Characterizing and interpreting genetic variation from personal genome sequencing

Methods in Molecular Biology

Volumn 838, Issue , 2012, Pages 343-367

  Johansson, Anna C V ^a   Feuk, Lars ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Copy number variation; Indel; Personal genomics; Whole genome sequencing

Indexed keywords

ALGORITHM; ARTICLE; CHROMOSOME BREAKAGE; CHROMOSOME MAP; COPY NUMBER VARIATION; DNA SEQUENCE; GENETICS; GENOMICS; HUMAN; HUMAN GENOME; HUMAN GENOME PROJECT; METHODOLOGY; NEOPLASM; REPRODUCIBILITY; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; CHROMOSOME BREAKPOINTS; CHROMOSOME MAPPING; DNA COPY NUMBER VARIATIONS; GENOME, HUMAN; GENOMICS; HUMAN GENOME PROJECT; HUMANS; NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 84856272334     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-507-7_17     Document Type: Article

References (69)

1. DeLisi, C. (2008) Meetings that changed the world: Santa Fe 1986: Human genome babysteps, Nature 455, 876-877.
2. Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., LeVine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J. P., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, J. C., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, R. H., Wilson, R. K., Hillier, L. W., McPherson, J. D., Marra, M. A., Mardis, E. R., Fulton, L. A., Chinwalla, A. T., Pepin, K. H., Gish, W. R., Chissoe, S. L., Wendl, M. C., Delehaunty, K. D., Miner, T. L., Delehaunty, A., Kramer, J. B., Cook, L. L., Fulton, R. S., Johnson, D. L., Minx, P. J., Clifton, S. W., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, J. F., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E., Frazier, M., Gibbs, R. A., Muzny, D. M., Scherer, S. E., Bouck, J. B., Sodergren, E. J., Worley, K. C., Rives, C. M., Gorrell, J. H., Metzker, M. L., Naylor, S. L., Kucherlapati, R. S., Nelson, D. L., Weinstock, G. M., Sakaki, Y., Fujiyama, A., Hattori, M., Yada, T., Toyoda, A., Itoh, T., Kawagoe, C., Watanabe, H., Totoki, Y., Taylor, T., Weissenbach, J., Heilig, R., Saurin, W., Artiguenave, F., Brottier, P., Bruls, T., Pelletier, E., Robert, C., Wincker, P., Smith, D. R., Doucette-Stamm, L., Rubenfi eld, M., Weinstock, K., Lee, H. M., Dubois, J., Rosenthal, A., Platzer, M., Nyakatura, G., Taudien, S., Rump, A., Yang, H., Yu, J., Wang, J., Huang, G., Gu, J., Hood, L., Rowen, L., Madan, A., Qin, S., Davis, R. W., Federspiel, N. A., Abola, A. P., Proctor, M. J., Myers, R. M., Schmutz, J., Dickson, M., Grimwood, J., Cox, D. R., Olson, M. V., Kaul, R., Shimizu, N., Kawasaki, K., Minoshima, S., Evans, G. A., Athanasiou, M., Schultz, R., Roe, B. A., Chen, F., Pan, H., Ramser, J., Lehrach, H., Reinhardt, R., McCombie, W. R., de la Bastide, M., Dedhia, N., Blocker, H., Hornischer, K., Nordsiek, G., Agarwala, R., Aravind, L., Bailey, J. A., Bateman, A., Batzoglou, S., Birney, E., Bork, P., Brown, D. G., Burge, C. B., Cerutti, L., Chen, H. C., Church, D., Clamp, M., Copley, R. R., Doerks, T., Eddy, S. R., Eichler, E. E., Furey, T. S., Galagan, J., Gilbert, J. G., Harmon, C., Hayashizaki, Y., Haussler, D., Hermjakob, H., Hokamp, K., Jang, W., Johnson, L. S., Jones, T. A., Kasif, S., Kaspryzk, A., Kennedy, S., Kent, W. J., Kitts, P., Koonin, E. V., Korf, I., Kulp, D., Lancet, D., Lowe, T. M., McLysaght, A., Mikkelsen, T., Moran, J. V., Mulder, N., Pollara, V. J., Ponting, C. P., Schuler, G., Schultz, J., Slater, G., Smit, A. F., Stupka, E., Szustakowski, J., Thierry-Mieg, D., Thierry-Mieg, J., Wagner, L., Wallis, J., Wheeler, R., Williams, A., Wolf, Y. I., Wolfe, K. H., Yang, S. P., Yeh, R. F., Collins, F., Guyer, M. S., Peterson, J., Felsenfeld, A., Wetterstrand, K. A., Patrinos, A., Morgan, M. J., de Jong, P., Catanese, J. J., Osoegawa, K., Shizuya, H., Choi, S., and Chen, Y. J. (2001) Initial sequencing and analysis of the human genome, Nature 409, 860-921. (Pubitemid 32165345)
3. Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., Gocayne, J. D., Amanatides, P., Ballew, R. M., Huson, D. H., Wortman, J. R., Zhang, Q., Kodira, C. D., Zheng, X. H., Chen, L., Skupski, M., Subramanian, G., Thomas, P. D., Zhang, J., Gabor Miklos, G. L., Nelson, C., Broder, S., Clark, A. G., Nadeau, J., McKusick, V. A., Zinder, N., Levine, A. J., Roberts, R. J., Simon, M., Slayman, C., Hunkapiller, M., Bolanos, R., Delcher, A., Dew, I., Fasulo, D., Flanigan, M., Florea, L., Halpern, A., Hannenhalli, S., Kravitz, S., Levy, S., Mobarry, C., Reinert, K., Remington, K., Abu-Threideh, J., Beasley, E., Biddick, K., Bonazzi, V., Brandon, R., Cargill, M., Chandramouliswaran, I., Charlab, R., Chaturvedi, K., Deng, Z., Di Francesco, V., Dunn, P., Eilbeck, K., Evangelista, C., Gabrielian, A. E., Gan, W., Ge, W., Gong, F., Gu, Z., Guan, P., Heiman, T. J., Higgins, M. E., Ji, R. R., Ke, Z., Ketchum, K. A., Lai, Z., Lei, Y., Li, Z., Li, J., Liang, Y., Lin, X., Lu, F., Merkulov, G. V., Milshina, N., Moore, H. M., Naik, A. K., Narayan, V. A., Neelam, B., Nusskern, D., Rusch, D. B., Salzberg, S., Shao, W., Shue, B., Sun, J., Wang, Z., Wang, A., Wang, X., Wang, J., Wei, M., Wides, R., Xiao, C., Yan, C., Yao, A., Ye, J., Zhan, M., Zhang, W., Zhang, H., Zhao, Q., Zheng, L., Zhong, F., Zhong, W., Zhu, S., Zhao, S., Gilbert, D., Baumhueter, S., Spier, G., Carter, C., Cravchik, A., Woodage, T., Ali, F., An, H., Awe, A., Baldwin, D., Baden, H., Barnstead, M., Barrow, I., Beeson, K., Busam, D., Carver, A., Center, A., Cheng, M. L., Curry, L., Danaher, S., Davenport, L., Desilets, R., Dietz, S., Dodson, K., Doup, L., Ferriera, S., Garg, N., Gluecksmann, A., Hart, B., Haynes, J., Haynes, C., Heiner, C., Hladun, S., Hostin, D., Houck, J., Howland, T., Ibegwam, C., Johnson, J., Kalush, F., Kline, L., Koduru, S., Love, A., Mann, F., May, D., McCawley, S., McIntosh, T., McMullen, I., Moy, M., Moy, L., Murphy, B., Nelson, K., Pfannkoch, C., Pratts, E., Puri, V., Qureshi, H., Reardon, M., Rodriguez, R., Rogers, Y. H., Romblad, D., Ruhfel, B., Scott, R., Sitter, C., Smallwood, M., Stewart, E., Strong, R., Suh, E., Thomas, R., Tint, N. N., Tse, S., Vech, C., Wang, G., Wetter, J., Williams, S., Williams, M., Windsor, S., Winn-Deen, E., Wolfe, K., Zaveri, J., Zaveri, K., Abril, J. F., Guigo, R., Campbell, M. J., Sjolander, K. V., Karlak, B., Kejariwal, A., Mi, H., Lazareva, B., Hatton, T., Narechania, A., Diemer, K., Muruganujan, A., Guo, N., Sato, S., Bafna, V., Istrail, S., Lippert, R., Schwartz, R., Walenz, B., Yooseph, S., Allen, D., Basu, A., Baxendale, J., Blick, L., Caminha, M., Carnes-Stine, J., Caulk, P., Chiang, Y. H., Coyne, M., Dahlke, C., Mays, A., Dombroski, M., Donnelly, M., Ely, D., Esparham, S., Fosler, C., Gire, H., Glanowski, S., Glasser, K., Glodek, A., Gorokhov, M., Graham, K., Gropman, B., Harris, M., Heil, J., Henderson, S., Hoover, J., Jennings, D., Jordan, C., Jordan, J., Kasha, J., Kagan, L., Kraft, C., Levitsky, A., Lewis, M., Liu, X., Lopez, J., Ma, D., Majoros, W., McDaniel, J., Murphy, S., Newman, M., Nguyen, T., Nguyen, N., Nodell, M., Pan, S., Peck, J., Peterson, M., Rowe, W., Sanders, R., Scott, J., Simpson, M., Smith, T., Sprague, A., Stockwell, T., Turner, R., Venter, E., Wang, M., Wen, M., Wu, D., Wu, M., Xia, A., Zandieh, A., and Zhu, X. (2001) The sequence of the human genome, Science 291, 1304-1351. (Pubitemid 32173090)
4. Consortium, I. H. G. S. (2004) Finishing the euchromatic sequence of the human genome, Nature 431, 931-945.
5. Sanger, F., Nicklen, S., and Coulson, A. R. (1977) DNA sequencing with chain-terminating inhibitors, Proc Natl Acad Sci USA 74, 5463-5467.
6. Istrail, S., Sutton, G. G., Florea, L., Halpern, A. L., Mobarry, C. M., Lippert, R., Walenz, B., Shatkay, H., Dew, I., Miller, J. R., Flanigan, M. J., Edwards, N. J., Bolanos, R., Fasulo, D., Halldorsson, B. V., Hannenhalli, S., Turner, R., Yooseph, S., Lu, F., Nusskern, D. R., Shue, B. C., Zheng, X. H., Zhong, F., Delcher, A. L., Huson, D. H., Kravitz, S. A., Mouchard, L., Reinert, K., Remington, K. A., Clark, A. G., Waterman, M. S., Eichler, E. E., Adams, M. D., Hunkapiller, M. W., Myers, E. W., and Venter, J. C. (2004) Whole-genome shotgun assembly and comparison of human genome assemblies, Proc Natl Acad Sci USA 101, 1916-1921. (Pubitemid 38228990)
7. Eichler, E. E., Clark, R. A., and She, X. (2004) An assessment of the sequence gaps: unfi nished business in a fi nished human genome, Nat Rev Genet 5, 345-354. (Pubitemid 38529406)
8. Bovee, D., Zhou, Y., Haugen, E., Wu, Z., Hayden, H. S., Gillett, W., Tuzun, E., Cooper, G. M., Sampas, N., Phelps, K., Levy, R., Morrison, V. A., Sprague, J., Jewett, D., Buckley, D., Subramaniam, S., Chang, J., Smith, D. R., Olson, M. V., Eichler, E. E., and Kaul, R. (2008) Closing gaps in the human genome with fosmid resources generated from multiple individuals, Nat Genet 40, 96-101.
9. Levy, S., Sutton, G., Ng, P. C., Feuk, L., Halpern, A. L., Walenz, B. P., Axelrod, N., Huang, J., Kirkness, E. F., Denisov, G., Lin, Y., MacDonald, J. R., Pang, A. W., Shago, M., Stockwell, T. B., Tsiamouri, A., Bafna, V., Bansal, V., Kravitz, S. A., Busam, D. A., Beeson, K. Y., McIntosh, T. C., Remington, K. A., Abril, J. F., Gill, J., Borman, J., Rogers, Y. H., Frazier, M. E., Scherer, S. W., Strausberg, R. L., and Venter, J. C. (2007) The diploid genome sequence of an individual human, PLoS Biol 5, e254.
10. Wheeler, D. A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., McGuire, A., He, W., Chen, Y. J., Makhijani, V., Roth, G. T., Gomes, X., Tartaro, K., Niazi, F., Turcotte, C. L., Irzyk, G. P., Lupski, J. R., Chinault, C., Song, X. Z., Liu, Y., Yuan, Y., Nazareth, L., Qin, X., Muzny, D. M., Margulies, M., Weinstock, G. M., Gibbs, R. A., and Rothberg, J. M. (2008) The complete genome of an individual by massively parallel DNA sequencing, Nature 452, 872-876. (Pubitemid 351550870)
11. 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., Boutell, J. M., Bryant, J., Carter, R. J., Keira Cheetham, R., Cox, A. J., Ellis, D. J., Flatbush, M. R., Gormley, N. A., Humphray, S. J., Irving, L. J., Karbelashvili, M. S., Kirk, S. M., Li, H., Liu, X., Maisinger, K. S., Murray, L. J., Obradovic, B., Ost, T., Parkinson, M. L., Pratt, M. R., Rasolonjatovo, I. M., Reed, M. T., Rigatti, R., Rodighiero, C., Ross, M. T., Sabot, A., Sankar, S. V., Scally, A., Schroth, G. P., Smith, M. E., Smith, V. P., Spiridou, A., Torrance, P. E., Tzonev, S. S., Vermaas, E. H., Walter, K., Wu, X., Zhang, L., Alam, M. D., Anastasi, C., Aniebo, I. C., Bailey, D. M., Bancarz, I. R., Banerjee, S., Barbour, S. G., Baybayan, P. A., Benoit, V. A., Benson, K. F., Bevis, C., Black, P. J., Boodhun, A., Brennan, J. S., Bridgham, J. A., Brown, R. C., Brown, A. A., Buermann, D. H., Bundu, A. A., Burrows, J. C., Carter, N. P., Castillo, N., Chiara, E. C. M., Chang, S., Neil Cooley, R., Crake, N. R., Dada, O. O., Diakoumakos, K. D., Dominguez-Fernandez, B., Earnshaw, D. J., Egbujor, U. C., Elmore, D. W., Etchin, S. S., Ewan, M. R., Fedurco, M., Fraser, L. J., Fuentes Fajardo, K. V., Scott Furey, W., George, D., Gietzen, K. J., Goddard, C. P., Golda, G. S., Granieri, P. A., Green, D. E., Gustafson, D. L., Hansen, N. F., Harnish, K., Haudenschild, C. D., Heyer, N. I., Hims, M. M., Ho, J. T., Horgan, A. M., Hoschler, K., Hurwitz, S., Ivanov, D. V., Johnson, M. Q., James, T., Huw Jones, T. A., Kang, G. D., Kerelska, T. H., Kersey, A. D., Khrebtukova, I., Kindwall, A. P., Kingsbury, Z., Kokko-Gonzales, P. I., Kumar, A., Laurent, M. A., Lawley, C. T., Lee, S. E., Lee, X., Liao, A. K., Loch, J. A., Lok, M., Luo, S., Mammen, R. M., Martin, J. W., McCauley, P. G., McNitt, P., Mehta, P., Moon, K. W., Mullens, J. W., Newington, T., Ning, Z., Ling Ng, B., Novo, S. M., ONeill, M. J., Osborne, M. A., Osnowski, A., Ostadan, O., Paraschos, L. L., Pickering, L., Pike, A. C., Chris Pinkard, D., Pliskin, D. P., Podhasky, J., Quijano, V. J., Raczy, C., Rae, V. H., Rawlings, S. R., Chiva Rodriguez, A., Roe, P. M., Rogers, J., Rogert Bacigalupo, M. C., Romanov, N., Romieu, A., Roth, R. K., Rourke, N. J., Ruediger, S. T., Rusman, E., Sanches-Kuiper, R. M., Schenker, M. R., Seoane, J. M., Shaw, R. J., Shiver, M. K., Short, S. W., Sizto, N. L., Sluis, J. P., Smith, M. A., Ernest Sohna Sohna, J., Spence, E. J., Stevens, K., Sutton, N., Szajkowski, L., Tregidgo, C. L., Turcatti, G., Vandevondele, S., Verhovsky, Y., Virk, S. M., Wakelin, S., Walcott, G. C., Wang, J., Worsley, G. J., Yan, J., Yau, L., Zuerlein, M., Mullikin, J. C., Hurles, M. E., McCooke, N. J., West, J. S., Oaks, F. L., Lundberg, P. L., Klenerman, D., Durbin, R., and Smith, A. J. (2008) Accurate whole human genome sequencing using reversible terminator chemistry, Nature 456, 53-59.
12. Wang, J., Wang, W., Li, R., Li, Y., Tian, G., Goodman, L., Fan, W., Zhang, J., Li, J., Guo, Y., Feng, B., Li, H., Lu, Y., Fang, X., Liang, H., Du, Z., Li, D., Zhao, Y., Hu, Y., Yang, Z., Zheng, H., Hellmann, I., Inouye, M., Pool, J., Yi, X., Zhao, J., Duan, J., Zhou, Y., Qin, J., Ma, L., Li, G., Zhang, G., Yang, B., Yu, C., Liang, F., Li, W., Li, S., Ni, P., Ruan, J., Li, Q., Zhu, H., Liu, D., Lu, Z., Li, N., Guo, G., Ye, J., Fang, L., Hao, Q., Chen, Q., Liang, Y., Su, Y., San, A., Ping, C., Yang, S., Chen, F., Li, L., Zhou, K., Ren, Y., Yang, L., Gao, Y., Yang, G., Li, Z., Feng, X., Kristiansen, K., Wong, G. K., Nielsen, R., Durbin, R., Bolund, L., Zhang, X., and Yang, H. (2008) The diploid genome sequence of an Asian individual, Nature 456, 60-65.
13. Pang, A. W., MacDonald, J. R., Pinto, D., Wei, J., Rafiq, M. A., Conrad, D. F., Park, H., Hurles, M. E., Lee, C., Venter, J. C., Kirkness, E. F., Levy, S., Feuk, L., and Scherer, S. W. (2010) Towards a comprehensive structural variation map of an individual human genome, Genome Biol 11, R52.
14. Ahn, S. M., Kim, T. H., Lee, S., Kim, D., Ghang, H., Kim, D. S., Kim, B. C., Kim, S. Y., Kim, W. Y., Kim, C., Park, D., Lee, Y. S., Kim, S., Reja, R., Jho, S., Kim, C. G., Cha, J. Y., Kim, K. H., Lee, B., Bhak, J., and Kim, S. J. (2009) The first Korean genome sequence and analysis: full genome sequencing for a socioethnic group, Genome Res 19, 1622-1629.
15. Kim, J. I., Ju, Y. S., Park, H., Kim, S., Lee, S., Yi, J. H., Mudge, J., Miller, N. A., Hong, D., Bell, C. J., Kim, H. S., Chung, I. S., Lee, W. C., Lee, J. S., Seo, S. H., Yun, J. Y., Woo, H. N., Lee, H., Suh, D., Kim, H. J., Yavartanoo, M., Kwak, M., Zheng, Y., Lee, M. K., Kim, J. Y., Gokcumen, O., Mills, R. E., Zaranek, A. W., Thakuria, J., Wu, X., Kim, R. W., Huntley, J. J., Luo, S., Schroth, G. P., Wu, T. D., Kim, H., Yang, K. S., Park, W. Y., Church, G. M., Lee, C., Kingsmore, S. F., and Seo, J. S. (2009) A highly annotated whole-genome sequence of a Korean individual, Nature 460, 1011-1015.
16. Schuster, S. C., Miller, W., Ratan, A., Tomsho, L. P., Giardine, B., Kasson, L. R., Harris, R. S., Petersen, D. C., Zhao, F., Qi, J., Alkan, C., Kidd, J. M., Sun, Y., Drautz, D. I., Bouffard, P., Muzny, D. M., Reid, J. G., Nazareth, L. V., Wang, Q., Burhans, R., Riemer, C., Wittekindt, N. E., Moorjani, P., Tindall, E. A., Danko, C. G., Teo, W. S., Buboltz, A. M., Zhang, Z., Ma, Q., Oosthuysen, A., Steenkamp, A. W., Oostuisen, H., Venter, P., Gajewski, J., Zhang, Y., Pugh, B. F., Makova, K. D., Nekrutenko, A., Mardis, E. R., Patterson, N., Pringle, T. H., Chiaromonte, F., Mullikin, J. C., Eichler, E. E., Hardison, R. C., Gibbs, R. A., Harkins, T. T., and Hayes, V. M. (2010) Complete Khoisan and Bantu genomes from southern Africa, Nature 463, 943-947.
17. McKernan, K. J., Peckham, H. E., Costa, G. L., McLaughlin, S. F., Fu, Y., Tsung, E. F., Clouser, C. R., Duncan, C., Ichikawa, J. K., Lee, C. C., Zhang, Z., Ranade, S. S., Dimalanta, E. T., Hyland, F. C., Sokolsky, T. D., Zhang, L., Sheridan, A., Fu, H., Hendrickson, C. L., Li, B., Kotler, L., Stuart, J. R., Malek, J. A., Manning, J. M., Antipova, A. A., Perez, D. S., Moore, M. P., Hayashibara, K. C., Lyons, M. R., Beaudoin, R. E., Coleman, B. E., Laptewicz, M. W., Sannicandro, A. E., Rhodes, M. D., Gottimukkala, R. K., Yang, S., Bafna, V., Bashir, A., MacBride, A., Alkan, C., Kidd, J. M., Eichler, E. E., Reese, M. G., De La Vega, F. M., and Blanchard, A. P. (2009) Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding, Genome Res 19, 1527-1541.
18. Consortium, T. I. H. (2003) The International HapMap Project, Nature 426, 789-796.
19. Drmanac, R., Sparks, A. B., Callow, M. J., Halpern, A. L., Burns, N. L., Kermani, B. G., Carnevali, P., Nazarenko, I., Nilsen, G. B., Yeung, G., Dahl, F., Fernandez, A., Staker, B., Pant, K. P., Baccash, J., Borcherding, A. P., Brownley, A., Cedeno, R., Chen, L., Chernikoff, D., Cheung, A., Chirita, R., Curson, B., Ebert, J. C., Hacker, C. R., Hartlage, R., Hauser, B., Huang, S., Jiang, Y., Karpinchyk, V., Koenig, M., Kong, C., Landers, T., Le, C., Liu, J., McBride, C. E., Morenzoni, M., Morey, R. E., Mutch, K., Perazich, H., Perry, K., Peters, B. A., Peterson, J., Pethiyagoda, C. L., Pothuraju, K., Richter, C., Rosenbaum, A. M., Roy, S., Shafto, J., Sharanhovich, U., Shannon, K. W., Sheppy, C. G., Sun, M., Thakuria, J. V., Tran, A., Vu, D., Zaranek, A. W., Wu, X., Drmanac, S., Oliphant, A. R., Banyai, W. C., Martin, B., Ballinger, D. G., Church, G. M., and Reid, C. A. (2010) Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays, Science 327, 78-81.
20. Pushkarev, D., Neff, N. F., and Quake, S. R. (2009) Single-molecule sequencing of an individual human genome, Nat Biotech 27, 847-850.
21. Roach, J. C., Glusman, G., Smit, A. F., Huff, C. D., Hubley, R., Shannon, P. T., Rowen, L., Pant, K. P., Goodman, N., Bamshad, M., Shendure, J., Drmanac, R., Jorde, L. B., Hood, L., and Galas, D. J. (2010) Analysis of genetic inheritance in a family quartet by wholegenome sequencing, Science 328, 636-639.
22. Ley, T. J., Mardis, E. R., Ding, L., Fulton, B., McLellan, M. D., Chen, K., Dooling, D., Dunford-Shore, B. H., McGrath, S., Hickenbotham, M., Cook, L., Abbott, R., Larson, D. E., Koboldt, D. C., Pohl, C., Smith, S., Hawkins, A., Abbott, S., Locke, D., Hillier, L. W., Miner, T., Fulton, L., Magrini, V., Wylie, T., Glasscock, J., Conyers, J., Sander, N., Shi, X., Osborne, J. R., Minx, P., Gordon, D., Chinwalla, A., Zhao, Y., Ries, R. E., Payton, J. E., Westervelt, P., Tomasson, M. H., Watson, M., Baty, J., Ivanovich, J., Heath, S., Shannon, W. D., Nagarajan, R., Walter, M. J., Link, D. C., Graubert, T. A., DiPersio, J. F., and Wilson, R. K. (2008) DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome, Nature 456, 66-72.
23. Mardis, E. R., Ding, L., Dooling, D. J., Larson, D. E., McLellan, M. D., Chen, K., Koboldt, D. C., Fulton, R. S., Delehaunty, K. D., McGrath, S. D., Fulton, L. A., Locke, D. P., Magrini, V. J., Abbott, R. M., Vickery, T. L., Reed, J. S., Robinson, J. S., Wylie, T., Smith, S. M., Carmichael, L., Eldred, J. M., Harris, C. C., Walker, J., Peck, J. B., Du, F., Dukes, A. F., Sanderson, G. E., Brummett, A. M., Clark, E., McMichael, J. F., Meyer, R. J., Schindler, J. K., Pohl, C. S., Wallis, J. W., Shi, X., Lin, L., Schmidt, H., Tang, Y., Haipek, C., Wiechert, M. E., Ivy, J. V., Kalicki, J., Elliott, G., Ries, R. E., Payton, J. E., Westervelt, P., Tomasson, M. H., Watson, M. A., Baty, J., Heath, S., Shannon, W. D., Nagarajan, R., Link, D. C., Walter, M. J., Graubert, T. A., DiPersio, J. F., Wilson, R. K., and Ley, T. J. (2009) Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome, N Engl J Med 361, 1058-1066.
24. Campbell, P. J., Stephens, P. J., Pleasance, E. D., OMeara, S., Li, H., Santarius, T., Stebbings, L. A., Leroy, C., Edkins, S., Hardy, C., Teague, J. W., Menzies, A., Goodhead, I., Turner, D. J., Clee, C. M., Quail, M. A., Cox, A., Brown, C., Durbin, R., Hurles, M. E., Edwards, P. A. W., Bignell, G. R., Stratton, M. R., and Futreal, P. A. (2008) Identifi cation of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing, Nat Genet 40, 722-729. (Pubitemid 351748860)
25. Pleasance, E. D., Stephens, P. J., OMeara, S., McBride, D. J., Meynert, A., Jones, D., Lin, M.-L., Beare, D., Lau, K. W., Greenman, C., Varela, I., Nik-Zainal, S., Davies, H. R., Ordonez, G. R., Mudie, L. J., Latimer, C., Edkins, S., Stebbings, L., Chen, L., Jia, M., Leroy, C., Marshall, J., Menzies, A., Butler, A., Teague, J. W., Mangion, J., Sun, Y. A., McLaughlin, S. F., Peckham, H. E., Tsung, E. F., Costa, G. L., Lee, C. C., Minna, J. D., Gazdar, A., Birney, E., Rhodes, M. D., McKernan, K. J., Stratton, M. R., Futreal, P. A., and Campbell, P. J. (2010) A small-cell lung cancer genome with complex signatures of tobacco exposure, Nature 463, 184-190.
26. Pleasance, E. D., Cheetham, R. K., Stephens, P. J., McBride, D. J., Humphray, S. J., Greenman, C. D., Varela, I., Lin, M.-L., Ordonez, G. R., Bignell, G. R., Ye, K., Alipaz, J., Bauer, M. J., Beare, D., Butler, A., Carter, R. J., Chen, L., Cox, A. J., Edkins, S., Kokko-Gonzales, P. I., Gormley, N. A., Grocock, R. J., Haudenschild, C. D., Hims, M. M., James, T., Jia, M., Kingsbury, Z., Leroy, C., Marshall, J., Menzies, A., Mudie, L. J., Ning, Z., Royce, T., Schulz-Trieglaff, O. B., Spiridou, A., Stebbings, L. A., Szajkowski, L., Teague, J., Williamson, D., Chin, L., Ross, M. T., Campbell, P. J., Bentley, D. R., Futreal, P. A., and Stratton, M. R. (2010) A comprehensive catalogue of somatic mutations from a human cancer genome, Nature 463, 191-196.
27. Consortium, T. I. C. G. (2010) International network of cancer genome projects, Nature 464, 993-998.
28. Gilbert, M. T., Kivisild, T., Gronnow, B., Andersen, P. K., Metspalu, E., Reidla, M., Tamm, E., Axelsson, E., Gotherstrom, A., Campos, P. F., Rasmussen, M., Metspalu, M., Higham, T. F., Schwenninger, J. L., Nathan, R., De Hoog, C. J., Koch, A., Moller, L. N., Andreasen, C., Meldgaard, M., Villems, R., Bendixen, C., and Willerslev, E. (2008) Paleo-Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland, Science 320, 1787-1789. (Pubitemid 351931295)
29. Rasmussen, M., Li, Y., Lindgreen, S., Pedersen, J. S., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., Bertalan, M., Nielsen, K., Gilbert, M. T., Wang, Y., Raghavan, M., Campos, P. F., Kamp, H. M., Wilson, A. S., Gledhill, A., Tridico, S., Bunce, M., Lorenzen, E. D., Binladen, J., Guo, X., Zhao, J., Zhang, X., Zhang, H., Li, Z., Chen, M., Orlando, L., Kristiansen, K., Bak, M., Tommerup, N., Bendixen, C., Pierre, T. L., Gronnow, B., Meldgaard, M., Andreasen, C., Fedorova, S. A., Osipova, L. P., Higham, T. F., Ramsey, C. B., Hansen, T. V., Nielsen, F. C., Crawford, M. H., Brunak, S., Sicheritz-Ponten, T., Villems, R., Nielsen, R., Krogh, A., Wang, J., and Willerslev, E. (2010) Ancient human genome sequence of an extinct Palaeo-Eskimo, Nature 463, 757-762.
30. Green, R. E., Malaspinas, A. S., Krause, J., Briggs, A. W., Johnson, P. L., Uhler, C., Meyer, M., Good, J. M., Maricic, T., Stenzel, U., Prufer, K., Siebauer, M., Burbano, H. A., Ronan, M., Rothberg, J. M., Egholm, M., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Wikstrom, M., Laakkonen, L., Kelso, J., Slatkin, M., and Paabo, S. (2008) A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing, Cell 134, 416-426.
31. Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H., Hansen, N. F., Durand, E. Y., Malaspinas, A. S., Jensen, J. D., Marques-Bonet, T., Alkan, C., Prufer, K., Meyer, M., Burbano, H. A., Good, J. M., Schultz, R., Aximu-Petri, A., Butthof, A., Hober, B., Hoffner, B., Siegemund, M., Weihmann, A., Nusbaum, C., Lander, E. S., Russ, C., Novod, N., Affourtit, J., Egholm, M., Verna, C., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Doronichev, V. B., Golovanova, L. V., Lalueza-Fox, C., de la Rasilla, M., Fortea, J., Rosas, A., Schmitz, R. W., Johnson, P. L., Eichler, E. E., Falush, D., Birney, E., Mullikin, J. C., Slatkin, M., Nielsen, R., Kelso, J., Lachmann, M., Reich, D., and Paabo, S. (2010) A draft sequence of the Neandertal genome, Science 328, 710-722.
32. Green, R. E., Krause, J., Ptak, S. E., Briggs, A. W., Ronan, M. T., Simons, J. F., Du, L., Egholm, M., Rothberg, J. M., Paunovic, M., and Paabo, S. (2006) Analysis of one million base pairs of Neanderthal DNA, Nature 444, 330-336. (Pubitemid 44764103)
33. Noonan, J. P., Coop, G., Kudaravalli, S., Smith, D., Krause, J., Alessi, J., Chen, F., Platt, D., Paabo, S., Pritchard, J. K., and Rubin, E. M. (2006) Sequencing and analysis of Neanderthal genomic DNA, Science 314, 1113-1118. (Pubitemid 44789035)
34. Burbano, H. A., Hodges, E., Green, R. E., Briggs, A. W., Krause, J., Meyer, M., Good, J. M., Maricic, T., Johnson, P. L. F., Xuan, Z., Rooks, M., Bhattacharjee, A., Brizuela, L., Albert, F. W., de la Rasilla, M., Fortea, J., Rosas, A., Lachmann, M., Hannon, G. J., and Paabo, S. (2010) Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture, Science 328, 723-725.
35. Ng, S. B., Turner, E. H., Robertson, P. D., Flygare, S. D., Bigham, A. W., Lee, C., Shaffer, T., Wong, M., Bhattacharjee, A., Eichler, E. E., Bamshad, M., Nickerson, D. A., and Shendure, J. (2009) Targeted capture and massively parallel sequencing of 12 human exomes, Nature 461, 272-276.
36. Ng, P. C., Levy, S., Huang, J., Stockwell, T. B., Walenz, B. P., Li, K., Axelrod, N., Busam, D. A., Strausberg, R. L., and Venter, J. C. (2008) Genetic variation in an individual human exome, PLoS Genet 4, e1000160.
37. Ng, S. B., Buckingham, K. J., Lee, C., Bigham, A. W., Tabor, H. K., Dent, K. M., Huff, C. D., Shannon, P. T., Jabs, E. W., Nickerson, D. A., Shendure, J., and Bamshad, M. J. (2010) Exome sequencing identifi es the cause of a mendelian disorder, Nat Genet 42, 30-35.
38. Choi, M., Scholl, U. I., Ji, W., Liu, T., Tikhonova, I. R., Zumbo, P., Nayir, A., Bakkaloglu, A., Ozen, S., Sanjad, S., Nelson-Williams, C., Farhi, A., Mane, S., and Lifton, R. P. (2009) Genetic diagnosis by whole exome capture and massively parallel DNA sequencing, Proc Natl Acad Sci USA 106, 19096-19101.
39. Rehman, A. U., Morell, R. J., Belyantseva, I. A., Khan, S. Y., Boger, E. T., Shahzad, M., Ahmed, Z. M., Riazuddin, S., Khan, S. N., and Friedman, T. B. (2010) Targeted capture and next-generation sequencing identifi es C9orf75, encoding taperin, as the mutated gene in nonsyndromic deafness DFNB79, Am J Hum Genet 86, 378-388.
40. Walsh, T., Shahin, H., Elkan-Miller, T., Lee, M. K., Thornton, A. M., Roeb, W., Abu Rayyan, A., Loulus, S., Avraham, K. B., King, M.-C., and Kanaan, M. Whole Exome Sequencing and Homozygosity Mapping Identify Mutation in the Cell Polarity Protein GPSM2 as the Cause of Nonsyndromic Hearing Loss DFNB82, The American Journal of Human Genetics In Press, Corrected Proof.
41. Lalonde, E., Albrecht, S., Ha, K. C. H., Jacob, K., Bolduc, N., Polychronakos, C., Dechelotte, P., Majewski, J., and Jabado, N. (2010) Unexpected allelic heterogeneity and spectrum of mutations in Fowler syndrome revealed by next-generation exome sequencing, Human Mutation 9999, n/a.
42. Hoischen, A., Gilissen, C., Arts, P., Wieskamp, N., Vliet, W. v. d., Vermeer, S., Steehouwer, M., Vries, P. d., Meijer, R., Seiqueros, J., Knoers, N. V. A. M., Buckley, M. F., Scheffer, H., and Veltman, J. A. (2010) Massively parallel sequencing of ataxia genes after arraybased enrichment, Human Mutation 31, 494-499.
43. Li, R., Li, Y., Zheng, H., Luo, R., Zhu, H., Li, Q., Qian, W., Ren, Y., Tian, G., Li, J., Zhou, G., Zhu, X., Wu, H., Qin, J., Jin, X., Li, D., Cao, H., Hu, X., Blanche, H., Cann, H., Zhang, X., Li, S., Bolund, L., Kristiansen, K., Yang, H., Wang, J., and Wang, J. (2010) Building the sequence map of the human pangenome, Nat Biotech 28, 57-63.
44. Khaja, R., Zhang, J., MacDonald, J. R., He, Y., Joseph-George, A. M., Wei, J., Rafiq, M. A., Qian, C., Shago, M., Pantano, L., Aburatani, H., Jones, K., Redon, R., Hurles, M., Armengol, L., Estivill, X., Mural, R. J., Lee, C., Scherer, S. W., and Feuk, L. (2006) Genome assembly comparison identifi es structural variants in the human genome, Nat Genet 38, 1413-1418. (Pubitemid 44837563)
45. Kidd, J. M., Sampas, N., Antonacci, F., Graves, T., Fulton, R., Hayden, H. S., Alkan, C., Malig, M., Ventura, M., Giannuzzi, G., Kallicki, J., Anderson, P., Tsalenko, A., Yamada, N. A., Tsang, P., Kaul, R., Wilson, R. K., Bruhn, L., and Eichler, E. E. (2010) Characterization of missing human genome sequences and copynumber polymorphic insertions, Nat Meth 7, 365-371.
46. Li, H., Ruan, J., and Durbin, R. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores, Genome Res 18, 1851-1858.
47. Hillier, L. W., Marth, G. T., Quinlan, A. R., Dooling, D., Fewell, G., Barnett, D., Fox, P., Glasscock, J. I., Hickenbotham, M., Huang, W., Magrini, V. J., Richt, R. J., Sander, S. N., Stewart, D. A., Stromberg, M., Tsung, E. F., Wylie, T., Schedl, T., Wilson, R. K., and Mardis, E. R. (2008) Whole-genome sequencing and variant discovery in C. elegans, Nat Meth 5, 183-188. (Pubitemid 351181748)
48. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and Genome Project Data Processing Subgroup. (2009) The Sequence Alignment/Map format and SAMtools, Bioinformatics 25, 2078-2079.
49. Li, R., Yu, C., Li, Y., Lam, T.-W., Yiu, S.-M., Kristiansen, K., and Wang, J. (2009) SOAP2: an improved ultrafast tool for short read alignment, Bioinformatics 25, 1966-1967.
50. Li, R., Li, Y., Kristiansen, K., and Wang, J. (2008) SOAP: short oligonucleotide alignment program, Bioinformatics 24, 713-714. (Pubitemid 351321217)
51. Tuzun, E., Sharp, A. J., Bailey, J. A., Kaul, R., Morrison, V. A., Pertz, L. M., Haugen, E., Hayden, H., Albertson, D., Pinkel, D., Olson, M. V., and Eichler, E. E. (2005) Fine-scale structural variation of the human genome, Nat Genet 37, 727-732. (Pubitemid 41754889)
52. Kidd, J. M., Cooper, G. M., Donahue, W. F., Hayden, H. S., Sampas, N., Graves, T., Hansen, N., Teague, B., Alkan, C., Antonacci, F., Haugen, E., Zerr, T., Yamada, N. A., Tsang, P., Newman, T. L., Tuzun, E., Cheng, Z., Ebling, H. M., Tusneem, N., David, R., Gillett, W., Phelps, K. A., Weaver, M., Saranga, D., Brand, A., Tao, W., Gustafson, E., McKernan, K., Chen, L., Malig, M., Smith, J. D., Korn, J. M., McCarroll, S. A., Altshuler, D. A., Peiffer, D. A., Dorschner, M., Stamatoyannopoulos, J., Schwartz, D., Nickerson, D. A., Mullikin, J. C., Wilson, R. K., Bruhn, L., Olson, M. V., Kaul, R., Smith, D. R., and Eichler, E. E. (2008) Mapping and sequencing of structural variation from eight human genomes, Nature 453, 56-64. (Pubitemid 351630326)
53. Lee, S., Hormozdiari, F., Alkan, C., and Brudno, M. (2009) MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions, Nat Meth 6, 473-474.
54. Korbel, J., Abyzov, A., Mu, X., Carriero, N., Cayting, P., Zhang, Z., Snyder, M., and Gerstein, M. (2009) PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data, Genome Biology 10, R23.
55. Chen, K., Wallis, J. W., McLellan, M. D., Larson, D. E., Kalicki, J. M., Pohl, C. S., McGrath, S. D., Wendl, M. C., Zhang, Q., Locke, D. P., Shi, X., Fulton, R. S., Ley, T. J., Wilson, R. K., Ding, L., and Mardis, E. R. (2009) BreakDancer: an algorithm for highresolution mapping of genomic structural variation, Nat Meth 6, 677-681.
56. Hajirasouliha, I., Hormozdiari, F., Alkan, C., Kidd, J. M., Birol, I., Eichler, E. E., and Sahinalp, S. C. (2010) Detection and characterization of novel sequence insertions using paired-end next-generation sequencing, Bioinformatics 26, 1277-1283.
57. Xie, C., and Tammi, M. T. (2009) CNV-seq, a new method to detect copy number variation using high-throughput sequencing, BMC Bioinformatics 10, 80.
58. Conrad, D. F., Bird, C., Blackburne, B., Lindsay, S., Mamanova, L., Lee, C., Turner, D. J., and Hurles, M. E. (2010) Mutation spectrum revealed by breakpoint sequencing of human germline CNVs, Nat Genet 42, 385-391.
59. Lam, H. Y., Mu, X. J., Stutz, A. M., Tanzer, A., Cayting, P. D., Snyder, M., Kim, P. M., Korbel, J. O., and Gerstein, M. B. (2010) Nucleotideresolution analysis of structural variants using BreakSeq and a breakpoint library, Nat Biotechnol 28, 47-55.
60. Korbel, J. O., Urban, A. E., Affourtit, J. P., Godwin, B., Grubert, F., Simons, J. F., Kim, P. M., Palejev, D., Carriero, N. J., Du, L., Taillon, B. E., Chen, Z., Tanzer, A., Saunders, A. C. E., Chi, J., Yang, F., Carter, N. P., Hurles, M. E., Weissman, S. M., Harkins, T. T., Gerstein, M. B., Egholm, M., and Snyder, M. (2007) Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome, Science 318, 420-426. (Pubitemid 47614521)
61. Ye, K., Schulz, M. H., Long, Q., Apweiler, R., and Ning, Z. (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from pairedend short reads, Bioinformatics 25, 2865-2871.
62. Ameur, A., Wetterbom, A., Feuk, L., and Gyllensten, U. (2010) Global and unbiased detection of splice junctions from RNA-seq data, Genome Biol 11, R34.
63. Feuk, L., Carson, A. R., and Scherer, S. W. (2006) Structural variation in the human genome, Nat Rev Genet 7, 85-97. (Pubitemid 43128895)
64. Chiang, D. Y., Getz, G., Jaffe, D. B., OKelly, M. J., Zhao, X., Carter, S. L., Russ, C., Nusbaum, C., Meyerson, M., and Lander, E. S. (2009) High-resolution mapping of copynumber alterations with massively parallel sequencing, Nat Methods 6, 99-103.
65. Lupski, J. R., Reid, J. G., Gonzaga-Jauregui, C., Rio Deiros, D., Chen, D. C., Nazareth, L., Bainbridge, M., Dinh, H., Jing, C., Wheeler, D. A., McGuire, A. L., Zhang, F., Stankiewicz, P., Halperin, J. J., Yang, C., Gehman, C., Guo, D., Irikat, R. K., Tom, W., Fantin, N. J., Muzny, D. M., and Gibbs, R. A. Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy, N Engl J Med 362, 1181-1191.
66. Frazer, K. A., Murray, S. S., Schork, N. J., and Topol, E. J. (2009) Human genetic variation and its contribution to complex traits, Nat Rev Genet 10, 241-251.
67. Klein, T. E., Chang, J. T., Cho, M. K., Easton, K. L., Fergerson, R., Hewett, M., Lin, Z., Liu, Y., Liu, S., Oliver, D. E., Rubin, D. L., Shafa, F., Stuart, J. M., and Altman, R. B. (2001) Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base, Pharmacogenomics J 1, 167-170. (Pubitemid 33756654)
68. Ng, P. C., Murray, S. S., Levy, S., and Venter, J. C. (2009) An agenda for personalized medicine, Nature 461, 724-726.
69. Ashley, E. A., Butte, A. J., Wheeler, M. T., Chen, R., Klein, T. E., Dewey, F. E., Dudley, J. T., Ormond, K. E., Pavlovic, A., Morgan, A. A., Pushkarev, D., Neff, N. F., Hudgins, L., Gong, L., Hodges, L. M., Berlin, D. S., Thorn, C. F., Sangkuhl, K., Hebert, J. M., Woon, M., Sagreiya, H., Whaley, R., Knowles, J. W., Chou, M. F., Thakuria, J. V., Rosenbaum, A. M., Zaranek, A. W., Church, G. M., Greely, H. T., Quake, S. R., and Altman, R. B. (2010) Clinical assessment incorporating a personal genome, Lancet 375, 1525-1535.