Giorgio Sirugo, Elizabeth A. Schaefer, Alieu Mendy, Pardis C. Sabeti, B West, Robin L. Bailey, Fabìo Macciardi, L. Zonta, Gijs Walraven,
... West AfricaSearch for more papers by this authorPardis Sabeti, Pardis Sabeti Wellcome Trust Centre for Human Genetics, University ... West AfricaSearch for more papers by this authorPardis Sabeti, Pardis Sabeti Wellcome Trust Centre for Human Genetics, University of ...
Tópico(s): Prenatal Screening and Diagnostics
2004 - Wiley | American Journal of Medical Genetics Part A
Christopher H. Tomkins-Tinch, Jennifer S. Daly, Adrianne Gladden-Young, Nicole Theodoropoulos, Michael P. Madaio, Neng Yu, Vijay K. Vanguri, Katherine J. Siddle, Gordon Adams, Lydia A. Krasilnikova, Babak Movahedi, Adel Bozorgzadeh, Karl Simin, Jacob E. Lemieux, Jeremy Luban, Daniel J. Park, Bronwyn MacInnis, Pardis C. Sabeti, Stuart M. Levitz,
... Daniel J. Park, PhD, Bronwyn L. MacInnis, PhD, Pardis C. Sabeti, MD, MSc, DPhil, and Stuart M. Levitz, MDChristopher ... Cambridge, MassachusettsSearch for more papers by this author, Pardis C. Sabeti, MD, MSc, DPhilThe Broad Institute of MIT and ... Daniel J. Park, PhD; Bronwyn L. MacInnis, PhD; Pardis C. Sabeti, MD, MSc, DPhil; Stuart M. Levitz, MDAffiliations: The ... MA 01605 (e-mail, stuart.levitz@umassmed.edu); Pardis C. Sabeti, MD, MSc, DPhil, 415 Main Street, Cambridge, MA 02142 (e-mail, pardis@broadinstitute.org); and Bronwyn L. MacInnis, PhD, 415 ...
Tópico(s): COVID-19 Clinical Research Studies
2021 - American College of Physicians | Annals of Internal Medicine
Adam Auton, Gonçalo R. Abecasis, David Altshuler, Richard Durbin, Gonçalo R. Abecasis, David Bentley, Aravinda Chakravarti, Andrew G. Clark, Peter Donnelly, Evan E. Eichler, Paul Flicek, Stacey Gabriel, Richard A. Gibbs, Eric D. Green, Matthew E. Hurles, Bartha Maria Knoppers, Jan O. Korbel, Eric S. Lander, Charles Lee, Hans Lehrach, Elaine R. Mardis, Gábor Marth, Gil McVean, Deborah A. Nickerson, Jeanette P. Schmidt, Stephen T. Sherry, Jun Wang, Richard K. Wilson, Richard A. Gibbs, Eric Boerwinkle, HarshaVardhan Doddapaneni, Yi Han, Viktoriya Korchina, Christie Kovar, Charles Lee, Donna M. Muzny, Jeffrey G. Reid, Yiming Zhu, Jun Wang, Yuqi Chang, Qiang Feng, Xiaodong Fang, Xiaosen Guo, Min Jian, Hui Jiang, Xin Jin, Tianming Lan, Guoqing Li, Jingxiang Li, Yingrui Li, Shengmao Liu, Xiao Liu, Yao Lu, Xuedi Ma, Meifang Tang, Bo Wang, Guangbiao Wang, Honglong Wu, Renhua Wu, Xun Xu, Ye Yin, Dandan Zhang, Wenwei Zhang, Jiao Zhao, Meiru Zhao, Xiaole Zheng, Eric S. Lander, David Altshuler, Stacey Gabriel, Namrata Gupta, Neda Gharani, Lorraine H. Toji, Norman P. Gerry, Alissa Resch, Paul Flicek, Juliet N. Barker, Laura Clarke, Laurent Gil, Sarah Hunt, Gavin Kelman, Eugene Kulesha, Rasko Leinonen, William McLaren, Rajesh Radhakrishnan, Asier Roa, Dmitriy Smirnov, Richard E. Smith, Ian Streeter, Anja Thormann, Iliana Toneva, Brendan Vaughan, Xiangqun Zheng-Bradley, David Bentley, Russell Grocock, Sean Humphray, Terena James, Zoya Kingsbury, Hans Lehrach, Ralf Sudbrak, Marcus W. Albrecht, Vyacheslav Amstislavskiy, Tatiana Borodina, Matthias Lienhard, Florian Mertes, Marc Sultan, Bernd Timmermann, Marie‐Laure Yaspo, Elaine R. Mardis, Richard K. Wilson, Lucinda Fulton, Robert S. Fulton, Stephen T. Sherry, Victor Ananiev, Zinaida Belaia, Dimitriy Beloslyudtsev, Nathan Bouk, Chao Chen, Deanna M. Church, Robert Cohen, Charles Cook, John Garner, Timothy Hefferon, Mikhail Kimelman, Chunlei Liu, John Lopez, Peter Meric, Chris O’Sullivan, Yuri Ostapchuk, Lon Phan, Sergiy Ponomarov, Valérie Schneider, Eugene Shekhtman, Karl Sirotkin, Douglas J. Slotta, Hua Zhang, Gil McVean, Richard Durbin, Senduran Balasubramaniam, John H. Burton, Petr Danecek, Thomas Keane, Anja Kolb‐Kokocinski, Shane McCarthy, James Stalker, Michael A. Quail, Jeanette P. Schmidt, Christopher J. Davies, Jeremy Gollub, Teresa Webster, Brant Wong, Yiping Zhan, Adam Auton, Christopher Campbell, Yu Kong, Anthony Marcketta, Richard A. Gibbs, Fuli Yu, Lilian Antunes, Matthew N. Bainbridge, Donna M. Muzny, Aniko Sabo, Zhuoyi Huang, Jun Wang, Lachlan Coin, Lin Fang, Xiaosen Guo, Xin Jin, Guoqing Li, Qibin Li, Yingrui Li, Zhenyu Li, Haoxiang Lin, Binghang Liu, Ruibang Luo, Haojing Shao, Yinlong Xie, Chen Ye, Chang Yu, Fan Zhang, Hancheng Zheng, Hongmei Zhu, Can Alkan, Elif Dal, Fatma Kahveci, Gábor Marth, Erik Garrison, Deniz Kural, Wan-Ping Lee, Wen Fung Leong, Michael P. Strömberg, Alistair Ward, Jiantao Wu, Mengyao Zhang, Mark J. Daly, Mark A. DePristo, Robert E. Handsaker, David Altshuler, Eric Banks, Gaurav Bhatia, Guillermo del Angel, Stacey Gabriel, Giulio Genovese, Namrata Gupta, Heng Li, Seva Kashin, Eric S. Lander, Steven A. McCarroll, James Nemesh, Ryan Poplin, Seungtai Yoon, Jayon Lihm, Vladimir Makarov, Andrew G. Clark, Srikanth Gottipati, Alon Keinan, Juan L. Rodriguez‐Flores, Jan O. Korbel, Tobias Rausch, Markus H. Fritz, Adrian M. Stütz, Paul Flicek, Kathryn Beal, Laura Clarke, Avik Datta, Javier Herrero, William McLaren, Graham R. S. Ritchie, Richard E. Smith, Daniel R. Zerbino, Xiangqun Zheng-Bradley, Pardis C. Sabeti, Ilya Shlyakhter, S. F. Schaffner, Joseph J. Vitti, D.N. Cooper, Edward V. Ball, Peter D. Stenson, David Bentley, Bret Barnes, Markus Bauer, R. Keira Cheetham, Anthony J. Cox, Michael A. Eberle, Sean Humphray, Scott D. Kahn, Lisa Murray, John F. Peden, Richard J. Shaw, Eimear E. Kenny, Mark A. Batzer, Miriam K. Konkel, Jerilyn A. Walker, Daniel G. MacArthur, Monkol Lek, Ralf Sudbrak, Vyacheslav Amstislavskiy, Ralf Herwig, Elaine R. Mardis, Li Ding, Daniel C. Koboldt, David E. Larson, Kai Ye, Simon Gravel, Anand Swaroop, Emily Y. Chew, Tuuli Lappalainen, Yaniv Erlich, Melissa Gymrek, Thomas Willems, Jared T. Simpson, Mark D. Shriver, Jeffrey Rosenfeld, Carlos D. Bustamante, Stephen B. Montgomery, Francisco M. De La Vega, Jake Byrnes, Andrew Carroll, Marianne K. DeGorter, Phil Lacroute, Brian K. Maples, Alicia R. Martin, Andrés Moreno‐Estrada, Suyash Shringarpure, Fouad Zakharia, Eran Halperin, Yael Baran, Charles Lee, Eliza Cerveira, Jaeho Hwang, Ankit Malhotra, Dariusz Plewczyński, Kamen Radew, Xian Mallory, Chengsheng Zhang, Fiona Hyland, David W. Craig,
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over ...
Nature Portfolio
Nathan L. Yozwiak, S. F. Schaffner, Pardis C. Sabeti,
... urge Nathan L. Yozwiak, Stephen F. Schaffner and Pardis C. Sabeti.
Tópico(s): COVID-19 epidemiological studies
2015 - Nature Portfolio | Nature
Roger A. Hoskins, Susanna Repo, Daniel Barsky, Gaia Andreoletti, John Moult, Steven E. Brenner,
... Potash, Clive R. Pullinger, Jasper Rine, Frederick Roth, Pardis Sabeti, Jeremy Sanford, Maria C. Scaini, Nicole Schmitt, Jay ...
Tópico(s): Race, Genetics, and Society
2017 - Wiley | Human Mutation
... investigators at the Broad Institute (Feng Zhang and Pardis Sabeti), the authors illustrate several applications for the SHERLOCK ...
Tópico(s): Viral Infections and Immunology Research
2018 - Cell Press | Cell Host & Microbe
Cormac M. Kinsella, Molly L. Paras, Sandra Smole, Samar Mehta, Vijay Ganesh, Lin H. Chen, Daniel P. McQuillen, Ruta Shah, Justin Chan, Matthew Osborne, Scott Hennigan, Frederic Halpern-Smith, Catherine Brown, Pardis Sabeti, Anne Piantadosi,
Jamestown Canyon virus (JCV) is a neuroinvasive arbovirus that is found throughout North America and increasingly recognized as a public health concern. From 2004 to 2012, an average of 1.7 confirmed cases were reported annually in the United States, whereas from 2013 to 2018 this figure increased over seventeen-fold to 29.2 cases per year. The rising number of reported human infections highlights the need for better understanding of the clinical manifestations and epidemiology of JCV. Here, we describe ...
Tópico(s): Vector-Borne Animal Diseases
2020 - Taylor & Francis | Emerging Microbes & Infections
James R. Xue, Ava Mackay-Smith, Kousuke Mouri, Meilín Fernández García, Michael X. Dong, Jared F. Akers, Mark Noble, Xue Li, Kerstin Lindblad‐Toh, Elinor K. Karlsson, James P. Noonan, Terence D. Capellini, Kristen Brennand, Ryan Tewhey, Pardis C. Sabeti, Steven K. Reilly, Gregory Andrews, Joel Armstrong, Matteo Bianchi, Bruce W. Birren, Kevin R. Bredemeyer, Ana M. Breit, Matthew J. Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X. Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M. Foley, Karin Forsberg‐Nilsson, Carlos J. Garcia, John Gatesy, Steven Gazal, Diane P. Genereux, Linda Goodman, Jenna Grimshaw, Michaela K. Halsey, Andrew J. Harris, Glenn Hickey, Michael Hiller, Allyson G. Hindle, Robert Hubley, Graham M. Hughes, Jeremy Johnson, David Juan, Irene M. Kaplow, Elinor K. Karlsson, Kathleen C. Keough, Bogdan Kirilenko, Klaus‐Peter Koepfli, Jennifer M. Korstian, Amanda Kowalczyk, Sergey V. Kozyrev, Alyssa J. Lawler, Colleen Lawless, Thomas Lehmann, Danielle L. Levesque, Harris A. Lewin, Xue Li, Abigail Lind, Kerstin Lindblad‐Toh, Ava Mackay-Smith, Voichita D. Marinescu, Tomás Marquès‐Bonet, Victor C. Mason, Jennifer R. S. Meadows, Wynn K. Meyer, Jill E. Moore, Lucas R. Moreira, Diana D. Moreno-Santillán, Kathleen M. Morrill, Gerard Muntané, William J. Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S. Paulat, Andreas Pfenning, BaDoi N. Phan, Katherine S. Pollard, Henry Pratt, David A. Ray, Steven K. Reilly, Jeb Rosen, Irina Ruf, Louise Ryan, Oliver A. Ryder, Pardis C. Sabeti, Daniel E. Schäffer, Aitor Serres, Beth Shapiro, Arian F. A. Smit, Mark S. Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M. Storer, Kevin A. Sullivan, Patrick F. Sullivan, Elisabeth Sundström, Megan A. Supple, Ross Swofford, Joy-El Talbot, Emma C. Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P. Wilder, Morgan Wirthlin, James R. Xue, Xiaomeng Zhang,
Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than ...
Tópico(s): RNA Research and Splicing
2023 - American Association for the Advancement of Science | Science
Matthew J. Christmas, Irene M. Kaplow, Diane P. Genereux, Michael X. Dong, Graham M. Hughes, Xue Li, Patrick F. Sullivan, Allyson G. Hindle, Gregory Andrews, Joel Armstrong, Matteo Bianchi, Ana M. Breit, Mark Diekhans, Cornelia Fanter, Nicole M. Foley, Daniel B. Goodman, Linda Goodman, Kathleen C. Keough, Bogdan Kirilenko, Amanda Kowalczyk, Colleen Lawless, Abigail Lind, Jennifer R. S. Meadows, Lucas R. Moreira, Ruby Redlich, Louise Ryan, Ross Swofford, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Ashley R. Brown, Joana Damas, Kaili Fan, John Gatesy, Jenna Grimshaw, Jeremy Johnson, Sergey V. Kozyrev, Alyssa J. Lawler, Voichita D. Marinescu, Kathleen M. Morrill, Austin Osmanski, Nicole S. Paulat, BaDoi N. Phan, Steven K. Reilly, Daniel E. Schäffer, Cynthia Steiner, Megan A. Supple, Aryn P. Wilder, Morgan Wirthlin, James R. Xue, Susan J. Birren, Steven Gazal, Robert Hubley, Klaus‐Peter Koepfli, Tomás Marquès‐Bonet, Wynn K. Meyer, Martin Nweeia, Pardis C. Sabeti, Beth Shapiro, Arian F. A. Smit, Mark S. Springer, Emma C. Teeling, Zhiping Weng, Michael Hiller, Danielle L. Levesque, Harris A. Lewin, William J. Murphy, Arcadi Navarro, Benedict Paten, Katherine S. Pollard, David A. Ray, Irina Ruf, Oliver A. Ryder, Andreas R. Pfenning, Kerstin Lindblad‐Toh, Elinor K. Karlsson, Gregory Andrews, Joel Armstrong, Matteo Bianchi, Susan J. Birren, Kevin R. Bredemeyer, Ana M. Breit, Matthew J. Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X. Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M. Foley, Karin Forsberg‐Nilsson, Carlos J. Garcia, John Gatesy, Steven Gazal, Diane P. Genereux, Linda Goodman, Jenna Grimshaw, Michaela K. Halsey, Andrew J. Harris, Glenn Hickey, Michael Hiller, Allyson G. Hindle, Robert Hubley, Graham M. Hughes, Jeremy Johnson, David Juan, Irene M. Kaplow, Elinor K. Karlsson, Kathleen C. Keough, Bogdan Kirilenko, Klaus‐Peter Koepfli, Jennifer M. Korstian, Amanda Kowalczyk, Sergey V. Kozyrev, Alyssa J. Lawler, Colleen Lawless, Thomas Lehmann, Danielle L. Levesque, Harris A. Lewin, Xue Li, Abigail Lind, Kerstin Lindblad‐Toh, Ava Mackay-Smith, Voichita D. Marinescu, Tomás Marquès‐Bonet, Victor C. Mason, Jennifer R. S. Meadows, Wynn K. Meyer, Jill E. Moore, Lucas R. Moreira, Diana D. Moreno-Santillán, Kathleen M. Morrill, Gerard Muntané, William J. Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S. Paulat, Andreas R. Pfenning, BaDoi N. Phan, Katherine S. Pollard, Henry Pratt, David A. Ray, Steven K. Reilly, Jeb Rosen, Irina Ruf, Louise Ryan, Oliver A. Ryder, Pardis C. Sabeti, Daniel E. Schäffer, Aitor Serres, Beth Shapiro, Arian F. A. Smit, Mark S. Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M. Storer, Kevin A. Sullivan, Patrick F. Sullivan, Elisabeth Sundström, Megan A. Supple, Ross Swofford, Joy-El Talbot, Emma C. Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P. Wilder, Morgan Wirthlin, James R. Xue, Xiaomeng Zhang,
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are ...
Tópico(s): Physiological and biochemical adaptations
2023 - American Association for the Advancement of Science | Science
Anne Piantadosi, Shibani S. Mukerji, Simon Ye, Michael J. Leone, Lisa M. Freimark, Daniel Park, Gordon Adams, Jacob E. Lemieux, Sanjat Kanjilal, Isaac H. Solomon, Asim A. Ahmed, Robert H. Goldstein, Vijay Ganesh, Bridget Ostrem, Kaelyn C. Cummins, Jesse Thon, Cormac M. Kinsella, Eric Rosenberg, Matthew P. Frosch, Marcia B. Goldberg, Tracey Cho, Pardis Sabeti,
Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures.
Tópico(s): Viral Infections and Immunology Research
2021 - American Society for Microbiology | mBio
Taane G. Clark, Andrew E. Fry, Sarah Auburn, Susana Campino, Mahamadou Diakité, Angela Green, Anna Richardson, Yik Ying Teo, Kerrin S. Small, Jonathan P. Wilson, Muminatou Jallow, Fatou Sisay-Joof, Margaret Pinder, Pardis C. Sabeti, Dominic Kwiatkowski, Kirk A. Rockett,
Several lines of evidence link glucose-6-phosphate dehydrogenase (G6PD) deficiency to protection from severe malaria. Early reports suggested most G6PD deficiency in sub-Saharan Africa was because of the 202A/376G G6PD A− allele, and recent association studies of G6PD deficiency have employed genotyping as a convenient way to determine enzyme status. However, further work has suggested that other G6PD deficiency alleles are relatively common in some regions of West Africa. To investigate the consequences ...
Tópico(s): Acute Lymphoblastic Leukemia research
2009 - Springer Nature | European Journal of Human Genetics
Andrew E. Fry, Anita Ghansa, Kerrin S. Small, A. Palma, Sarah Auburn, Mahamadou Diakité, Angela Green, Susana Campino, Yik Ying Teo, Taane G. Clark, Anna E. Jeffreys, Jonathan P. Wilson, Muminatou Jallow, Fatou Sisay-Joof, Margaret Pinder, Michael J. Griffiths, Norbert Peshu, Thomas N. Williams, Charles R. Newton, Kevin Marsh, Malcolm E. Molyneux, Terrie E. Taylor, Kwadwo A. Koram, Abraham Oduro, William O. Rogers, Kirk A. Rockett, Pardis C. Sabeti, Dominic Kwiatkowski,
The prevalence of CD36 deficiency in East Asian and African populations suggests that the causal variants are under selection by severe malaria. Previous analysis of data from the International HapMap Project indicated that a CD36 haplotype bearing a nonsense mutation (T1264G; rs3211938) had undergone recent positive selection in the Yoruba of Nigeria. To investigate the global distribution of this putative selection event, we genotyped T1264G in 3420 individuals from 66 populations. We confirmed ...
Tópico(s): Hepatitis C virus research
2009 - Oxford University Press | Human Molecular Genetics
Regina C. LaRocque, Pardis C. Sabeti, Priya Duggal, Fahima Chowdhury, A I Khan, Lauren M. Lebrun, Jason B. Harris, Edward T. Ryan, Firdausi Qadri, Stephen B. Calderwood,
Tópico(s): Viral gastroenteritis research and epidemiology
2009 - Springer Nature | Genes and Immunity
Tracey L. Petryshen, Pardis C. Sabeti, Kimberly A. Aldinger, Ben Fry, Jinbo B. Fan, S. F. Schaffner, Skye G. Waggoner, A R Tahl, Pamela Sklar,
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 all studies support these findings, and overall the evidence for the association of BDNF with disease risk is weak. As differences in population genetic structure between patient samples could cause discrepant or spurious association results, we investigated this possibility by carrying ...
Tópico(s): Genetics and Neurodevelopmental Disorders
2009 - Springer Nature | Molecular Psychiatry
Pardis C. Sabeti, S Usen, Shelli Farhadian, Muminatou Jallow, T. Doherty, Melanie J. Newport, M Pinder, R. H. Ward, Dominic Kwiatkowski,
CD40 ligand (CD40L), a glycoprotein involved in B cell proliferation, antigen presenting cell activation, and Ig class switching, is important in the immune response to infection. Rare coding mutations in CD40L can lead to life-threatening immunodeficiency but the potential for common variants to alter disease susceptibility remains to be explored. To identify polymorphisms in CD40L, we sequenced 2.3 kb of the 5′ flanking region and the first exon of the gene in DNA samples from 36 Gambian females ...
Tópico(s): Invertebrate Immune Response Mechanisms
2002 - Springer Nature | Genes and Immunity
Pardis C. Sabeti, David Reich, John M. Higgins, Haninah Z. P. Levine, Daniel J. Richter, S. F. Schaffner, Stacey Gabriel, Jill Platko, Nick Patterson, Gavin J. McDonald, Hans Ackerman, Sarah J. Campbell, David Altshuler, Richard Cooper, Dominic Kwiatkowski, Ryk Ward, Eric S. Lander,
Tópico(s): Genetic diversity and population structure
2002 - Nature Portfolio | Nature
Sarah J. Campbell, Pardis C. Sabeti, Katherine Fielding, Jackson Sillah, Boubacar Bah, Per Gustafson, Kebba Manneh, Ida Maria Lisse, Giorgio Sirugo, Richard Bellamy, Steve Bennett, Peter Aaby, Keith McAdam, Oumou Bah‐Sow, Christian Lienhardt, Adrian V. S. Hill,
Tópico(s): Immunodeficiency and Autoimmune Disorders
2003 - Springer Science+Business Media | Immunogenetics
Produção Nacional
Revisado por pares
Daniel E. Neafsey, S. F. Schaffner, Sarah K. Volkman, Daniel Park, Philip Montgomery, Danny A. Milner, Amanda K. Lukens, David W. Rosen, Rachel F. Daniels, Nathan Houde, Joseph F. Cortese, Erin Tyndall, Casey Gates, Nicole Stange-Thomann, Ousmane Sarr, Daouda Ndiaye, Omar Ndir, Soulyemane Mboup, Marcelo U. Ferreira, Sandra do Lago Moraes, Aditya Prasad Dash, Chetan E. Chitnis, Roger C. Wiegand, Daniel L. Hartl, Bruce W. Birren, Eric S. Lander, Pardis C. Sabeti, Dyann F. Wirth,
Abstract Background The malaria parasite Plasmodium falciparum exhibits abundant genetic diversity, and this diversity is key to its success as a pathogen. Previous efforts to study genetic diversity in P. falciparum have begun to elucidate the demographic history of the species, as well as patterns of population structure and patterns of linkage disequilibrium within its genome. Such studies will be greatly enhanced by new genomic tools and recent large-scale efforts to map genomic variation. To ...
Tópico(s): Vector-borne infectious diseases
2008 - BioMed Central | Genome biology
Rachel F. Daniels, Sarah K. Volkman, Danny A. Milner, Nira Mahesh, Daniel E. Neafsey, Daniel J. Park, David Rosen, Elaine Angelino, Pardis C. Sabeti, Dyann F. Wirth, Roger C. Wiegand,
Abstract Background Single nucleotide polymorphism (SNP) genotyping provides the means to develop a practical, rapid, inexpensive assay that will uniquely identify any Plasmodium falciparum parasite using a small amount of DNA. Such an assay could be used to distinguish recrudescence from re-infection in drug trials, to monitor the frequency and distribution of specific parasites in a patient population undergoing drug treatment or vaccine challenge, or for tracking samples and determining purity ...
Tópico(s): Antibiotic Resistance in Bacteria
2008 - BioMed Central | Malaria Journal
Sharon R. Grossman, Ilya Shylakhter, Elinor K. Karlsson, Elizabeth H. Byrne, Shannon J. Morales, Gabriel Frieden, Elizabeth Hostetter, Elaine Angelino, Manuel Garber, Or Zuk, Eric S. Lander, S. F. Schaffner, Pardis C. Sabeti,
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 method, composite of multiple signals (CMS), that combines tests for multiple signals of selection and increases resolution by up to 100-fold. By applying CMS to candidate regions from the International Haplotype Map, we localized population-specific selective signals to 55 kilobases ( ...
Tópico(s): Fractal and DNA sequence analysis
2010 - American Association for the Advancement of Science | Science
David Altshuler, Richard A Gibbs, Leena Peltonen, David Altshuler, Richard A Gibbs, Leena Peltonen, Emmanouil T. Dermitzakis, S. F. Schaffner, Fuli Yu, Leena Peltonen, Emmanouil T. Dermitzakis, Penelope E. Bonnen, David Altshuler, Richard A Gibbs, Paul I. W. de Bakker, Panos Deloukas, Stacey B. Gabriel, Rhian Gwilliam, Sarah Hunt, Michael Inouye, Xiaoming Jia, Aarno Palotie, Melissa Parkin, Pamela Whittaker, Fuli Yu, Kyle Chang, Alicia Hawes, Lora Lewis, Yanru Ren, David A. Wheeler, Richard A. Gibbs, Donna M. Muzny, C. Barnes, Katayoon Darvishi, Matthew E. Hurles, Joshua M. Korn, Kati Kristiansson, Charles Lee, Steven A. McCarrol, James Nemesh, Emmanouil T. Dermitzakis, Alon Keinan, Stephen B. Montgomery, Samuela Pollack, Alkes L. Price, Nicole Soranzo, Penelope E. Bonnen, Richard A Gibbs, Claudia Gonzaga‐Jauregui, Alon Keinan, Alkes L. Price, Fuli Yu, Verneri Anttila, Wendy Brodeur, Mark J. Daly, Stephen Leslie, Gil McVean, Loukas Moutsianas, Huy Nguyen, S. F. Schaffner, Qingrun Zhang, Mohammed J. R. Ghori, Ralph McGinnis, William McLaren, Samuela Pollack, Alkes L. Price, S. F. Schaffner, Fumihiko Takeuchi, Sharon R. Grossman, Ilya Shlyakhter, Elizabeth Hostetter, Pardis C. Sabeti, Clement Adebamowo, Morris W. Foster, Deborah R Gordon, Júlio Licinio, María Cristina Manca, Patricia A. Marshall, Ichiro Matsuda, Duncan Ngare, Vivian Ota Wang, Deepa Reddy, Charles N. Rotimi, Charmaine Royal, Richard R. Sharp, Changqing Zeng, Lisa Brooks, Jean E. McEwen,
Despite great progress in identifying genetic variants that influence human disease, most inherited risk remains unexplained. A more complete understanding requires genome-wide studies that fully examine less common alleles in populations with a wide range of ancestry. To inform the design and interpretation of such studies, we genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations, and sequenced ten 100-kilobase regions in 692 ...
Tópico(s): Genomic variations and chromosomal abnormalities
2010 - Nature Portfolio | Nature
Ann Demogines, Alysia M. East, Ji‐Hoon Lee, Sharon R. Grossman, Pardis C. Sabeti, Tanya T. Paull, Sara L. Sawyer,
In human cells, DNA double-strand breaks are repaired primarily by the non-homologous end joining (NHEJ) pathway. Given their critical nature, we expected NHEJ proteins to be evolutionarily conserved, with relatively little sequence change over time. Here, we report that while critical domains of these proteins are conserved as expected, the sequence of NHEJ proteins has also been shaped by recurrent positive selection, leading to rapid sequence evolution in other protein domains. In order to characterize ...
Tópico(s): HIV Research and Treatment
2010 - Public Library of Science | PLoS Genetics
Kelly A. Frazer, Dennis G. Ballinger, David R. Cox, David A. Hinds, Laura L. Stuvé, Richard A. Gibbs, John W. Belmont, Andrew Boudreau, Paul Hardenbol, Suzanne M. Leal, Shiran Pasternak, David A. Wheeler, T. D. Willis, Fuli Yu, Huanming Yang, Changqing Zeng, Yang Gao, Haoran Hu, Weitao Hu, Chaohua Li, Wei Lin, Siqi Liu, Hao Pan, Xiaoli Tang, Jian Wang, Wei Wang, Jun Yu, Bo Zhang, Qingrun Zhang, Hongbin Zhao, Hui Zhao, Jun Zhou, Stacey Gabriel, Rachel Barry, Brendan Blumenstiel, Amy L. Camargo, Matthew DeFelice, Maura Faggart, Mary Goyette, Supriya Gupta, Jamie Moore, Huy Nguyen, Robert C. Onofrio, Melissa Parkin, Jessica Roy, Erich Stahl, Ellen Winchester, Liuda Ziaugra, David Altshuler, Yan Shen, Zhijian Yao, Wei Huang, Xun Chu, Yungang He, Jin Li, Yangfan Liu, Yayun Shen, Weiwei Sun, Haifeng Wang, Yi Wang, Ying Wang, Xiaoyan Xiong, Liang Xu, Mary Miu Yee Waye, Stephen Kwok‐Wing Tsui, Hong Xue, J. Tze‐Fei Wong, Luana Galver, Jian-Bing Fan, Kevin L. Gunderson, Sarah S. Murray, Arnold Oliphant, Mark S. Chee, Alexandre Montpetit, Fanny Chagnon, Vincent Ferretti, Martin Leboeuf, Jean François Olivier, Michael Phillips, Stéphanie Roumy, Clémentine Sallée, Andrei Verner, Thomas J. Hudson, Pui‐Yan Kwok, Dongmei Cai, Daniel C. Koboldt, Raymond D. Miller, Ludmila Pawlikowska, Patricia Taillon‐Miller, Ming Xiao, Lap Chee Tsui, William Mak, You‐Qiang Song, Paul Kwong Hang Tam, Yusuke Nakamura, Takahisa Kawaguchi, Takuya Kitamoto, Takashi Morizono, Atsushi Nagashima, Yozo Ohnishi, Akihiro Sekine, Toshihiro Tanaka, Tatsuhiko Tsunoda, Panos Deloukas, Christine Bird, Marcos Delgado, Emmanouil T. Dermitzakis, Rhian Gwilliam, Sarah Hunt, Jonathan J. Morrison, Don Powell, Barbara E. Stranger, Pamela Whittaker, David Bentley, Mark J. Daly, Paul I. W. de Bakker, Jeff Barrett, Yves Chrétien, Julian Maller, Steve McCarroll, Hon‐Cheong So, Itsik Pe’er, Alkes L. Price, Shaun Purcell, Daniel J. Richter, Pardis C. Sabeti, Richa Saxena, S. F. Schaffner, Pak C. Sham, Patrick Varilly, Lincoln D. Stein, Lalitha Krishnan, Albert V. Smith, Marcela K. Tello-Ruiz, Guðmundur Á. Þórisson, Aravinda Chakravarti, Peter E. Chen, David J. Cutler, Carl Kashuk, Shin Lin, Gonçalo R. Abecasis, Weihua Guan, Yun Li, Heather M. Munro, Zhaohui Qin, Daryl J. Thomas, Gil McVean, Adam Auton, Leonardo Bottolo, Niall J. Cardin, S. Eyheramendy, Colin Freeman, Jonathan Marchini, Simon Myers, Chris Spencer, Matthew Stephens, Peter Donnelly, Lon R. Cardon, Geraldine M Clarke, David M. Evans, Andrew P. Morris, Bruce S. Weir, Todd A. Johnson, James C. Mullikin, Stephen T. Sherry, Michael Feolo, Andrew D. Skol, Houcan Zhang, Ichiro Matsuda, Yoshimitsu Fukushima, Darryl Macer, Eiko Suda, Charles N. Rotimi, Clement Adebamowo, IkeOluwapo O. Ajayi, Toyin Aniagwu, Patricia A. Marshall, Chibuzor Nkwodimmah, Charmaine Royal, Mark Leppert, Missy Dixon, Andy Peiffer, Renzong Qiu, Alastair Kent, Yoshihiro Kato, Norio Niikawa, Isaac F. Adewole, Bartha Maria Knoppers, Morris W. Foster, Ellen Wright Clayton, Jessica Watkin, Donna M. Muzny, Lynne Nazareth, Erica Sodergren, George M. Weinstock, Imtaz Yakub, Bruce W. Birren, Richard K. Wilson, Lucinda Fulton, Jane Rogers, John H. Burton, Nigel P. Carter, Christopher M. Clee, Mark Griffiths, Matthew Jones, Kirsten McLay, R. W. Plumb, Mark T. Ross, Sarah K. Sims, David L. Willey, Zhu Chen, Hua Han, Le Kang, Martin Godbout, John C. Wallenburg, Paul L'Archevêque, Guy Bellemare, K. Saeki, Hongguang Wang, Daochang An, Hongbo Fu, Qing Li, Zhen Wang, Renwu Wang, Arthur L. Holden, Lisa D. Brooks, Jean E. McEwen, Mark S. Guyer, Vivian Ota Wang, Jane L. Peterson, Michael Shi, Jack Spiegel, Lawrence M. Sung, Lynn F. Zacharia, Francis S. Collins, Karen Kennedy, Ruth Jamieson, John Stewart,
We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25–35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase ...
Tópico(s): Genetic Mapping and Diversity in Plants and Animals
2007 - Nature Portfolio | Nature
Michelle M. A. Fernando, Christine Stevens, Pardis C. Sabeti, Emily C. Walsh, Alasdair McWhinnie, Anila Shah, Todd J. Green, John D. Rioux, Timothy J. Vyse,
The association of the major histocompatibility complex (MHC) with SLE is well established yet the causal variants arising from this region remain to be identified, largely due to inadequate study design and the strong linkage disequilibrium demonstrated by genes across this locus. The majority of studies thus far have identified strong association with classical class II alleles, in particular HLA-DRB1*0301 and HLA-DRB1*1501. Additional associations have been reported with class III alleles; specifically, ...
Tópico(s): Immune Cell Function and Interaction
2007 - Public Library of Science | PLoS Genetics
Pardis C. Sabeti, Patrick Varilly, Ben Fry, Jason Lohmueller, Elizabeth Hostetter, Chris Cotsapas, Xiaohui Xie, Elizabeth H. Byrne, Steven A. McCarroll, Rachelle Gaudet, S. F. Schaffner, Eric S. Lander,
The International HapMap Consortium has produced a second-generation version of its remarkable haplotype map of the human genome. The Phase II HapMap charts human genetic variation even more extensively than the original, tripling of the number of genetic markers included. The original HapMap was instrumental in making large-scale genome-wide association studies possible. An indication of how this type of work will be extended with 'HapMap2' is presented in this issue: Sabeti et al. build on previous ...
Tópico(s): Genetics, Aging, and Longevity in Model Organisms
2007 - Nature Portfolio | Nature
Fuli Yu, Robert Hill, S. F. Schaffner, Pardis C. Sabeti, Eric T. Wang, André A. Mignault, Russell J. Ferland, Robert K. Moyzis, Christopher A. Walsh, David Reich,
Mekel-Bobrov et al . (Reports, 9 September 2005, p. 1720) suggested that ASPM , a gene associated with microcephaly, underwent natural selection within the last 500 to 14,100 years. Their analyses based on comparison with computer simulations indicated that ASPM had an unusual pattern of variation. However, when we compare ASPM empirically to a large number of other loci, its variation is not unusual and does not support selection.
Tópico(s): Genetic diversity and population structure
2007 - American Association for the Advancement of Science | Science
Simon Gravel, Brenna M. Henn, Ryan N. Gutenkunst, Amit Indap, Gábor Marth, Andrew G. Clark, Fuli Yu, Richard A. Gibbs, Carlos D. Bustamante, David L. Altshuler, Richard Durbin, Gonçalo R. Abecasis, David Bentley, Aravinda Chakravarti, Andrew G. Clark, Francis S. Collins, Francisco M. De La Vega, Peter Donnelly, Michael D. Miller, Paul Flicek, Stacey Gabriel, Richard A. Gibbs, Bartha Maria Knoppers, Eric S. Lander, Hans Lehrach, Elaine R. Mardis, Gil McVean, Debbie A. Nickerson, Leena Peltonen, Alan J. Schafer, Stephen T. Sherry, Jun Wang, Richard K. Wilson, Richard A. Gibbs, David Rio Deiros, Mike Metzker, Donna M. Muzny, Jeff Reid, David A. Wheeler, Jun Wang, Jingxiang Li, Min Jian, Guoqing Li, Ruiqiang Li, Huiqing Liang, Geng Tian, Bó Wáng, Jian Wang, Wei Wang, Huanming Yang, Xiuqing Zhang, Huisong Zheng, Eric S. Lander, David L. Altshuler, Lauren Ambrogio, Toby Bloom, Kristian Cibulskis, Tim Fennell, Stacey Gabriel, David B. Jaffe, Erica Shefler, Carrie Sougnez, David Bentley, Niall Gormley, Sean Humphray, Zoya Kingsbury, Paula Koko-Gonzales, Jennifer Stone, Kevin McKernan, Gina L. Costa, Jeffry K. Ichikawa, Clarence Lee, Ralf Sudbrak, Hans Lehrach, Tatiana Borodina, Andreas Dahl, Alexey N. Davydov, P Marquardt, Florian Mertes, Wilfiried Nietfeld, Philip Rosenstiel, Stefan Schreiber, Aleksey V. Soldatov, Bernd Timmermann, Marius Tolzmann, Michael D. Miller, Jason P. Affourtit, Dana Ashworth, Said Attiya, Melissa Bachorski, Eli Buglione, Adam Burke, Amanda Caprio, Christopher Celone, Andrew G. Clark, David Conners, Brian Desany, Lisa Gu, Lorri Guccione, Kalvin Kao, Andrew Kebbel, Jennifer Knowlton, Matthew T. Labrecque, Louise McDade, Craig Mealmaker, Melissa Minderman, Anne Nawrocki, Faheem Niazi, Kristen Pareja, Ravi Ramenani, David W. H. Riches, Wanmin Song, Cynthia Turcotte, Shally Wang, Elaine R. Mardis, Richard K. Wilson, David J. Dooling, Lucinda Fulton, Robert E. Fulton, George M. Weinstock, Richard Durbin, John H. Burton, David M. Carter, Carol Churcher, Alison J. Coffey, Anthony J. Cox, Aarno Palotie, Michael A. Quail, Tom Skelly, James Stalker, Harold Swerdlow, Daniel J. Turner, Anniek De Witte, Shane Giles, Richard A. Gibbs, David A. Wheeler, Matthew N. Bainbridge, Danny Challis, Aniko Sabo, Fuli Yu, Jin Yu, Jun Wang, Xiaodong Fang, Xiaosen Guo, Ruiqiang Li, Yingrui Li, Ruibang Luo, Shuaishuai Tai, Honglong Wu, Hancheng Zheng, Xiaole Zheng, Yan Zhou, Guoqing Li, Jian Wang, Huanming Yang, Gábor Marth, Erik Garrison, Weichun Huang, Amit Indap, Deniz Kural, Wan‐Ping Lee, Wen Fung Leong, Aaron R. Quinlan, Chip Stewart, Michael P. Strömberg, Alistair Ward, Jiantao Wu, Charles Lee, Ryan E. Mills, Xinghua Shi, Mark J. Daly, Mark A. DePristo, David L. Altshuler, Aaron D. Ball, Eric Banks, Toby Bloom, Brian L. Browning, Kristian Cibulskis, Tim Fennell, Kiran Garimella, Sharon R. Grossman, Robert E. Handsaker, Matt Hanna, Christopher Hartl, David B. Jaffe, Andrew Kernytsky, Joshua M. Korn, Heng Li, Jared Maguire, Steven A. McCarroll, Aaron McKenna, James Nemesh, Anthony Philippakis, Ryan Poplin, Alkes L. Price, Manuel A. Rivas, Pardis C. Sabeti, S. F. Schaffner, Erica Shefler, Ilya Shlyakhter, D.N. Cooper, Edward V. Ball, Matthew Mort, Andrew D. Phillips, Peter D. Stenson, Jonathan Sebat, Vladimir Makarov, Kenny Ye, Seungtai Yoon, Carlos D. Bustamante, Andrew G. Clark, Adam R. Boyko, Jeremiah D. Degenhardt, Simon Gravel, Ryan N. Gutenkunst, Mark Kaganovich, Alon Keinan, Phil Lacroute, Xin Ma, Andy Reynolds, Laura Clarke, Paul Flicek, Fiona Cunningham, Javier Herrero, Stephen Keenen, Eugene Kulesha, Rasko Leinonen, William McLaren, Rajesh Radhakrishnan, Richard E. Smith, Vadim Zalunin, Xiangqun Zheng-Bradley, Jan O. Korbel, Adrian M. Stütz, Sean Humphray, Markus Bauer, R. Keira Cheetham, Tony Cox, Michael A. Eberle, Terena James, Scott D. Kahn, Lisa Murray, Aravinda Chakravarti, Kai Ye, Francisco M. De La Vega, Yutao Fu, Fiona Hyland, Jonathan M. Manning, Stephen F. McLaughlin, Heather E. Peckham, Onur Sakarya, Yongming Sun, Eric F. Tsung, Mark A. Batzer, Miriam K. Konkel, Jerilyn A. Walker, Ralf Sudbrak, Marcus W. Albrecht, Vyacheslav Amstislavskiy, Ralf Herwig, Dimitri V. Parkhomchuk, Stephen T. Sherry, Richa Agarwala, Hoda Khouri, Aleksandr Morgulis, Justin Paschall, Lon Phan, Kirill E. Rotmistrovsky, Robert D. Sanders, Martin Shumway, Chunlin Xiao, Gil McVean, Adam Auton, Zamin Iqbal, Gerton Lunter, Jonathan Marchini, Loukas Moutsianas, Simon Myers, Afidalina Tumian, Brian Desany, James Knight, Roger Winer, David W. Craig, Steve M. Beckstrom-Sternberg, Alexis Christoforides, Ahmet Kurdoglu, John V. Pearson, Shripad Sinari, Waibhav Tembe, David Haussler, Angie S. Hinrichs, Sol Katzman, Andrew D. Kern, Robert M. Kuhn, Molly Przeworski, Ryan D. Hernandez,
High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to data generated by the pilot phase of the Thousand Genomes Project, including whole-genome 2–4× coverage data for 179 samples from HapMap European, Asian, ...
National Academy of Sciences
David N. Reshef, Yakir Reshef, Hilary K. Finucane, Sharon R. Grossman, Gil McVean, Peter J. Turnbaugh, Eric S. Lander, Michael Mitzenmacher, Pardis C. Sabeti,
A statistical method reveals relationships among variables in complex data sets.
Tópico(s): Bioinformatics and Genomic Networks
2011 - American Association for the Advancement of Science | Science
Gaurav Bhatia, Nick Patterson, Bogdan Paşaniuc, Noah Zaitlen, Giulio Genovese, Samuela Pollack, Swapan Mallick, Simon Myers, Arti Tandon, Chris C. A. Spencer, Lyle J. Palmer, Adebowale Adeyemo, Ermeg L. Akylbekova, L. Adrienne Cupples, Jasmin Divers, Myriam Fornage, W.H. Linda Kao, Leslie A. Lange, Mingyao Li, Solomon K. Musani, Josyf C. Mychaleckyj, Adesola Ogunniyi, George Papanicolaou, Charles N. Rotimi, Jerome I. Rotter, Ingo Ruczinski, Babatunde Salako, David S. Siscovick, Bamidele O. Tayo, Qiong Yang, Steve McCarroll, Pardis C. Sabeti, Guillaume Lettre, Phil De Jager, Joel N. Hirschhorn, Xiaofeng Zhu, Stephen S. Rich, David Reich, James G. Wilson, Alkes L. Price,
The study of recent natural selection in human populations has important applications to human history and medicine. Positive natural selection drives the increase in beneficial alleles and plays a role in explaining diversity across human populations. By discovering traits subject to positive selection, we can better understand the population level response to environmental pressures including infectious disease. Our study examines unusual population differentiation between three large data sets ...
Tópico(s): Epigenetics and DNA Methylation
2011 - Elsevier BV | The American Journal of Human Genetics
Daria Van Tyne, Daniel J. Park, S. F. Schaffner, Daniel E. Neafsey, Elaine Angelino, Joseph F. Cortese, Kayla G. Barnes, David M. Rosen, Amanda K. Lukens, Rachel F. Daniels, Danny A. Milner, Charles A. Johnson, Ilya Shlyakhter, Sharon R. Grossman, Justin S. Becker, Daniel Yamins, Elinor K. Karlsson, Daouda Ndiaye, Ousmane Sarr, Souleymane Mboup, Christian T. Happi, Nicholas A. Furlotte, Eleazar Eskin, Hyun Min Kang, Daniel L. Hartl, Bruce W. Birren, Roger C. Wiegand, Eric S. Lander, Dyann F. Wirth, Sarah K. Volkman, Pardis C. Sabeti,
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 of these adaptations is critical to intervening successfully against malaria. To that end, we created a high-density genotyping array that assays over 17,000 single nucleotide polymorphisms (∼1 SNP/kb), and applied it to 57 culture-adapted parasites from three continents. We characterized ...
Tópico(s): Complement system in diseases
2011 - Public Library of Science | PLoS Genetics