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12 results on '"Delehaunty K"'

1. Integrated genomic analyses of ovarian carcinoma

Author

Bell, D., Berchuck, A., Birrer, M., Chien, J., Cramer, D. W., Dao, F., Dhir, R., DiSaia, P., Gabra, H., Glenn, P., Godwin, A. K., Gross, J., Hartmann, L., Huang, M., Huntsman, D. G., Iacocca, M., Imielinski, M., Kalloger, S., Karlan, B. Y., Morrison, C., Mutch, D., Olvera, N., Orsulic, S., Park, K., Petrelli, N., Rabeno, B., Rader, J. S., Sikic, B. I., Smith-McCune, K., Sood, A. K., Bowtell, D., Testa, J. R., Chang, K., Dinh, H. H., Drummond, J. A., Fowler, G., Gunaratne, P., Hawes, A. C., Kovar, C. L., Lewis, L. R., Morgan, M. B., Newsham, I. F., Santibanez, J., Reid, J. G., Trevino, L. R., Wu, Y.-Q., Wang, M., Muzny, D. M., Wheeler, D. A., Gibbs, R. A., Sivachenko, A. Y., Sougnez, C., Wilkinson, J., Bloom, T., Fennell, T., Baldwin, J., Gabriel, S., Lander, E. S., Ding, L., Fulton, R. S., Koboldt, D. C., McLellan, M. D., Wylie, T., Walker, J., O’Laughlin, M., Dooling, D. J., Fulton, L., Abbott, R., Dees, N. D., Zhang, Q., Kandoth, C., Wendl, M., Schierding, W., Shen, D., Harris, C. C., Schmidt, H., Kalicki, J., Delehaunty, K. D., Fronick, C. C., Demeter, R., Cook, L., Wallis, J. W., Lin, L., Magrini, V. J., Hodges, J. S., Eldred, J. M., Smith, S. M., Pohl, C. S., Vandin, F., Raphael, B. J., Weinstock, G. M., Mardis, E. R., Wilson, R. K., Meyerson, M., Winckler, W., Verhaak, R. G. W., Carter, S. L., Mermel, C. H., Nguyen, H., Onofrio, R. C., Hubbard, D., Gupta, S., Crenshaw, A., Ramos, A. H., Protopopov, A., Zhang, Juinhua, Kim, T. M., Perna, I., Xiao, Y., Ren, G., Sathiamoorthy, N., Lee, E., Park, P. J., Kucherlapati, R., Absher, D. M., Waite, L., Sherlock, G., Brooks, J. D., Li, J. Z., Xu, J., Myers, R. M., Laird, P. W., Cope, L., Herman, J. G., Shen, H., Weisenberger, D. J., Noushmehr, H., Pan, F., Triche, T., Jr, Berman, B. P., Van Den Berg, D. J., Buckley, J., Baylin, S. B., Jakkula, L. R., Dorton, S., Marr, H., Choi, Y. G., Wang, V., Wang, N. J., Ngai, J., Conboy, J. G., Feiler, H. S., Socci, N. D., Liang, Y., Lash, A. E., Brennan, C., Viale, A., Meng, S., Shi, Y., Li, L., Turman, Y. J., Zang, D., Helms, E. B., Zhou, X., Wu, J., Topal, M. D., Zhang, Junihua, Wu, C. J., Shukla, S., Sivachenko, A., Jing, R., Liu, Y., Noble, M., Carter, H., Kim, D., Karchin, R., Korkola, J. E., Heiser, L. M., Cho, R. J., Hu, Z., Parvin, B., Cerami, E., Olshen, A., Reva, B., Antipin, Y., Shen, R., Mankoo, P., Sheridan, R., Ciriello, G., Chang, W. K., Bernanke, J. A., Haussler, D., Benz, C. C., Stuart, J. M., Benz, S. C., Sanborn, J. Z., Vaske, C. J., Zhu, J., Szeto, C., Scott, G. K., Yau, C., Wilkerson, M. D., Zhang, N., Akbani, R., Baggerly, K. A., Yung, W. K., Weinstein, J. N., Shelton, T., Grimm, D., Hatfield, M., Morris, S., Yena, P., Rhodes, P., Sherman, M., Paulauskis, J., Millis, S., Kahn, A., Greene, J. M., Sfeir, R., Jensen, M. A., Chen, J., Whitmore, J., Alonso, S., Jordan, J., Chu, A., Zhang, Jinghui, Barker, A., Compton, C., Eley, G., Ferguson, M., Fielding, P., Gerhard, D. S., Myles, R., Schaefer, C., Mills Shaw, K. R., Vaught, J., Vockley, J. B., Good, P. J., Guyer, M. S., Ozenberger, B., Peterson, J., and Thomson, E.

Published
2011
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2. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

Author

Hoadley, K., Yau, C., Wolf, D., Cherniack, A., Tamborero, D., Ng, S., Leiserson, M., Niu, B., McLellan, M., Uzunangelov, V., Zhang, J., Kandoth, C., Akbani, R., Shen, H., Omberg, L., Chu, A., Margolin, A., van't Veer, L., Lopez-Bigas, N., Laird, P., Raphael, B., Ding, L., Robertson, A., Byers, L., Mills, G., Weinstein, J., Van Waes, C., Chen, Z., Collisson, E., Benz, C., Perou, C., Stuart, J., Abbott, R., Abbott, S., Aksoy, B., Aldape, K., Ally, A., Amin, S., Anastassiou, D., Auman, J., Baggerly, K., Balasundaram, M., Balu, S., Baylin, S., Benz, S., Berman, B., Bernard, B., Bhatt, A., Birol, I., Black, A., Bodenheimer, T., Bootwalla, M., Bowen, J., Bressler, R., Bristow, C., Brooks, A., Broom, B., Buda, E., Burton, R., Butterfield, Y., Carlin, D., Carter, S., Casasent, T., Chang, K., Chanock, S., Chin, L., Cho, D., Cho, J., Chuah, E., Chun, H., Cibulskis, K., Ciriello, G., Cleland, J., Cline, M., Craft, B., Creighton, C., Danilova, L., Davidsen, T., Davis, C., Dees, N., Delehaunty, K., Demchok, J., Dhalla, N., DiCara, D., Dinh, H., Dobson, J., Dodda, D., Doddapaneni, H., Donehower, L., Dooling, D., Dresdner, G., Drummond, J., Eakin, A., Edgerton, M., Eldred, J., Eley, G., Ellrott, K., Fan, C., Fei, S., Felau, I., Frazer, S., Freeman, S., Frick, J., Fronick, C., Fulton, L., Fulton, R., Gabriel, S., Gao, J., Gastier-Foster, J., Gehlenborg, N., George, M., Getz, G., Gibbs, R., Goldman, M., Gonzalez-Perez, A., Gross, B., Guin, R., Gunaratne, P., Hadjipanayis, A., Hamilton, M., Hamilton, S., Han, L., Han, Y., Harper, H., Haseley, P., Haussler, D., Hayes, D., Heiman, D., Helman, E., Helsel, C., Herbrich, S., Herman, J., Hinoue, T., Hirst, C., Hirst, M., Holt, R., Hoyle, A., Iype, L., Jacobsen, A., Jeffreys, S., Jensen, M., Jones, C., Jones, S., Ju, Z., Jung, J., Kahles, A., Kahn, A., Kalicki-Veizer, J., Kalra, D., Kanchi, K., Kane, D., Kim, H., Kim, J., Knijnenburg, T., Koboldt, D., Kovar, C., Kramer, R., Kreisberg, R., Kucherlapati, R., Ladanyi, M., Lander, E., Larson, D., Lawrence, M., Lee, D., Lee, E., Lee, S., Lee, W., Lehmann, K., Leinonen, K., Leraas, K., Lerner, S., Levine, D., Lewis, L., Ley, T., Li, H., Li, J., Li, W., Liang, H., Lichtenberg, T., Lin, J., Lin, L., Lin, P., Liu, W., Liu, Y., Lorenzi, P., Lu, C., Lu, Y., Luquette, L., Ma, S., Magrini, V., Mahadeshwar, H., Mardis, E., Marra, M., Mayo, M., McAllister, C., McGuire, S., McMichael, J., Melott, J., Meng, S., Meyerson, M., Mieczkowski, P., Miller, C., Miller, M., Moore, R., Morgan, M., Morton, D., Mose, L., Mungall, A., Muzny, D., Nguyen, L., Noble, M., Noushmehr, H., O'Laughlin, M., Ojesina, A., Yang, T., Ozenberger, B., Pantazi, A., Parfenov, M., Park, P., Parker, J., Paull, E., Pedamallu, C., Pihl, T., Pohl, C., Pot, D., Protopopov, A., Przytycka, T., Radenbaugh, A., Ramirez, N., Ramirez, R., Ratsch, G., Reid, J., Ren, X., Reva, B., Reynolds, S., Rhie, S., Roach, J., Rovira, H., Ryan, M., Saksena, G., Salama, S., Sander, C., Santoso, N., Schein, J., Schmidt, H., Schultz, N., Schumacher, S., Seidman, J., Senbabaoglu, Y., Seth, S., Sharpe, S., Shen, R., Sheth, M., Shi, Y., Shmulevich, I., Silva, G., Simons, J., Sinha, R., Sipahimalani, P., Smith, S., Sofia, H., Sokolov, A., Soloway, M., Song, X., Sougnez, C., Spellman, P., Staudt, L., Stewart, C., Stojanov, P., Su, X., Sumer, S., Sun, Y., Swatloski, T., Tabak, B., Tam, A., Tan, D., Tang, J., Tarnuzzer, R., Taylor, B., Thiessen, N., Thorsson, V., Triche, T., Van Den Berg, D., Vandin, F., Varhol, Richard, Vaske, C., Veluvolu, U., Verhaak, R., Voet, D., Walker, J., Wallis, J., Waltman, P., Wan, Y., Wang, M., Wang, W., Wang, Z., Waring, S., Weinhold, N., Weisenberger, D., Wendl, M., Wheeler, D., Wilkerson, M., Wilson, R., Wise, L., Wong, A., Wu, C., Wu, H., Wu, J., Wylie, T., Xi, L., Xi, R., Xia, Z., Xu, A., Yang, D., Yang, L., Yang, Y., Yao, J., Yao, R., Ye, K., Yoshihara, K., Yuan, Y., Yung, A., Zack, T., Zeng, D., Zenklusen, J., Zhang, H., Zhang, N., Zhang, Q., Zhang, W., Zhao, W., Zheng, S., Zhu, J., Zmuda, E., Zou, L., Hoadley, K., Yau, C., Wolf, D., Cherniack, A., Tamborero, D., Ng, S., Leiserson, M., Niu, B., McLellan, M., Uzunangelov, V., Zhang, J., Kandoth, C., Akbani, R., Shen, H., Omberg, L., Chu, A., Margolin, A., van't Veer, L., Lopez-Bigas, N., Laird, P., Raphael, B., Ding, L., Robertson, A., Byers, L., Mills, G., Weinstein, J., Van Waes, C., Chen, Z., Collisson, E., Benz, C., Perou, C., Stuart, J., Abbott, R., Abbott, S., Aksoy, B., Aldape, K., Ally, A., Amin, S., Anastassiou, D., Auman, J., Baggerly, K., Balasundaram, M., Balu, S., Baylin, S., Benz, S., Berman, B., Bernard, B., Bhatt, A., Birol, I., Black, A., Bodenheimer, T., Bootwalla, M., Bowen, J., Bressler, R., Bristow, C., Brooks, A., Broom, B., Buda, E., Burton, R., Butterfield, Y., Carlin, D., Carter, S., Casasent, T., Chang, K., Chanock, S., Chin, L., Cho, D., Cho, J., Chuah, E., Chun, H., Cibulskis, K., Ciriello, G., Cleland, J., Cline, M., Craft, B., Creighton, C., Danilova, L., Davidsen, T., Davis, C., Dees, N., Delehaunty, K., Demchok, J., Dhalla, N., DiCara, D., Dinh, H., Dobson, J., Dodda, D., Doddapaneni, H., Donehower, L., Dooling, D., Dresdner, G., Drummond, J., Eakin, A., Edgerton, M., Eldred, J., Eley, G., Ellrott, K., Fan, C., Fei, S., Felau, I., Frazer, S., Freeman, S., Frick, J., Fronick, C., Fulton, L., Fulton, R., Gabriel, S., Gao, J., Gastier-Foster, J., Gehlenborg, N., George, M., Getz, G., Gibbs, R., Goldman, M., Gonzalez-Perez, A., Gross, B., Guin, R., Gunaratne, P., Hadjipanayis, A., Hamilton, M., Hamilton, S., Han, L., Han, Y., Harper, H., Haseley, P., Haussler, D., Hayes, D., Heiman, D., Helman, E., Helsel, C., Herbrich, S., Herman, J., Hinoue, T., Hirst, C., Hirst, M., Holt, R., Hoyle, A., Iype, L., Jacobsen, A., Jeffreys, S., Jensen, M., Jones, C., Jones, S., Ju, Z., Jung, J., Kahles, A., Kahn, A., Kalicki-Veizer, J., Kalra, D., Kanchi, K., Kane, D., Kim, H., Kim, J., Knijnenburg, T., Koboldt, D., Kovar, C., Kramer, R., Kreisberg, R., Kucherlapati, R., Ladanyi, M., Lander, E., Larson, D., Lawrence, M., Lee, D., Lee, E., Lee, S., Lee, W., Lehmann, K., Leinonen, K., Leraas, K., Lerner, S., Levine, D., Lewis, L., Ley, T., Li, H., Li, J., Li, W., Liang, H., Lichtenberg, T., Lin, J., Lin, L., Lin, P., Liu, W., Liu, Y., Lorenzi, P., Lu, C., Lu, Y., Luquette, L., Ma, S., Magrini, V., Mahadeshwar, H., Mardis, E., Marra, M., Mayo, M., McAllister, C., McGuire, S., McMichael, J., Melott, J., Meng, S., Meyerson, M., Mieczkowski, P., Miller, C., Miller, M., Moore, R., Morgan, M., Morton, D., Mose, L., Mungall, A., Muzny, D., Nguyen, L., Noble, M., Noushmehr, H., O'Laughlin, M., Ojesina, A., Yang, T., Ozenberger, B., Pantazi, A., Parfenov, M., Park, P., Parker, J., Paull, E., Pedamallu, C., Pihl, T., Pohl, C., Pot, D., Protopopov, A., Przytycka, T., Radenbaugh, A., Ramirez, N., Ramirez, R., Ratsch, G., Reid, J., Ren, X., Reva, B., Reynolds, S., Rhie, S., Roach, J., Rovira, H., Ryan, M., Saksena, G., Salama, S., Sander, C., Santoso, N., Schein, J., Schmidt, H., Schultz, N., Schumacher, S., Seidman, J., Senbabaoglu, Y., Seth, S., Sharpe, S., Shen, R., Sheth, M., Shi, Y., Shmulevich, I., Silva, G., Simons, J., Sinha, R., Sipahimalani, P., Smith, S., Sofia, H., Sokolov, A., Soloway, M., Song, X., Sougnez, C., Spellman, P., Staudt, L., Stewart, C., Stojanov, P., Su, X., Sumer, S., Sun, Y., Swatloski, T., Tabak, B., Tam, A., Tan, D., Tang, J., Tarnuzzer, R., Taylor, B., Thiessen, N., Thorsson, V., Triche, T., Van Den Berg, D., Vandin, F., Varhol, Richard, Vaske, C., Veluvolu, U., Verhaak, R., Voet, D., Walker, J., Wallis, J., Waltman, P., Wan, Y., Wang, M., Wang, W., Wang, Z., Waring, S., Weinhold, N., Weisenberger, D., Wendl, M., Wheeler, D., Wilkerson, M., Wilson, R., Wise, L., Wong, A., Wu, C., Wu, H., Wu, J., Wylie, T., Xi, L., Xi, R., Xia, Z., Xu, A., Yang, D., Yang, L., Yang, Y., Yao, J., Yao, R., Ye, K., Yoshihara, K., Yuan, Y., Yung, A., Zack, T., Zeng, D., Zenklusen, J., Zhang, H., Zhang, N., Zhang, Q., Zhang, W., Zhao, W., Zheng, S., Zhu, J., Zmuda, E., and Zou, L.

Abstract

© 2014 Elsevier Inc. Recent genomic analyses of pathologically defined tumor types identify 'within-a-tissue' disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-oforigin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head and neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pancancer subtypes. The multiplatform classification, while correlated with tissue-of-origin, provides independent information for predicting clinical outcomes. All data sets are available for data-mining from a unified resource to support further biological discoveries and insights into novel therapeutic strategies.

Published
2014

3. Genome analysis of the platypus reveals unique signatures of evolution (Nature (2008) 453, (175-183))

Author

Warren, WC, Hillier, LW, Marshall Graves, JA, Birney, E, Ponting, CP, Grützner, F, Belov, K, Miller, W, Clarke, L, Chinwalla, AT, Yang, S-P, Heger, A, Locke, DP, Miethke, P, Waters, PD, Veyrunes, F, Fulton, L, Fulton, B, Graves, T, Wallis, J, Puente, XS, López-Otín, C, Ordó̃ez, GR, Eichler, EE, Chen, L, Cheng, Z, Deakin, JE, Alsop, A, Thompson, K, Kirby, P, Papenfuss, AT, Wakefield, MJ, Olender, T, Lancet, D, Huttley, GA, Smit, AFA, Pask, A, Temple-Smith, P, Batzer, MA, Walker, JA, Konkel, MK, Harris, RS, Whittington, CM, Wong, ESW, Gemmell, NJ, Buschiazzo, E, Vargas Jentzsch, IM, Merkel, A, Schmitz, J, Zemann, A, Churakov, G, Kriegs, JO, Brosius, J, Murchison, EP, Sachidanandam, R, Smith, C, Hannon, GJ, Tsend-Ayush, E, McMillan, D, Attenborough, R, Rens, W, Ferguson-Smith, M, Lefèvre, CM, Sharp, JA, Nicholas, KR, Ray, DA, Kube, M, Reinhardt, R, Pringle, TH, Taylor, J, Jones, RC, Nixon, B, Dacheux, J-L, Niwa, H, Sekita, Y, Huang, X, Stark, A, Kheradpour, P, Kellis, M, Flicek, P, Chen, Y, Webber, C, Hardison, R, Nelson, J, Hallsworth-Pepin, K, Delehaunty, K, Markovic, C, Minx, P, Feng, Y, Kremitzki, C, Mitreva, M, Glasscock, J, Wylie, T, Wohldmann, P, Thiru, P, Nhan, MN, Pohl, CS, Smith, SM, Hou, S, Nefedov, M, De Jong, PJ, Renfree, MB, Mardis, ER, and Wilson, RK

Published
2008

4. Comprehensive molecular characterization of human colon and rectal cancer

Author

Muzny, D., Bainbridge, M., Chang, K., Dinh, H., Drummond, J., Fowler, G., Kovar, C., Lewis, L., Morgan, M., Newsham, I., Reid, J., Santibanez, J., Shinbrot, E., Trevino, L., Wu, Y., Wang, M., Gunaratne, P., Donehower, L., Creighton, C., Wheeler, D., Gibbs, R., Lawrence, M., Voet, D., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E., Gabriel, S., Ding, L., Fulton, R., Koboldt, D., Wylie, T., Walker, J., Dooling, D., Fulton, L., Delehaunty, K., Fronick, C., Demeter, R., Mardis, E., Wilson, R., Chu, A., Chun, H., Mungall, A., Pleasance, E., Gordon Robertson, A., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y., Chuah, E., Coope, R., Dhalla, N., Guin, R., Hirst, C., Hirst, M., Holt, R., Lee, D., Li, H., Mayo, M., Moore, R., Schein, J., Slobodan, J., Tam, A., Thiessen, N., Varhol, Richard, Zeng, T., Zhao, Y., Jones, S., Marra, M., Bass, A., Ramos, A., Saksena, G., Cherniack, A., Schumacher, S., Tabak, B., Carter, S., Pho, N., Nguyen, H., Onofrio, R., Crenshaw, A., Ardlie, K., Muzny, D., Bainbridge, M., Chang, K., Dinh, H., Drummond, J., Fowler, G., Kovar, C., Lewis, L., Morgan, M., Newsham, I., Reid, J., Santibanez, J., Shinbrot, E., Trevino, L., Wu, Y., Wang, M., Gunaratne, P., Donehower, L., Creighton, C., Wheeler, D., Gibbs, R., Lawrence, M., Voet, D., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E., Gabriel, S., Ding, L., Fulton, R., Koboldt, D., Wylie, T., Walker, J., Dooling, D., Fulton, L., Delehaunty, K., Fronick, C., Demeter, R., Mardis, E., Wilson, R., Chu, A., Chun, H., Mungall, A., Pleasance, E., Gordon Robertson, A., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y., Chuah, E., Coope, R., Dhalla, N., Guin, R., Hirst, C., Hirst, M., Holt, R., Lee, D., Li, H., Mayo, M., Moore, R., Schein, J., Slobodan, J., Tam, A., Thiessen, N., Varhol, Richard, Zeng, T., Zhao, Y., Jones, S., Marra, M., Bass, A., Ramos, A., Saksena, G., Cherniack, A., Schumacher, S., Tabak, B., Carter, S., Pho, N., Nguyen, H., Onofrio, R., Crenshaw, A., and Ardlie, K.

Abstract

To characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and microRNA expression. A subset of these samples (97) underwent low-depth-of-coverage whole-genome sequencing. In total, 16% of colorectal carcinomas were found to be hypermutated: three-quarters of these had the expected high microsatellite instability, usually with hypermethylation and MLH1 silencing, and one-quarter had somatic mismatch-repair gene and polymerase µ (POLE) mutations. Excluding the hypermutated cancers, colon and rectum cancers were found to have considerably similar patterns of genomic alteration. Twenty-four genes were significantly mutated, and in addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9 and FAM123B. Recurrent copy-number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include the fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive colorectal carcinoma and an important role for MYC-directed transcriptional activation and repression. © 2012 Macmillan Publishers Limited. All rights reserved.

Published
2012

5. A high-resolution map of human evolutionary constraint using 29 mammals.

Author

Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, and Kellis M

Subjects
Animals, Disease, Exons genetics, Genomics, Health, Humans, Molecular Sequence Annotation, Phylogeny, RNA classification, RNA genetics, Selection, Genetic genetics, Sequence Alignment, Sequence Analysis, DNA, Evolution, Molecular, Genome genetics, Genome, Human genetics, Mammals genetics
Abstract

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.

Published
2011
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6. Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome.

Author

Baxter L, Tripathy S, Ishaque N, Boot N, Cabral A, Kemen E, Thines M, Ah-Fong A, Anderson R, Badejoko W, Bittner-Eddy P, Boore JL, Chibucos MC, Coates M, Dehal P, Delehaunty K, Dong S, Downton P, Dumas B, Fabro G, Fronick C, Fuerstenberg SI, Fulton L, Gaulin E, Govers F, Hughes L, Humphray S, Jiang RHY, Judelson H, Kamoun S, Kyung K, Meijer H, Minx P, Morris P, Nelson J, Phuntumart V, Qutob D, Rehmany A, Rougon-Cardoso A, Ryden P, Torto-Alalibo T, Studholme D, Wang Y, Win J, Wood J, Clifton SW, Rogers J, Van den Ackerveken G, Jones JDG, McDowell JM, Beynon J, and Tyler BM

Subjects
Adaptation, Physiological, Amino Acid Sequence, Enzymes genetics, Gene Dosage, Genes, Host-Pathogen Interactions, Metabolic Networks and Pathways genetics, Molecular Sequence Data, Oomycetes pathogenicity, Oomycetes physiology, Phytophthora genetics, Polymorphism, Single Nucleotide, Proteins genetics, Selection, Genetic, Sequence Analysis, DNA, Spores physiology, Synteny, Virulence Factors genetics, Arabidopsis parasitology, Evolution, Molecular, Genome, Oomycetes genetics, Oomycetes growth & development, Plant Diseases parasitology
Abstract

Many oomycete and fungal plant pathogens are obligate biotrophs, which extract nutrients only from living plant tissue and cannot grow apart from their hosts. Although these pathogens cause substantial crop losses, little is known about the molecular basis or evolution of obligate biotrophy. Here, we report the genome sequence of the oomycete Hyaloperonospora arabidopsidis (Hpa), an obligate biotroph and natural pathogen of Arabidopsis thaliana. In comparison with genomes of related, hemibiotrophic Phytophthora species, the Hpa genome exhibits dramatic reductions in genes encoding (i) RXLR effectors and other secreted pathogenicity proteins, (ii) enzymes for assimilation of inorganic nitrogen and sulfur, and (iii) proteins associated with zoospore formation and motility. These attributes comprise a genomic signature of evolution toward obligate biotrophy.

Published
2010
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7. The B73 maize genome: complexity, diversity, and dynamics.

Author

Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, and Wilson RK

Subjects
Base Sequence, Centromere genetics, Chromosome Mapping, Chromosomes, Plant genetics, Crops, Agricultural genetics, DNA Copy Number Variations, DNA Methylation, DNA Transposable Elements, DNA, Plant genetics, Genes, Plant, Inbreeding, MicroRNAs genetics, Molecular Sequence Data, Ploidies, RNA, Plant genetics, Recombination, Genetic, Retroelements, Genetic Variation, Genome, Plant, Sequence Analysis, DNA, Zea mays genetics
Abstract

We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

Published
2009
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8. The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism.

Author

Dieterich C, Clifton SW, Schuster LN, Chinwalla A, Delehaunty K, Dinkelacker I, Fulton L, Fulton R, Godfrey J, Minx P, Mitreva M, Roeseler W, Tian H, Witte H, Yang SP, Wilson RK, and Sommer RJ

Subjects
Amino Acid Sequence, Animals, Caenorhabditis elegans genetics, Evolution, Molecular, Exons genetics, Host-Parasite Interactions, Introns genetics, Molecular Sequence Data, Phylogeny, Sequence Homology, Amino Acid, Chromosome Mapping, Coleoptera parasitology, Genes, Helminth, Genome, Helminth, Intestines parasitology, Nematoda physiology
Abstract

Here we present a draft genome sequence of the nematode Pristionchus pacificus, a species that is associated with beetles and is used as a model system in evolutionary biology. With 169 Mb and 23,500 predicted protein-coding genes, the P. pacificus genome is larger than those of Caenorhabditis elegans and the human parasite Brugia malayi. Compared to C. elegans, the P. pacificus genome has more genes encoding cytochrome P450 enzymes, glucosyltransferases, sulfotransferases and ABC transporters, many of which were experimentally validated. The P. pacificus genome contains genes encoding cellulase and diapausin, and cellulase activity is found in P. pacificus secretions, indicating that cellulases can be found in nematodes beyond plant parasites. The relatively higher number of detoxification and degradation enzymes in P. pacificus is consistent with its necromenic lifestyle and might represent a preadaptation for parasitism. Thus, comparative genomics analysis of three ecologically distinct nematodes offers a unique opportunity to investigate the association between genome structure and lifestyle.

Published
2008
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9. Evolution of genes and genomes on the Drosophila phylogeny.

Author

Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, and MacCallum I

Subjects
Animals, Codon genetics, DNA Transposable Elements genetics, Drosophila immunology, Drosophila metabolism, Drosophila Proteins genetics, Gene Order genetics, Genome, Mitochondrial genetics, Immunity genetics, Multigene Family genetics, RNA, Untranslated genetics, Reproduction genetics, Sequence Alignment, Sequence Analysis, DNA, Synteny genetics, Drosophila classification, Drosophila genetics, Evolution, Molecular, Genes, Insect genetics, Genome, Insect genetics, Genomics, Phylogeny
Abstract

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

Published
2007
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10. Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid.

Author

McClelland M, Sanderson KE, Clifton SW, Latreille P, Porwollik S, Sabo A, Meyer R, Bieri T, Ozersky P, McLellan M, Harkins CR, Wang C, Nguyen C, Berghoff A, Elliott G, Kohlberg S, Strong C, Du F, Carter J, Kremizki C, Layman D, Leonard S, Sun H, Fulton L, Nash W, Miner T, Minx P, Delehaunty K, Fronick C, Magrini V, Nhan M, Warren W, Florea L, Spieth J, and Wilson RK

Subjects
Base Sequence, Gene Library, Genome Components genetics, Humans, Microarray Analysis, Molecular Sequence Data, Pseudogenes genetics, Sequence Analysis, DNA, Species Specificity, Evolution, Molecular, Genetic Variation, Genome, Bacterial, Mutation genetics, Salmonella paratyphi A genetics, Salmonella typhi genetics
Abstract

Salmonella enterica serovars often have a broad host range, and some cause both gastrointestinal and systemic disease. But the serovars Paratyphi A and Typhi are restricted to humans and cause only systemic disease. It has been estimated that Typhi arose in the last few thousand years. The sequence and microarray analysis of the Paratyphi A genome indicates that it is similar to the Typhi genome but suggests that it has a more recent evolutionary origin. Both genomes have independently accumulated many pseudogenes among their approximately 4,400 protein coding sequences: 173 in Paratyphi A and approximately 210 in Typhi. The recent convergence of these two similar genomes on a similar phenotype is subtly reflected in their genotypes: only 30 genes are degraded in both serovars. Nevertheless, these 30 genes include three known to be important in gastroenteritis, which does not occur in these serovars, and four for Salmonella-translocated effectors, which are normally secreted into host cells to subvert host functions. Loss of function also occurs by mutation in different genes in the same pathway (e.g., in chemotaxis and in the production of fimbriae).

Published
2004
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11. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes.

Author

Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T, Chinwalla A, Delehaunty A, Delehaunty K, Du H, Fewell G, Fulton L, Fulton R, Graves T, Hou SF, Latrielle P, Leonard S, Mardis E, Maupin R, McPherson J, Miner T, Nash W, Nguyen C, Ozersky P, Pepin K, Rock S, Rohlfing T, Scott K, Schultz B, Strong C, Tin-Wollam A, Yang SP, Waterston RH, Wilson RK, Rozen S, and Page DC

Subjects
Chromosomes, Human, X genetics, Crossing Over, Genetic genetics, DNA Transposable Elements genetics, Euchromatin genetics, Female, Gene Amplification genetics, Gene Conversion genetics, Genes genetics, Heterochromatin genetics, Humans, In Situ Hybridization, Fluorescence, Male, Models, Genetic, Multigene Family genetics, Organ Specificity, Pseudogenes genetics, Sequence Homology, Nucleic Acid, Sex Characteristics, Species Specificity, Testis metabolism, Transcription, Genetic genetics, Chromosomes, Human, Y genetics, Evolution, Molecular, Sex Determination Processes, Transducin
Abstract

The male-specific region of the Y chromosome, the MSY, differentiates the sexes and comprises 95% of the chromosome's length. Here, we report that the MSY is a mosaic of heterochromatic sequences and three classes of euchromatic sequences: X-transposed, X-degenerate and ampliconic. These classes contain all 156 known transcription units, which include 78 protein-coding genes that collectively encode 27 distinct proteins. The X-transposed sequences exhibit 99% identity to the X chromosome. The X-degenerate sequences are remnants of ancient autosomes from which the modern X and Y chromosomes evolved. The ampliconic class includes large regions (about 30% of the MSY euchromatin) where sequence pairs show greater than 99.9% identity, which is maintained by frequent gene conversion (non-reciprocal transfer). The most prominent features here are eight massive palindromes, at least six of which contain testis genes.

Published
2003
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12. Initial sequencing and analysis of the human genome.

Author

Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, 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 JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, 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 JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, 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 DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, 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 RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, and Szustakowki J

Subjects
Animals, Chromosome Mapping, Conserved Sequence, CpG Islands, DNA Transposable Elements, Databases, Factual, Drug Industry, Evolution, Molecular, Forecasting, GC Rich Sequence, Gene Duplication, Genes, Genetic Diseases, Inborn, Genetics, Medical, Humans, Mutation, Private Sector, Proteins genetics, Proteome, Public Sector, RNA genetics, Repetitive Sequences, Nucleic Acid, Species Specificity, Genome, Human, Human Genome Project, Sequence Analysis, DNA methods
Abstract

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Published
2001
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