Access the full text.
Sign up today, get DeepDyve free for 14 days.
Loading next page...
/lp/springer-journals/building-the-sequence-map-of-the-human-pan-genome-dUL670iFGE
References (39)
-
D. Falush, M. Stephens, J. Pritchard (2007)
Inference of population structure using multilocus genotype data: dominant markers and null allelesMolecular Ecology Notes, 7
-
D. Falush, M. Stephens, J. Pritchard (2003)
Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.Genetics, 164 4
-
P. Underhill, T. Kivisild (2007)
Use of y chromosome and mitochondrial DNA population structure in tracing human migrations.Annual review of genetics, 41
-
D. Wheeler, Maithreyan Srinivasan, M. Egholm, Yufeng Shen, Lei Chen, A. McGuire, Wenshe He, Yi-Ju Chen, V. Makhijani, G. Roth, Xavier Gomes, K. Tartaro, K. Tartaro, Faheem Niazi, C. Turcotte, G. Irzyk, J. Lupski, J. Lupski, C. Chinault, Xing-Zhi Song, Yue Liu, Ye Yuan, L. Nazareth, X. Qin, D. Muzny, M. Margulies, G. Weinstock, G. Weinstock, R. Gibbs, R. Gibbs, J. Rothberg, J. Rothberg (2008)
The complete genome of an individual by massively parallel DNA sequencingNature, 452
-
J. Dekker, J. Rossen, H. Büller, A. Einerhand (2002)
The MUC family: an obituary.Trends in biochemical sciences, 27 3
-
Ravi Sachidanandam, David Weissman, Steven Schmidt, Jerzy Kakol, Lincoln Stein, Gabor Marth, Steve Sherry, J. Mullikin, B. Mortimore, David Willey, S. Hunt, Charlotte Cole, Penny Coggill, C. Rice, Zemin Ning, J. Rogers, D. Bentley, Pui-Yan Kwok, E. Mardis, Raymond Yeh, Brian Schultz, L. Cook, Ruth Davenport, M. Dante, L. Fulton, L. Hillier, Robert Waterston, J. Mcpherson, Brian Gilman, Stephen Schaffner, W. Etten, David Reich, J. Higgins, Mark Daly, B. Blumenstiel, J. Baldwin, N. Stange-thomann, M. Zody, L. Linton, Eric Lander, D. Altshuler (2001)
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphismsNature, 409
-
Sijia Wang, Cecil Lewis, M. Jakobsson, Sohini Ramachandran, N. Ray, G. Bedoya, W. Rojas, M. Parra, J. Molina, C. Gallo, G. Mazzotti, G. Poletti, K. Hill, A. Hurtado, D. Labuda, W. Klitz, R. Barrantes, M. Bortolini, F. Salzano, M. Petzl-Erler, L. Tsuneto, E. Llop, F. Rothhammer, L. Excoffier, M. Feldman, N. Rosenberg, A. Ruiz-Linares (2007)
Genetic Variation and Population Structure in Native AmericansPLoS Genetics, 3
-
J. Bonfield, J. Galagan (2004)
Finishing the euchromatic sequence of the human genomeNature, 431
-
G. Wong, Zhiyong Yang, D. Passey, M. Kibukawa, Marcia Paddock, Chun-Rong Liu, L. Bolund, Jun Yu (2003)
A population threshold for functional polymorphisms.Genome research, 13 8
-
J. Sebat, B. Lakshmi, J. Troge, Joan Alexander, Janet Young, P. Lundin, S. Månér, H. Massa, M. Walker, M. Chi, N. Navin, R. Lucito, J. Healy, J. Hicks, Kenny Ye, Andrew Reiner, T. Gilliam, B. Trask, N. Patterson, A. Zetterberg, M. Wigler (2004)
Large-Scale Copy Number Polymorphism in the Human GenomeScience, 305
-
M. Olivier (2003)
A haplotype map of the human genome.Nature, 437 7063
-
D. Hinds, L. Stuve, Geoffrey Nilsen, E. Halperin, E. Eskin, D. Ballinger, K. Frazer, D. Cox (2005)
Whole-Genome Patterns of Common DNA Variation in Three Human PopulationsScience, 307
-
Jun Li, D. Absher, Hua Tang, Audrey Southwick, A. Casto, Sohini Ramachandran, H. Cann, G. Barsh, M. Feldman, L. Cavalli-Sforza, R. Myers
Supporting Online Material Materials and Methods Figs. S1 to S3 Tables S1 to S5 References Worldwide Human Relationships Inferred from Genome-wide Patterns of Variation -
PW Holland, HA Booth, EA Bruford (2007)
Classification and nomenclature of all human homeobox genesBMC Biol., 5
-
S. Krishna, I. Majumdar, N. Grishin (2003)
Structural classification of zinc fingers: survey and summary.Nucleic acids research, 31 2
-
Marie-Claire Beckers, Jan Gabriëls, S. Maarel, A. Vriese, Rune Frants, D. Collen, Alexandra Belayew (2001)
Active genes in junk DNA? Characterization of DUX genes embedded within 3.3 kb repeated elements.Gene, 264 1
-
Donald Bovee, Yang Zhou, E. Haugen, Zaining Wu, H. Hayden, W. Gillett, Eray Tuzun, Gregory Cooper, N. Sampas, K. Phelps, R. Levy, V Morrison, James Sprague, Donald Jewett, D. Buckley, Sandhya Subramaniam, Jean Chang, Douglas Smith, M. Olson, Evan Eichler, R. Kaul (2008)
Closing gaps in the human genome with fosmid resources generated from multiple individualsNature Genetics, 40
-
JZ Li (2008)
Worldwide human relationships inferred from genome-wide patterns of variationScience, 319
-
Yingrui Li, Jun Wang (2009)
Faster human genome sequencingNature Biotechnology, 27
-
J. Hirschhorn, M. Daly (2005)
Genome-wide association studies for common diseases and complex traitsNature Reviews Genetics, 6
-
W. Kent (2002)
BLAT--the BLAST-like alignment tool.Genome research, 12 4
-
Ruiqiang Li, Hong-mei Zhu, Jue Ruan, W. Qian, X. Fang, Z. Shi, Yingrui Li, Shengting Li, Gao Shan, K. Kristiansen, Songgang Li, Huanming Yang, Jian Wang, Jun Wang (2010)
De novo assembly of human genomes with massively parallel short read sequencing.Genome research, 20 2
-
D. Bentley, S. Balasubramanian, H. Swerdlow, G. Smith, J. Milton, Clive Brown, K. Hall, D. Evers, C. Barnes, Helen Bignell, J. Boutell, J. Bryant, Richard Carter, R. Cheetham, A. Cox, D. Ellis, Michael Flatbush, N. Gormley, S. Humphray, Leslie Irving, Mirian Karbelashvili, Scott Kirk, Heng Li, Xiaohai Liu, K. Maisinger, L. Murray, B. Obradovic, T. Ost, Michael Parkinson, Mark Pratt, I. Rasolonjatovo, M. Reed, R. Rigatti, C. Rodighiero, M. Ross, A. Sabot, S. Sankar, A. Scally, G. Schroth, Mark Smith, Vincent Smith, Anastassia Spiridou, Peta Torrance, Svilen Tzonev, Eric Vermaas, Klaudia Walter, Xiaolin Wu, Lu Zhang, Mohammed Alam, C. Anastasi, I. Aniebo, D. Bailey, I. Bancarz, Saibal Banerjee, Selena Barbour, P. Baybayan, Vincent Benoit, Kevin Benson, Claire Bevis, Phillip Black, Asha Boodhun, J. Brennan, J. Bridgham, Rob Brown, A. Brown, Dale Buermann, Abass Bundu, James Burrows, N. Carter, Nestor Castillo, M. Catenazzi, Simon Chang, R. Cooley, Natasha Crake, Olubunmi Dada, Konstantinos Diakoumakos, Belen Dominguez-Fernandez, D. Earnshaw, Ugonna Egbujor, Dave Elmore, S. Etchin, Mark Ewan, M. Fedurco, Louise Fraser, K. Fajardo, W. Furey, Dave George, Kimberley Gietzen, Colin Goddard, G. Golda, Philip Granieri, David Green, D. Gustafson, Nancy Hansen, K. Harnish, C. Haudenschild, Narinder Heyer, Matthew Hims, Johnny Ho, Adrian Horgan, Katya Hoschler, Steve Hurwitz, D. Ivanov, Maria Johnson, Terena James, T. Jones, Gyoung-Dong Kang, Tzvetana Kerelska, A. Kersey, I. Khrebtukova, A. Kindwall, Z. Kingsbury, P. Kokko-Gonzales, Anil Kumar, M. Laurent, C. Lawley, Sarah Lee, X. Lee, A. Liao, Jennifer Loch, Mitch Lok, Shujun Luo, Radhika Mammen, J. Martin, P. McCauley, P. McNitt, Parul Mehta, Keith Moon, Joe Mullens, T. Newington, Z. Ning, B. Ng, Sonia Novo, Michael O'neill, M. Osborne, A. Osnowski, Omead Ostadan, L. Paraschos, L. Pickering, Andrew Pike, A. Pike, D. Pinkard, Daniel Pliskin, Joe Podhasky, Victor Quijano, C. Raczy, Vicki Rae, S. Rawlings, Ana Rodriguez, Phyllida Roe, J. Rogers, M. Bacigalupo, Nikolai Romanov, A. Romieu, Rithy Roth, Natalie Rourke, Silke Ruediger, E. Rusman, Raquel Sanches-Kuiper, M. Schenker, J. Seoane, Richard Shaw, Mitch Shiver, S. Short, N. Sizto, Johannes Sluis, M. Smith, J. Sohna, Eric Spence, K. Stevens, Neil Sutton, L. Szajkowski, C. Tregidgo, G. Turcatti, S. Vandevondele, Yuli Verhovsky, Selene Virk, S. Wakelin, Gregory Walcott, Jingwen Wang, G. Worsley, Juying Yan, L. Yau, Mike Zuerlein, J. Rogers, J. Mullikin, M. Hurles, N. McCooke, John West, F. Oaks, Peter Lundberg, D. Klenerman, R. Durbin, Anthony Smith (2008)
Accurate Whole Human Genome Sequencing using Reversible Terminator ChemistryNature, 456
-
N. Rosenberg, J. Pritchard, J. Weber, H. Cann, K. Kidd, L. Zhivotovsky, M. Feldman (2002)
Genetic Structure of Human PopulationsScience, 298
-
S. Tishkoff, F. Reed, F. Friedlaender, C. Ehret, A. Ranciaro, A. Froment, J. Hirbo, A. Awomoyi, J. Bodo, O. Doumbo, M. Ibrahim, Abdalla Juma, M. Kotze, Godfrey Lema, J. Moore, Holly Mortensen, T. Nyambo, S. Omar, Kweli Powell, G. Pretorius, Michael Smith, M. Thera, C. Wambebe, J. Weber, Scott Williams (2009)
The Genetic Structure and History of Africans and African AmericansScience, 324
-
S. Altschul, W. Gish, W. Miller, E. Myers, D. Lipman (1990)
Basic local alignment search tool.Journal of molecular biology, 215 3
-
Jun Wang, Wei Wang, Ruiqiang Li, Yingrui Li, G. Tian, L. Goodman, Wei Fan, Junqing Zhang, Jun Li, Juanbin Zhang, Yiran Guo, Binxiao Feng, Heng Li, Yao Lu, X. Fang, Huiqing Liang, Zhenglin Du, Dong Li, Yiqing Zhao, Yujie Hu, Zhenzhen Yang, Hancheng Zheng, Ines Hellmann, M. Inouye, J. Pool, X. Yi, J. Zhao, Jinjie Duan, Yan Zhou, J. Qin, Lijia Ma, Guoqing Li, Zhentao Yang, Guojie Zhang, Bin Yang, Chang Yu, Fang Liang, Wen-jie Li, Shaochuan Li, Dawei Li, Peixiang Ni, Jue Ruan, Qibin Li, Hong-mei Zhu, Dongyuan Liu, Zhike Lu, Ning Li, Guangwu Guo, Jianguo Zhang, Jia Ye, L. Fang, Qin Hao, Quan Chen, Yuxi Liang, Yeyang Su, A. San, Cuo Ping, Shuang Yang, Fang Chen, Li Li, Ke Zhou, Hongkun Zheng, Yuanyuan Ren, Ling Yang, Yang Gao, Guohua Yang, Zhuo Li, Xiaoli Feng, K. Kristiansen, G. Wong, R. Nielsen, R. Durbin, L. Bolund, Xiuqing Zhang, Songgang Li, Huanming Yang, Jian Wang (2008)
The diploid genome sequence of an Asian individualNature, 456
-
H. Cann, C. Toma, L. Cazes, Marie‐Fernande Legrand, Valerie Morel, L. Piouffre, J. Bodmer, W. Bodmer, B. Bonné-Tamir, A. Cambon-Thomsen, Zhu Chen, Jiayou Chu, C. Carcassi, L. Contu, R. Du, L. Excoffier, G. Ferrara, Jonathan Friedlaender, H. Groot, D. Gurwitz, T. Jenkins, R. Herrera, Xiaoyi Huang, J. Kidd, K. Kidd, A. Langaney, A. Lin, S. Mehdi, P. Parham, A. Piazza, M. Pistillo, Y. Qian, Qunfang Shu, Jiujin Xu, S. Zhu, J. Weber, H. Greely, M. Feldman, G. Thomas, J. Dausset, L. Cavalli-Sforza (2002)
A Human Genome Diversity Cell Line PanelScience, 296
-
(2007)
BMC Biology BioMed Central Research article Classification and nomenclature of all human homeobox genes -
A. Iafrate, L. Feuk, Miguel Rivera, M. Listewnik, Patricia Donahoe, Y. Qi, Stephen Scherer, Charles Lee (2004)
Detection of large-scale variation in the human genomeNature Genetics, 36
-
M. Jakobsson, Sonja Scholz, P. Scheet, J. Gibbs, Jenna Vanliere, H. Fung, Zachary Szpiech, J. Degnan, Kai Wang, R. Guerreiro, J. Bras, Jennifer Schymick, D. Hernandez, B. Traynor, J. Simón-Sánchez, M. Matarin, A. Britton, J. Leemput, Ian Rafferty, M. Bucan, H. Cann, J. Hardy, N. Rosenberg, A. Singleton (2008)
Genotype, haplotype and copy-number variation in worldwide human populationsNature, 451
-
S. Levy, G. Sutton, P. Ng, L. Feuk, A. Halpern, B. Walenz, Nelson Axelrod, Jiaqi Huang, E. Kirkness, Gennady Denisov, Yuan Lin, J. MacDonald, Andy Wing, Chun Pang, M. Shago, Timothy Stockwell, Alexia Tsiamouri, V. Bafna, V. Bansal, S. Kravitz, D. Busam, K. Beeson, T. McIntosh, K. Remington, J. Abril, J. Gill, Jon Borman, Y. Rogers, M. Frazier, S. Scherer, R. Strausberg, J. Venter (2007)
The Diploid Genome Sequence of an Individual HumanPLoS Biology, 5
-
L. Cavalli-Sforza (2005)
The Human Genome Diversity Project: past, present and futureNature Reviews Genetics, 6
-
J. Kidd, G. Cooper, W. Donahue, H. Hayden, N. Sampas, T. Graves, Nancy Hansen, Brian Teague, C. Alkan, F. Antonacci, E. Haugen, Troy Zerr, N. Yamada, P. Tsang, Tera Newman, Eray Tüzün, Ze Cheng, H. Ebling, N. Tusneem, R. David, W. Gillett, K. Phelps, M. Weaver, David Saranga, A. Brand, Wei Tao, E. Gustafson, K. McKernan, Lin Chen, M. Malig, Joshua Smith, Joshua Korn, S. Mccarroll, D. Altshuler, D. Peiffer, M. Dorschner, J. Stamatoyannopoulos, D. Schwartz, D. Nickerson, Jim Mullikin, R. Wilson, L. Bruhn, M. Olson, R. Kaul, Douglas Smith, E. Eichler (2008)
Mapping and sequencing of structural variation from eight human genomesNature, 453
-
R. Khaja, Junjun Zhang, J. MacDonald, Yongshu He, Ann Joseph-George, John Wei, M. Rafiq, Cheng Qian, M. Shago, L. Pantano, H. Aburatani, K. Jones, R. Redon, M. Hurles, L. Armengol, X. Estivill, R. Mural, Charles Lee, S. Scherer, L. Feuk (2006)
Genome assembly comparison identifies structural variants in the human genomeNature Genetics, 38
-
Sung‐Min Ahn, Tae-Hyung Kim, Sunghoon Lee, Deokhoon Kim, H. Ghang, Dae-Soo Kim, Byoung-Chul Kim, Sang-Yoon Kim, Woo-Yeon Kim, Chulhong Kim, Daeui Park, Y. Lee, Sangsoo Kim, Rohit Reja, S. Jho, Chang Kim, J. Cha, Kyung-Hee Kim, B. Lee, J. Bhak, Seong-Jin Kim (2009)
The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group.Genome research, 19 9
-
K. Frazer, S. Murray, N. Schork, E. Topol (2009)
Human genetic variation and its contribution to complex traitsNature Reviews Genetics, 10
-
M. Cargill, D. Altshuler, J. Ireland, P. Sklar, K. Ardlie, N. Patil, C. Lane, Esther Lim, Nilesh Kalyanaraman, J. Nemesh, L. Ziaugra, L. Friedland, A. Rolfe, J. Warrington, R. Lipshutz, G. Daley, E. Lander (1999)
Characterization of single-nucleotide polymorphisms in coding regions of human genesNature Genetics, 22
-
Janet Young, Raelynn Endicott, Sean Parghi, M. Walker, J. Kidd, B. Trask (2008)
Extensive copy-number variation of the human olfactory receptor gene family.American journal of human genetics, 83 2
- Publisher
- Springer Journals
- Copyright
- Copyright © 2010 by Nature Publishing Group
- Subject
- Life Sciences; Life Sciences, general; Biotechnology; Biomedicine, general; Agriculture; Biomedical Engineering/Biotechnology; Bioinformatics
- ISSN
- 1087-0156
- eISSN
- 1546-1696
- DOI
- 10.1038/nbt.1596
- Publisher site
- See Article on Publisher Site
Abstract
Here we integrate the de novo assembly of an Asian and an African genome with the NCBI reference human genome, as a step toward constructing the human pan-genome. We identified ∼5 Mb of novel sequences not present in the reference genome in each of these assemblies. Most novel sequences are individual or population specific, as revealed by their comparison to all available human DNA sequence and by PCR validation using the human genome diversity cell line panel. We found novel sequences present in patterns consistent with known human migration paths. Cross-species conservation analysis of predicted genes indicated that the novel sequences contain potentially functional coding regions. We estimate that a complete human pan-genome would contain ∼19–40 Mb of novel sequence not present in the extant reference genome. The extensive amount of novel sequence contributing to the genetic variation of the pan-genome indicates the importance of using complete genome sequencing and de novo assembly.
Journal
Nature Biotechnology – Springer Journals
Published: Dec 7, 2009