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4. Genome Maps 7: The Human Transcript Map

Author

Jasny, Barbara R., Schuler, G. D., Boguski, M. S., Hudson, T. J., Hui, L., Ma, J., Castle, A. B., Wu, X., Silva, J., Nusbaum, H. C., Birren, B. B., Slonim, D. K., Rozen, S., Stein, L. D., Page, D., Lander, E. S., Stewart, E. A., Aggarwal, A., Bajorek, E., Brady, S., Chu, A., Fang, N., Hadley, D., Harris, M., Hussain, S., Maratukulam, A., Perkins, S., Piercy, M., Qin, F., Reif, T., Sanders, C., She, X., Sun, W. L., Tabar, P., Voyticky, S., Mader, C., McKusick, K. B., Fan, J. B., Cowles, S., Quackenbush, J., Vollrath, D., Myers, R. M., Cox, D. R., Butler, A., Clee, C., Dibling, T., East, C., Edwards, C., Garrett, C., Green, L., Harrison, P., Hicks, A., Holloway, E., Ranby, S., MacGilvery, A., Mungall, A., Peck, A., Wilmer, T., Soderlund, C., Rice, K., Dunham, I., Bentley, D., Deloukas, P., Gyapay, G., Chiannilkulchai, N., Fizames, C., Bentolila, S., Duprat, S., Vega-Czarny, N., Muselet, D., Drouot, N., Morissette, J., Beckmann, J., Weissenbach., J., James, M. R., White, R. E., Thangarajah, T., Day, P. J. R., Goodfellow, P. N., Schmitt, K., Walter, N. A. R., Berry, R., Iorio, K. R., Sikela, J. M., Polymeropoulos, M. H., Torres, R., Ide, S. S. E., Dehejia, A., Houlgatte, R., Auffray, C., Adams, M. D., Phillips, C., Brandon, R., Sandusky, M., Venter, J. C., Seki, N., Nagase, T., Ishikawa, K., Nomura, N., Rodriguez-Tome, P., Matise, T. C., Lee, W. Y., Swanson, K. A., and Hudson, J. R.

Published
1996

5. A Gene Map of the Human Genome

Author

Schuler, G. D., Boguski, M. S., Stewart, E. A., Stein, L. D., Gyapay, G., Rice, K., White, R. E., Rodriguez-Tomé, P., Aggarwal, A., Bajorek, E., Bentolila, S., Birren, B. B., Butler, A., Castle, A. B., Chiannilkulchai, N., Chu, A., Clee, C., Cowles, S., Day, P. J. R., Dibling, T., Drouot, N., Dunham, I., Duprat, S., East, C., Edwards, C., Fang, N., Fizames, C., Garrett, C., Green, L., Hadley, D., Harris, M., Harrison, P., Brady, S., Hicks, A., Holloway, E., Hui, L., Hussain, S., Ma, J., MacGilvery, A., Mader, C., Maratukulam, A., Matise, T. C., McKusick, K. B., Morissette, J., Mungall, A., Muselet, D., Nusbaum, H. C., Page, D. C., Peck, A., Perkins, S., Piercy, M., Qin, F., Quackenbush, J., Ranby, S., Reif, T., Rozen, S., Sanders, C., She, X., Silva, J., Slonim, D. K., Soderlund, C., Tabar, P., Thangarajah, T., Vega-Czarny, N., Vollrath, D., Voyticky, S., Wilmer, T., Wu, X., Adams, M. D., Aufiray, C., Walter, N. A. R., Brandon, R., Dehejia, A., Goodfellow, P. N., Houlgatte, R., Hudson, J. R., Ide, S. E., Iorio, K. R., Lee, W. Y., Seki, N., Nagase, T., Ishikawa, K., Nomura, N., Phillips, C., Polymeropoulos, M. H., Sandusky, M., Schmitt, K., Berry, R., Swanson, K., Torres, R., Venter, J. C., Sikela, J. M., Beckmann, J. S., Weissenbach, J., Myers, R. M., Cox, D. R., James, M. R., Bentley, D., Deloukas, P., Lander, E. S., and Hudson, T. J.

Published
1996

7. A Physical Map of 30,000 Human Genes

Author

Deloukas, P., Schuler, G. D., Gyapay, G., Beasley, E. M., Soderlund, C., Rodriguez-Tomé, P., Hui, L., Matise, T. C., McKusick, K. B., Beckmann, J. S., Bentolila, S., Birren, B. B., Browne, J., Butler, A., Castle, A. B., Chiannilkulchai, N., Clee, C., Day, P. J. R., Dehejia, A., Dibling, T., Drouot, N., Duprat, S., Fizames, C., Fox, S., Gelling, S., Green, L., Harrison, P., Hocking, R., Holloway, E., Hunt, S., Keil, S., Lijnzaad, P., Ma, J., Mendis, A., Miller, J., Morissette, J., Muselet, D., Nusbaum, H. C., Peck, A., Rozen, S., Simon, D., Slonim, D. K., Staples, R., Stein, L. D., Stewart, E. A., Suchard, M. A., Thangarajah, T., Vega-Czarny, N., Webber, C., Wu, X., Hudson, J., Auffray, C., Nomura, N., Sikela, J. M., Polymeropoulous, M. H., James, M. R., Lander, E. S., Hudson, T. J., Myers, R. M., Cox, D. R., Weissenbach, J., Boguski, M. S., and Bentley, D. R.

Published
1998

9. Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse

Author

Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, Wade, C. M., Giulotto, E., Sigurdsson, S., Zoli, M., Gnerre, S., Imsland, F., Lear, T. L., Adelson, D. L., Bailey, E., Bellone, R. R., Blöcker, H., Distl, O., Edgar, R. C., Garber, M., Leeb, T., Mauceli, E., MacLeod, J. N., Penedo, M. C. T., Raison, J. M., Sharpe, T., Vogel, J., Andersson, L., Antczak, D. F., Biagi, T., Binns, M. M., Chowdhary, B. P., Coleman, S. J., Valle, G. Delia, Fryc, S., Guérin, G., Hasegawa, T., Hill, E. W., Jurka, J., Kiialainen, A., Lindgren, G., Liu, J., Magnani, E., Mickelson, J. R., Murray, J., Nergadze, S. G., Onofrio, R., Pedroni, S., Piras, M. F., Raudsepp, T., Rocchi, M., Røed, K. H., Ryder, O. A., Searle, S., Skow, L., Swinburne, J. E., Syvänen, A. C., Tozaki, T., Valberg, S. J., Vaudin, M., White, J. R., Zody, M. C., Lander, E. S., and Lindblad-Toh, K.

Published
2009
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12. Correction: Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation

Author

BIS, J. C., JIAN, X., KUNKLE, B. W., CHEN, Y., HAMILTON-NELSON, K. L., BUSH, W. S., SALERNO, W. J., LANCOUR, D., MA, Y., RENTON, A. E., MARCORA, E., FARRELL, J. J., ZHAO, Y., QU, L., AHMAD, S., AMIN, N., AMOUYEL, P., BEECHAM, G. W., BELOW, J. E., CAMPION, D., CANTWELL, L., CHARBONNIER, C., CHUNG, J., CRANE, P. K., CRUCHAGA, C., CUPPLES, L. A., DARTIGUES, Jean-Francois, DEBETTE, Stéphanie, DELEUZE, J. F., FULTON, L., GABRIEL, S. B., GENIN, E., GIBBS, R. A., GOATE, A., GRENIER-BOLEY, B., GUPTA, N., HAINES, J. L., HAVULINNA, A. S., HELISALMI, S., HILTUNEN, M., HOWRIGAN, D. P., IKRAM, M. A., KAPRIO, J., KONRAD, J., KUZMA, A., LANDER, E. S., LATHROP, M., LEHTIMAKI, T., LIN, H., MATTILA, K., MAYEUX, R., MUZNY, D. M., NASSER, W., NEALE, B., NHO, K., NICOLAS, G., PATEL, D., PERICAK-VANCE, M. A., PEROLA, M., PSATY, B. M., QUENEZ, O., RAJABLI, F., REDON, R., REITZ, C., REMES, A. M., SALOMAA, V., SARNOWSKI, C., SCHMIDT, H., SCHMIDT, M., SCHMIDT, R., SOININEN, H., THORNTON, T. A., TOSTO, G., TZOURIO, Christophe, VAN DER LEE, S. J., VAN DUIJN, C. M., VALLADARES, O., VARDARAJAN, B., WANG, L. S., WANG, W., WIJSMAN, E., WILSON, R. K., WITTEN, D., WORLEY, K. C., ZHANG, X., BELLENGUEZ, C., LAMBERT, J. C., KURKI, M. I., PALOTIE, A., DALY, M., BOERWINKLE, E., LUNETTA, K. L., DESTEFANO, A. L., DUPUIS, J., MARTIN, E. R., SCHELLENBERG, G. D., SESHADRI, S., NAJ, A. C., FORNAGE, M., and FARRER, L. A.

Subjects
0301 basic medicine, Computational biology, Biology, SEPIA, 03 medical and health sciences, Cellular and Molecular Neuroscience, Psychiatry and Mental health, 030104 developmental biology, 0302 clinical medicine, Immune system, VINTAGE, Transcriptional regulation, HEALTHY, Molecular Biology, 030217 neurology & neurosurgery, Exome sequencing
Abstract

Following publication, the authors noticed that ‘Laura Cantwell’, ‘Otto Valladares’, and ‘Li-San Wang’ were inadvertently omitted from the author list. These authors have now been added to the author list in 21st, 77th, and 79th position, respectively. This has been corrected in both the PDF and HTML versions of the article.

Published
2020

14. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Author

Okazaki, Y., Furuno, M., Kasukawa, T., Adachi, J., Bono, H., Kondo, S., Nikaido, I., Osato, N., Saito, R., Suzuki, H., Yamanaka, I., Kiyosawa, H., Yagi, K., Tomaru, Y., Hasegawa, Y., Nogami, A., Schonbach, C., Gojobori, T., Baldarelli, R., Hill, D. P., Bult, C., Hume, D. A., Quackenbush, J., Schriml, L. M., Kanapin, A., Matsuda, H., Batalov, S., Beisel, K. W., Blake, J. A., Bradt, D., Brusic, V., Chothia, C., Corbani, L. E., Cousins, S., Dalla, E., Dragani, T. A., Fletcher, C. F., Forrest, A., Frazer, K. S., Gaasterland, T., Gariboldi, M., Gissi, C., Godzik, A., Gough, J., Grimmond, S., Gustincich, S., Hirokawa, N., Jackson, I. J., Jarvis, E. D., Kanai, A., Kawaji, H., Kawasawa, Y., Kedzierski, R. M., King, B. L., Konagaya, A., Kurochkin, I. V., Lee, Y., Lenhard, B., Lyons, P. A., Maglott, D. R., Maltais, L., Marchionni, L., McKenzie, L., Miki, H., Nagashima, T., Numata, K., Okido, T., Pavan, W. J., Pertea, G., Pesole, G., Petrovsky, N., Pillai, R., Pontius, J. U., Qi, D., Ramachandran, S., Ravasi, T., Reed, J. C., Reed, D. J., Reid, J., Ring, B. Z., Ringwald, M., Sandelin, A., Schneider, C., Semple, C. A. M., Setou, M., Shimada, K., Sultana, R., Takenaka, Y., Taylor, M. S., Teasdale, R. D., Tomita, M., Verardo, R., Wagner, L., Wahlestedt, C., Wang, Y., Watanabe, Y., Wells, C., Wilming, L. G., Wynshaw-Boris, A., Yanagisawa, M., Yang, I., Yang, L., Yuan, Z., Zavolan, M., Zhu, Y., Zimmer, A., Carninci, P., Hayatsu, N., Hirozane-Kishikawa, T., Konno, H., Nakamura, M., Sakazume, N., Sato, K., Shiraki, T., Waki, K., Kawai, J., Aizawa, K., Arakawa, T., Fukuda, S., Hara, A., Hashizume, W., Imotani, K., Ishii, Y., Itoh, M., Kagawa, I., Miyazaki, A., Sakai, K., Sasaki, D., Shibata, K., Shinagawa, A., Yasunishi, A., Yoshino, M., Waterston, R., Lander, E. S., Rogers, J., Birney, E., and Hayashizaki, Y.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): The FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I & II Team*; FANTOM Consortium:; Y. Okazaki [1, 2]; M. Furuno [1]; T. Kasukawa [1, 3]; J. [...]

Published
2002
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16. 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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18. Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse

Author

Wade, C. M., Giulotto, E., Sigurdsson, S., Zoti, M., Gnerre, S., Imsland, F., Lear, T. L., Adelson, D. L., Bailey, E., Bellone, R. R., Blocker, H., Distl, O., Edgar, R. C., Garber, M., Leeb, T., Mauceli, E., MacLeod, J. N., T. Penedo, M. C., Raison, J. M., Sharpe, T., Vogel, J., Andersson, L., Antczak, D. F., Biagi, T., Binns, M. M., Chowdhary, B. P., Coleman, S. J., Valle, Delia G., Fryc, S., Guérin, G., Hasegawa, T., Hill, E. W., Jurka, J., Kiialainen, A., Lindgren, G., Liu, J., Magnani, E., Mickelson, J. R., Murray, J., Nergadze, S. G., Onofrio, R., Pedroni, S., Piras, M. F., Raudsepp, T., Rocchi, M., Reed, K. H., Ryder, O. A., Searle, S., Skow, L., Swinburne, J. E., Syvanen, A. C., Tozaki, T., Valberg, S. J., Vaudin, M., White, J. R., Zody, M. C., Lander, E. S., and Lindblad-Toh, K.

Published
2009

19. Rare germline variants in ATM are associated with chronic lymphocytic leukemia

Author

Tiao, G., Improgo, M. R., Kasar, S., Poh, W., Kamburov, A., Landau, D-A, Tausch, E., Taylor-Weiner, A., Cibulskis, C., Bahl, S., Fernandes, S. M., Hoang, K., Rheinbay, E., Kim, H. T., Bahlo, J., Robrecht, S., Fischer, K., Hallek, M., Gabriel, S., Lander, E. S., Stilgenbauer, S., Wu, C. J., Kiezun, A., Getz, G., Brown, J. R., Tiao, G., Improgo, M. R., Kasar, S., Poh, W., Kamburov, A., Landau, D-A, Tausch, E., Taylor-Weiner, A., Cibulskis, C., Bahl, S., Fernandes, S. M., Hoang, K., Rheinbay, E., Kim, H. T., Bahlo, J., Robrecht, S., Fischer, K., Hallek, M., Gabriel, S., Lander, E. S., Stilgenbauer, S., Wu, C. J., Kiezun, A., Getz, G., and Brown, J. R.

Published
2017

20. Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution

Author

Kasar, S., primary, Kim, J., additional, Improgo, R., additional, Tiao, G., additional, Polak, P., additional, Haradhvala, N., additional, Lawrence, M. S., additional, Kiezun, A., additional, Fernandes, S. M., additional, Bahl, S., additional, Sougnez, C., additional, Gabriel, S., additional, Lander, E. S., additional, Kim, H. T., additional, Getz, G., additional, and Brown, J. R., additional

Published
2015
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21. Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany

Author

Grad, Y. H., primary, Lipsitch, M., additional, Griggs, A. D., additional, Haas, B. J., additional, Shea, T. P., additional, McCowan, C., additional, Montmayeur, A., additional, FitzGerald, M., additional, Wortman, J. R., additional, Krogfelt, K. A., additional, Bingen, E., additional, Weill, F.-X., additional, Tietze, E., additional, Flieger, A., additional, Lander, E. S., additional, Nusbaum, C., additional, Birren, B. W., additional, Hung, D. T., additional, and Hanage, W. P., additional

Published
2012
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22. Genome maps 7. The human transcript map. Wall chart

Author

Schuler, G. D., Boguski, M. S., Hudson, T. J., Hui, L., Ma, J., Castle, A. B., Wu, X., Silva, J., Nusbaum, H. C., Birren, B. B., Slonim, D. K., Steven G. Rozen, Stein, L. D., Page, D., Lander, E. S., Stewart, E. A., Aggarwal, A., Bajorek, E., Brady, S., Chu, S., Fang, N., Hadley, D., Harris, M., Hussain, S., and Hudson Jr, J. R.

Subjects
Genetic Markers, DNA, Complementary, Genome, Human, Human Genome Project, Genetic Diseases, Inborn, Chromosome Mapping, Gene Expression, Humans, RNA, Messenger, Gene Library, Sequence Tagged Sites
Published
1996

23. A locus for Fanconi anemia on 16q determined by homozygosity mapping

Author

Gschwend, M., Levran, O., Kruglyak, L., Ranade, K., Verlander, P. C., Shen, S., Faure, S., Weissenbach, J., Altay, C., Lander, E. S., Arleen Auerbach, and Botstein, D.

Subjects
Genetic Markers, Genotype, Genome, Human, Homozygote, Chromosome Mapping, Pedigree, Consanguinity, Fanconi Anemia, Gene Frequency, Humans, Genetic Testing, Lod Score, Chromosomes, Human, Pair 16, Research Article
Abstract

We report the results of a genomewide scan using homozygosity mapping to identify genes causing Fanconi anemia, a genetically heterogeneous recessive disorder. By studying 23 inbred families, we detected linkage to a locus causing Fanconi anemia near marker D16S520 (16q24.3). Although -65% of our families displayed clear linkage to D16S520, we found strong evidence (P = .0013) of genetic heterogeneity. This result independently confirms the recent mapping of the FAA gene to chromosome 16 by Pronk et al. Family ascertainment was biased against a previously identified FAC gene on chromosome 9, and no linkage was observed to this locus. Simultaneous search analysis suggested several additional chromosomal regions that could account for a small fraction of Fanconi anemia in our families, but the sample size is insufficient to provide statistical significance. We also demonstrate the strong effect of marker allele frequencies on LOD scores obtained in homozygosity mapping and discuss ways to avoid false positives arising from this effect.

Published
1996

25. Atelosteogenesis type II is caused by mutations in the diastrophic dysplasia sulfate-transporter gene (DTDST): evidence for a phenotypic series involving three chondrodysplasias

Author

Hästbacka, J., Superti-Furga, A., Wilcox, W. R., Rimoin, D. L., Cohn, D. H., and Lander, E. S.

Subjects
Heterozygote, Base Sequence, Sulfates, Anion Transport Proteins, Molecular Sequence Data, Infant, Newborn, Gene Expression, Membrane Transport Proteins, Biological Transport, Fibroblasts, Osteochondrodysplasias, Bone and Bones, Osteogenesis, Sulfate Transporters, Humans, Point Mutation, Proteoglycans, Cloning, Molecular, Carrier Proteins, Sequence Analysis, Research Article, Sequence Deletion
Abstract

Atelosteogenesis type II (AO II) is a neonatally lethal chondrodysplasia whose clinical and histological characteristics resemble those of another chondrodysplasia, the much less severe diastrophic dysplasia (DTD). The similarity suggests a shared pathogenesis involving lesions in the same biochemical pathway and perhaps the same gene. DTD is caused by mutations in the recently identified diastrophic dysplasia sulfate-transporter gene (DTDST). Here, we report that AOII patients also have DTDST mutations, which lead to defective uptake of inorganic sulfate and insufficient sulfation of macromolecules by patient mesenchymal cells in vitro. Together with our recent observation that a third even more severe chondrodysplasia, achondrogenesis type IB, is also caused by mutations in DTDST, these results demonstrate a phenotypic series of three chondrodysplasias of increasing severity caused by lesions in a single sulfate-transporter gene. The severity of the phenotype appears to be correlated with the predicted effect of the mutations on the residual activity of the DTDST protein.

Published
1996

26. Complete multipoint sib-pair analysis of qualitative and quantitative traits

Author

Kruglyak, L and Lander, E S

Subjects
Genetic Markers, Heterozygote, Diabetes Mellitus, Type 1, Models, Statistical, Letter, Models, Genetic, Genetic Linkage, Genetic Diseases, Inborn, Chromosome Mapping, Humans, Software, Research Article
Abstract

Sib-pair analysis is an increasingly important tool for genetic dissection of complex traits. Current methods for sib-pair analysis are primarily based on studying individual genetic markers one at a time and thus fail to use the full inheritance information provided by multipoint linkage analysis. In this paper, we describe how to extract the complete multipoint inheritance information for each sib pair. We then describe methods that use this information to map loci affecting traits, thereby providing a unified approach to both qualitative and quantitative traits. Specifically, complete multipoint approaches are presented for (1) exclusion mapping of qualitative traits; (2) maximum-likelihood mapping of qualitative traits; (3) information-content mapping, showing the extent to which all inheritance information has been extracted at each location in the genome; and (4) quantitative-trait mapping, by two parametric methods and one nonparametric method. In addition, we explore the effects of marker density, marker polymorphism, and availability of parents on the information content of a study. We have implemented the analysis methods in a new computer package, MAPMAKER/SIBS. With this computer package, complete multipoint analysis with dozens of markers in hundreds of sib pairs can be carried out in minutes.

Published
1995

28. cDNA Sequences for Transcription Factors and Signaling Proteins of the HemichordateSaccoglossus kowalevskii: Efficacy of the Expressed Sequence Tag (EST) Approach for Evolutionary and Developmental Studies of a New Organism

Author

Freeman, R. M., primary, Wu, M., additional, Cordonnier-Pratt, M-M., additional, Pratt, L. H., additional, Gruber, C. E., additional, Smith, M., additional, Lander, E. S., additional, Stange-Thomann, N., additional, Lowe, C. J., additional, Gerhart, J., additional, and Kirschner, M., additional

Published
2008
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30. Gene-based anchoring of the rat genetic linkage and cytogenetic maps: new regional localizations, orientation of the linkage groups, and insights into mammalian chromosome evolution.

Author

Szpirer, Claude, Szpirer, Josiane, Van Vooren, Pascale, Tissir, F, Simon, Jason, Koike, G., Jacob, H J, Lander, E S, Helou, Khalil, Klinga-Levan, K, Levan, G, Szpirer, Claude, Szpirer, Josiane, Van Vooren, Pascale, Tissir, F, Simon, Jason, Koike, G., Jacob, H J, Lander, E S, Helou, Khalil, Klinga-Levan, K, and Levan, G

Abstract

In order to generate anchor points connecting the rat cytogenetic and genetic maps, the cytogenetic position of 62 rat markers (including 55 genes) already localized genetically was determined by fluorescence in situ hybridization. Whenever possible, markers located near one end of the linkage groups were included. These new localizations allowed us to unambiguously orient the 20 autosomal and the X chromosome linkage groups. The position of the centromere in the linkage map could also be determined in the case of several metacentric chromosomes. In addition, the regional localization of 15 other rat genes was determined. These new data bring useful information with respect to comparative mapping with the mouse and the human and to mammalian evolution. They illustrate, for instance, that groups of genes can remain syntenic during mammalian evolution while being subjected to intrachromosomal rearrangements in some lineages (synteny is conserved while gene order is not). This analysis also disclosed cases of synteny conservation in one the two rodent species and the human, while the synteny is split in the other rodent species: such configurations are likely examples of lineage-specific interchromosomal rearrangements associated with speciation., Journal Article, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, P.H.S., info:eu-repo/semantics/published

Published
1998

31. A genetic map of the laboratory rat

Author

Jacob, H J, Brown, D, Bunker, R, Daly, M, Dzau, V, Szpirer, Claude, Szpirer, Josiane, Lander, E S, Jacob, H J, Brown, D, Bunker, R, Daly, M, Dzau, V, Szpirer, Claude, Szpirer, Josiane, and Lander, E S

Abstract

info:eu-repo/semantics/published

Published
1995

32. Genetic identification of Mcs-1, a rat mammary carcinoma suppressor gene.

Author

Hsu, L C, Kennan, W S, Shepel, L A, Jacob, H J, Szpirer, Claude, Szpirer, Josiane, Lander, E S, Gould, M N, Hsu, L C, Kennan, W S, Shepel, L A, Jacob, H J, Szpirer, Claude, Szpirer, Josiane, Lander, E S, and Gould, M N

Abstract

Women have inherited differences in their susceptibility to breast cancer, but the genes underlying this variation are difficult to identify. We have approached the problem of identifying breast cancer susceptibility genes by using a rat model. Inbred rat strains display differential susceptibilities to mammary carcinogenesis; the Copenhagen (COP) rat is resistant, while the Wistar-Furth (WF) rat is susceptible to induction of mammary tumors by 7,12-dimethylbenz[a]anthracene. Genetic breeding studies have shown that tumor resistance in the COP rat is a dominant phenotype, termed the rat mammary carcinoma suppressor trait. As a step toward defining the basis of this resistance, we undertook genetic mapping of this phenotype in a (WF x COP)F1 x WF backcross by studying a large collection of microsatellite and minisatellite polymorphisms. A total of 114 genetic markers, covering approximately 75% of the rat genome, were genotyped in the backcross progeny. A marker on rat chromosome 2 was found to show linkage to the resistance phenotype. Genetic linkage was demonstrated both in a qualitative analysis (in which rats were defined as resistant if they developed 0 tumors and sensitive if they developed two or more tumors; LOD score, 4.0) and in a quantitative trait locus analysis (in which tumor number was used as the quantitative phenotype; LOD score, 3.8). We infer the existence of a gene, Mcs-1, on rat chromosome 2 that suppresses mammary carcinogenesis., Journal Article, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, P.H.S., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
1994

44. The 1.4-Mb CMT1A duplication/HNPP deletion genomic region reveals unique genome architectural features and provides insights into the recent evolution of new genes.

Author

Inoue, K, Dewar, K, Katsanis, N, Reiter, L T, Lander, E S, Devon, K L, Wyman, D W, Lupski, J R, and Birren, B

Abstract

Duplication and deletion of the 1.4-Mb region in 17p12 that is delimited by two 24-kb low copy number repeats (CMT1A-REPs) represent frequent genomic rearrangements resulting in two common inherited peripheral neuropathies, Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsy (HNPP). CMT1A and HNPP exemplify a paradigm for genomic disorders wherein unique genome architectural features result in susceptibility to DNA rearrangements that cause disease. A gene within the 1.4-Mb region, PMP22, is responsible for these disorders through a gene-dosage effect in the heterozygous duplication or deletion. However, the genomic structure of the 1.4-Mb region, including other genes contained within the rearranged genomic segment, remains essentially uncharacterized. To delineate genomic structural features, investigate higher-order genomic architecture, and identify genes in this region, we constructed PAC and BAC contigs and determined the complete nucleotide sequence. This CMT1A/HNPP genomic segment contains 1,421,129 bp of DNA. A low copy number repeat (LCR) was identified, with one copy inside and two copies outside of the 1.4-Mb region. Comparison between physical and genetic maps revealed a striking difference in recombination rates between the sexes with a lower recombination frequency in males (0.67 cM/Mb) versus females (5.5 cM/Mb). Hypothetically, this low recombination frequency in males may enable a chromosomal misalignment at proximal and distal CMT1A-REPs and promote unequal crossing over, which occurs 10 times more frequently in male meiosis. In addition to three previously described genes, five new genes (TEKT3, HS3ST3B1, NPD008/CGI-148, CDRT1, and CDRT15) and 13 predicted genes were identified. Most of these predicted genes are expressed only in embryonic stages. Analyses of the genomic region adjacent to proximal CMT1A-REP indicated an evolutionary mechanism for the formation of proximal CMT1A-REP and the creation of novel genes by DNA rearrangement during primate speciation.

Published
2001
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45. Human and mouse gene structure: comparative analysis and application to exon prediction.

Author

Batzoglou, S, Pachter, L, Mesirov, J P, Berger, B, and Lander, E S

Abstract

We describe a novel analytical approach to gene recognition based on cross-species comparison. We first undertook a comparison of orthologous genomic loci from human and mouse, studying the extent of similarity in the number, size and sequence of exons and introns. We then developed an approach for recognizing genes within such orthologous regions by first aligning the regions using an iterative global alignment system and then identifying genes based on conservation of exonic features at aligned positions in both species. The alignment and gene recognition are performed by new programs called and, respectively. performed well at exact identification of coding exons in 117 orthologous pairs tested.

Published
2000

46. Sequencing a genome by walking with clone-end sequences: a mathematical analysis.

Author

Batzoglou, S, Berger, B, Mesirov, J, and Lander, E S

Abstract

One approach to sequencing a large genome is (1) to sequence a collection of nonoverlapping "seeds" chosen from a genomic library of large-insert clones [such as bacterial artificial chromosomes (BACs)] and then (2) to take successive "walking" steps by selecting and sequencing minimally overlapping clones, using information such as clone-end sequences to identify the overlaps. In this paper we analyze the strategic issues involved in using this approach. We derive formulas showing how two key factors, the initial density of seed clones and the depth of the genomic library used for walking, affect the cost and time of a sequencing project-that is, the amount of redundant sequencing and the number of steps to cover the vast majority of the genome. We also discuss a variant strategy in which a second genomic library with clones having a somewhat smaller insert size is used to close gaps. This approach can dramatically decrease the amount of redundant sequencing, without affecting the rate at which the genome is covered.

Published
1999
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47. Rescue of the hairless phenotype in nude mice by transgenic insertion of the wild-type Hfh11 genomic locus.

Author

Kurooka, H, Segre, J A, Hirano, Y, Nemhauser, J L, Nishimura, H, Yoneda, K, Lander, E S, and Honjo, T

Abstract

Mice and rats homozygous for mutations at the nude (nu) locus exhibit the pleiotropic phenotypes of hairlessness and athymia. A recent positional cloning study identified, as a nude gene, a novel fork head transcription factor, Hfh11 (also called whn), that is expressed in skin and thymus, and is mutated in nude rodents. To obtain the direct biological proof that this gene is responsible for nude phenotype, we microinjected a cosmid clone containing the wild-type Hfh11 genomic locus into fertilized nude eggs. Two independent founder lines of transgenic mice were generated that corrected the hairless phenotype, but not the thymic defect. This partial rescue demonstrates that Hfh11 is the gene responsible for the hairless defect in the nude mouse. Taken together with previous genetic studies, this complementation result indicates that Hfh11 is indeed the nude gene and the Hfh11 locus is likely to be subject to complicated regulation.

Published
1996
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48. Restriction fragment length polymorphism linkage map for Arabidopsis thaliana.

Author

Chang, C, Bowman, J L, DeJohn, A W, Lander, E S, and Meyerowitz, E M

Abstract

We have constructed a restriction fragment length polymorphism linkage map for the nuclear genome of the flowering plant Arabidopsis thaliana. The map, containing 90 randomly distributed molecular markers, is physically very dense; greater than 50% of the genome is within 1.9 centimorgans, or approximately 270 kilobase pairs, of the mapped DNA fragments. The map was based on the meiotic segregation of markers in two different crosses. The restriction fragment length polymorphism linkage groups were integrated with the five classically mapped linkage groups by virtue of mapped mutations included in these crosses. Markers consist of both cloned Arabidopsis genes and random low-copy-number genomic DNA clones that are able to detect polymorphisms with the restriction enzymes EcoRI, Bgl II, and/or Xba I. These cloned markers can serve as starting points for chromosome walking, allowing for the isolation of Arabidopsis genes of known map location. The restriction fragment length polymorphism map also can associate clones of unknown gene function with mutant phenotypes, and vice versa.

Published
1988
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49. Strategies for studying heterogeneous genetic traits in humans by using a linkage map of restriction fragment length polymorphisms.

Author

Lander, E S and Botstein, D

Abstract

Simple single-gene disorders in humans can be genetically mapped by using traditional methods of linkage analysis and increasingly abundant restriction fragment length polymorphisms (RFLPs). Many human diseases and traits, however, can be expected to be genetically heterogeneous (i.e., caused by any one of several genes), and traditional linkage analysis is much less effective in such circumstances. We present two methods, interval mapping and simultaneous search, designed to exploit the full power of a linkage map of the DNA markers. For the simplest situations, only 1/3 as many affected families are needed to map a heterogeneous trait by using these methods. Only 1/5-1/50 as many are needed to detect that genetic heterogeneity is present.

Published
1986
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50. Construction of multilocus genetic linkage maps in humans.

Author

Lander, E S and Green, P

Abstract

Human genetic linkage maps are most accurately constructed by using information from many loci simultaneously. Traditional methods for such multilocus linkage analysis are computationally prohibitive in general, even with supercomputers. The problem has acquired practical importance because of the current international collaboration aimed at constructing a complete human linkage map of DNA markers through the study of three-generation pedigrees. We describe here several alternative algorithms for constructing human linkage maps given a specified gene order. One method allows maximum-likelihood multilocus linkage maps for dozens of DNA markers in such three-generation pedigrees to be constructed in minutes.

Published
1987
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