600 results on '"Pearson, Richard D"'
Search Results
2. Genomic analysis of Plasmodium vivax describes patterns of connectivity and putative drivers of adaptation in Ethiopia
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Kebede, Alebachew Messele, Sutanto, Edwin, Trimarsanto, Hidayat, Benavente, Ernest Diez, Barnes, Mariana, Pearson, Richard D., Siegel, Sasha V., Erko, Berhanu, Assefa, Ashenafi, Getachew, Sisay, Aseffa, Abraham, Petros, Beyene, Lo, Eugenia, Mohammed, Rezika, Yilma, Daniel, Rumaseb, Angela, Nosten, Francois, Noviyanti, Rintis, Rayner, Julian C., Kwiatkowski, Dominic P., Price, Ric N., Golassa, Lemu, and Auburn, Sarah
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- 2023
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3. Genomics of Plasmodium vivax in Colombia reveals evidence of local bottle-necking and inter-country connectivity in the Americas
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Sutanto, Edwin, Pava, Zuleima, Echeverry, Diego F., Lopera-Mesa, Tatiana M., Montenegro, Lidia Madeline, Yasnot-Acosta, Maria F., Benavente, Ernest Diez, Pearson, Richard D., Herrera, Sócrates, Arévalo-Herrera, Myriam, Trimarsanto, Hidayat, Rumaseb, Angela, Noviyanti, Rintis, Kwiatkowski, Dominic P., Price, Ric N., and Auburn, Sarah
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- 2023
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4. Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum
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Kümpornsin, Krittikorn, Kochakarn, Theerarat, Yeo, Tomas, Okombo, John, Luth, Madeline R., Hoshizaki, Johanna, Rawat, Mukul, Pearson, Richard D., Schindler, Kyra A., Mok, Sachel, Park, Heekuk, Uhlemann, Anne-Catrin, Jana, Gouranga P., Maity, Bikash C., Laleu, Benoît, Chenu, Elodie, Duffy, James, Moliner Cubel, Sonia, Franco, Virginia, Gomez-Lorenzo, Maria G., Gamo, Francisco Javier, Winzeler, Elizabeth A., Fidock, David A., Chookajorn, Thanat, and Lee, Marcus C. S.
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- 2023
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5. Chloroquine resistance evolution in Plasmodium falciparum is mediated by the putative amino acid transporter AAT1
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Amambua-Ngwa, Alfred, Button-Simons, Katrina A., Li, Xue, Kumar, Sudhir, Brenneman, Katelyn Vendrely, Ferrari, Marco, Checkley, Lisa A., Haile, Meseret T., Shoue, Douglas A., McDew-White, Marina, Tindall, Sarah M., Reyes, Ann, Delgado, Elizabeth, Dalhoff, Haley, Larbalestier, James K., Amato, Roberto, Pearson, Richard D., Taylor, Alexander B., Nosten, François H., D’Alessandro, Umberto, Kwiatkowski, Dominic, Cheeseman, Ian H., Kappe, Stefan H. I., Avery, Simon V., Conway, David J., Vaughan, Ashley M., Ferdig, Michael T., and Anderson, Timothy J. C.
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- 2023
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6. Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination.
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Jacob, Christopher G, Thuy-Nhien, Nguyen, Mayxay, Mayfong, Maude, Richard J, Quang, Huynh Hong, Hongvanthong, Bouasy, Vanisaveth, Viengxay, Ngo Duc, Thang, Rekol, Huy, van der Pluijm, Rob, von Seidlein, Lorenz, Fairhurst, Rick, Nosten, François, Hossain, Md Amir, Park, Naomi, Goodwin, Scott, Ringwald, Pascal, Chindavongsa, Keobouphaphone, Newton, Paul, Ashley, Elizabeth, Phalivong, Sonexay, Maude, Rapeephan, Leang, Rithea, Huch, Cheah, Dong, Le Thanh, Nguyen, Kim-Tuyen, Nhat, Tran Minh, Hien, Tran Tinh, Nguyen, Hoa, Zdrojewski, Nicole, Canavati, Sara, Sayeed, Abdullah Abu, Uddin, Didar, Buckee, Caroline, Fanello, Caterina I, Onyamboko, Marie, Peto, Thomas, Tripura, Rupam, Amaratunga, Chanaki, Myint Thu, Aung, Delmas, Gilles, Landier, Jordi, Parker, Daniel M, Chau, Nguyen Hoang, Lek, Dysoley, Suon, Seila, Callery, James, Jittamala, Podjanee, Hanboonkunupakarn, Borimas, Pukrittayakamee, Sasithon, Phyo, Aung Pyae, Smithuis, Frank, Lin, Khin, Thant, Myo, Hlaing, Tin Maung, Satpathi, Parthasarathi, Satpathi, Sanghamitra, Behera, Prativa K, Tripura, Amar, Baidya, Subrata, Valecha, Neena, Anvikar, Anupkumar R, Ul Islam, Akhter, Faiz, Abul, Kunasol, Chanon, Drury, Eleanor, Kekre, Mihir, Ali, Mozam, Love, Katie, Rajatileka, Shavanthi, Jeffreys, Anna E, Rowlands, Kate, Hubbart, Christina S, Dhorda, Mehul, Vongpromek, Ranitha, Kotanan, Namfon, Wongnak, Phrutsamon, Almagro Garcia, Jacob, Pearson, Richard D, Ariani, Cristina V, Chookajorn, Thanat, Malangone, Cinzia, Nguyen, T, Stalker, Jim, Jeffery, Ben, Keatley, Jonathan, Johnson, Kimberly J, Muddyman, Dawn, Chan, Xin Hui S, Sillitoe, John, Amato, Roberto, Simpson, Victoria, Gonçalves, Sonia, Rockett, Kirk, Day, Nicholas P, Dondorp, Arjen M, Kwiatkowski, Dominic P, and Miotto, Olivo
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asia ,drug resistance ,epidemiology ,genetic surveillance ,global health ,infectious disease ,malaria ,microbiology ,Biochemistry and Cell Biology - Abstract
BackgroundNational Malaria Control Programmes (NMCPs) currently make limited use of parasite genetic data. We have developed GenRe-Mekong, a platform for genetic surveillance of malaria in the Greater Mekong Subregion (GMS) that enables NMCPs to implement large-scale surveillance projects by integrating simple sample collection procedures in routine public health procedures.MethodsSamples from symptomatic patients are processed by SpotMalaria, a high-throughput system that produces a comprehensive set of genotypes comprising several drug resistance markers, species markers and a genomic barcode. GenRe-Mekong delivers Genetic Report Cards, a compendium of genotypes and phenotype predictions used to map prevalence of resistance to multiple drugs.ResultsGenRe-Mekong has worked with NMCPs and research projects in eight countries, processing 9623 samples from clinical cases. Monitoring resistance markers has been valuable for tracking the rapid spread of parasites resistant to the dihydroartemisinin-piperaquine combination therapy. In Vietnam and Laos, GenRe-Mekong data have provided novel knowledge about the spread of these resistant strains into previously unaffected provinces, informing decision-making by NMCPs.ConclusionsGenRe-Mekong provides detailed knowledge about drug resistance at a local level, and facilitates data sharing at a regional level, enabling cross-border resistance monitoring and providing the public health community with valuable insights. The project provides a rich open data resource to benefit the entire malaria community.FundingThe GenRe-Mekong project is funded by the Bill and Melinda Gates Foundation (OPP11188166, OPP1204268). Genotyping and sequencing were funded by the Wellcome Trust (098051, 206194, 203141, 090770, 204911, 106698/B/14/Z) and Medical Research Council (G0600718). A proportion of samples were collected with the support of the UK Department for International Development (201900, M006212), and Intramural Research Program of the National Institute of Allergy and Infectious Diseases.
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- 2021
7. Genetic surveillance ofPlasmodium falciparumreveals rapid population changes following first-line treatment policy revisions in the Greater Mekong Subregion
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Verschuuren, Tess D, primary, Wasakul, Varanya, additional, Thuy-Nhien, Nguyen, additional, Booth, Ethan, additional, Quang, Huynh Hong, additional, Thang, Ngo Duc, additional, Chindavongsa, Keobouphaphone, additional, Sovannaroth, Siv, additional, Banouvong, Virasak, additional, Sengsavath, Viengphone, additional, Mayxay, Mayfong, additional, Tuyen, Nguyen Thi Kim, additional, Phuong, Vo Ngoc Lam, additional, Trung, Pham Duc, additional, Goncalves, Sonia, additional, Chen, Soun, additional, Phalivong, Sonexay, additional, Xayvanghang, Saiamphone, additional, Mahaphontrakoon, Supaporn, additional, Pearson, Richard D, additional, Newton, Paul N, additional, Maude, Richard J, additional, Ashley, Elizabeth A, additional, Ariani, Cristina, additional, Simpson, Victoria J, additional, Day, Nicholas P, additional, Dondorp, Arjen M, additional, and Miotto, Olivo, additional
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- 2024
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8. Malaria outbreak in Laos driven by a selective sweep for Plasmodium falciparum kelch13 R539T mutants: a genetic epidemiology analysis
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Wasakul, Varanya, Disratthakit, Areeya, Mayxay, Mayfong, Chindavongsa, Keobouphaphone, Sengsavath, Viengphone, Thuy-Nhien, Nguyen, Pearson, Richard D, Phalivong, Sonexay, Xayvanghang, Saiamphone, Maude, Richard J, Gonçalves, Sónia, Day, Nicholas P, Newton, Paul N, Ashley, Elizabeth A, Kwiatkowski, Dominic P, Dondorp, Arjen M, and Miotto, Olivo
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- 2023
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9. Frequent expansion of Plasmodium vivax Duffy Binding Protein in Ethiopia and its epidemiological significance.
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Lo, Eugenia, Hostetler, Jessica B, Yewhalaw, Delenasaw, Pearson, Richard D, Hamid, Muzamil MA, Gunalan, Karthigayan, Kepple, Daniel, Ford, Anthony, Janies, Daniel A, Rayner, Julian C, Miller, Louis H, and Yan, Guiyun
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Erythrocytes ,Humans ,Plasmodium vivax ,Malaria ,Vivax ,Receptors ,Cell Surface ,Protozoan Proteins ,Antigens ,Protozoan ,Duffy Blood-Group System ,Genome ,Protozoan ,Ethiopia ,Female ,Male ,DNA Copy Number Variations ,Antigens ,Protozoan ,Genome ,Malaria ,Vivax ,Receptors ,Cell Surface ,Biological Sciences ,Medical and Health Sciences ,Tropical Medicine - Abstract
Plasmodium vivax invasion of human erythrocytes depends on the Duffy Binding Protein (PvDBP) which interacts with the Duffy antigen. PvDBP copy number has been recently shown to vary between P. vivax isolates in Sub-Saharan Africa. However, the extent of PvDBP copy number variation, the type of PvDBP multiplications, as well as its significance across broad samples are still unclear. We determined the prevalence and type of PvDBP duplications, as well as PvDBP copy number variation among 178 Ethiopian P. vivax isolates using a PCR-based diagnostic method, a novel quantitative real-time PCR assay and whole genome sequencing. For the 145 symptomatic samples, PvDBP duplications were detected in 95 isolates, of which 81 had the Cambodian and 14 Malagasy-type PvDBP duplications. PvDBP varied from 1 to >4 copies. Isolates with multiple PvDBP copies were found to be higher in symptomatic than asymptomatic infections. For the 33 asymptomatic samples, PvDBP was detected with two copies in two of the isolates, and both were the Cambodian-type PvDBP duplication. PvDBP copy number in Duffy-negative heterozygotes was not significantly different from that in Duffy-positives, providing no support for the hypothesis that increased copy number is a specific association with Duffy-negativity, although the number of Duffy-negatives was small and further sampling is required to test this association thoroughly.
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- 2019
10. A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria
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Trimarsanto, Hidayat, Amato, Roberto, Pearson, Richard D., Sutanto, Edwin, Noviyanti, Rintis, Trianty, Leily, Marfurt, Jutta, Pava, Zuleima, Echeverry, Diego F., Lopera-Mesa, Tatiana M., Montenegro, Lidia M., Tobón-Castaño, Alberto, Grigg, Matthew J., Barber, Bridget, William, Timothy, Anstey, Nicholas M., Getachew, Sisay, Petros, Beyene, Aseffa, Abraham, Assefa, Ashenafi, Rahim, Awab G., Chau, Nguyen H., Hien, Tran T., Alam, Mohammad S., Khan, Wasif A., Ley, Benedikt, Thriemer, Kamala, Wangchuck, Sonam, Hamedi, Yaghoob, Adam, Ishag, Liu, Yaobao, Gao, Qi, Sriprawat, Kanlaya, Ferreira, Marcelo U., Laman, Moses, Barry, Alyssa, Mueller, Ivo, Lacerda, Marcus V. G., Llanos-Cuentas, Alejandro, Krudsood, Srivicha, Lon, Chanthap, Mohammed, Rezika, Yilma, Daniel, Pereira, Dhelio B., Espino, Fe E. J., Chu, Cindy S., Vélez, Iván D., Namaik-larp, Chayadol, Villegas, Maria F., Green, Justin A., Koh, Gavin, Rayner, Julian C., Drury, Eleanor, Gonçalves, Sónia, Simpson, Victoria, Miotto, Olivo, Miles, Alistair, White, Nicholas J., Nosten, Francois, Kwiatkowski, Dominic P., Price, Ric N., and Auburn, Sarah
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- 2022
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11. Malaria protection due to sickle haemoglobin depends on parasite genotype
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Band, Gavin, Leffler, Ellen M., Jallow, Muminatou, Sisay-Joof, Fatoumatta, Ndila, Carolyne M., Macharia, Alexander W., Hubbart, Christina, Jeffreys, Anna E., Rowlands, Kate, Nguyen, Thuy, Gonçalves, Sónia, Ariani, Cristina V., Stalker, Jim, Pearson, Richard D., Amato, Roberto, Drury, Eleanor, Sirugo, Giorgio, d’Alessandro, Umberto, Bojang, Kalifa A., Marsh, Kevin, Peshu, Norbert, Saelens, Joseph W., Diakité, Mahamadou, Taylor, Steve M., Conway, David J., Williams, Thomas N., Rockett, Kirk A., and Kwiatkowski, Dominic P.
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- 2022
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12. Disseminated Cutaneous Leishmaniasis and Alcohol Misuse, Northeast Brazil, 2015-2018
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Sousa, Anastacio Q., Filho, Pedro D.T. Sindeaux, Cavalcante, Diane I.M., Frutuoso, Mercia S., Pereira, Francisco F., Lima, Jose W.O., Santos, Laecio P.S., Queiroz, Jose A.N., Maguire, James H., Pearson, Richard D., and Pompeu, Margarida M.L.
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Alcoholism -- Statistics -- Complications and side effects ,Leishmaniasis, Cutaneous -- Statistics -- Risk factors ,Health - Abstract
Leishmaniasis is a parasitic disease caused by infection with Leishmania parasites, which are transmitted by the bites of phlebotomine sand flies. Localized cutaneous leishmaniasis (LCL), disseminated cutaneous leishmaniasis (DCL), and [...]
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- 2021
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13. Erratum: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.
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Flannick, Jason, Fuchsberger, Christian, Mahajan, Anubha, Teslovich, Tanya M, Agarwala, Vineeta, Gaulton, Kyle J, Caulkins, Lizz, Koesterer, Ryan, Ma, Clement, Moutsianas, Loukas, McCarthy, Davis J, Rivas, Manuel A, Perry, John RB, Sim, Xueling, Blackwell, Thomas W, Robertson, Neil R, Rayner, N William, Cingolani, Pablo, Locke, Adam E, Tajes, Juan Fernandez, Highland, Heather M, Dupuis, Josee, Chines, Peter S, Lindgren, Cecilia M, Hartl, Christopher, Jackson, Anne U, Chen, Han, Huyghe, Jeroen R, van de Bunt, Martijn, Pearson, Richard D, Kumar, Ashish, Müller-Nurasyid, Martina, Grarup, Niels, Stringham, Heather M, Gamazon, Eric R, Lee, Jaehoon, Chen, Yuhui, Scott, Robert A, Below, Jennifer E, Chen, Peng, Huang, Jinyan, Go, Min Jin, Stitzel, Michael L, Pasko, Dorota, Parker, Stephen CJ, Varga, Tibor V, Green, Todd, Beer, Nicola L, Day-Williams, Aaron G, Ferreira, Teresa, Fingerlin, Tasha, Horikoshi, Momoko, Hu, Cheng, Huh, Iksoo, Ikram, Mohammad Kamran, Kim, Bong-Jo, Kim, Yongkang, Kim, Young Jin, Kwon, Min-Seok, Lee, Juyoung, Lee, Selyeong, Lin, Keng-Han, Maxwell, Taylor J, Nagai, Yoshihiko, Wang, Xu, Welch, Ryan P, Yoon, Joon, Zhang, Weihua, Barzilai, Nir, Voight, Benjamin F, Han, Bok-Ghee, Jenkinson, Christopher P, Kuulasmaa, Teemu, Kuusisto, Johanna, Manning, Alisa, Ng, Maggie CY, Palmer, Nicholette D, Balkau, Beverley, Stančáková, Alena, Abboud, Hanna E, Boeing, Heiner, Giedraitis, Vilmantas, Prabhakaran, Dorairaj, Gottesman, Omri, Scott, James, Carey, Jason, Kwan, Phoenix, Grant, George, Smith, Joshua D, Neale, Benjamin M, Purcell, Shaun, Butterworth, Adam S, Howson, Joanna MM, Lee, Heung Man, Lu, Yingchang, Kwak, Soo-Heon, Zhao, Wei, Danesh, John, and Lam, Vincent KL
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This corrects the article DOI: 10.1038/sdata.2017.179.
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- 2018
14. Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.
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Flannick, Jason, Fuchsberger, Christian, Mahajan, Anubha, Teslovich, Tanya M, Agarwala, Vineeta, Gaulton, Kyle J, Caulkins, Lizz, Koesterer, Ryan, Ma, Clement, Moutsianas, Loukas, McCarthy, Davis J, Rivas, Manuel A, Perry, John RB, Sim, Xueling, Blackwell, Thomas W, Robertson, Neil R, Rayner, N William, Cingolani, Pablo, Locke, Adam E, Tajes, Juan Fernandez, Highland, Heather M, Dupuis, Josee, Chines, Peter S, Lindgren, Cecilia M, Hartl, Christopher, Jackson, Anne U, Chen, Han, Huyghe, Jeroen R, van de Bunt, Martijn, Pearson, Richard D, Kumar, Ashish, Müller-Nurasyid, Martina, Grarup, Niels, Stringham, Heather M, Gamazon, Eric R, Lee, Jaehoon, Chen, Yuhui, Scott, Robert A, Below, Jennifer E, Chen, Peng, Huang, Jinyan, Go, Min Jin, Stitzel, Michael L, Pasko, Dorota, Parker, Stephen CJ, Varga, Tibor V, Green, Todd, Beer, Nicola L, Day-Williams, Aaron G, Ferreira, Teresa, Fingerlin, Tasha, Horikoshi, Momoko, Hu, Cheng, Huh, Iksoo, Ikram, Mohammad Kamran, Kim, Bong-Jo, Kim, Yongkang, Kim, Young Jin, Kwon, Min-Seok, Lee, Juyoung, Lee, Selyeong, Lin, Keng-Han, Maxwell, Taylor J, Nagai, Yoshihiko, Wang, Xu, Welch, Ryan P, Yoon, Joon, Zhang, Weihua, Barzilai, Nir, Voight, Benjamin F, Han, Bok-Ghee, Jenkinson, Christopher P, Kuulasmaa, Teemu, Kuusisto, Johanna, Manning, Alisa, Ng, Maggie CY, Palmer, Nicholette D, Balkau, Beverley, Stančáková, Alena, Abboud, Hanna E, Boeing, Heiner, Giedraitis, Vilmantas, Prabhakaran, Dorairaj, Gottesman, Omri, Scott, James, Carey, Jason, Kwan, Phoenix, Grant, George, Smith, Joshua D, Neale, Benjamin M, Purcell, Shaun, Butterworth, Adam S, Howson, Joanna MM, Lee, Heung Man, Lu, Yingchang, Kwak, Soo-Heon, Zhao, Wei, Danesh, John, and Lam, Vincent KL
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Humans ,Diabetes Mellitus ,Type 2 ,European Continental Ancestry Group ,Genetic Variation ,Diabetes ,Human Genome ,Genetics ,2.1 Biological and endogenous factors ,Metabolic and endocrine - Abstract
To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.
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- 2017
15. A complexPlasmodium falciparumcryptotype circulating at low frequency across the African continent
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Miotto, Olivo, primary, Amambua-Ngwa, Alfred, additional, Amenga-Etego, Lucas, additional, Abdel Hamid, Muzamil M, additional, Adam, Ishag, additional, Aninagyei, Enoch, additional, Apinjoh, Tobias, additional, Awandare, Gordon A, additional, Bejon, Philip, additional, Bertin, Gwladys I, additional, Bouyou-Akotet, Marielle, additional, Claessens, Antoine, additional, Conway, David J, additional, D’Alessandro, Umberto, additional, Diakite, Mahamadou, additional, Djimdé, Abdoulaye, additional, Dondorp, Arjen M, additional, Duffy, Patrick, additional, Fairhurst, Rick M, additional, Fanello, Caterina I, additional, Ghansah, Anita, additional, Ishengoma, Deus, additional, Lawniczak, Mara, additional, Maïga-Ascofaré, Oumou, additional, Auburn, Sarah, additional, Rosanas-Urgell, Anna, additional, Wasakul, Varanya, additional, White, Nina FD, additional, Almagro-Garcia, Jacob, additional, Pearson, Richard D, additional, Goncalves, Sonia, additional, Ariani, Cristina, additional, Bozdech, Zbynek, additional, Hamilton, William, additional, Simpson, Victoria, additional, and Kwiatkowski, Dominic P, additional
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- 2024
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16. A Low-Frequency Inactivating Akt2 Variant Enriched in the Finnish Population is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk.
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Manning, Alisa, Highland, Heather M, Gasser, Jessica, Sim, Xueling, Tukiainen, Taru, Fontanillas, Pierre, Grarup, Niels, Rivas, Manuel A, Mahajan, Anubha, Locke, Adam E, Cingolani, Pablo, Pers, Tune H, Viñuela, Ana, Brown, Andrew A, Wu, Ying, Flannick, Jason, Fuchsberger, Christian, Gamazon, Eric R, Gaulton, Kyle J, Im, Hae Kyung, Teslovich, Tanya M, Blackwell, Thomas W, Bork-Jensen, Jette, Burtt, Noël P, Chen, Yuhui, Green, Todd, Hartl, Christopher, Kang, Hyun Min, Kumar, Ashish, Ladenvall, Claes, Ma, Clement, Moutsianas, Loukas, Pearson, Richard D, Perry, John RB, Rayner, N William, Robertson, Neil R, Scott, Laura J, van de Bunt, Martijn, Eriksson, Johan G, Jula, Antti, Koskinen, Seppo, Lehtimäki, Terho, Palotie, Aarno, Raitakari, Olli T, Jacobs, Suzanne BR, Wessel, Jennifer, Chu, Audrey Y, Scott, Robert A, Goodarzi, Mark O, Blancher, Christine, Buck, Gemma, Buck, David, Chines, Peter S, Gabriel, Stacey, Gjesing, Anette P, Groves, Christopher J, Hollensted, Mette, Huyghe, Jeroen R, Jackson, Anne U, Jun, Goo, Justesen, Johanne Marie, Mangino, Massimo, Murphy, Jacquelyn, Neville, Matt, Onofrio, Robert, Small, Kerrin S, Stringham, Heather M, Trakalo, Joseph, Banks, Eric, Carey, Jason, Carneiro, Mauricio O, DePristo, Mark, Farjoun, Yossi, Fennell, Timothy, Goldstein, Jacqueline I, Grant, George, Hrabé de Angelis, Martin, Maguire, Jared, Neale, Benjamin M, Poplin, Ryan, Purcell, Shaun, Schwarzmayr, Thomas, Shakir, Khalid, Smith, Joshua D, Strom, Tim M, Wieland, Thomas, Lindstrom, Jaana, Brandslund, Ivan, Christensen, Cramer, Surdulescu, Gabriela L, Lakka, Timo A, Doney, Alex SF, Nilsson, Peter, Wareham, Nicholas J, Langenberg, Claudia, Varga, Tibor V, Franks, Paul W, Rolandsson, Olov, Rosengren, Anders H, and Farook, Vidya S
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Genetics ,Diabetes ,Aetiology ,2.1 Biological and endogenous factors ,Metabolic and endocrine ,Black or African American ,Alleles ,Asian People ,Case-Control Studies ,Diabetes Mellitus ,Type 2 ,Fasting ,Finland ,Gene Frequency ,Genetic Predisposition to Disease ,Genotype ,Hispanic or Latino ,Humans ,Insulin ,Insulin Resistance ,Odds Ratio ,Proto-Oncogene Proteins c-akt ,White People ,Medical and Health Sciences ,Endocrinology & Metabolism - Abstract
To identify novel coding association signals and facilitate characterization of mechanisms influencing glycemic traits and type 2 diabetes risk, we analyzed 109,215 variants derived from exome array genotyping together with an additional 390,225 variants from exome sequence in up to 39,339 normoglycemic individuals from five ancestry groups. We identified a novel association between the coding variant (p.Pro50Thr) in AKT2 and fasting plasma insulin (FI), a gene in which rare fully penetrant mutations are causal for monogenic glycemic disorders. The low-frequency allele is associated with a 12% increase in FI levels. This variant is present at 1.1% frequency in Finns but virtually absent in individuals from other ancestries. Carriers of the FI-increasing allele had increased 2-h insulin values, decreased insulin sensitivity, and increased risk of type 2 diabetes (odds ratio 1.05). In cellular studies, the AKT2-Thr50 protein exhibited a partial loss of function. We extend the allelic spectrum for coding variants in AKT2 associated with disorders of glucose homeostasis and demonstrate bidirectional effects of variants within the pleckstrin homology domain of AKT2.
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- 2017
17. Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic study
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van der Pluijm, Rob W, Imwong, Mallika, Chau, Nguyen Hoang, Hoa, Nhu Thi, Thuy-Nhien, Nguyen Thanh, Thanh, Ngo Viet, Jittamala, Podjanee, Hanboonkunupakarn, Borimas, Chutasmit, Kitipumi, Saelow, Chalermpon, Runjarern, Ratchadaporn, Kaewmok, Weerayuth, Tripura, Rupam, Peto, Thomas J, Yok, Sovann, Suon, Seila, Sreng, Sokunthea, Mao, Sivanna, Oun, Savuth, Yen, Sovannary, Amaratunga, Chanaki, Lek, Dysoley, Huy, Rekol, Dhorda, Mehul, Chotivanich, Kesinee, Ashley, Elizabeth A, Mukaka, Mavuto, Waithira, Naomi, Cheah, Phaik Yeong, Maude, Richard J, Amato, Roberto, Pearson, Richard D, Gonçalves, Sónia, Jacob, Christopher G, Hamilton, William L, Fairhurst, Rick M, Tarning, Joel, Winterberg, Markus, Kwiatkowski, Dominic P, Pukrittayakamee, Sasithon, Hien, Tran Tinh, Day, Nicholas PJ, Miotto, Olivo, White, Nicholas J, and Dondorp, Arjen M
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- 2019
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18. Evolution and expansion of multidrug-resistant malaria in southeast Asia: a genomic epidemiology study
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Hamilton, William L, Amato, Roberto, van der Pluijm, Rob W, Jacob, Christopher G, Quang, Huynh Hong, Thuy-Nhien, Nguyen Thanh, Hien, Tran Tinh, Hongvanthong, Bouasy, Chindavongsa, Keobouphaphone, Mayxay, Mayfong, Huy, Rekol, Leang, Rithea, Huch, Cheah, Dysoley, Lek, Amaratunga, Chanaki, Suon, Seila, Fairhurst, Rick M, Tripura, Rupam, Peto, Thomas J, Sovann, Yok, Jittamala, Podjanee, Hanboonkunupakarn, Borimas, Pukrittayakamee, Sasithon, Chau, Nguyen Hoang, Imwong, Mallika, Dhorda, Mehul, Vongpromek, Ranitha, Chan, Xin Hui S, Maude, Richard J, Pearson, Richard D, Nguyen, T, Rockett, Kirk, Drury, Eleanor, Gonçalves, Sónia, White, Nicholas J, Day, Nicholas P, Kwiatkowski, Dominic P, Dondorp, Arjen M, and Miotto, Olivo
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- 2019
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19. Next generation proton PDFs with deuteron and nuclear uncertainties
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Rosalyn L. Pearson, Richard D. Ball, Emanuele R. Nocera
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Physics ,QC1-999 - Abstract
As data become more precise, estimating theoretical uncertainties in global PDF determinations is likely to become increasingly necessary to obtain correspondingly precise PDFs. Here we present a next generation of global proton PDFs (NNPDF4.0) that include theoretical uncertainties due to the use of heavy nuclear and deuteron data in the fit. We estimate these uncertainties by comparing the values of the nuclear observables computed with the nuclear PDFs against those computed with proton PDFs. For heavy nuclear PDFs we use the nuclear nNNPDF2.0 set, while for deuteron PDFs we develop an iterative procedure to determine proton and deuteron PDFs simultaneously, each including the uncertainties in the other. Accounting for nuclear uncertainties resolves some of the tensions in the global fit of the proton PDFs, especially those between the nuclear data and the extended LHC data set used in NNPDF4.0.
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- 2022
- Full Text
- View/download PDF
20. The South Asian genome.
- Author
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Chambers, John C, Abbott, James, Zhang, Weihua, Turro, Ernest, Scott, William R, Tan, Sian-Tsung, Afzal, Uzma, Afaq, Saima, Loh, Marie, Lehne, Benjamin, O'Reilly, Paul, Gaulton, Kyle J, Pearson, Richard D, Li, Xinzhong, Lavery, Anita, Vandrovcova, Jana, Wass, Mark N, Miller, Kathryn, Sehmi, Joban, Oozageer, Laticia, Kooner, Ishminder K, Al-Hussaini, Abtehale, Mills, Rebecca, Grewal, Jagvir, Panoulas, Vasileios, Lewin, Alexandra M, Northwood, Korrinne, Wander, Gurpreet S, Geoghegan, Frank, Li, Yingrui, Wang, Jun, Aitman, Timothy J, McCarthy, Mark I, Scott, James, Butcher, Sarah, Elliott, Paul, and Kooner, Jaspal S
- Subjects
Humans ,Sequence Analysis ,DNA ,Genetics ,Population ,Genotype ,Polymorphism ,Single Nucleotide ,Alleles ,Genome ,Human ,Asian Continental Ancestry Group ,European Continental Ancestry Group ,Asia ,Genetic Variation ,Genome-Wide Association Study ,Genetics ,Population ,Genome ,Human ,Polymorphism ,Single Nucleotide ,Sequence Analysis ,DNA ,General Science & Technology - Abstract
The genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world's population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians.
- Published
- 2014
21. Transferrin receptor 1 is a reticulocyte-specific receptor for Plasmodium vivax
- Author
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Gruszczyk, Jakub, Kanjee, Usheer, Chan, Li-Jin, Menant, Sébastien, Malleret, Benoit, Lim, Nicholas T. Y., Schmidt, Christoph Q., Mok, Yee-Foong, Lin, Kai-Min, Pearson, Richard D., Rangel, Gabriel, Smith, Brian J., Call, Melissa J., Weekes, Michael P., Griffin, Michael D. W., Murphy, James M., Abraham, Jonathan, Sriprawat, Kanlaya, Menezes, Maria J., Ferreira, Marcelo U., Russell, Bruce, Renia, Laurent, Duraisingh, Manoj T., and Tham, Wai-Hong
- Published
- 2018
22. Genome-wide association analysis identifies 13 new risk loci for schizophrenia
- Author
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Donnelly, Peter, Barroso, Ines, Blackwell, Jenefer M, Bramon, Elvira, Brown, Matthew A, Casas, Juan P, Corvin, Aiden P, Deloukas, Panos, Duncanson, Audrey, Jankowski, Janusz, Markus, Hugh S, Mathew, Christopher G, Palmer, Colin NA, Plomin, Robert, Rautanen, Anna, Sawcer, Stephen J, Trembath, Richard C, Viswanathan, Ananth C, Wood, Nicholas W, Spencer, Chris CA, Band, Gavin, Bellenguez, Céline, Freeman, Colin, Hellenthal, Garrett, Giannoulatou, Eleni, Pirinen, Matti, Pearson, Richard D, Strange, Amy, Su, Zhan, Vukcevic, Damjan, Langford, Cordelia, Hunt, Sarah E, Edkins, Sarah, Gwilliam, Rhian, Blackburn, Hannah, Bumpstead, Suzannah J, Dronov, Serge, Gillman, Matthew, Gray, Emma, Hammond, Naomi, Jayakumar, Alagurevathi, McCann, Owen T, Liddle, Jennifer, Potter, Simon C, Ravindrarajah, Radhi, Ricketts, Michelle, Tashakkori-Ghanbaria, Avazeh, Waller, Matthew J, Weston, Paul, Widaa, Sara, Whittaker, Pamela, and McCarthy, Mark I
- Subjects
Mental health ,Case-Control Studies ,Female ,Genetic Predisposition to Disease ,Genome-Wide Association Study ,Humans ,Male ,Polymorphism ,Single Nucleotide ,Schizophrenia ,Sweden ,Multicenter Genetic Studies of Schizophrenia Consortium ,Psychosis Endophenotypes International Consortium ,Wellcome Trust Case Control Consortium 2 ,Biological Sciences ,Medical and Health Sciences ,Developmental Biology - Abstract
Schizophrenia is an idiopathic mental disorder with a heritable component and a substantial public health impact. We conducted a multi-stage genome-wide association study (GWAS) for schizophrenia beginning with a Swedish national sample (5,001 cases and 6,243 controls) followed by meta-analysis with previous schizophrenia GWAS (8,832 cases and 12,067 controls) and finally by replication of SNPs in 168 genomic regions in independent samples (7,413 cases, 19,762 controls and 581 parent-offspring trios). We identified 22 loci associated at genome-wide significance; 13 of these are new, and 1 was previously implicated in bipolar disorder. Examination of candidate genes at these loci suggests the involvement of neuronal calcium signaling. We estimate that 8,300 independent, mostly common SNPs (95% credible interval of 6,300-10,200 SNPs) contribute to risk for schizophrenia and that these collectively account for at least 32% of the variance in liability. Common genetic variation has an important role in the etiology of schizophrenia, and larger studies will allow more detailed understanding of this disorder.
- Published
- 2013
23. Host Defenses Against Prototypical Intracellular Protozoans, the Leishmania
- Author
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Pearson, Richard D., primary and Wilson, Mary E., additional
- Published
- 2020
- Full Text
- View/download PDF
24. Origins of the current outbreak of multidrug-resistant malaria in southeast Asia: a retrospective genetic study
- Author
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Amato, Roberto, Pearson, Richard D, Almagro-Garcia, Jacob, Amaratunga, Chanaki, Lim, Pharath, Suon, Seila, Sreng, Sokunthea, Drury, Eleanor, Stalker, Jim, Miotto, Olivo, Fairhurst, Rick M, and Kwiatkowski, Dominic P
- Published
- 2018
- Full Text
- View/download PDF
25. Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity
- Author
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Tsoi, Lam C, Spain, Sarah L, Knight, Jo, Ellinghaus, Eva, Stuart, Philip E, Capon, Francesca, Ding, Jun, Li, Yanming, Tejasvi, Trilokraj, Gudjonsson, Johann E, Kang, Hyun M, Allen, Michael H, McManus, Ross, Novelli, Giuseppe, Samuelsson, Lena, Schalkwijk, Joost, Ståhle, Mona, Burden, A David, Smith, Catherine H, Cork, Michael J, Estivill, Xavier, Bowcock, Anne M, Krueger, Gerald G, Weger, Wolfgang, Worthington, Jane, Tazi-Ahnini, Rachid, Nestle, Frank O, Hayday, Adrian, Hoffmann, Per, Winkelmann, Juliane, Wijmenga, Cisca, Langford, Cordelia, Edkins, Sarah, Andrews, Robert, Blackburn, Hannah, Strange, Amy, Band, Gavin, Pearson, Richard D, Vukcevic, Damjan, Spencer, Chris CA, Deloukas, Panos, Mrowietz, Ulrich, Schreiber, Stefan, Weidinger, Stephan, Koks, Sulev, Kingo, Külli, Esko, Tonu, Metspalu, Andres, Lim, Henry W, Voorhees, John J, Weichenthal, Michael, Wichmann, H Erich, Chandran, Vinod, Rosen, Cheryl F, Rahman, Proton, Gladman, Dafna D, Griffiths, Christopher EM, Reis, Andre, Kere, Juha, Nair, Rajan P, Franke, Andre, Barker, Jonathan NWN, Abecasis, Goncalo R, Elder, James T, and Trembath, Richard C
- Subjects
Genetics ,Autoimmune Disease ,Human Genome ,Psoriasis ,Aetiology ,2.1 Biological and endogenous factors ,Skin ,CARD Signaling Adaptor Proteins ,Core Binding Factor Alpha 3 Subunit ,DEAD Box Protein 58 ,DEAD-box RNA Helicases ,GTPase-Activating Proteins ,Genetic Loci ,Genetic Predisposition to Disease ,Genome-Wide Association Study ,Guanylate Cyclase ,Humans ,Immunity ,Innate ,Membrane Proteins ,Oligonucleotide Array Sequence Analysis ,Polymorphism ,Single Nucleotide ,Receptors ,Immunologic ,STAT3 Transcription Factor ,T-Lymphocytes ,White People ,Collaborative Association Study of Psoriasis ,Genetic Analysis of Psoriasis Consortium ,Psoriasis Association Genetics Extension ,Wellcome Trust Case Control Consortium 2 ,Biological Sciences ,Medical and Health Sciences ,Developmental Biology - Abstract
To gain further insight into the genetic architecture of psoriasis, we conducted a meta-analysis of 3 genome-wide association studies (GWAS) and 2 independent data sets genotyped on the Immunochip, including 10,588 cases and 22,806 controls. We identified 15 new susceptibility loci, increasing to 36 the number associated with psoriasis in European individuals. We also identified, using conditional analyses, five independent signals within previously known loci. The newly identified loci shared with other autoimmune diseases include candidate genes with roles in regulating T-cell function (such as RUNX3, TAGAP and STAT3). Notably, they included candidate genes whose products are involved in innate host defense, including interferon-mediated antiviral responses (DDX58), macrophage activation (ZC3H12C) and nuclear factor (NF)-κB signaling (CARD14 and CARM1). These results portend a better understanding of shared and distinctive genetic determinants of immune-mediated inflammatory disorders and emphasize the importance of the skin in innate and acquired host defense.
- Published
- 2012
26. Intrinsic multiplication rate variation and plasticity of human blood stage malaria parasites
- Author
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Stewart, Lindsay B., Diaz-Ingelmo, Ofelia, Claessens, Antoine, Abugri, James, Pearson, Richard D., Goncalves, Sonia, Drury, Eleanor, Kwiatkowski, Dominic P., Awandare, Gordon A., and Conway, David J.
- Published
- 2020
- Full Text
- View/download PDF
27. The Practice of Travel Medicine: Guidelines by the Infectious Diseases Society of America
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Hill, David R., Pearson, Richard D., Freedman, David O., Fischer, Philip R., and Ryan, Edward T.
- Published
- 2006
28. 315 - Antiparasitic Therapy
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Budge, Philip J. and Pearson, Richard D.
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- 2024
- Full Text
- View/download PDF
29. Infected Physicians and Invasive Procedures: Safe Practice Management
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Moreno, Jonathan D., Pearson, Richard D., Sawyer, Robert G., and Lombardo, Paul A.
- Published
- 2005
30. T-cell activation, senescence, and exhaustion in asymptomatic HIV/Leishmania infantumco-infection
- Author
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de Oliveira Mendes-Aguiar, Carolina, primary, do Monte Alves, Manoella, additional, Lopes Machado, Amanda de Albuquerque, additional, de Góis Monteiro, Glória Regina, additional, Medeiros, Iara Marques, additional, Queiroz, Jose Wilton, additional, Lima, Iraci Duarte, additional, Pearson, Richard D., additional, Wilson, Mary E., additional, Glesby, Marshall J., additional, do Nascimento, Eliana Lúcia Tomaz, additional, and Bezerra Jerônimo, Selma Maria, additional
- Published
- 2023
- Full Text
- View/download PDF
31. Genomic Analysis Reveals a Common Breakpoint in Amplifications of the Plasmodium vivax Multidrug Resistance 1 Locus in Thailand
- Author
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Auburn, Sarah, Serre, David, Pearson, Richard D., Amato, Roberto, Sriprawat, Kanlaya, To, Sheren, Handayuni, Irene, Suwanarusk, Rossarin, Russell, Bruce, Drury, Eleanor, Stalker, Jim, Miotto, Olivo, Kwiatkowski, Dominic P., Nosten, Francois, and Price, Ric N.
- Published
- 2016
32. Genetic markers associated with dihydroartemisinin–piperaquine failure in Plasmodium falciparum malaria in Cambodia: a genotype–phenotype association study
- Author
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Amato, Roberto, Lim, Pharath, Miotto, Olivo, Amaratunga, Chanaki, Dek, Dalin, Pearson, Richard D, Almagro-Garcia, Jacob, Neal, Aaron T, Sreng, Sokunthea, Suon, Seila, Drury, Eleanor, Jyothi, Dushyanth, Stalker, Jim, Kwiatkowski, Dominic P, and Fairhurst, Rick M
- Published
- 2017
- Full Text
- View/download PDF
33. Infected Physicians and Invasive Procedures: National Policy and Legal Reality
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Tereskerz, Patti Miller, Pearson, Richard D., and Jagger, Janine
- Published
- 1999
34. Cryo-EM structure of an essential Plasmodium vivax invasion complex
- Author
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Gruszczyk, Jakub, Huang, Rick K., Chan, Li-Jin, Menant, Sébastien, Hong, Chuan, Murphy, James M., Mok, Yee-Foong, Griffin, Michael D. W., Pearson, Richard D., Wong, Wilson, Cowman, Alan F., Yu, Zhiheng, and Tham, Wai-Hong
- Published
- 2018
- Full Text
- View/download PDF
35. Nanopore sequencing for real-time genomic surveillance ofPlasmodium falciparum
- Author
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Girgis, Sophia T., primary, Adika, Edem, additional, Nenyewodey, Felix E., additional, Senoo Jnr, Dodzi K., additional, Ngoi, Joyce M., additional, Bandoh, Kukua, additional, Lorenz, Oliver, additional, van de Steeg, Guus, additional, Nsoh, Sebastian, additional, Judge, Kim, additional, Pearson, Richard D., additional, Almagro-Garcia, Jacob, additional, Saiid, Samirah, additional, Atampah, Solomon, additional, Amoako, Enock K., additional, Morang’a, Collins M., additional, Asoala, Victor, additional, Adjei, Elrmion S., additional, Burden, William, additional, Roberts-Sengier, William, additional, Drury, Eleanor, additional, Gonçalves, Sónia, additional, Awandare, Gordon A., additional, Kwiatkowski, Dominic P., additional, Amenga-Etego, Lucas N., additional, and Hamilton, William L., additional
- Published
- 2022
- Full Text
- View/download PDF
36. Clinical Spectrum of Leishmaniasis
- Author
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Pearson, Richard D.
- Published
- 1996
37. An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples
- Author
-
Adam, Ishag, Alam, Mohammad Shafiul, Alemu, Sisay, Amaratunga, Chanaki, Amato, Roberto, Andrianaranjaka, Voahangy, Anstey, Nicholas M, Aseffa, Abraham, Ashley, Elizabeth, Assefa, Ashenafi, Auburn, Sarah, Barber, Bridget E, Barry, Alyssa, Batista Pereira, Dhelio, Cao, Jun, Chau, Nguyen Hoang, Chotivanich, Kesinee, Chu, Cindy, Dondorp, Arjen M, Drury, Eleanor, Echeverry, Diego F, Erko, Berhanu, Espino, Fe, Fairhurst, Rick, Faiz, Abdul, Fernanda Villegas, María, Gao, Qi, Golassa, Lemu, Goncalves, Sonia, Grigg, Matthew J, Hamedi, Yaghoob, Hien, Tran Tinh, Htut, Ye, Johnson, Kimberly J, Karunaweera, Nadira, Khan, Wasif, Krudsood, Srivicha, Kwiatkowski, Dominic P, Lacerda, Marcus, Ley, Benedikt, Lim, Pharath, Liu, Yaobao, Llanos-Cuentas, Alejandro, Lon, Chanthap, Lopera-Mesa, Tatiana, Marfurt, Jutta, Michon, Pascal, Miotto, Olivo, Mohammed, Rezika, Mueller, Ivo, Namaik-Larp, Chayadol, Newton, Paul N, Nguyen, Thuy-Nhien, Nosten, Francois, Noviyanti, Rintis, Pava, Zuleima, Pearson, Richard D, Petros, Beyene, Phyo, Aung P, Price, Ric N, Pukrittayakamee, Sasithon, Rahim, Awab Ghulam, Randrianarivelojosia, Milijaona, Rayner, Julian C, Rumaseb, Angela, Siegel, Sasha V, Simpson, Victoria J, Thriemer, Kamala, Tobon-Castano, Alberto, Trimarsanto, Hidayat, Urbano Ferreira, Marcelo, Vélez, Ivan D, Wangchuk, Sonam, Wellems, Thomas E, White, Nicholas J, William, Timothy, Yasnot, Maria F, Yilma, Daniel, Alam, Mohammad Shafiul [0000-0001-8330-5499], Ashley, Elizabeth [0000-0002-7620-4822], Barber, Bridget E [0000-0003-1066-7960], Batista Pereira, Dhelio [0000-0002-7761-5498], Chu, Cindy [0000-0001-9465-8214], Dondorp, Arjen M [0000-0001-5190-2395], Echeverry, Diego F [0000-0003-0301-4478], Espino, Fe [0000-0003-1690-1711], Faiz, Abdul [0000-0002-3460-7535], Golassa, Lemu [0000-0002-1216-8711], Grigg, Matthew J [0000-0001-9914-8352], Karunaweera, Nadira [0000-0003-3985-1817], Kwiatkowski, Dominic P [0000-0002-5023-0176], Ley, Benedikt [0000-0002-5734-0845], Miotto, Olivo [0000-0001-8060-6771], Nguyen, Thuy-Nhien [0000-0002-4101-5706], Nosten, Francois [0000-0002-7951-0745], Pearson, Richard D [0000-0002-7386-3566], Phyo, Aung P [0000-0002-0383-9624], Price, Ric N [0000-0003-2000-2874], Rayner, Julian C [0000-0002-9835-1014], Urbano Ferreira, Marcelo [0000-0002-5293-9090], Wellems, Thomas E [0000-0003-3899-8454], Yasnot, Maria F [0000-0001-8081-4212], Yilma, Daniel [0000-0001-6058-2696], and Apollo - University of Cambridge Repository
- Subjects
parasitic diseases ,Genomics ,Genomic Epidemiology ,Plasmodium vivax ,Malaria ,Data Resource - Abstract
This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.
- Published
- 2022
38. Malaria outbreak in Laos driven by a selective sweep for Plasmodium falciparum kelch13 R539T mutants: a genetic epidemiology analysis
- Author
-
Wasakul, Varanya, primary, Disratthakit, Areeya, additional, Mayxay, Mayfong, additional, Chindavongsa, Keobouphaphone, additional, Sengsavath, Viengphone, additional, Thuy-Nhien, Nguyen, additional, Pearson, Richard D, additional, Phalivong, Sonexay, additional, Xayvanghang, Saiamphone, additional, Maude, Richard J, additional, Gonçalves, Sónia, additional, Day, Nicholas P, additional, Newton, Paul N, additional, Ashley, Elizabeth A, additional, Kwiatkowski, Dominic P, additional, Dondorp, Arjen M, additional, and Miotto, Olivo, additional
- Published
- 2022
- Full Text
- View/download PDF
39. Postmortem findings for 7 neonates with congenital Zika virus infection
- Author
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Sousa, Anastacio Q., Cavalcante, Diane I.M., Franco, Luciano M., Araujo, Fernanda M.C., Sousa, Emilia T., Valenca-Junior, Jose Telmo, Rolim, Dionne B., Melo, Maria E.L., Sindeaux, Pedro D.T., Araujo, Marialva T.F., Pearson, Richard D., Wilson, Mary E., and Pompeu, Margarida M.L.
- Subjects
Newborn infants ,Zika virus ,Guillain-Barre syndrome -- Research ,Neurons ,Health - Abstract
From the discovery of Zika virus in Uganda in 1947 through 2007, when an outbreak occurred on Yap Island, Micronesia, only sporadic cases of human infection had been reported (1). [...]
- Published
- 2017
- Full Text
- View/download PDF
40. An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples
- Author
-
MalariaGEN, Adam, Ishag, Alam, Mohammad Shafiul, Alemu, Sisay, Amaratunga, Chanaki, Amato, Roberto, Andrianaranjaka, Voahangy, Anstey, Nicholas M, Aseffa, Abraham, Ashley, Elizabeth, Assefa, Ashenafi, Auburn, Sarah, Barber, Bridget E, Barry, Alyssa, Batista Pereira, Dhelio, Cao, Jun, Chau, Nguyen Hoang, Chotivanich, Kesinee, Chu, Cindy, Dondorp, Arjen M, Drury, Eleanor, Echeverry, Diego F, Erko, Berhanu, Espino, Fe, Fairhurst, Rick, Faiz, Abdul, Fernanda Villegas, María, Gao, Qi, Golassa, Lemu, Goncalves, Sonia, Grigg, Matthew J, Hamedi, Yaghoob, Hien, Tran Tinh, Htut, Ye, Johnson, Kimberly J, Karunaweera, Nadira, Khan, Wasif, Krudsood, Srivicha, Kwiatkowski, Dominic P, Lacerda, Marcus, Ley, Benedikt, Lim, Pharath, Liu, Yaobao, Llanos-Cuentas, Alejandro, Lon, Chanthap, Lopera-Mesa, Tatiana, Marfurt, Jutta, Michon, Pascal, Miotto, Olivo, Mohammed, Rezika, Mueller, Ivo, Namaik-Larp, Chayadol, Newton, Paul N, Nguyen, Thuy-Nhien, Nosten, Francois, Noviyanti, Rintis, Pava, Zuleima, Pearson, Richard D, Petros, Beyene, Phyo, Aung P, Price, Ric N, Pukrittayakamee, Sasithon, Rahim, Awab Ghulam, Randrianarivelojosia, Milijaona, Rayner, Julian C, Rumaseb, Angela, Siegel, Sasha V, Simpson, Victoria J, Thriemer, Kamala, Tobon-Castano, Alberto, Trimarsanto, Hidayat, Urbano Ferreira, Marcelo, Vélez, Ivan D, Wangchuk, Sonam, Wellems, Thomas E, White, Nicholas J, William, Timothy, Yasnot, Maria F, Yilma, Daniel, AII - Infectious diseases, Intensive Care Medicine, MalariaGEN, Alam, Mohammad Shafiul [0000-0001-8330-5499], Ashley, Elizabeth [0000-0002-7620-4822], Barber, Bridget E [0000-0003-1066-7960], Batista Pereira, Dhelio [0000-0002-7761-5498], Chu, Cindy [0000-0001-9465-8214], Dondorp, Arjen M [0000-0001-5190-2395], Echeverry, Diego F [0000-0003-0301-4478], Espino, Fe [0000-0003-1690-1711], Faiz, Abdul [0000-0002-3460-7535], Golassa, Lemu [0000-0002-1216-8711], Karunaweera, Nadira [0000-0003-3985-1817], Kwiatkowski, Dominic P [0000-0002-5023-0176], Ley, Benedikt [0000-0002-5734-0845], Miotto, Olivo [0000-0001-8060-6771], Nguyen, Thuy-Nhien [0000-0002-4101-5706], Nosten, Francois [0000-0002-7951-0745], Pearson, Richard D [0000-0002-7386-3566], Phyo, Aung P [0000-0002-0383-9624], Price, Ric N [0000-0003-2000-2874], Rayner, Julian C [0000-0002-9835-1014], Urbano Ferreira, Marcelo [0000-0002-5293-9090], Wellems, Thomas E [0000-0003-3899-8454], Yasnot, Maria F [0000-0001-8081-4212], Yilma, Daniel [0000-0001-6058-2696], and Apollo - University of Cambridge Repository
- Subjects
Data resource ,parasitic diseases ,Medicine (miscellaneous) ,Genomics ,Genomic epidemiology ,Plasmodium vivax ,General Biochemistry, Genetics and Molecular Biology ,Malaria - Abstract
This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.
- Published
- 2022
41. Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum
- Author
-
Kümpornsin, Krittikorn, primary, Kochakarn, Theerarat, additional, Yeo, Tomas, additional, Luth, Madeline R, additional, Pearson, Richard D, additional, Hoshizaki, Johanna, additional, Schindler, Kyra A, additional, Mok, Sachel, additional, Park, Heekuk, additional, Uhlemann, Anne-Catrin, additional, Cubel, Sonia Moliner, additional, Franco, Virginia, additional, Gomez-Lorenzo, Maria G, additional, Gamo, Francisco Javier, additional, Winzeler, Elizabeth A, additional, Fidock, David A, additional, Chookajorn, Thanat, additional, and Lee, Marcus CS, additional
- Published
- 2022
- Full Text
- View/download PDF
42. Genetic analysis of a malaria outbreak in Laos driven by a selective sweep for Plasmodium falciparum kelch13 R539T mutants
- Author
-
Wasakul, Varanya, primary, Disratthakit, Areeya, additional, Mayxay, Mayfong, additional, Chindavongsa, Keobouphaphone, additional, Sengsavath, Viengphone, additional, Thuy-Nhien, Nguyen, additional, Pearson, Richard D, additional, Phalivong, Sonexay, additional, Xayvanghang, Saiamphone, additional, Gonçalves, Sonia, additional, Day, Nicholas P, additional, Newton, Paul N, additional, Ashley, Elizabeth A, additional, Kwiatkowski, Dominic P, additional, Dondorp, Arjen M, additional, and Miotto, Olivo, additional
- Published
- 2022
- Full Text
- View/download PDF
43. Geographical distribution and genetic diversity of Plasmodium vivax reticulocyte binding protein 1a correlates with patient antigenicity
- Author
-
Park, Ji-Hoon, primary, Kim, Min-Hee, additional, Sutanto, Edwin, additional, Na, Seok-Won, additional, Kim, Min-Jae, additional, Yeom, Joon Sup, additional, Nyunt, Myat Htut, additional, Abbas Elfaki, Mohammed Mohieldien, additional, Abdel Hamid, Muzamil Mahdi, additional, Cha, Seok Ho, additional, Alemu, Sisay Getachew, additional, Sriprawat, Kanlaya, additional, Anstey, Nicholas M., additional, Grigg, Matthew J., additional, Barber, Bridget E., additional, William, Timothy, additional, Gao, Qi, additional, Liu, Yaobao, additional, Pearson, Richard D., additional, Price, Ric N., additional, Nosten, Francois, additional, Yoon, Sung-Il, additional, No, Joo Hwan, additional, Han, Eun-Taek, additional, Auburn, Sarah, additional, Russell, Bruce, additional, and Han, JinHee, additional
- Published
- 2022
- Full Text
- View/download PDF
44. Genetic diversity of the African malaria vector Anopheles gambiae
- Author
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Miles, Alistair, Harding, Nicholas J., Bottà, Giordano, Clarkson, Chris S., Antão, Tiago, Kozak, Krzysztof, Schrider, Daniel R., Kern, Andrew D., Redmond, Seth, Sharakhov, Igor, Pearson, Richard D., Bergey, Christina, Fontaine, Michael C., Donnelly, Martin J., Lawniczak, Mara K. N., Kwiatkowski, Dominic P., Ayala, Diego, Besansky, Nora J., Burt, Austin, Caputo, Beniamino, della Torre, Alessandra, Godfray, H. Charles J., Hahn, Matthew W., Midega, Janet, Neafsey, Daniel E., O’Loughlin, Samantha, Pinto, João, Riehle, Michelle M., Vernick, Kenneth D., Weetman, David, Wilding, Craig S., White, Bradley J., Troco, Arlete D., Diabaté, Abdoulaye, Costantini, Carlo, Rohatgi, Kyanne R., Elissa, Nohal, Coulibaly, Boubacar, Dinis, João, Mbogo, Charles, Bejon, Philip, Mawejje, Henry D., Stalker, Jim, Rockett, Kirk, Drury, Eleanor, Mead, Daniel, Jeffreys, Anna, Hubbart, Christina, Rowlands, Kate, Isaacs, Alison T., Jyothi, Dushyanth, Malangone, Cinzia, Vauterin, Paul, Jeffery, Ben, Wright, Ian, Hart, Lee, Kluczyński, Krzysztof, Cornelius, Victoria, MacInnis, Bronwyn, Henrichs, Christa, and Giacomantonio, Rachel
- Published
- 2017
- Full Text
- View/download PDF
45. Changing epidemiology of visceral leishmaniasis in northeastern Brazil: a 25-year follow-up of an urban outbreak
- Author
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Lima, Ádila L M, de Lima, Iraci D, Coutinho, José F V, de Sousa, Úrsula P S T, Rodrigues, Marcos A G, Wilson, Mary E, Pearson, Richard D, Queiroz, José W, and Jerônimo, Selma M B
- Published
- 2017
- Full Text
- View/download PDF
46. The genetic architecture of type 2 diabetes
- Author
-
Fuchsberger, Christian, Flannick, Jason, Teslovich, Tanya M., Mahajan, Anubha, Agarwala, Vineeta, Gaulton, Kyle J., Ma, Clement, Fontanillas, Pierre, Moutsianas, Loukas, McCarthy, Davis J., Rivas, Manuel A., Perry, John R. B., Sim, Xueling, Blackwell, Thomas W., Robertson, Neil R., Rayner, N. William, Cingolani, Pablo, Locke, Adam E., Tajes, Juan Fernandez, Highland, Heather M., Dupuis, Josee, Chines, Peter S., Lindgren, Cecilia M., Hartl, Christopher, Jackson, Anne U., Chen, Han, Huyghe, Jeroen R., van de Bunt, Martijn, Pearson, Richard D., Kumar, Ashish, Müller-Nurasyid, Martina, Grarup, Niels, Stringham, Heather M., Gamazon, Eric R., Lee, Jaehoon, Chen, Yuhui, Scott, Robert A., Below, Jennifer E., Chen, Peng, Huang, Jinyan, Go, Min Jin, Stitzel, Michael L., Pasko, Dorota, Parker, Stephen C. J., Varga, Tibor V., Green, Todd, Beer, Nicola L., Day-Williams, Aaron G., Ferreira, Teresa, Fingerlin, Tasha, Horikoshi, Momoko, Hu, Cheng, Huh, Iksoo, Ikram, Mohammad Kamran, Kim, Bong-Jo, Kim, Yongkang, Kim, Young Jin, Kwon, Min-Seok, Lee, Juyoung, Lee, Selyeong, Lin, Keng-Han, Maxwell, Taylor J., Nagai, Yoshihiko, Wang, Xu, Welch, Ryan P., Yoon, Joon, Zhang, Weihua, Barzilai, Nir, Voight, Benjamin F., Han, Bok-Ghee, Jenkinson, Christopher P., Kuulasmaa, Teemu, Kuusisto, Johanna, Manning, Alisa, Ng, Maggie C. Y., Palmer, Nicholette D., Balkau, Beverley, Stančáková, Alena, Abboud, Hanna E., Boeing, Heiner, Giedraitis, Vilmantas, Prabhakaran, Dorairaj, Gottesman, Omri, Scott, James, Carey, Jason, Kwan, Phoenix, Grant, George, Smith, Joshua D., Neale, Benjamin M., Purcell, Shaun, Butterworth, Adam S., Howson, Joanna M. M., Lee, Heung Man, Lu, Yingchang, Kwak, Soo-Heon, Zhao, Wei, Danesh, John, Lam, Vincent K. L., Park, Kyong Soo, Saleheen, Danish, So, Wing Yee, Tam, Claudia H. T., Afzal, Uzma, Aguilar, David, Arya, Rector, Aung, Tin, Chan, Edmund, Navarro, Carmen, Cheng, Ching-Yu, Palli, Domenico, Correa, Adolfo, Curran, Joanne E., Rybin, Denis, Farook, Vidya S., Fowler, Sharon P., Freedman, Barry I., Griswold, Michael, Hale, Daniel Esten, Hicks, Pamela J., Khor, Chiea-Chuen, Kumar, Satish, Lehne, Benjamin, Thuillier, Dorothée, Lim, Wei Yen, Liu, Jianjun, van der Schouw, Yvonne T., Loh, Marie, Musani, Solomon K., Puppala, Sobha, Scott, William R., Yengo, Loïc, Tan, Sian-Tsung, Taylor Jr., Herman A., Thameem, Farook, Wilson, Gregory, Wong, Tien Yin, Njølstad, Pål Rasmus, Levy, Jonathan C., Mangino, Massimo, Bonnycastle, Lori L., Schwarzmayr, Thomas, Fadista, João, Surdulescu, Gabriela L., Herder, Christian, Groves, Christopher J., Wieland, Thomas, Bork-Jensen, Jette, Brandslund, Ivan, Christensen, Cramer, Koistinen, Heikki A., Doney, Alex S. F., Kinnunen, Leena, Esko, Tõnu, Farmer, Andrew J., Hakaste, Liisa, Hodgkiss, Dylan, Kravic, Jasmina, Lyssenko, Valeriya, Hollensted, Mette, Jørgensen, Marit E., Jørgensen, Torben, Ladenvall, Claes, Justesen, Johanne Marie, Käräjämäki, Annemari, Kriebel, Jennifer, Rathmann, Wolfgang, Lannfelt, Lars, Lauritzen, Torsten, Narisu, Narisu, Linneberg, Allan, Melander, Olle, Milani, Lili, Neville, Matt, Orho-Melander, Marju, Qi, Lu, Qi, Qibin, Roden, Michael, Rolandsson, Olov, Swift, Amy, Rosengren, Anders H., Stirrups, Kathleen, Wood, Andrew R., Mihailov, Evelin, Blancher, Christine, Carneiro, Mauricio O., Maguire, Jared, Poplin, Ryan, Shakir, Khalid, Fennell, Timothy, DePristo, Mark, Hrabé de Angelis, Martin, Deloukas, Panos, Gjesing, Anette P., Jun, Goo, Nilsson, Peter, Murphy, Jacquelyn, Onofrio, Robert, Thorand, Barbara, Hansen, Torben, Meisinger, Christa, Hu, Frank B., Isomaa, Bo, Karpe, Fredrik, Liang, Liming, Peters, Annette, Huth, Cornelia, O’Rahilly, Stephen P., Palmer, Colin N. A., Pedersen, Oluf, Rauramaa, Rainer, Tuomilehto, Jaakko, Salomaa, Veikko, Watanabe, Richard M., Syvänen, Ann-Christine, Bergman, Richard N., Bharadwaj, Dwaipayan, Bottinger, Erwin P., Cho, Yoon Shin, Chandak, Giriraj R., Chan, Juliana C. N., Chia, Kee Seng, Daly, Mark J., Ebrahim, Shah B., Langenberg, Claudia, Elliott, Paul, Jablonski, Kathleen A., Lehman, Donna M., Jia, Weiping, Ma, Ronald C. W., Pollin, Toni I., Sandhu, Manjinder, Tandon, Nikhil, Froguel, Philippe, Barroso, Inês, Teo, Yik Ying, Zeggini, Eleftheria, Loos, Ruth J. F., Small, Kerrin S., Ried, Janina S., DeFronzo, Ralph A., Grallert, Harald, Glaser, Benjamin, Metspalu, Andres, Wareham, Nicholas J., Walker, Mark, Banks, Eric, Gieger, Christian, Ingelsson, Erik, Im, Hae Kyung, Illig, Thomas, Franks, Paul W., Buck, Gemma, Trakalo, Joseph, Buck, David, Prokopenko, Inga, Mägi, Reedik, Lind, Lars, Farjoun, Yossi, Owen, Katharine R., Gloyn, Anna L., Strauch, Konstantin, Tuomi, Tiinamaija, Kooner, Jaspal Singh, Lee, Jong-Young, Park, Taesung, Donnelly, Peter, Morris, Andrew D., Hattersley, Andrew T., Bowden, Donald W., Collins, Francis S., Atzmon, Gil, Chambers, John C., Spector, Timothy D., Laakso, Markku, Strom, Tim M., Bell, Graeme I., Blangero, John, Duggirala, Ravindranath, Tai, E. Shyong, McVean, Gilean, Hanis, Craig L., Wilson, James G., Seielstad, Mark, Frayling, Timothy M., Meigs, James B., Cox, Nancy J., Sladek, Rob, Lander, Eric S., Gabriel, Stacey, Burtt, Noël P., Mohlke, Karen L., Meitinger, Thomas, Groop, Leif, Abecasis, Goncalo, Florez, Jose C., Scott, Laura J., Morris, Andrew P., Kang, Hyun Min, Boehnke, Michael, Altshuler, David, and McCarthy, Mark I.
- Published
- 2016
- Full Text
- View/download PDF
47. An amino acid transporter AAT1 plays a pivotal role in chloroquine resistance evolution in malaria parasites
- Author
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Amambua-Ngwa, Alfred, primary, Button-Simons, Katrina A., additional, Li, Xue, additional, Kumar, Sudhir, additional, Brenneman, Katelyn Vendrely, additional, Ferrari, Marco, additional, Checkley, Lisa A., additional, Haile, Meseret T., additional, Shoue, Douglas A., additional, McDew-White, Marina, additional, Tindall, Sarah M., additional, Reyes, Ann, additional, Delgado, Elizabeth, additional, Dalhoff, Haley, additional, Larbalestier, James K., additional, Amato, Roberto, additional, Pearson, Richard D., additional, Taylor, Alexander B., additional, Nosten, François H., additional, D’Alessandro, Umberto, additional, Kwiatkowski, Dominic, additional, Cheeseman, Ian H., additional, Kappe, Stefan H. I., additional, Avery, Simon V., additional, Conway, David J., additional, Vaughan, Ashley M., additional, Ferdig, Michael T., additional, and Anderson, Timothy J. C., additional
- Published
- 2022
- Full Text
- View/download PDF
48. Table S1: Additional antimalarial drug resistant mutations identified in PfCRT, PfDHFR, PfDHPS, and PfMDR1
- Author
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Omedo, Irene, Bartilol, Brian, Kimani, Domtila, Gon��alves, S��nia, Drury, Eleanor, Rono, Martin, Abdi, Abdirahman I., Almagro-Garcia, Jacob, Amato, Roberto, Pearson, Richard D., Ochola-Oyier, Lynette Isabella, P Kwiatkowski, Dominic, and Bejon, Philip
- Subjects
parasitic diseases - Abstract
These mutations have been associated with resistance to Plasmodium falciparum parasites in vitro, although their effect in vivo has not been confirmed.
- Published
- 2022
- Full Text
- View/download PDF
49. Reply to Torres and Suárez
- Author
-
Sousa, Anastácio Q., Pompeu, Margarida M. L., Frutuoso, Mércia S., Moraes, Elisabete A., and Pearson, Richard D.
- Published
- 2012
- Full Text
- View/download PDF
50. A metabolic network approach for the identification and prioritization of antimicrobial drug targets
- Author
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Chavali, Arvind K., D’Auria, Kevin M., Hewlett, Erik L., Pearson, Richard D., and Papin, Jason A.
- Published
- 2012
- Full Text
- View/download PDF
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