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171 results on '"Maslen, G"'

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. Dominant negative mutations in human PPAR-gamma associated with severe insulin resistance, diabetes mellitus and hypertension

Author

Barroso, I., Gurnell, M., Crowley, V.E.F., Agostini, M., Schwabe, J.W., Soos, M.A., Maslen, G. Ll, Williams, T.D.M., Lewis, H., Schafer, A.J., Chatterjee, V.K.K., and O'Rahilly, S.

Subjects
Diabetes -- Genetic aspects, Hypertension -- Genetic aspects, Insulin resistance -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

It has been possible to identify the first examples of naturally occurring loss-of-function germline mutations in human PPAR-gamma. There is a strong association between these mutations and an unusual syndrome of strong insulin resistance, early onset diabetes and hypertension. It is possible that residual PPAR-gamma activity, possibly controlled by high endogenous ligand concentrations in adipocytes, is sufficient to maintain adipogenesis. There is a possible causal connection between the PPAR-gamma mutation and early onset hypertension through effects on vascular tone.

Published
1999

4. 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

6. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

Author

Manske, M, Miotto, O, Campino, S, Auburn, S, Almagro-Garcia, J, Maslen, G, O'Brien, J, Djimde, A, Doumbo, O, Zongo, I, Ouedraogo, JB, Michon, P, Mueller, I, Siba, P, Nzila, A, Borrmann, S, Kiara, SM, Marsh, K, Jiang, H, Su, XZ, Amaratunga, C, Fairhurst, R, Socheat, D, Nosten, F, Imwong, M, White, NJ, Sanders, M, Anastasi, E, Alcock, D, Drury, E, Oyola, S, Quail, MA, Turner, DJ, Ruano-Rubio, V, Jyothi, D, Amenga-Etego, L, Hubbart, C, Jeffreys, A, Rowlands, K, Sutherland, C, Roper, C, Mangano, V, Modiano, D, Tan, JC, Ferdig, MT, Amambua-Ngwa, A, Conway, DJ, Takala-Harrison, S, Plowe, CV, Rayner, JC, Rockett, KA, Clark, TG, Newbold, CI, Berriman, M, MacInnis, B, and Kwiatkowski, DP

Subjects
Genotype, 030231 tropical medicine, Population, Plasmodium falciparum, Genomics, Biology, Polymorphism, Single Nucleotide, Deep sequencing, Article, 03 medical and health sciences, 0302 clinical medicine, parasitic diseases, Humans, Genetic variability, Malaria, Falciparum, education, Genotyping, Alleles, Phylogeny, 030304 developmental biology, Genetics, Whole genome sequencing, 0303 health sciences, Genetic diversity, education.field_of_study, Principal Component Analysis, Multidisciplinary, High-Throughput Nucleotide Sequencing, Biodiversity, biology.organism_classification, 3. Good health, Genome, Protozoan
Abstract

methods for the large-scale analysis of genetic variation in Plasmodium falciparum by deep sequencing of parasite DNA obtained from the blood of patients with malaria, either directly or after short-term culture. Analysis of 86,158 exonic single nucleotide polymorphisms that passed genotyping quality control in 227 samples from Africa, Asia and Oceania provides genomewide estimates of allele frequency distribution, population structure and linkage disequilibrium. By comparing the genetic diversity of individual infections with that of the local parasite population, we derive a metric of within-host diversity that is related to the level of inbreeding in the population. An open-access web application has been established for the exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome. The genetic diversity and evolutionary plasticity of P. falciparum are major obstacles for malaria elimination. New forms of resistance against antimalarial drugs are continually emerging 1,2 , and new forms of antigenic variation are a critical point of vulnerability for future malaria vaccines. Effective tools are needed to detect evolutionary changes in the parasite population and to monitor the spread of genetic variants that affect malaria control. Here we describe the use of deep sequencing to analyse P. falciparum diversity, using blood samples from patients with malaria. The P. falciparum genome has several unusual features that greatly complicate sequence analysis, such as extreme AT bias, large tracts of nonunique sequence and several large families of intensely polymorphic genes 3 . Our aim was therefore not to determine the entire genome sequence of individual field samples—which would be prohibitively expensive with current technologies—but to define an initial set of single nucleotide polymorphisms (SNPs) distributed across the P. falciparum genome, whose genotype can be ascertained with confidence in parasitized blood samples by deep sequencing. An additional complication in the analysis of P. falciparum genome variation is that the billions of haploid parasites that infect a single individual can be a complex mixture of genetic types. Previous studies 4–8 have largely focused on laboratory-adapted parasite clones, but the within-host diversity of natural infections is of fundamental biological interest. Parasites in the blood replicate asexually, but when they are taken up in the blood meal of an Anopheles mosquito they undergo sexual mating. If the parasites in the blood are of diverse genetic types, this process of sexual mating can generate novel recombinant forms. Deep sequencing provides new ways of investigating within-host diversity and the role of sexual recombination in parasite evolution.

Published
2016

7. Genome-wide and fine-resolution association analysis of malaria in West Africa

Author

Muminatou, Jallow, Yik Ying Teo, Small, Kerrin S., Rockett, Kirk A., Panos, Deloukas, Clark, Taane G., Katja, Kivinen, Bojang, Kalifa A., Conway, David J., Margaret, Pinder, Giorgio, Sirugo, Fatou Sisay Joof, Stanley, Usen, Sarah, Auburn, Bumpstead, Suzannah J., Susana, Campino, Alison, Coffey, Andrew, Dunham, Fry, Andrew E., Angela, Green, Rhian, Gwilliam, Hunt, Sarah E., Michael, Inouye, Jeffreys, Anna E., Alieu, Mendy, Aarno, Palotie, Simon, Potter, Jiannis, Ragoussis, Jane, Rogers, Kate, Rowlands, Elilan, Somaskantharajah, Pamela, Whittaker, Claire, Widden, Peter, Donnelly, Bryan, Howie, Jonathan, Marchini, Andrew, Morris, Miguel, Sanjoaquin, Eric Akum Achidi, Tsiri, Agbenyega, Angela, Allen, Olukemi, Amodu, Patrick, Corran, Abdoulaye, Djimde, Amagana, Dolo, Doumbo, Ogobara K., Chris, Drakeley, Sarah, Dunstan, Jennifer, Evans, Jeremy, Farrar, Hien Tt, Fernando D., Horstmann, R. D., Ibrahim, M., Karunaweera, N., Kokwaro, G., Koram, K. A., Lemnge, M., Makani, J., Marsh, K., Michon, P., David, Modiano, Molyneux, M. E., Mueller, I., Parker, M., Peshu, N., Plowe, C. V., Puijalon, O., Reeder, J., Reyburn, H., Riley, E. M., Sakuntabhai, A., Singhasivanon, P., Sirima, S., Tall, A., Taylor, T. E., Thera, M., Troye Blomberg, M., Williams, T. N., Wilson, M., Wellcome Trust Case Control Consortium Kwiatkowski, D. P., Epidemiology Network: Achidi, Malaria Genomic E. A., Agbenyega, T., Ahmad, T., Alcock, D., Allen, S., Amenga Etego, L., Amodu, O., Apinjoh, T. O., Attwood, A. P., Auburn, S., Ball, S. G., Balmforth, A. J., Ban, M., Barbour, J., Barnwell, D., Barrett, J. C., Barrett, J. H., Barton, A., Bentley, D., Bishop, D. T., Bojang, K., Boorman, J. P., Bougouma, E., Bradbury, L. A., Braga Marcano, C. A., Braund, P. S., Bredin, F., Breen, G., Brown, M. A., Brown, M. J., Bruce, I. N., Bryan, C., Bull, S., Bumpstead, S. J., Burke, B., Burton, P. R., Caesar, S., Campino, S., Cant, B., Cardin, N. J., Cardon, L. R., Carucci, D., Caulfield, M., Chaney, A., Clark, T., Clayton, D. G., Collier, D. A., Compston, A., Compston, D. A., Connell, J., Conway, D., Cook, K., Corran, P., Craddock, N., Cummings, F. R., Davison, D., Deloukas, P., Devries, J., Dewasurendra, R., Diakite, M., Dixon, R. J., Djimde, A., Dobson, R., Dolo, A., Dominiczak, A., Donnelly, P., Donovan, H., Doumbo, O., Downes, K., Doyle, A., Drakeley, C., Drummond, H., Duffy, P., Duncanson, A., Dunger, D. B., Dunstan, S., Duombo, O., Easton, D., Elkin, A., Elliott, K. S., Elzein, A., Enimil, A., Evans, D., Evans, J., Everson, U., Eyre, S., Farmer, A., Farrall, M., Farrar, C., Farrar, J., Fernando, D., Ferreira, T., Ferrier, I. N., Fisher, S. A., Fitzpatrick, K., Forbes, A., Franklyn, J. A., Fraser, C., Frayling, T. M., Freathy, R. M., Ghansah, A., Ghori, J., Gilbert, P. D., Gordon Smith, K., Goris, A., Gottlieb, M., Gough, S. C., Green, A., Green, E. K., Groves, C. J., Grozeva, D., Gungadoo, J., Gwilliam, R., Hall, A. S., Hallgrimsdóttir, I. B., Hamshere, M. L., Hart, L., Hattersley, A. T., Heward, J. M., Hider, S. L., Tran Tinh Hien, Hill, A. V., Hilton, E., Hinks, A. M., Hitman, G. A., Holmans, P. A., Horstmann, Rolf D., Howie, B. N., Hubbart, C., Hughes, C., Hunt, S. E., Hussein, A., Hussey, J. M., Muntaser, Ibrahim, Iles, M. M., Inouye, M., Ishengoma, D., Jallow, M., Jeffreys, A. E., Jewell, D. P., John, Sl, Jolley, J. D., Jones, I. R., Jones, L., Jones, R. W., Nadira, Karunaweera, Keniry, A., King, E., Kirov, G., Kivinen, K., Knight, A. S., Koch, K., Gilbert, Kokwaro, Koram, Kwadwo A., Lango, H., Lathrop, G. M., Lee, K. L., Lees, C. W., Martha, Lemnge, Leung, H. T., Lewis, C. M., Lin, E., Lindgren, C. M., Ly, A., Macinnis, B., Julie, Makani, Mangano, Valentina, Mangino, M., Manjurano, A., Manning, L., Mansfield, J. C., Manske, M., Maqbool, A., Marchini, J. L., Kevin, Marsh, Maslen, G., Mathew, C. G., Mcardle, W. L., Mccarthy, M. I., Mccreight, M., Mcginnis, R., Mcguffin, P., Meech, E., Mendy, A., Pascal, Michon, Mohiuddin, M. K., Molyneux, Malcolm E., Morris, A. P., Moskvina, V., Moyes, C., Ivo, Mueller, Munroe, P. B., Mutabingwa, T., Ndila, C. M., Newhouse, S. J., Newport, M., Nikolov, I., Nimmo, E. R., Nutland, S., Nyirongo, V., O'Donovan, M. C., Oluoch, T., Onipinla, A., Onnie, C. M., Ouwehand, W. H., Owen, M. J., Michael, Parker, Parkes, M., Pembrey, M., Pereira Gale, J., Perry, J. R., Norbert, Peshu, Plowe, Christopher V., Pointon, J. J., Potter, C., Potter, S., Prescott, N. J., Prowse, C. V., Odile, Puijalon, Quyen, N. T., Ragoussis, J., Rahman, N., Ravindrarajah, R., Rayner, N. W., John, Reeder, Hugh, Reyburn, Riley, Eleanor M., Ring, S. M., Risley, P., Rockett, K. A., Rogers, J., Rowlands, K., Anavaj, Sakuntabhai, Samani, N. J., Sanderson, J., Sanjoaquin, M., Satsangi, J., Sawcer, S. J., Seal, S., Shields, B. M., Silman, A. J., Simmonds, M. J., Pratap, Singhasivanon, Sodiomon, Sirima, Sirugo, G., Small, K. S., Somaskantharajah, E., Spencer, C. C., St Clair, D., Stevens, H. E., Stevens, M., Stevens, S., Strachan, D. P., Stratton, M. R., Su, Z., Suriyaphol, P., Symmons, D. P., Adama, Tall, Taylor, N. C., Taylor, Terrie E., Teo, Y., Teo, Y. Y., Mahamadou, Thera, Thompson, J. R., Thomson, W., Timpson, N. J., Tobin, M. D., Todd, J. A., Todhunter, C. E., Toure, O., Tremelling, M., Marita Troye Blomberg, Vanderwal, A., Vukcevic, D., Walker, M., Walker, N. M., Wallace, C., Walters, G. R., Walton, R., Watkins, N. A., Watson, R., Webster, J., Weedon, M. N., Whittaker, P., Widmer, B., Williams, Thomas N., Williamson, R., Michael, Wilson, Winzer, T., Withers, D., Wordsworth, P., Worthington, J., Wrigley, R., Xue, M., Young, A. H., Yuldasheva, N., and Zeggini, E.

Subjects
Linkage disequilibrium, Hemoglobin, Sickle, Population, Genome-wide association study, Locus (genetics), Biology, Population stratification, Polymorphism, Single Nucleotide, Severity of Illness Index, Linkage Disequilibrium, Article, Gene mapping, Reference Values, Ethnicity, Genetics, Humans, education, Genetic association, education.field_of_study, Polymorphism, Genetic, Chromosome Mapping, Genetic Variation, Malaria, Gambia, Imputation (genetics), Genome-Wide Association Study
Abstract

We report a genome-wide association (GWA) study of severe malaria in The Gambia. The initial GWA scan included 2,500 children genotyped on the Affymetrix 500K GeneChip, and a replication study included 3,400 children. We used this to examine the performance of GWA methods in Africa. We found considerable population stratification, and also that signals of association at known malaria resistance loci were greatly attenuated owing to weak linkage disequilibrium (LD). To investigate possible solutions to the problem of low LD, we focused on the HbS locus, sequencing this region of the genome in 62 Gambian individuals and then using these data to conduct multipoint imputation in the GWA samples. This increased the signal of association, from P = 4 × 10(-7) to P = 4 × 10(-14), with the peak of the signal located precisely at the HbS causal variant. Our findings provide proof of principle that fine-resolution multipoint imputation, based on population-specific sequencing data, can substantially boost authentic GWA signals and enable fine mapping of causal variants in African populations.

Published
2009
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8. Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

Author

Neafsey, DE, Waterhouse, RM, Abai, MR, Aganezov, SS, Alekseyev, MA, Allen, JE, Amon, J, Arcà, B, Arensburger, P, Artemov, G, Assour, LA, Basseri, H, Berlin, A, Birren, BW, Blandin, SA, Brockman, AI, Burkot, TR, Burt, A, Chan, CS, Chauve, C, Chiu, JC, Christensen, M, Costantini, C, Davidson, VLM, Deligianni, E, Dottorini, T, Dritsou, V, Gabriel, SB, Guelbeogo, WM, Hall, AB, Han, MV, Hlaing, T, Hughes, DST, Jenkins, AM, Jiang, X, Jungreis, I, Kakani, EG, Kamali, M, Kemppainen, P, Kennedy, RC, Kirmitzoglou, IK, Koekemoer, LL, Laban, N, Langridge, N, Lawniczak, MKN, Lirakis, M, Lobo, NF, Lowy, E, MacCallum, RM, Mao, C, Maslen, G, Mbogo, C, McCarthy, J, Michel, K, Mitchell, SN, Moore, W, Murphy, KA, Naumenko, AN, Nolan, T, Novoa, EM, O'Loughlin, S, Oringanje, C, Oshaghi, MA, Pakpour, N, Papathanos, PA, Peery, AN, Povelones, M, Prakash, A, Price, DP, Rajaraman, A, Reimer, LJ, Rinker, DC, Rokas, A, Russell, TL, Sagnon, N, Sharakhova, MV, Shea, T, Simão, FA, Simard, F, Slotman, MA, Somboon, P, Stegniy, V, Struchiner, CJ, and Thomas, GWC

Abstract

© 2015, american association for the advancement of science. All rigths reserved. Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ∼100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.

Published
2015
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9. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes

Author

Neafsey, D. E., Waterhouse, R. M., Abai, M. R., Aganezov, S. S., Alekseyev, M. A., Allen, J. E., Amon, J., Arca, B., Arensburger, P., Artemov, G., Assour, L. A., Basseri, H., Berlin, A., Birren, B. W., Blandin, S. A., Brockman, A. I., Burkot, T. R., Burt, A., Chan, C. S., Chauve, C., Chiu, J. C., Christensen, M., Costantini, C., Davidson, V. L., Deligianni, E., Dottorini, T., Dritsou, V., Gabriel, S. B., Guelbeogo, W. M., Hall, A. B., Han, M. V., Hlaing, T., Hughes, D. S., Jenkins, A. M., Jiang, X., Jungreis, I., Kakani, E. G., Kamali, M., Kemppainen, P., Kennedy, R. C., Kirmitzoglou, I. K., Koekemoer, L. L., Laban, N., Langridge, N., Lawniczak, M. K., Lirakis, M., Lobo, N. F., Lowy, E., MacCallum, R. M., Mao, C., Maslen, G., Mbogo, C., McCarthy, J., Michel, K., Mitchell, S. N., Moore, W., Murphy, K. A., Naumenko, A. N., Nolan, T., Novoa, E. M., O'Loughlin, S., Oringanje, C., Oshaghi, M. A., Pakpour, N., Papathanos, P. A., Peery, A. N., Povelones, M., Prakash, A., Price, D. P., Rajaraman, A., Reimer, L. J., Rinker, D. C., Rokas, A., Russell, T. L., Sagnon, N., Sharakhova, M. V., Shea, T., Simao, F. A., Simard, F., Slotman, M. A., Somboon, P., Stegniy, V., Struchiner, C. J., Thomas, G. W., Tojo Castro, Marta, Topalis, P., Tubio, J. M., Unger, M. F., Vontas, J., Walton, C., Wilding, C. S., Willis, J. H., Wu, Y. C., Yan, G., Zdobnov, E. M., Zhou, X., Catteruccia, F., Christophides, G. K., Collins, F. H., Cornman, R. S., Crisanti, A., Donnelly, M. J., Emrich, S. J., Fontaine, M. C., Gelbart, W., Hahn, M. W., Hansen, I. A., Howell, P. I., Kafatos, F. C., Kellis, M., Lawson, D., Louis, C., Luckhart, S., Muskavitch, M. A., Ribeiro, J. M., Riehle, M. A., Sharakhov, I. V., Tu, Z., Zwiebel, L. J., and Besansky, N. J.

Subjects
EXPRESSION, SEX-CHROMOSOME EVOLUTION, ANTENNAL TRANSCRIPTOME PROFILES, Base Sequence, R CONSENSUS, Genome, Insect, Molecular Sequence Data, GAMBIAE, CUTICULAR PROTEIN GENES, AEDES-AEGYPTI, DROSOPHILA, ANNOTATION, FAMILY, Malari, Chromosomes, Insect, Insect Vectors, Evolution, Molecular, Anopheles, Animals, Humans, Drosophila, Sequence Alignment, Phylogeny
Abstract

Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.

Published
2015

11. High throughput SNP discovery in candidate genes

Author

Valdes, A.M., Barroso, I., Baynes, C., Cubberley, R., Cutts, T., Durham, J., Greenham, J., Elliot, A., Jones, K., Lightning, J., Loudon, I., Maslen, G., Palmer, M., Reed, J., Ring, H., Swarbrick, P., Thomas, K., Townley, D., Varley, A., and Schafer, A.

Subjects
Genetic research -- Analysis, Human genetics -- Research, Chromosome mapping -- Research, Genetic polymorphisms -- Research, Biological sciences
Published
2000

12. Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi

Author

Jiang, X., Peery, A., Hall, B., Sharma, A., Chen, X.-G., Waterhouse, R. M., Komissarov, A., Riehle, M. M., Shouche, Y., Sharakhova, Maria V., Lawson, D., Pakpour, Nazzy, Arensburger, Peter, Davidson, V. L. M., Eiglmeier, K., Emrich, S., George, P., Kennedy, R. C., Mane, S. P., Maslen, G., Oringanje, C., Qi, Y., Settlage, Robert E., Tojo, M., Tubio, J. M. C., Unger, Maria F., Wang, B., Vernick, K. D., Ribeiro, J. C., James, A. A., Michel, K., Riehle, M. A., Luckhart, Shirley, Sharakhov, Igor V., Tu, Zhijian Jake, and Biological Systems Engineering

Subjects
Genetics & Heredity, Biotechnology & Applied Microbiology, PLASMODIUM-FALCIPARUM, WEB SERVER, parasitic diseases, INVERSION POLYMORPHISMS, RNA-SEQ, IN-SILICO, NUCLEAR LAMINS, AEDES-AEGYPTI, GENE, EVOLUTION, CHROMOSOMAL REARRANGEMENT
Abstract

Background: Anopheles stephensi is the key vector of malaria throughout the Indian subcontinent and Middle East and an emerging model for molecular and genetic studies of mosquito-parasite interactions. The type form of the species is responsible for the majority of urban malaria transmission across its range. Results: Here, we report the genome sequence and annotation of the Indian strain of the type form of An. stephensi. The 221 Mb genome assembly represents more than 92% of the entire genome and was produced using a combination of 454, Illumina, and PacBio sequencing. Physical mapping assigned 62% of the genome onto chromosomes, enabling chromosome-based analysis. Comparisons between An. stephensi and An. gambiae reveal that the rate of gene order reshuffling on the X chromosome was three times higher than that on the autosomes. An. stephensi has more heterochromatin in pericentric regions but less repetitive DNA in chromosome arms than An. gambiae. We also identify a number of Y-chromosome contigs and BACs. Interspersed repeats constitute 7.1% of the assembled genome while LTR retrotransposons alone comprise more than 49% of the Y contigs. RNA-seq analyses provide new insights into mosquito innate immunity, development, and sexual dimorphism. Conclusions: The genome analysis described in this manuscript provides a resource and platform for fundamental and translational research into a major urban malaria vector. Chromosome-based investigations provide unique perspectives on Anopheles chromosome evolution. RNA-seq analysis and studies of immunity genes offer new insights into mosquito biology and mosquito-parasite interactions. Published version

Published
2014

15. Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi

Author

Biological Systems Engineering, Jiang, X., Peery, A., Hall, B., Sharma, A., Chen, X.-G., Waterhouse, R. M., Komissarov, A., Riehle, M. M., Shouche, Y., Sharakhova, Maria V., Lawson, D., Pakpour, Nazzy, Arensburger, Peter, Davidson, V. L. M., Eiglmeier, K., Emrich, S., George, P., Kennedy, R. C., Mane, S. P., Maslen, G., Oringanje, C., Qi, Y., Settlage, Robert E., Tojo, M., Tubio, J. M. C., Unger, Maria F., Wang, B., Vernick, K. D., Ribeiro, J. C., James, A. A., Michel, K., Riehle, M. A., Luckhart, Shirley, Sharakhov, Igor V., Tu, Zhijian Jake, Biological Systems Engineering, Jiang, X., Peery, A., Hall, B., Sharma, A., Chen, X.-G., Waterhouse, R. M., Komissarov, A., Riehle, M. M., Shouche, Y., Sharakhova, Maria V., Lawson, D., Pakpour, Nazzy, Arensburger, Peter, Davidson, V. L. M., Eiglmeier, K., Emrich, S., George, P., Kennedy, R. C., Mane, S. P., Maslen, G., Oringanje, C., Qi, Y., Settlage, Robert E., Tojo, M., Tubio, J. M. C., Unger, Maria F., Wang, B., Vernick, K. D., Ribeiro, J. C., James, A. A., Michel, K., Riehle, M. A., Luckhart, Shirley, Sharakhov, Igor V., and Tu, Zhijian Jake

Abstract

Background: Anopheles stephensi is the key vector of malaria throughout the Indian subcontinent and Middle East and an emerging model for molecular and genetic studies of mosquito-parasite interactions. The type form of the species is responsible for the majority of urban malaria transmission across its range. Results: Here, we report the genome sequence and annotation of the Indian strain of the type form of An. stephensi. The 221 Mb genome assembly represents more than 92% of the entire genome and was produced using a combination of 454, Illumina, and PacBio sequencing. Physical mapping assigned 62% of the genome onto chromosomes, enabling chromosome-based analysis. Comparisons between An. stephensi and An. gambiae reveal that the rate of gene order reshuffling on the X chromosome was three times higher than that on the autosomes. An. stephensi has more heterochromatin in pericentric regions but less repetitive DNA in chromosome arms than An. gambiae. We also identify a number of Y-chromosome contigs and BACs. Interspersed repeats constitute 7.1% of the assembled genome while LTR retrotransposons alone comprise more than 49% of the Y contigs. RNA-seq analyses provide new insights into mosquito innate immunity, development, and sexual dimorphism. Conclusions: The genome analysis described in this manuscript provides a resource and platform for fundamental and translational research into a major urban malaria vector. Chromosome-based investigations provide unique perspectives on Anopheles chromosome evolution. RNA-seq analysis and studies of immunity genes offer new insights into mosquito biology and mosquito-parasite interactions.

Published
2014

16. A global network for genomic epidemiology of malaria

Author

Malaria Genomic Epidemiology Network, Achidi, Ea, Agbenyega, T, Allen, S, Amodu, O, Bojang, K, Conway, D, Corran, P, Deloukas, P, Djimde, A, Dolo, A, Doumbo, O, Drakeley, C, Duffy, P, Dunstan, S, Evans, J, Farrar, J, Fernando, D, Tran, Th, Horstmann, R, Ibrahim, M, Karunaweera, N, Kokwaro, G, Koram, K, Kwiatkowski, D, Lemnge, M, Makani, J, Marsh, K, Michon, P, Modiano, D, Molyneux, Me, Mueller, I, Mutabingwa, T, Parker, M, Peshu, N, Plowe, C, Puijalon, O, Ragoussis, J, Reeder, J, Reyburn, H, Riley, E, Rogers, J, Sakuntabhai, A, Singhasivanon, P, Sirima, S, Sirugo, G, Tall, A, Taylor, T, Thera, M, Troye Blomberg, M, Williams, T, Wilson, M, Amenga Etego, L, Apinjoh, To, Bougouma, E, Dewasurendra, R, Diakite, M, Enimil, A, Hussein, A, Ishengoma, D, Jallow, M, Lin, E, Ly, A, Mangano, Valentina, Manjurano, A, Manning, L, Ndila, Cm, Nyirongo, V, Oluoch, T, Nguyen, Tn, Suriyaphol, P, Toure, O, Rockett, Ka, Vanderwal, A, Clark, T, Wrigley, R, Alcock, D, Auburn, S, Barnwell, D, Bull, S, Campino, S, Devries, J, Elzein, A, Fitzpatrick, K, Ghansah, A, Green, A, Hart, L, Hilton, E, Hubbart, C, Hughes, C, Jeffreys, Ae, Kivinen, K, Macinnis, B, Manske, M, Maslen, G, Mccreight, M, Mendy, A, Moyes, C, Nyika, A, Potter, C, Risley, P, Rowlands, K, Sanjoaquin, M, Small, K, Somaskantharajah, E, Stevens, M, Teo, Y, Watson, R, Carucci, D, Cook, K, Doyle, A, Duombo, O, Gottlieb, M, and Kwiatkowski, D.

Published
2008

17. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

Author

Manske, M, Miotto, O, Campino, S, Auburn, S, Almagro-Garcia, J, Maslen, G, O'Brien, J, Djimde, A, Doumbo, O, Zongo, I, Ouedraogo, J-B, Michon, P, Mueller, I, Siba, P, Nzila, A, Borrmann, S, Kiara, SM, Marsh, K, Jiang, H, Su, X-Z, Amaratunga, C, Fairhurst, R, Socheat, D, Nosten, F, Imwong, M, White, NJ, Sanders, M, Anastasi, E, Alcock, D, Drury, E, Oyola, S, Quail, MA, Turner, DJ, Ruano-Rubio, V, Jyothi, D, Amenga-Etego, L, Hubbart, C, Jeffreys, A, Rowlands, K, Sutherland, C, Roper, C, Mangano, V, Modiano, D, Tan, JC, Ferdig, MT, Amambua-Ngwa, A, Conway, DJ, Takala-Harrison, S, Plowe, CV, Rayner, JC, Rockett, KA, Clark, TG, Newbold, CI, Berriman, M, MacInnis, B, Kwiatkowski, DP, Manske, M, Miotto, O, Campino, S, Auburn, S, Almagro-Garcia, J, Maslen, G, O'Brien, J, Djimde, A, Doumbo, O, Zongo, I, Ouedraogo, J-B, Michon, P, Mueller, I, Siba, P, Nzila, A, Borrmann, S, Kiara, SM, Marsh, K, Jiang, H, Su, X-Z, Amaratunga, C, Fairhurst, R, Socheat, D, Nosten, F, Imwong, M, White, NJ, Sanders, M, Anastasi, E, Alcock, D, Drury, E, Oyola, S, Quail, MA, Turner, DJ, Ruano-Rubio, V, Jyothi, D, Amenga-Etego, L, Hubbart, C, Jeffreys, A, Rowlands, K, Sutherland, C, Roper, C, Mangano, V, Modiano, D, Tan, JC, Ferdig, MT, Amambua-Ngwa, A, Conway, DJ, Takala-Harrison, S, Plowe, CV, Rayner, JC, Rockett, KA, Clark, TG, Newbold, CI, Berriman, M, MacInnis, B, and Kwiatkowski, DP

Abstract

Malaria elimination strategies require surveillance of the parasite population for genetic changes that demand a public health response, such as new forms of drug resistance. Here we describe methods for the large-scale analysis of genetic variation in Plasmodium falciparum by deep sequencing of parasite DNA obtained from the blood of patients with malaria, either directly or after short-term culture. Analysis of 86,158 exonic single nucleotide polymorphisms that passed genotyping quality control in 227 samples from Africa, Asia and Oceania provides genome-wide estimates of allele frequency distribution, population structure and linkage disequilibrium. By comparing the genetic diversity of individual infections with that of the local parasite population, we derive a metric of within-host diversity that is related to the level of inbreeding in the population. An open-access web application has been established for the exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome.

Published
2012

18. Integrated outcrop, drill core, borehole and seismic stratigraphic architecture of a cyclothemic, shallow-marine depositional system, Wanganui Basin, New Zealand

Author

Naish, T. R., Field, B. D., Zhu, H., Melhuish, A., Carter, R. M., Abbott, S. T., Edwards, S., Alloway, B. V., Wilson, G. S., Niessen, Frank, Barker, A., Brone, G. H., Maslen, G., Naish, T. R., Field, B. D., Zhu, H., Melhuish, A., Carter, R. M., Abbott, S. T., Edwards, S., Alloway, B. V., Wilson, G. S., Niessen, Frank, Barker, A., Brone, G. H., and Maslen, G.

Published
2005

19. Quaternary glacio-eustatic sea-level fluctuations from Wanganui Basin, New Zealand

Author

Naish, T., Carter, B., Abbott, S., Field, B., Zhu, H., Wilson, G., Alloway, B., Edwards, S., Pillans, B., Barker, A., Niessen, Frank, Maslen, G., Beu, A., Naish, T., Carter, B., Abbott, S., Field, B., Zhu, H., Wilson, G., Alloway, B., Edwards, S., Pillans, B., Barker, A., Niessen, Frank, Maslen, G., and Beu, A.

Published
2004

23. Integrated outcrop, drill core, borehole and seismic stratigraphic architecture of a cyclothemic, shallow‐marine depositional system, Wanganui Basin, New Zealand

Author

Naish, T. R., primary, Field, B. D., additional, Zhu, H., additional, Melhuish, A., additional, Carter, R. M., additional, Abbott, S. T., additional, Edwards, S., additional, Alloway, B. V., additional, Wilson, G. S., additional, Niessen, F., additional, Barker, A., additional, Browne, G. H, additional, and Maslen, G., additional

Published
2005
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24. From Long Range Mapping to Sequence-Ready Contigs on Human Chromosome 6

Author

Mungall, A. J., primary, Humphray, S. J., additional, Ranby, S. A., additional, Edwards, C. A., additional, Heathcott, R. W., additional, Clee, C. M., additional, Holloway, E., additional, Peck, A. I., additional, Harrison, P., additional, Green, L. D., additional, Butler, A. P., additional, Langford, C. F., additional, Gwilliam, R., additional, Huckle, E. J., additional, Baron, L., additional, Smith, A., additional, Leversha, M. A., additional, Ramsey, Y. H., additional, Clegg, S. M., additional, Rice, C. M., additional, Maslen, G. L., additional, Hunt, S. E., additional, Scott, C. E., additional, Soderlund, C. A., additional, Theaker, A. J., additional, Carter, N. P., additional, Ross, M. T., additional, Deloukas, P., additional, Bentley, D. R., additional, and Dunham, I., additional

Published
1997
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25. The Chromosome 6 Database at the Sanger Centre

Author

Theaker, A. J., primary, Maslen, G. L., additional, Scott, C. E., additional, Rice, C. M., additional, Hunt, S. E., additional, King, A., additional, Mungall, A. J., additional, Dunham, I., additional, and Beck, S., additional

Published
1997
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27. Report of the DNA committee and catalogues of cloned and mapped genes, markers formatted for PCR and DNA polymorphisms (Part 14 of 27)

Author

Williamson, R., primary, Bowcock, A., additional, Kidd, K., additional, Pearson, P., additional, Schmidtke, J., additional, Ceverha, P., additional, Chipperfield, M., additional, Cooper, D.N., additional, Coutelle, C., additional, Hewitt, J., additional, Klinger, K., additional, Langley, K., additional, Beckmann, J., additional, Tolley, M., additional, Maidak, B., additional, Hewett, D., additional, Linch, C., additional, and Maslen, G., additional

Published
1991
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28. Report of the DNA committee and catalogues of cloned and mapped genes, markers formatted for PCR and DNA polymorphisms (Part 21 of 27)

Author

Williamson, R., primary, Bowcock, A., additional, Kidd, K., additional, Pearson, P., additional, Schmidtke, J., additional, Ceverha, P., additional, Chipperfield, M., additional, Cooper, D.N., additional, Coutelle, C., additional, Hewitt, J., additional, Klinger, K., additional, Langley, K., additional, Beckmann, J., additional, Tolley, M., additional, Maidak, B., additional, Hewett, D., additional, Linch, C., additional, and Maslen, G., additional

Published
1991
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29. Report of the DNA committee and catalogues of cloned and mapped genes, markers formatted for PCR and DNA polymorphisms (Part 3 of 27)

Author

Williamson, R., primary, Bowcock, A., additional, Kidd, K., additional, Pearson, P., additional, Schmidtke, J., additional, Ceverha, P., additional, Chipperfield, M., additional, Cooper, D.N., additional, Coutelle, C., additional, Hewitt, J., additional, Klinger, K., additional, Langley, K., additional, Beckmann, J., additional, Tolley, M., additional, Maidak, B., additional, Hewett, D., additional, Linch, C., additional, and Maslen, G., additional

Published
1991
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30. Report of the DNA committee and catalogues of cloned and mapped genes, markers formatted for PCR and DNA polymorphisms (Part 9 of 27)

Author

Williamson, R., primary, Bowcock, A., additional, Kidd, K., additional, Pearson, P., additional, Schmidtke, J., additional, Ceverha, P., additional, Chipperfield, M., additional, Cooper, D.N., additional, Coutelle, C., additional, Hewitt, J., additional, Klinger, K., additional, Langley, K., additional, Beckmann, J., additional, Tolley, M., additional, Maidak, B., additional, Hewett, D., additional, Linch, C., additional, and Maslen, G., additional

Published
1991
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31. Report of the DNA committee and catalogues of cloned and mapped genes, markers formatted for PCR and DNA polymorphisms (Part 4 of 27)

Author

Williamson, R., primary, Bowcock, A., additional, Kidd, K., additional, Pearson, P., additional, Schmidtke, J., additional, Ceverha, P., additional, Chipperfield, M., additional, Cooper, D.N., additional, Coutelle, C., additional, Hewitt, J., additional, Klinger, K., additional, Langley, K., additional, Beckmann, J., additional, Tolley, M., additional, Maidak, B., additional, Hewett, D., additional, Linch, C., additional, and Maslen, G., additional

Published
1991
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32. Report of the DNA committee and catalogues of cloned and mapped genes, markers formatted for PCR and DNA polymorphisms (Part 8 of 27)

Author

Williamson, R., primary, Bowcock, A., additional, Kidd, K., additional, Pearson, P., additional, Schmidtke, J., additional, Ceverha, P., additional, Chipperfield, M., additional, Cooper, D.N., additional, Coutelle, C., additional, Hewitt, J., additional, Klinger, K., additional, Langley, K., additional, Beckmann, J., additional, Tolley, M., additional, Maidak, B., additional, Hewett, D., additional, Linch, C., additional, and Maslen, G., additional

Published
1991
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33. Report of the DNA committee and catalogues of cloned and mapped genes, markers formatted for PCR and DNA polymorphisms (Part 6 of 27)

Author

Williamson, R., primary, Bowcock, A., additional, Kidd, K., additional, Pearson, P., additional, Schmidtke, J., additional, Ceverha, P., additional, Chipperfield, M., additional, Cooper, D.N., additional, Coutelle, C., additional, Hewitt, J., additional, Klinger, K., additional, Langley, K., additional, Beckmann, J., additional, Tolley, M., additional, Maidak, B., additional, Hewett, D., additional, Linch, C., additional, and Maslen, G., additional

Published
1991
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34. Report of the DNA committee and catalogues of cloned and mapped genes, markers formatted for PCR and DNA polymorphisms (Part 5 of 27)

Author

Williamson, R., primary, Bowcock, A., additional, Kidd, K., additional, Pearson, P., additional, Schmidtke, J., additional, Ceverha, P., additional, Chipperfield, M., additional, Cooper, D.N., additional, Coutelle, C., additional, Hewitt, J., additional, Klinger, K., additional, Langley, K., additional, Beckmann, J., additional, Tolley, M., additional, Maidak, B., additional, Hewett, D., additional, Linch, C., additional, and Maslen, G., additional

Published
1991
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35. Report of the DNA committee and catalogues of cloned and mapped genes, markers formatted for PCR and DNA polymorphisms (Part 7 of 27)

Author

Williamson, R., primary, Bowcock, A., additional, Kidd, K., additional, Pearson, P., additional, Schmidtke, J., additional, Ceverha, P., additional, Chipperfield, M., additional, Cooper, D.N., additional, Coutelle, C., additional, Hewitt, J., additional, Klinger, K., additional, Langley, K., additional, Beckmann, J., additional, Tolley, M., additional, Maidak, B., additional, Hewett, D., additional, Linch, C., additional, and Maslen, G., additional

Published
1991
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46. High-resolution landmark framework for the sequence-ready mapping of Xq23-q26.1.

Author

Steingruber, H E, Dunham, A, Coffey, A J, Clegg, S M, Howell, G R, Maslen, G L, Scott, C E, Gwilliam, R, Hunt, P J, Sotheran, E C, Huckle, E J, Hunt, S E, Dhami, P, Soderlund, C, Leversha, M A, Bentley, D R, and Ross, M T

Abstract

We have established a landmark framework map over 20-25 Mb of the long arm of the human X chromosome using yeast artificial chromosome (YAC) clones. The map has approximately one landmark per 45 kb of DNA and stretches from DXS7531 in proximal Xq23 to DXS895 in proximal Xq26, connecting to published framework maps on its proximal and distal sides. There are three gaps in the framework map resulting from the failure to obtain clone coverage from the YAC resources available. Estimates of the maximum sizes of these gaps have been obtained. The four YAC contigs have been positioned and oriented using somatic-cell hybrids and fluorescence in situ hybridization, and the largest is estimated to cover approximately 15 Mb of DNA. The framework map is being used to assemble a sequence-ready map in large-insert bacterial clones, as part of an international effort to complete the sequence of the X chromosome. PAC and BAC contigs currently cover 18 Mb of the region, and from these, 12 Mb of finished sequence is available.

Published
1999

48. The Chromosome 6 Database at the Sanger Centre

Author

Theaker, A. J., Maslen, G. L., Scott, C. E., Rice, C. M., Hunt, S. E., King, A., Mungall, A. J., Dunham, I., and Beck, S.

Abstract

The Sanger Centre Chromosome 6 Database (6ace) has been developed as the primary means of release of annotated sequencing and mapping information for human chromosome 6 from the Sanger Centre. It is also being used to curate global data from published and unpublished external sources. The rationale behind the development of 6ace is described, together with information as to how to access the database.

Published
1997
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49. From Long Range Mapping to Sequence-Ready Contigs on Human Chromosome 6

Author

Mungall, A. J., Humphray, S. J., Ranby, S. A., Edwards, C. A., Heathcott, R. W., Clee, C. M., Holloway, E., Peck, A. I., Harrison, P., Green, L. D., Butler, A. P., Langford, C. F., Gwilliam, R., Huckle, E. J., Baron, L., Smith, A., Leversha, M. A., Ramsey, Y. H., Clegg, S. M., Rice, C. M., Maslen, G. L., Hunt, S. E., Scott, C. E., Soderlund, C. A., Theaker, A. J., Carter, N. P., Ross, M. T., Deloukas, P., Bentley, D. R., and Dunham, I.

Abstract

Our aim is to construct physical clone maps covering those regions of chromosome 6 that are not currently extensively mapped, and use these to determine the DNA sequence of the whole chromosome. The strategy we are following involves establishing a high density framework map of the order of 15 markers per Megabase using radiation hybrid (RH) mapping. The markers are then used to identify large-insert genomic bacterial clones covering the chromosome, which are assembled into sequence-ready contigs by restriction enzyme fingerprinting and sequence tagged site (STS) content analysis. Contig gap closure is performed by walking experiments using STSs developed from the end sequences of the clone inserts.

Published
1997
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