Browsing by Author "Schaffner, Stephen"

Now showing items 1-17 of 17

    • Clinical Illness and Outcomes in Patients with Ebola in Sierra Leone 

      Schieffelin, John S.; Shaffer, Jeffrey G.; Goba, Augustine; Gbakie, Michael; Gire, Stephen; Colubri, Andres; SEALFON, RACHEL; Kanneh, Lansana; Moigboi, Alex; Momoh, Mambu; Fullah, Mohammed; Moses, Lina M.; Brown, Bethany L.; Andersen, Kristian G; Winnicki, Sarah M.; Schaffner, Stephen; Park, Daniel John; Yozwiak, Nathan; Jiang, Pan-Pan Xueke; Kargbo, David; Jalloh, Simbirie; Fonnie, Mbalu; Sinnah, Vandi; French, Issa; Kovoma, Alice; Kamara, Fatima K.; Tucker, Veronica; Konuwa, Edwin; Sellu, Josephine; Mustapha, Ibrahim; Foday, Momoh; Yillah, Mohamed; Kanneh, Franklyn; Saffa, Sidiki; Massally, James L.B.; Boisen, Matt L.; Branco, Luis M.; Vandi, Mohamed A.; Grant, Donald S.; Happi, Christian Tientcha; Gevao, Sahr M.; Fletcher, Thomas E.; Fowler, Robert A.; Bausch, Daniel G.; Sabeti, Pardis Christine; Khan, S. Humarr; Garry, Robert F. (New England Journal of Medicine (NEJM/MMS), 2014)
      Background;Limited clinical and laboratory data are available on patients with Ebola virus disease (EVD). The Kenema Government Hospital in Sierra Leone, which had an existing infrastructure for research regarding viral ...

    • A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection 

      Shylakhter, Ilya; Karlsson, Elinor Kathryn; Byrne, Elizabeth Hockfield; Morales, Shannon; Frieden, Gabriel; Hostetter, Elizabeth; Angelino, Elaine Lee; Garber, Manuel; Zuk, Or; Lander, Eric Steven; Schaffner, Stephen; Sabeti, Pardis Christine; Grossman, Sharon Rachel (American Association for Advancement of Science, 2010)
      The human genome contains hundreds of regions whose patterns of genetic variation indicate recent positive natural selection, yet for most the underlying gene and the advantageous mutation remain unknown. We developed a ...

    • Ebola Virus Epidemiology and Evolution in Nigeria 

      Folarin, Onikepe A.; Ehichioya, Deborah; Schaffner, Stephen F.; Winnicki, Sarah M.; Wohl, Shirlee; Eromon, Philomena; West, Kendra L.; Gladden-Young, Adrianne; Oyejide, Nicholas E.; Matranga, Christian B.; Deme, Awa Bineta; James, Ayorinde; Tomkins-Tinch, Christopher; Onyewurunwa, Kenneth; Ladner, Jason T.; Palacios, Gustavo; Nosamiefan, Iguosadolo; Andersen, Kristian G.; Omilabu, Sunday; Park, Daniel J.; Yozwiak, Nathan L.; Nasidi, Abdusallam; Garry, Robert F.; Tomori, Oyewale; Sabeti, Pardis C.; Happi, Christian T. (Oxford University Press, 2016)
      Containment limited the 2014 Nigerian Ebola virus (EBOV) disease outbreak to 20 reported cases and 8 fatalities. We present here clinical data and contact information for at least 19 case patients, and full-length EBOV ...

    • Genetic Surveillance Detects Both Clonal and Epidemic Transmission of Malaria following Enhanced Intervention in Senegal 

      Daniels, Rachel Fath; Chang, Hsiao-Han; Séne, Papa Diogoye; Park, Danny C.; Neafsey, Daniel Edward; Schaffner, Stephen; Hamilton, Elizabeth Julia; Lukens, Amanda Kathleen; Van Tyne, Daria Natalie; Mboup, Souleymane; Sabeti, Pardis Christine; Ndiaye, Daouda; Wirth, Dyann Fergus; Hartl, Daniel L.; Cooke, Sarah Volkman (Public Library of Science, 2013)
      Using parasite genotyping tools, we screened patients with mild uncomplicated malaria seeking treatment at a clinic in Thiès, Senegal, from 2006 to 2011. We identified a growing frequency of infections caused by genetically ...

    • Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak 

      Gire, Stephen; Goba, A.; Andersen, Kristian G; Sealfon, R. S. G.; Park, D. J.; Kanneh, L.; Jalloh, S.; Momoh, M.; Fullah, M.; Dudas, G.; Wohl, Shirlee; Moses, L. M.; Yozwiak, Nathan; Winnicki, Sarah M.; Matranga, C. B.; Malboeuf, C. M.; Qu, J.; Gladden, Adrianne Deanna; Schaffner, Stephen; Yang, X.; Jiang, P.-P.; Nekoui, M.; Colubri, Andres; Coomber, M. R.; Fonnie, M.; Moigboi, A.; Gbakie, M.; Kamara, F. K.; Tucker, V.; Konuwa, E.; Saffa, S.; Sellu, J.; Jalloh, A. A.; Kovoma, A.; Koninga, J.; Mustapha, I.; Kargbo, K.; Foday, M.; Yillah, M.; Kanneh, F.; Robert, W.; Massally, J. L. B.; Chapman, S. B.; Bochicchio, J.; Murphy, C.; Nusbaum, C.; Young, S.; Birren, B. W.; Grant, D. S.; Scheiffelin, J. S.; Lander, Eric Steven; Happi, Christian Tientcha; Gevao, S. M.; Gnirke, A.; Rambaut, A.; Garry, R. F.; Khan, S. H.; Sabeti, Pardis Christine (American Association for the Advancement of Science (AAAS), 2014)
      In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78 patients in Sierra Leone to ~2000× coverage. We observed a rapid ...

    • Human Cerebral Malaria and Plasmodium falciparum Genotypes in Malawi 

      Milner, Danny Arnold; Vareta, Jimmy; Valim, Clarissa; Montgomery, Jacqui; Daniels, Rachel Fath; Cooke, Sarah Volkman; Neafsey, Daniel Edward; Park, Daniel John; Schaffner, Stephen; Mahesh, Nira C; Barnes, Kayla G; Rosen, David M; Lukens, Amanda Kathleen; Van-Tyne, Daria; Wiegand, Roger C.; Sabeti, Pardis Christine; Seydel, Karl B; Glover, Simon J; Kamiza, Steve; Molyneux, Malcolm E; Taylor, Terrie E; Wirth, Dyann Fergus (BioMed Central, 2012)
      Background: Cerebral malaria, a severe form of Plasmodium falciparum infection, is an important cause of mortality in sub-Saharan African children. A Taqman 24 Single Nucleotide Polymorphisms (SNP) molecular barcode assay ...

    • Identification and Functional Validation of the Novel Antimalarial Resistance Locus PF10_0355 in Plasmodium falciparum 

      Van Tyne, Daria Natalie; Park, Daniel John; Schaffner, Stephen; Neafsey, Daniel Edward; Angelino, Elaine Lee; Cortese, Joseph F.; Barnes, Kayla G.; Rosen, David M.; Lukens, Amanda Kathleen; Daniels, Rachel Fath; Milner, Danny Arnold; Johnson, Charles A.; Shlyakhter, Ilya; Grossman, Sharon Rachel; Becker, Justin S.; Yamins, Daniel Louis Kanef; Karlsson, Elinor Kathryn; Ndiaye, Daouda; Sarr, Ousmane; Mboup, Souleymane; Happi, Christian Tientcha; Furlotte, Nicholas A.; Eskin, Eleazar; Kang, Hyun Min; Hartl, Daniel L.; Birren, Bruce W.; Wiegand, Roger C.; Lander, Eric Steven; Wirth, Dyann Fergus; Cooke, Sarah Volkman; Sabeti, Pardis Christine (Public Library of Science, 2011)
      The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis ...

    • Identifying Recent Adaptations in Large-Scale Genomic Data 

      Grossman, Shamai Aaron; Andersen, Kristian G; Shlyakhter, Ilya; Tabrizi, Shervin; Winnicki, Sarah M.; Yen, Angela; Park, Daniel J.; Griesemer, Dustin Shahab; Karlsson, Elinor Kathryn; Wong, Sunny H.; Cabili, Moran; Adegbola, Richard A.; Bamezai, Rameshwar N.K.; Hill, Adrian V.S.; Vannberg, Fredrik O.; Rinn, John L; Lander, Eric Steven; Schaffner, Stephen; Sabeti, Pardis Christine (Elsevier BV, 2013)
      Summary: Although several hundred regions of the human genome harbor signals of positive natural selection, few of the relevant adaptive traits and variants have been elucidated. Using full-genome sequence variation from ...

    • A Map of Human Genome Variation from Population Scale Sequencing 

      Altshuler, David Matthew; Lander, Eric Steven; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Lee, Charles; Mills, Ryan Edward; Shi, Xinghua; Daly, Mark Joseph; DePristo, Mark A.; Ball, Aaron D.; Banks, Eric; Browning, Brian L.; Garimella, Kiran V.; Grossman, Sharon Rachel; Handsaker, Robert E; Hanna, Matt; Hartl, Chris; Kernytsky, Andrew M.; Korn, Joshua M.; Li, Heng; Maguire, Jared R.; McCarroll, Steven A.; Nemesh, James C.; McKenna, Aaron; Philippakis, Anthony Andrew; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis Christine; Schaffner, Stephen; Shlyakhter, Ilya (Nature Publishing Group, 2010)
      The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot ...

    • Mapping Copy Number Variation by Population Scale Genome Sequencing 

      Mills, Ryan Edward; Handsaker, Robert E; Korn, Joshua; Nemesh, James; Shi, Xinghua; Lee, Charles; McCarroll, Steven A.; Altshuler, David Matthew; Gabriel, Stacey B.; Lander, Eric Steven; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Daly, Mark Joseph; DePristo, Mark A.; Ball, Aaron D.; Banks, Eric; Bloom, Toby; Browning, Brian L.; Garimella, Kiran V.; Grossman, Sharon Rachel; Handsaker, Robert E; Hanna, Matt; Hartl, Chris; Kernytsky, Andrew M.; Li, Heng; Maguire, Jared R.; McKenna, Aaron; Philippakis, Anthony Andrew; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis Christine; Schaffner, Stephen; Shlyakhter, Ilya; DePristo, Mark A.; Wilkinson, Jane (Nature Publishing Group, 2011)
      Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of ...

    • Modeling malaria genomics reveals transmission decline and rebound in Senegal 

      Daniels, Rachel Fath; Schaffner, Stephen; Wenger, Edward A.; Proctor, Joshua L.; Chang, Hsiao-Han; Wong, Wesley Philip; Baro, Nicholas; Ndiaye, Daouda; Fall, Fatou Ba; Ndiop, Medoune; Ba, Mady; Milner, Danny Arnold; Taylor, Terrie E.; Neafsey, Daniel Edward; Cooke, Sarah K.; Eckhoff, Philip A.; Hartl, Daniel L.; Wirth, Dyann F. (Proceedings of the National Academy of Sciences, 2015)
      To study the effects of malaria-control interventions on parasite population genomics, we examined a set of 1,007 samples of the malaria parasite Plasmodium falciparum collected in Thiès, Senegal between 2006 and 2013. The ...

    • Natural Selection in a Bangladeshi Population from the Cholera-Endemic Ganges River Delta 

      Karlsson, Elinor Kathryn; Harris, J. B.; Tabrizi, Shervin; Rahman, A.; Shlyakhter, Ilya; Patterson, N.; O, C.; Schaffner, Stephen; Gupta, S.; Chowdhury, F.; Sheikh, A.; Shin, O. S.; Ellis, C.; Becker, C. E.; Stuart, L. M.; Calderwood, Stephen Beaven; Ryan, Edward Thomas; Qadri, F.; Sabeti, Pardis Christine; Larocque, Regina Celes (American Association for the Advancement of Science (AAAS), 2013)
      As an ancient disease with high fatality, cholera has likely exerted strong selective pressure on affected human populations. We performed a genome-wide study of natural selection in a population from the Ganges River ...

    • Population Genetic Study of the Brain-Derived Neurotrophic Factor (BDNF) Gene 

      Petryshen, Tracey Lynn; Sabeti, Pardis Christine; Aldinger, Kimberly A.; Fry, Ben; Fan, Jinbo B.; Schaffner, Stephen; Waggoner, Skye G.; Tahl, Anthony R.; Sklar, Pamela (Nature Publishing Group, 2010)
      Genetic variants in the brain-derived neurotrophic factor (BDNF) gene, predominantly the functional Val66Met polymorphism, have been associated with risk of bipolar disorder and other psychiatric disorders. However, not ...

    • Sequence-Based Association and Selection Scans Identify Drug Resistance Loci in the Plasmodium Falciparum Malaria Parasite 

      Park, Daniel John; Lukens, Amanda Kathleen; Neafsey, Daniel Edward; Schaffner, Stephen; Chang, Hsiao-Han; Valim, Clarissa; Ribacke, Ulf Erik; Van Tyne, Daria Natalie; Galinsky, Kevin Joseph; Galligan, Meghan; Becker, Justin S.; Ndiaye, Daouda; Mboup, Souleymane; Wiegand, Roger C.; Hartl, Daniel L.; Sabeti, Pardis Christine; Wirth, Dyann F.; Cooke, Sarah K. (Proceedings of the National Academy of Sciences, 2012)
      Through rapid genetic adaptation and natural selection, the Plasmodium falciparum parasite—the deadliest of those that cause malaria—is able to develop resistance to antimalarial drugs, thwarting present efforts to control ...

    • SNP Genotyping Identifies New Signatures of Selection in a Deep Sample of West African Plasmodium falciparum Malaria Parasites 

      Amambua-Ngwa, Alfred; Barnes, Kayla G.; Sene, Papa; Conway, David J.; Park, Daniel John; Volkman, Sarah; Bei, Amy Kristine; Lukens, Amanda Kathleen; Van Tyne, Daria Natalie; Ndiaye, Daouda; Wirth, Dyann Fergus; Neafsey, Daniel Edward; Schaffner, Stephen (Oxford University Press, 2012)
      We used a high-density single-nucleotide polymorphism array to genotype 75 Plasmodium falciparum isolates recently collected from Senegal and The Gambia to search for signals of selection in this malaria endemic region. ...

    • Virus genomes reveal factors that spread and sustained the Ebola epidemic 

      Dudas, Gytis; Carvalho, Luiz Max; Bedford, Trevor; Tatem, Andrew J.; Baele, Guy; Faria, Nuno R.; Park, Daniel; Ladner, Jason T.; Arias, Armando; Asogun, Danny; Bielejec, Filip; Caddy, Sarah L.; Cotten, Matthew; D’Ambrozio, Jonathan; Dellicour, Simon; Di Caro, Antonino; Diclaro, Joseph W.; Duraffour, Sophie; Elmore, Michael J.; Fakoli, Lawrence S.; Faye, Ousmane; Gilbert, Merle L.; Gevao, Sahr M.; Gire, Stephen; Gladden-Young, Adrianne; Gnirke, Andreas; Goba, Augustine; Grant, Donald S.; Haagmans, Bart L.; Hiscox, Julian A.; Jah, Umaru; Kugelman, Jeffrey R.; Liu, Di; Lu, Jia; Malboeuf, Christine M.; Mate, Suzanne; Matthews, David A.; Matranga, Christian B.; Meredith, Luke W.; Qu, James; Quick, Joshua; Pas, Suzan D.; Phan, My V. T.; Pollakis, Georgios; Reusken, Chantal B.; Sanchez-Lockhart, Mariano; Schaffner, Stephen; Schieffelin, John S.; SEALFON, RACHEL; Simon-Loriere, Etienne; Smits, Saskia L.; Stoecker, Kilian; Thorne, Lucy; Tobin, Ekaete Alice; Vandi, Mohamed A.; Watson, Simon J.; West, Kendra Leigh; Whitmer, Shannon; Wiley, Michael R.; Winnicki, Sarah M.; Wohl, Shirlee; Wölfel, Roman; Yozwiak, Nathan; Andersen, Kristian; Blyden, Sylvia O.; Bolay, Fatorma; Carroll, Miles W.; Dahn, Bernice; Diallo, Boubacar; Formenty, Pierre; Fraser, Christophe; Gao, George F.; Garry, Robert F.; Goodfellow, Ian; Günther, Stephan; Happi, Christian Tientcha; Holmes, Edward C.; Kargbo, Brima; Keïta, Sakoba; Kellam, Paul; Koopmans, Marion P. G.; Kuhn, Jens H.; Loman, Nicholas J.; Magassouba, N’Faly; Naidoo, Dhamari; Nichol, Stuart T.; Nyenswah, Tolbert; Palacios, Gustavo; Pybus, Oliver G.; Sabeti, Pardis; Sall, Amadou; Ströher, Ute; Wurie, Isatta; Suchard, Marc A.; Lemey, Philippe; Rambaut, Andrew (Springer Science and Business Media LLC, 2017-04)
      The 2013–2016 epidemic of Ebola virus disease was of unprecedented magnitude, duration and impact. Analysing 1610 Ebola virus genomes, representing over 5% of known cases, we reconstruct the dispersal, proliferation and ...

    • Zika virus evolution and spread in the Americas 

      Metsky, Hayden C; Matranga, Christian B; Wohl, Shirlee; Schaffner, Stephen; Freije, Catherine Amanda; Winnicki, Sarah M.; West, Kendra Leigh; Qu, James; Baniecki, Mary; Gladden-Young, Adrianne; Lin, Aaron Eric; Tomkins-Tinch, Christopher Holiday; Ye, Simon H; Park, Daniel Sangsoon; Luo, Cynthia; Barnes, Kayla G.; Shah, Rickey; Chak, Bridget; Barbosa-Lima, Giselle; Delatorre, Edson; Vieira, Yasmine R; Paul, Lauren M; Tan, Amanda L; Barcellona, Carolyn M; Porcelli, Mario C; Vasquez, Chalmers; Cannons, Andrew C; Cone, Marshall R; Hogan, Kelly N; Kopp, Edgar W; Anzinger, Joshua J; Garcia, Kimberly F; Parham, Leda A; Gelvez Ramirez, Rosa Margarita; Miranda Montoya, Maria Consuelo; Rojas, Diana P; Brown, Catherine M; Hennigan, Scott; Sabina, Brandon; Scotland, Sarah; Gangavarapu, Karthik; Grubaugh, Nathan D; Oliveira, Glenn; Robles-Sikisaka, Refugio; Rambaut, Andrew; Gehrke, Lee; Smole, Sandra; Halloran, M Elizabeth; Villar Centeno, Luis Angel; Mattar, Salim; Lorenzana, Ivette; Cerbino-Neto, Jose; Valim, Clarissa; Degrave, Wim; Bozza, Patricia T; Gnirke, Andreas; Andersen, Kristian G; Isern, Sharon; Michael, Scott; Bozza, Fernando A; Souza, Thiago ML; Bosch, Irene; Yozwiak, Nathan L; MacInnis, Bronwyn L; Sabeti, Pardis Christine (SpringerNature, 2017)
      Despite great attention given to the recent Zika virus (ZIKV) epidemic in the Americas, much remains unknown about its epidemiology and evolution, in part due to a lack of genomic data. We applied multiple sequencing ...