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1. Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data

Author

Romagnoni, A., Jegou, S., Van Steen, K., Wainrib, G., Hugot, J. -P., Peyrin-Biroulet, L., Chamaillard, M., Colombel, J. -F., Cottone, M., D'Amato, M., D'Inca, R., Halfvarson, J., Henderson, P., Karban, A., Kennedy, N. A., Khan, M. A., Lemann, M., Levine, A., Massey, D., Milla, M., S. M. E., Ng, Oikonomou, I., Peeters, H., Proctor, D. D., Rahier, J. -F., Rutgeerts, P., Seibold, F., Stronati, L., Taylor, K. M., Torkvist, L., Ublick, K., Van Limbergen, J., Van Gossum, A., Vatn, M. H., Zhang, H., Zhang, W., Andrews, J. M., Bampton, P. A., Barclay, M., Florin, T. H., Gearry, R., Krishnaprasad, K., Lawrance, I. C., Mahy, G., Montgomery, G. W., Radford-Smith, G., Roberts, R. L., Simms, L. A., Hanigan, K., Croft, A., Amininijad, L., Cleynen, I., Dewit, O., Franchimont, D., Georges, M., Laukens, D., Theatre, E., Vermeire, S., Aumais, G., Baidoo, L., Barrie, A. M., Beck, K., Bernard, E. -J., Binion, D. G., Bitton, A., Brant, S. R., Cho, J. H., Cohen, A., Croitoru, K., Daly, M. J., Datta, L. W., Deslandres, C., Duerr, R. H., Dutridge, D., Ferguson, J., Fultz, J., Goyette, P., Greenberg, G. R., Haritunians, T., Jobin, G., Katz, S., Lahaie, R. G., Mcgovern, D. P., Nelson, L., S. M., Ng, Ning, K., Pare, P., Regueiro, M. D., Rioux, J. D., Ruggiero, E., Schumm, L. P., Schwartz, M., Scott, R., Sharma, Y., Silverberg, M. S., Spears, D., Steinhart, A. H., Stempak, J. M., Swoger, J. M., Tsagarelis, C., Zhang, C., Zhao, H., Aerts, J., Ahmad, T., Arbury, H., Attwood, A., Auton, A., Ball, S. G., Balmforth, A. J., Barnes, C., Barrett, J. C., Barroso, I., Barton, A., Bennett, A. J., Bhaskar, S., Blaszczyk, K., Bowes, J., Brand, O. J., Braund, P. S., Bredin, F., Breen, G., Brown, M. J., Bruce, I. N., Bull, J., Burren, O. S., Burton, J., Byrnes, J., Caesar, S., Cardin, N., Clee, C. M., Coffey, A. J., MC Connell, J., Conrad, D. F., Cooper, J. D., Dominiczak, A. F., Downes, K., Drummond, H. E., Dudakia, D., Dunham, A., Ebbs, B., Eccles, D., Edkins, S., Edwards, C., Elliot, A., Emery, P., Evans, D. M., Evans, G., Eyre, S., Farmer, A., Ferrier, I. N., Flynn, E., Forbes, A., Forty, L., Franklyn, J. A., Frayling, T. M., Freathy, R. M., Giannoulatou, E., Gibbs, P., Gilbert, P., Gordon-Smith, K., Gray, E., Green, E., Groves, C. J., Grozeva, D., Gwilliam, R., Hall, A., Hammond, N., Hardy, M., Harrison, P., Hassanali, N., Hebaishi, H., Hines, S., Hinks, A., Hitman, G. A., Hocking, L., Holmes, C., Howard, E., Howard, P., Howson, J. M. M., Hughes, D., Hunt, S., Isaacs, J. D., Jain, M., Jewell, D. P., Johnson, T., Jolley, J. D., Jones, I. R., Jones, L. A., Kirov, G., Langford, C. F., Lango-Allen, H., Lathrop, G. M., Lee, J., Lee, K. L., Lees, C., Lewis, K., Lindgren, C. M., Maisuria-Armer, M., Maller, J., Mansfield, J., Marchini, J. L., Martin, P., Massey, D. C., Mcardle, W. L., Mcguffin, P., Mclay, K. E., Mcvean, G., Mentzer, A., Mimmack, M. L., Morgan, A. E., Morris, A. P., Mowat, C., Munroe, P. B., Myers, S., Newman, W., Nimmo, E. R., O'Donovan, M. C., Onipinla, A., Ovington, N. R., Owen, M. J., Palin, K., Palotie, A., Parnell, K., Pearson, R., Pernet, D., Perry, J. R., Phillips, A., Plagnol, V., Prescott, N. J., Prokopenko, I., Quail, M. A., Rafelt, S., Rayner, N. W., Reid, D. M., Renwick, A., Ring, S. M., Robertson, N., Robson, S., Russell, E., Clair, D. S., Sambrook, J. G., Sanderson, J. D., Sawcer, S. J., Schuilenburg, H., Scott, C. E., Seal, S., Shaw-Hawkins, S., Shields, B. M., Simmonds, M. J., Smyth, D. J., Somaskantharajah, E., Spanova, K., Steer, S., Stephens, J., Stevens, H. E., Stirrups, K., Stone, M. A., Strachan, D. P., Su, Z., Symmons, D. P. M., Thompson, J. R., Thomson, W., Tobin, M. D., Travers, M. E., Turnbull, C., Vukcevic, D., Wain, L. V., Walker, M., Walker, N. M., Wallace, C., Warren-Perry, M., Watkins, N. A., Webster, J., Weedon, M. N., Wilson, A. G., Woodburn, M., Wordsworth, B. P., Yau, C., Young, A. H., Zeggini, E., Brown, M. A., Burton, P. R., Caulfield, M. J., Compston, A., Farrall, M., Gough, S. C. L., Hall, A. S., Hattersley, A. T., Hill, A. V. S., Mathew, C. G., Pembrey, M., Satsangi, J., Stratton, M. R., Worthington, J., Hurles, M. E., Duncanson, A., Ouwehand, W. H., Parkes, M., Rahman, N., Todd, J. A., Samani, N. J., Kwiatkowski, D. P., Mccarthy, M. I., Craddock, N., Deloukas, P., Donnelly, P., Blackwell, J. M., Bramon, E., Casas, J. P., Corvin, A., Jankowski, J., Markus, H. S., Palmer, C. N., Plomin, R., Rautanen, A., Trembath, R. C., Viswanathan, A. C., Wood, N. W., Spencer, C. C. A., Band, G., Bellenguez, C., Freeman, C., Hellenthal, G., Pirinen, M., Strange, A., Blackburn, H., Bumpstead, S. J., Dronov, S., Gillman, M., Jayakumar, A., Mccann, O. T., Liddle, J., Potter, S. C., Ravindrarajah, R., Ricketts, M., Waller, M., Weston, P., Widaa, S., Whittaker, P., Romagnoni, A., Jegou, S., Van Steen, K., Wainrib, G., Hugot, J. -P., Peyrin-Biroulet, L., Chamaillard, M., Colombel, J. -F., Cottone, M., D'Amato, M., D'Inca, R., Halfvarson, J., Henderson, P., Karban, A., Kennedy, N. A., Khan, M. A., Lemann, M., Levine, A., Massey, D., Milla, M., Ng, S. M. E., Oikonomou, I., Peeters, H., Proctor, D. D., Rahier, J. -F., Rutgeerts, P., Seibold, F., Stronati, L., Taylor, K. M., Torkvist, L., Ublick, K., Van Limbergen, J., Van Gossum, A., Vatn, M. H., Zhang, H., Zhang, W., Andrews, J. M., Bampton, P. A., Barclay, M., Florin, T. H., Gearry, R., Krishnaprasad, K., Lawrance, I. C., Mahy, G., Montgomery, G. W., Radford-Smith, G., Roberts, R. L., Simms, L. A., Hanigan, K., Croft, A., Amininijad, L., Cleynen, I., Dewit, O., Franchimont, D., Georges, M., Laukens, D., Theatre, E., Vermeire, S., Aumais, G., Baidoo, L., Barrie, A. M., Beck, K., Bernard, E. -J., Binion, D. G., Bitton, A., Brant, S. R., Cho, J. H., Cohen, A., Croitoru, K., Daly, M. J., Datta, L. W., Deslandres, C., Duerr, R. H., Dutridge, D., Ferguson, J., Fultz, J., Goyette, P., Greenberg, G. R., Haritunians, T., Jobin, G., Katz, S., Lahaie, R. G., Mcgovern, D. P., Nelson, L., Ng, S. M., Ning, K., Pare, P., Regueiro, M. D., Rioux, J. D., Ruggiero, E., Schumm, L. P., Schwartz, M., Scott, R., Sharma, Y., Silverberg, M. S., Spears, D., Steinhart, A. H., Stempak, J. M., Swoger, J. M., Tsagarelis, C., Zhang, C., Zhao, H., Aerts, J., Ahmad, T., Arbury, H., Attwood, A., Auton, A., Ball, S. G., Balmforth, A. J., Barnes, C., Barrett, J. C., Barroso, I., Barton, A., Bennett, A. J., Bhaskar, S., Blaszczyk, K., Bowes, J., Brand, O. J., Braund, P. S., Bredin, F., Breen, G., Brown, M. J., Bruce, I. N., Bull, J., Burren, O. S., Burton, J., Byrnes, J., Caesar, S., Cardin, N., Clee, C. M., Coffey, A. J., MC Connell, J., Conrad, D. F., Cooper, J. D., Dominiczak, A. F., Downes, K., Drummond, H. E., Dudakia, D., Dunham, A., Ebbs, B., Eccles, D., Edkins, S., Edwards, C., Elliot, A., Emery, P., Evans, D. M., Evans, G., Eyre, S., Farmer, A., Ferrier, I. N., Flynn, E., Forbes, A., Forty, L., Franklyn, J. A., Frayling, T. M., Freathy, R. M., Giannoulatou, E., Gibbs, P., Gilbert, P., Gordon-Smith, K., Gray, E., Green, E., Groves, C. J., Grozeva, D., Gwilliam, R., Hall, A., Hammond, N., Hardy, M., Harrison, P., Hassanali, N., Hebaishi, H., Hines, S., Hinks, A., Hitman, G. A., Hocking, L., Holmes, C., Howard, E., Howard, P., Howson, J. M. M., Hughes, D., Hunt, S., Isaacs, J. D., Jain, M., Jewell, D. P., Johnson, T., Jolley, J. D., Jones, I. R., Jones, L. A., Kirov, G., Langford, C. F., Lango-Allen, H., Lathrop, G. M., Lee, J., Lee, K. L., Lees, C., Lewis, K., Lindgren, C. M., Maisuria-Armer, M., Maller, J., Mansfield, J., Marchini, J. L., Martin, P., Massey, D. C., Mcardle, W. L., Mcguffin, P., Mclay, K. E., Mcvean, G., Mentzer, A., Mimmack, M. L., Morgan, A. E., Morris, A. P., Mowat, C., Munroe, P. B., Myers, S., Newman, W., Nimmo, E. R., O'Donovan, M. C., Onipinla, A., Ovington, N. R., Owen, M. J., Palin, K., Palotie, A., Parnell, K., Pearson, R., Pernet, D., Perry, J. R., Phillips, A., Plagnol, V., Prescott, N. J., Prokopenko, I., Quail, M. A., Rafelt, S., Rayner, N. W., Reid, D. M., Renwick, A., Ring, S. M., Robertson, N., Robson, S., Russell, E., Clair, D. S., Sambrook, J. G., Sanderson, J. D., Sawcer, S. J., Schuilenburg, H., Scott, C. E., Seal, S., Shaw-Hawkins, S., Shields, B. M., Simmonds, M. J., Smyth, D. J., Somaskantharajah, E., Spanova, K., Steer, S., Stephens, J., Stevens, H. E., Stirrups, K., Stone, M. A., Strachan, D. P., Su, Z., Symmons, D. P. M., Thompson, J. R., Thomson, W., Tobin, M. D., Travers, M. E., Turnbull, C., Vukcevic, D., Wain, L. V., Walker, M., Walker, N. M., Wallace, C., Warren-Perry, M., Watkins, N. A., Webster, J., Weedon, M. N., Wilson, A. G., Woodburn, M., Wordsworth, B. P., Yau, C., Young, A. H., Zeggini, E., Brown, M. A., Burton, P. R., Caulfield, M. J., Compston, A., Farrall, M., Gough, S. C. L., Hall, A. S., Hattersley, A. T., Hill, A. V. S., Mathew, C. G., Pembrey, M., Satsangi, J., Stratton, M. R., Worthington, J., Hurles, M. E., Duncanson, A., Ouwehand, W. H., Parkes, M., Rahman, N., Todd, J. A., Samani, N. J., Kwiatkowski, D. P., Mccarthy, M. I., Craddock, N., Deloukas, P., Donnelly, P., Blackwell, J. M., Bramon, E., Casas, J. P., Corvin, A., Jankowski, J., Markus, H. S., Palmer, C. N., Plomin, R., Rautanen, A., Trembath, R. C., Viswanathan, A. C., Wood, N. W., Spencer, C. C. A., Band, G., Bellenguez, C., Freeman, C., Hellenthal, G., Pirinen, M., Strange, A., Blackburn, H., Bumpstead, S. J., Dronov, S., Gillman, M., Jayakumar, A., Mccann, O. T., Liddle, J., Potter, S. C., Ravindrarajah, R., Ricketts, M., Waller, M., Weston, P., Widaa, S., Whittaker, P., Daly, Mark J. [0000-0002-0949-8752], Apollo - University of Cambridge Repository, Hugot, Jean-Pierre [0000-0002-8446-6056], UCL - SSS/IREC/GAEN - Pôle d'Hépato-gastro-entérologie, UCL - (MGD) Service de gastro-entérologie, Romagnoni, A, Jegou, S, VAN STEEN, Kristel, Wainrib, G, Hugot, JP, Peyrin-Biroulet, L, Chamaillard, M, Colombel, JF, Cottone, M, D'Amato, M, D'Inca, R, Halfvarson, J, Henderson, P, Karban, A, Kennedy, NA, Khan, MA, Lemann, M, Levine, A, Massey, D, Milla, M, Ng, SME, Oikonomou, I, Peeters, H, Proctor, DD, Rahier, JF, Rutgeerts, P, Seibold, F, Stronati, L, Taylor, KM, Torkvist, L, Ublick, K, Van Limbergen, J, Van Gossum, A, Vatn, MH, Zhang, H, Zhang, W, Andrews, JM, Bampton, PA, Barclay, M, Florin, TH, Gearry, R, Krishnaprasad, K, Lawrance, IC, Mahy, G, Montgomery, GW, Radford-Smith, G, Roberts, RL, Simms, LA, Hanigan, K, Croft, A, Amininijad, L, Cleynen, I, Dewit, O, Franchimont, D, Georges, M, Laukens, D, Theatre, E, Vermeire, S, Aumais, G, Baidoo, L, Barrie, AM, Beck, K, Bernard, EJ, Binion, DG, Bitton, A, Brant, SR, Cho, JH, Cohen, A, Croitoru, K, Daly, MJ, Datta, LW, Deslandres, C, Duerr, RH, Dutridge, D, Ferguson, J, Fultz, J, Goyette, P, Greenberg, GR, Haritunians, T, Jobin, G, Katz, S, Lahaie, RG, McGovern, DP, Nelson, L, Ng, SM, Ning, K, Pare, P, Regueiro, MD, Rioux, JD, Ruggiero, E, Schumm, LP, Schwartz, M, Scott, R, Sharma, Y, Silverberg, MS, Spears, D, Steinhart, AH, Stempak, JM, Swoger, JM, Tsagarelis, C, Zhang, C, Zhao, HY, AERTS, Jan, Ahmad, T, Arbury, H, Attwood, A, Auton, A, Ball, SG, Balmforth, AJ, Barnes, C, Barrett, JC, Barroso, I, Barton, A, Bennett, AJ, Bhaskar, S, Blaszczyk, K, Bowes, J, Brand, OJ, Braund, PS, Bredin, F, Breen, G, Brown, MJ, Bruce, IN, Bull, J, Burren, OS, Burton, J, Byrnes, J, Caesar, S, Cardin, N, Clee, CM, Coffey, AJ, Mc Connell, J, Conrad, DF, Cooper, JD, Dominiczak, AF, Downes, K, Drummond, HE, Dudakia, D, Dunham, A, Ebbs, B, Eccles, D, Edkins, S, Edwards, C, Elliot, A, Emery, P, Evans, DM, Evans, G, Eyre, S, Farmer, A, Ferrier, IN, Flynn, E, Forbes, A, Forty, L, Franklyn, JA, Frayling, TM, Freathy, RM, Giannoulatou, E, Gibbs, P, Gilbert, P, Gordon-Smith, K, Gray, E, Green, E, Groves, CJ, Grozeva, D, Gwilliam, R, Hall, A, Hammond, N, Hardy, M, Harrison, P, Hassanali, N, Hebaishi, H, Hines, S, Hinks, A, Hitman, GA, Hocking, L, Holmes, C, Howard, E, Howard, P, Howson, JMM, Hughes, D, Hunt, S, Isaacs, JD, Jain, M, Jewell, DP, Johnson, T, Jolley, JD, Jones, IR, Jones, LA, Kirov, G, Langford, CF, Lango-Allen, H, Lathrop, GM, Lee, J, Lee, KL, Lees, C, Lewis, K, Lindgren, CM, Maisuria-Armer, M, Maller, J, Mansfield, J, Marchini, JL, Martin, P, Massey, DCO, McArdle, WL, McGuffin, P, McLay, KE, McVean, G, Mentzer, A, Mimmack, ML, Morgan, AE, Morris, AP, Mowat, C, Munroe, PB, Myers, S, Newman, W, Nimmo, ER, O'Donovan, MC, Onipinla, A, Ovington, NR, Owen, MJ, Palin, K, Palotie, A, Parnell, K, Pearson, R, Pernet, D, Perry, JRB, Phillips, A, Plagnol, V, Prescott, NJ, Prokopenko, I, Quail, MA, Rafelt, S, Rayner, NW, Reid, DM, Renwick, A, Ring, SM, Robertson, N, Robson, S, Russell, E, St Clair, D, Sambrook, JG, Sanderson, JD, Sawcer, SJ, Schuilenburg, H, Scott, CE, Seal, S, Shaw-Hawkins, S, Shields, BM, Simmonds, MJ, Smyth, DJ, Somaskantharajah, E, Spanova, K, Steer, S, Stephens, J, Stevens, HE, Stirrups, K, Stone, MA, Strachan, DP, Su, Z, Symmons, DPM, Thompson, JR, Thomson, W, Tobin, MD, Travers, ME, Turnbull, C, Vukcevic, D, Wain, LV, Walker, M, Walker, NM, Wallace, C, Warren-Perry, M, Watkins, NA, Webster, J, Weedon, MN, Wilson, AG, Woodburn, M, Wordsworth, BP, Yau, C, Young, AH, Zeggini, E, Brown, MA, Burton, PR, Caulfield, MJ, Compston, A, Farrall, M, Gough, SCL, Hall, AS, Hattersley, AT, Hill, AVS, Mathew, CG, Pembrey, M, Satsangi, J, Stratton, MR, Worthington, J, Hurles, ME, Duncanson, A, Ouwehand, WH, Parkes, M, Rahman, N, Todd, JA, Samani, NJ, Kwiatkowski, DP, McCarthy, MI, Craddock, N, Deloukas, P, Donnelly, P, Blackwell, JM, Bramon, E, Casas, JP, Corvin, A, Jankowski, J, Markus, HS, Palmer, CNA, Plomin, R, Rautanen, A, Trembath, RC, Viswanathan, AC, Wood, NW, Spencer, CCA, Band, G, Bellenguez, C, Freeman, C, Hellenthal, G, Pirinen, M, Strange, A, Blackburn, H, Bumpstead, SJ, Dronov, S, Gillman, M, Jayakumar, A, McCann, OT, Liddle, J, Potter, SC, Ravindrarajah, R, Ricketts, M, Waller, M, Weston, P, Widaa, S, Whittaker, P, and Kwiatkowski, D

Subjects
Male, 692/4020/1503/257/1402, Genotype, Genotyping Techniques, LOCI, 45/43, lcsh:Medicine, Polymorphism, Single Nucleotide, Crohn's disease, genetics, genome wide association, Article, Deep Learning, Crohn Disease, INDEL Mutation, Genetics research, Humans, genetics, Genetic Predisposition to Disease, 129, lcsh:Science, Alleles, Science & Technology, genome wide association, RISK PREDICTION, 45, Models, Genetic, lcsh:R, Decision Trees, 692/308/2056, ASSOCIATION, Multidisciplinary Sciences, Crohn's disease, Logistic Models, Nonlinear Dynamics, ROC Curve, Area Under Curve, Science & Technology - Other Topics, lcsh:Q, Female, Neural Networks, Computer, INFLAMMATORY-BOWEL-DISEASE, Genome-Wide Association Study
Abstract

Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers. Tis work was supported by Fondation pour la Recherche Médical (ref DEI20151234405) and Investissements d’Avenir programme ANR-11-IDEX-0005-02, Sorbonne Paris Cite, Laboratoire d’excellence INFLAMEX. Te authors thank the students that participated to the wisdom of the crowd exercise.

Published
2019

2. The DNA sequence and analysis of human chromosome 6

Author

Mungall, A. J., Palmer, S. A., Sims, S. K., Edwards, C. A., Ashurst, J. L., Wilming, L., Jones, M. C., Horton, R., Hunt, S. E., Scott, C. E., Gilbert, J. G. R., Clamp, M. E., Bethel, G., Milne, S., Ainscough, R., Almeida, J. P., Ambrose, K. D., Andrews, T. D., Ashwell, R. I. S., Babbage, A. K., Bagguley, C. L., Bailey, J., Banerjee, R., Barker, D. J., Barlow, K. F., Bates, K., Beare, D. M., Beasley, H., Beasley, O., Bird, C. P., Blakey, S., Bray-Allen, S., Brook, J., Brown, A. J., Brown, J. Y., Burford, D. C., Burrill, W., Burton, J., Carder, C., Carter, N. P., Chapman, J. C., Clark, S. Y., Clark, G., Clee, C. M., Clegg, S., Cobley, V., Collier, R. E., Collins, J. E., Colman, L. K., Corby, N. R., Coville, G. J., Culley, K. M., Dhami, P., Davies, J., Dunn, M., Earthrowl, M. E., Ellington, A. E., Evans, K. A., Faulkner, L., Francis, M. D., Frankish, A., Frankland, J., French, L., Garner, P., Garnett, J., Ghori, M. J. R., Gilby, L. M., Gillson, C. J., Glithero, R. J., Grafham, D. V., Grant, M., Gribble, S., Griffiths, C., Griffiths, M., Hall, R., Halls, K. S., Hammond, S., Harley, J. L., Hart, E. A., Heath, P. D., Heathcott, R., Holmes, S. J., Howden, P. J., Howe, K. L., Howell, G. R., Huckle, E., Humphray, S. J., Humphries, M. D., Hunt, A. R., Johnson, C. M., Joy, A. A., Kay, M., Keenan, S. J., Kimberley, A. M., King, A., Laird, G. K., Langford, C., Lawlor, S., Leongamornlert, D. A., Leversha, M., Lloyd, C. R., Lloyd, D. M., Loveland, J. E., Lovell, J., Martin, S., Mashreghi-Mohammadi, M., Maslen, G. L., Matthews, L., McCann, O. T., McLaren, S. J., McLay, K., McMurray, A., Moore, M. J. F., Mullikin, J. C., Niblett, D., Nickerson, T., Novik, K. L., Oliver, K., Overton-Larty, E. K., Parker, A., Patel, R., Pearce, A. V., Peck, A. I., Phillimore, B., Phillips, S., Plumb, R. W., Porter, K. M., Ramsey, Y., Ranby, S. A., Rice, C. M., Ross, M. T., Searle, S. M., Sehra, H. K., Sheridan, E., Skuce, C. D., Smith, S., Smith, M., Spraggon, L., Squares, S. L., Steward, C. A., Sycamore, N., Tamlyn-Hall, G., Tester, J., Theaker, A. J., Thomas, D. W., Thorpe, A., Tracey, A., Tromans, A., Tubby, B., Wall, M., Wallis, J. M., West, A. P., White, S. S., Whitehead, S. L., Whittaker, H., Wild, A., Willey, D. J., Wilmer, T. E., Wood, J. M., Wray, P. W., Wyatt, J. C., Young, L., Younger, R. M., Bentley, D. R., Coulson, A., Durbin, R., Hubbard, T., Sulston, J. E., Dunham, I., Rogers, J., and Beck, S.

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

Author(s): A. J. Mungall (corresponding author) [1, 2]; S. A. Palmer [1]; S. K. Sims [1]; C. A. Edwards [1]; J. L. Ashurst [1]; L. Wilming [1]; M. C. Jones [...]

Published
2003
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3. The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X

Author

Bentley, D. R., Deloukas, P., Dunham, A., French, L., Gregory, S. G., Humphray, S. J., Mungall, A. J., Ross, M. T., Carter, N. P., Dunham, I., Scott, C. E., Ashcroft, K. J., Atkinson, A. L., Aubin, K., Beare, D. M., Bethel, G., Brady, N., Brook, J. C., Burford, D. C., Burrill, W. D., Burrows, C., Butler, A. P., Carder, C., Catanese, J. J., Clee, C. M., Clegg, S. M., Cobley, V., Coffey, A. J., Cole, C. G., Collins, J. E., Conquer, J. S., Cooper, R. A., Culley, K. M., Dawson, E., Dearden, F. L., Durbin, R. M., de Jong, P. J., Dhami, P. D., Earthrowl, M. E., Edwards, C. A., Evans, R. S., Gillson, C. J., Ghori, J., Green, L., Gwilliam, R., Halls, K. S., Hammond, S., Harper, G. L., Heathcott, R. W., Holden, J. L., Holloway, E., Hopkins, B. L., Howard, P. J., Howell, G. R., Huckle, E. J., Hughes, J., Hunt, P. J., Hunt, S. E., Izmajlowicz, M., Jones, C. A., Joseph, S. S., Laird, G., Langford, C. F., Lehvaslaiho, M. H., Leversha, M. A., McCann, O. T., McDonald, L. M., McDowall, J., Maslen, G. L., Mistry, D., Moschonas, N. K., Neocleous, V., Pearson, D. M., Phillips, K. J., Porter, K. M., Prathalingam, S. R., Ramsey, Y. H., Ranby, S. A., Rice, C. M., Rogers, J., Rogers, L. J., Sarafidou, T., Scott, D. J., Sharp, G. J., Shaw-Smith, C. J., Smink, L. J., Soderlund, C., Sotheran, E. C., Steingruher, H. E., Sulston, J. E., Taylor, A., Taylor, R. G., Thorpe, A. A., Tinsley, E., Warry, G. L., Whittaker, A., Whittaker, P., Williams, S. H., Wilmer, T. E., Wooster, R., and Wright, C. L.

Published
2001

4. The DNA sequence of human chromosome 22

Author

Dunham, I., primary, Hunt, A. R., additional, Collins, J. E., additional, Bruskiewich, R., additional, Beare, D. M., additional, Clamp, M., additional, Smink, L. J., additional, Ainscough, R., additional, Almeida, J. P., additional, Babbage, A., additional, Bagguley, C., additional, Bailey, J., additional, Barlow, K., additional, Bates, K. N., additional, Beasley, O., additional, Bird, C. P., additional, Blakey, S., additional, Bridgeman, A. M., additional, Buck, D., additional, Burgess, J., additional, Burrill, W. D., additional, Burton, J., additional, Carder, C., additional, Carter, N. P., additional, Chen, Y., additional, Clark, G., additional, Clegg, S. M., additional, Cobley, V., additional, Cole, C. G., additional, Collier, R. E., additional, Connor, R. E., additional, Conroy, D., additional, Corby, N., additional, Coville, G. J., additional, Cox, A. V., additional, Davis, J., additional, Dawson, E., additional, Dhami, P. D., additional, Dockree, C., additional, Dodsworth, S. J., additional, Durbin, R. M., additional, Ellington, A., additional, Evans, K. L., additional, Fey, J. M., additional, Fleming, K., additional, French, L., additional, Garner, A. A., additional, Gilbert, J. G. R., additional, Goward, M. E., additional, Grafham, D., additional, Griffiths, M. N., additional, Hall, C., additional, Hall, R., additional, Hall-Tamlyn, G., additional, Heathcott, R. W., additional, Ho, S., additional, Holmes, S., additional, Hunt, S. E., additional, Jones, M. C., additional, Kershaw, J., additional, Kimberley, A., additional, King, A., additional, Laird, G. K., additional, Langford, C. F., additional, Leversha, M. A., additional, Lloyd, C., additional, Lloyd, D. M., additional, Martyn, I. D., additional, Mashreghi-Mohammadi, M., additional, Matthews, L., additional, McCann, O. T., additional, McClay, J., additional, McLaren, S., additional, McMurray, A. A., additional, Milne, S. A., additional, Mortimore, B. J., additional, Odell, C. N., additional, Pavitt, R., additional, Pearce, A. V., additional, Pearson, D., additional, Phillimore, B. J., additional, Phillips, S. H., additional, Plumb, R. W., additional, Ramsay, H., additional, Ramsey, Y., additional, Rogers, L., additional, Ross, M. T., additional, Scott, C. E., additional, Sehra, H. K., additional, Skuce, C. D., additional, Smalley, S., additional, Smith, M. L., additional, Soderlund, C., additional, Spragon, L., additional, Steward, C. A., additional, Sulston, J. E., additional, Swann, R. M., additional, Vaudin, M., additional, Wall, M., additional, Wallis, J. M., additional, Whiteley, M. N., additional, Willey, D., additional, Williams, L., additional, Williams, S., additional, Williamson, H., additional, Wilmer, T. E., additional, Wilming, L., additional, Wright, C. L., additional, Hubbard, T., additional, Bentley, D. R., additional, Beck, S., additional, Rogers, J., additional, Shimizu, N., additional, Minoshima, S., additional, Kawasaki, K., additional, Sasaki, T., additional, Asakawa, S., additional, Kudoh, J., additional, Shintani, A., additional, Shibuya, K., additional, Yoshizaki, Y., additional, Aoki, N., additional, Mitsuyama, S., additional, Roe, B. A., additional, Chen, F., additional, Chu, L., additional, Crabtree, J., additional, Deschamps, S., additional, Do, A., additional, Do, T., additional, Dorman, A., additional, Fang, F., additional, Fu, Y., additional, Hu, P., additional, Hua, A., additional, Kenton, S., additional, Lai, H., additional, Lao, H. I., additional, Lewis, J., additional, Lewis, S., additional, Lin, S.-P., additional, Loh, P., additional, Malaj, E., additional, Nguyen, T., additional, Pan, H., additional, Phan, S., additional, Qi, S., additional, Qian, Y., additional, Ray, L., additional, Ren, Q., additional, Shaull, S., additional, Sloan, D., additional, Song, L., additional, Wang, Q., additional, Wang, Y., additional, Wang, Z., additional, White, J., additional, Willingham, D., additional, Wu, H., additional, Yao, Z., additional, Zhan, M., additional, Zhang, G., additional, Chissoe, S., additional, Murray, J., additional, Miller, N., additional, Minx, P., additional, Fulton, R., additional, Johnson, D., additional, Bemis, G., additional, Bentley, D., additional, Bradshaw, H., additional, Bourne, S., additional, Cordes, M., additional, Du, Z., additional, Fulton, L., additional, Goela, D., additional, Graves, T., additional, Hawkins, J., additional, Hinds, K., additional, Kemp, K., additional, Latreille, P., additional, Layman, D., additional, Ozersky, P., additional, Rohlfing, T., additional, Scheet, P., additional, Walker, C., additional, Wamsley, A., additional, Wohldmann, P., additional, Pepin, K., additional, Nelson, J., additional, Korf, I., additional, Bedell, J. A., additional, Hillier, L., additional, Mardis, E., additional, Waterston, R., additional, Wilson, R., additional, Emanuel, B. S., additional, Shaikh, T., additional, Kurahashi, H., additional, Saitta, S., additional, Budarf, M. L., additional, McDermid, H. E., additional, Johnson, A., additional, Wong, A. C. C., additional, Morrow, B. E., additional, Edelmann, L., additional, Kim, U. J., additional, Shizuya, H., additional, Simon, M. I., additional, Dumanski, J. P., additional, Peyrard, M., additional, Kedra, D., additional, Seroussi, E., additional, Fransson, I., additional, Tapia, I., additional, Bruder, C. E., additional, and O'Brien, K. P., additional

Published
1999
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5. A physical map of the human genome.

Author

McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK, Fulton R, Kucaba TA, Wagner-McPherson C, Barbazuk WB, Gregory SG, Humphray SJ, French L, Evans RS, Bethel G, Whittaker A, Holden JL, McCann OT, Dunham A, Soderlund C, Scott CE, Bentley DR, Schuler G, Chen HC, Jang W, Green ED, Idol JR, Maduro VV, Montgomery KT, Lee E, Miller A, Emerling S, Kucherlapati, Gibbs R, Scherer S, Gorrell JH, Sodergren E, Clerc-Blankenburg K, Tabor P, Naylor S, Garcia D, de Jong PJ, Catanese JJ, Nowak N, Osoegawa K, Qin S, Rowen L, Madan A, Dors M, Hood L, Trask B, Friedman C, Massa H, Cheung VG, Kirsch IR, Reid T, Yonescu R, Weissenbach J, Bruls T, Heilig R, Branscomb E, Olsen A, Doggett N, Cheng JF, Hawkins T, Myers RM, Shang J, Ramirez L, Schmutz J, Velasquez O, Dixon K, Stone NE, Cox DR, Haussler D, Kent WJ, Furey T, Rogic S, Kennedy S, Jones S, Rosenthal A, Wen G, Schilhabel M, Gloeckner G, Nyakatura G, Siebert R, Schlegelberger B, Korenberg J, Chen XN, Fujiyama A, Hattori M, Toyoda A, Yada T, Park HS, Sakaki Y, Shimizu N, Asakawa S, Kawasaki K, Sasaki T, Shintani A, Shimizu A, Shibuya K, Kudoh J, Minoshima S, Ramser J, Seranski P, Hoff C, Poustka A, Reinhardt R, and Lehrach H

Subjects
Chromosomes, Artificial, Bacterial, Cloning, Molecular, DNA Fingerprinting, Gene Duplication, Humans, In Situ Hybridization, Fluorescence, Repetitive Sequences, Nucleic Acid, Contig Mapping, Genome, Human
Abstract

The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.

Published
2001
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