by 72
Self-citationMohajeri, K., Cantsilieris, S., Huddleston, J., Nelson, B. J., Coe, B. P., Campbell, C. D., Baker, C., Harshman, L., Munson, K. M., Kronenberg, Z. N., et al. (2016) · Genome Research · doi:10.1101/gr.211284.116 · Cited by 42
Self-citationRozenfeld, C., Blanca, J., Gallego, V., García-Carpintero, V., Herranz-Jusdado, J. G., Pérez, L., Asturiano, J. F., Cañizares, J., & Peñaranda, D. S. (2019) · PLOS ONE · doi:10.1371/journal.pone.0218085 · Cited by 28
Human-specific gene expansions contribute to brain evolution
(2025) · doi:10.1016/j.cell.2025.06.037 · Cited by 25
High performance of a GPU-accelerated variant calling tool in genome data analysis
Zhang, Q., Liu, H., & Bu, F. (2021) · doi:10.1101/2021.12.12.472266 · Cited by 13
Network spectra for drug-target identification in complex diseases: new guns against old foes
Rai, A., Shinde, P., & Jalan, S. (2018) · Applied Network Science · doi:10.1007/s41109-018-0107-y · Cited by 12
Accuracy Assessment of Diploid Consensus Sequences
Kim, J., Waterman, M., & Li, L. (2007) · IEEE/ACM Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2007.1007 · Cited by 11
Metadata
- Authors
- Bailey, J. A., Gu, Z., Clark, R. A., Reinert, K., Samonte, R. V., Schwartz, S., Adams, M. D., Myers, E. W., Li, P. W., & Eichler, E. E.
- Venue
- Science
- Published
- 2002-08-09
- Volume
- 297
- Issue
- 5583
- Pages
- 1003-1007
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2045040686
- Cited by
- 1,352
- References
- 0
- FWCI
- 49.86
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
