15 results on '"Adam Felsenfeld"'
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2. Centers for Mendelian Genomics: A decade of facilitating gene discovery
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Samantha M. Baxter, Jennifer E. Posey, Nicole J. Lake, Nara Sobreira, Jessica X. Chong, Steven Buyske, Elizabeth E. Blue, Lisa H. Chadwick, Zeynep H. Coban-Akdemir, Kimberly F. Doheny, Colleen P. Davis, Monkol Lek, Christopher Wellington, Shalini N. Jhangiani, Mark Gerstein, Richard A. Gibbs, Richard P. Lifton, Daniel G. MacArthur, Tara C. Matise, James R. Lupski, David Valle, Michael J. Bamshad, Ada Hamosh, Shrikant Mane, Deborah A. Nickerson, Heidi L. Rehm, Anne O’Donnell-Luria, Marcia Adams, François Aguet, Gulsen Akay, Peter Anderson, Corina Antonescu, Harindra M. Arachchi, Mehmed M. Atik, Christina A. Austin-Tse, Larry Babb, Tamara J. Bacus, Vahid Bahrambeigi, Suganthi Balasubramanian, Yavuz Bayram, Arthur L. Beaudet, Christine R. Beck, John W. Belmont, Jennifer E. Below, Kaya Bilguvar, Corinne D. Boehm, Eric Boerwinkle, Philip M. Boone, Sara J. Bowne, Harrison Brand, Kati J. Buckingham, Alicia B. Byrne, Daniel Calame, Ian M. Campbell, Xiaolong Cao, Claudia Carvalho, Varuna Chander, Jaime Chang, Katherine R. Chao, Ivan K. Chinn, Declan Clarke, Ryan L. Collins, Beryl Cummings, Zain Dardas, Moez Dawood, Kayla Delano, Stephanie P. DiTroia, Harshavardhan Doddapaneni, Haowei Du, Renqian Du, Ruizhi Duan, Mohammad Eldomery, Christine M. Eng, Eleina England, Emily Evangelista, Selin Everett, Jawid Fatih, Adam Felsenfeld, Laurent C. Francioli, Christian D. Frazar, Jack Fu, Emmanuel Gamarra, Tomasz Gambin, Weiniu Gan, Mira Gandhi, Vijay S. Ganesh, Kiran V. Garimella, Laura D. Gauthier, Danielle Giroux, Claudia Gonzaga-Jauregui, Julia K. Goodrich, William W. Gordon, Sean Griffith, Christopher M. Grochowski, Shen Gu, Sanna Gudmundsson, Stacey J. Hall, Adam Hansen, Tamar Harel, Arif O. Harmanci, Isabella Herman, Kurt Hetrick, Hadia Hijazi, Martha Horike-Pyne, Elvin Hsu, Jianhong Hu, Yongqing Huang, Jameson R. Hurless, Steve Jahl, Gail P. Jarvik, Yunyun Jiang, Eric Johanson, Angad Jolly, Ender Karaca, Michael Khayat, James Knight, J. Thomas Kolar, Sushant Kumar, Seema Lalani, Kristen M. Laricchia, Kathryn E. Larkin, Suzanne M. Leal, Gabrielle Lemire, Richard A. Lewis, He Li, Hua Ling, Rachel B. Lipson, Pengfei Liu, Alysia Kern Lovgren, Francesc López-Giráldez, Melissa P. MacMillan, Brian E. Mangilog, Stacy Mano, Dana Marafi, Beth Marosy, Jamie L. Marshall, Renan Martin, Colby T. Marvin, Michelle Mawhinney, Sean McGee, Daniel J. McGoldrick, Michelle Mehaffey, Betselote Mekonnen, Xiaolu Meng, Tadahiro Mitani, Christina Y. Miyake, David Mohr, Shaine Morris, Thomas E. Mullen, David R. Murdock, Mullai Murugan, Donna M. Muzny, Ben Myers, Juanita Neira, Kevin K. Nguyen, Patrick M. Nielsen, Natalie Nudelman, Emily O’Heir, Melanie C. O’Leary, Chrissie Ongaco, Jordan Orange, Ikeoluwa A. Osei-Owusu, Ingrid S. Paine, Lynn S. Pais, Justin Paschall, Karynne Patterson, Davut Pehlivan, Benjamin Pelle, Samantha Penney, Jorge Perez de Acha Chavez, Emma Pierce-Hoffman, Cecilia M. Poli, Jaya Punetha, Aparna Radhakrishnan, Matthew A. Richardson, Eliete Rodrigues, Gwendolin T. Roote, Jill A. Rosenfeld, Erica L. Ryke, Aniko Sabo, Alice Sanchez, Isabelle Schrauwen, Daryl A. Scott, Fritz Sedlazeck, Jillian Serrano, Chad A. Shaw, Tameka Shelford, Kathryn M. Shively, Moriel Singer-Berk, Joshua D. Smith, Hana Snow, Grace Snyder, Matthew Solomonson, Rachel G. Son, Xiaofei Song, Pawel Stankiewicz, Taylorlyn Stephan, V. Reid Sutton, Abigail Sveden, Diana Cornejo Sánchez, Monica Tackett, Michael Talkowski, Machiko S. Threlkeld, Grace Tiao, Miriam S. Udler, Laura Vail, Zaheer Valivullah, Elise Valkanas, Grace E. VanNoy, Qingbo S. Wang, Gao Wang, Lu Wang, Michael F. Wangler, Nicholas A. Watts, Ben Weisburd, Jeffrey M. Weiss, Marsha M. Wheeler, Janson J. White, Clara E. Williamson, Michael W. Wilson, Wojciech Wiszniewski, Marjorie A. Withers, Dane Witmer, Lauren Witzgall, Elizabeth Wohler, Monica H. Wojcik, Isaac Wong, Jordan C. Wood, Nan Wu, Jinchuan Xing, Yaping Yang, Qian Yi, Bo Yuan, Jordan E. Zeiger, Chaofan Zhang, Peng Zhang, Yan Zhang, Xiaohong Zhang, Yeting Zhang, Shifa Zhang, Huda Zoghbi, and Igna van den Veyver
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Phenotype ,Exome Sequencing ,Humans ,Exome ,Genomics ,Article ,Genetic Association Studies ,Genetics (clinical) - Abstract
PURPOSE: Mendelian disease genomic research has undergone a massive transformation over the past decade. With increasing availability of exome and genome sequencing, the role of Mendelian research has expanded beyond data collection, sequencing, and analysis to worldwide data sharing and collaboration. METHODS: Over the past 10 years, the National Institutes of Health–supported Centers for Mendelian Genomics (CMGs) have played a major role in this research and clinical evolution. RESULTS: We highlight the cumulative gene discoveries facilitated by the program, biomedical research leveraged by the approach, and the larger impact on the research community. Beyond generating a list of gene-phenotype relationships and participating in widespread data sharing, the CMGs have created resources, tools, and training for the larger community to foster understanding of genes and genome variation. The CMGs have participated in a wide range of data sharing activities, including deposition of all eligible CMG data into the Analysis, Visualization, and Informatics Lab-space (AnVIL), sharing candidate genes through the Matchmaker Exchange and the CMG website, and sharing variants in Genotypes to Mendelian Phenotypes (Geno2MP) and VariantMatcher. CONCLUSION: The work is far from complete; strengthening communication between research and clinical realms, continued development and sharing of knowledge and tools, and improving access to richly characterized data sets are all required to diagnose the remaining molecularly undiagnosed patients.
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- 2022
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3. Strategic vision for improving human health at The Forefront of Genomics
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Paul P. Liu, Allison Mandich, Chris Gunter, Elise A. Feingold, Adam Felsenfeld, Teri A. Manolio, Valentina Di Francesco, Kris A. Wetterstrand, Daniel L. Kastner, Leslie G. Biesecker, Jyoti G. Dayal, Britny J. Kish, Vence L. Bonham, Anastasia L. Wise, Elaine A. Ostrander, William A. Gahl, Benjamin D. Solomon, Susan Vasquez, William J. Pavan, Laura Lyman Rodriguez, David J. Kaufman, Carla Easter, Lawrence C. Brody, Adam M. Phillippy, Sarah A. Bates, Eric D. Green, Christopher Wellington, Carolyn M. Hutter, Bettie J. Graham, and Darryl Leja
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0301 basic medicine ,medicine.medical_specialty ,Biomedical Research ,Process (engineering) ,Genomics ,Translational research ,Article ,Translational Research, Biomedical ,03 medical and health sciences ,0302 clinical medicine ,Political science ,medicine ,Mainstream ,Humans ,Social Change ,Everyday life ,Strategic planning ,Multidisciplinary ,Genome, Human ,Public health ,COVID-19 ,Human genetics ,United States ,National Human Genome Research Institute (U.S.) ,030104 developmental biology ,Engineering ethics ,Public Health ,030217 neurology & neurosurgery - Abstract
Starting with the launch of the Human Genome Project three decades ago, genomics has become progressively entrenched within the bedrock of the biomedical research enterprise. Capitalizing on the momentum of the project’s successful completion in 2003, genomics now regularly plays a central and catalytic role in basic and translational research, and studies increasingly demonstrate the vital role that genomic information can play in clinical care. Looking ahead, the anticipated advances in technology development, biological insights, and clinical applications (among others) will lead to more widespread integration of genomics into virtually all areas of biomedical research, the adoption of genomics into mainstream medical and public-health practices, and an increasing relevance of genomics in everyday life. On behalf of the research community, the National Human Genome Research Institute recently completed a multi-year process of strategic engagement to capture input about the future research priorities and opportunities in human genomics, with an emphasis on health applications. Here we articulate the highest-priority elements envisioned for the cutting-edge of human genomics going forward – that is, at “The Forefront of Genomics.”
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- 2020
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4. F1‐01‐02: Alzheimer's Disease Sequencing Project: Search for Alzheimer's Disease Resilience Genes That May Modify Disease Susceptibility in Specific Apoe Genotype Backgrounds
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Marilyn M. Miller, Adam C. Naj, Joshua C. Bis, Li-San Wang, Gary W. Beecham, Richard Mayeux, Myriam Fornage, Manav Kapoor, Gerard D. Schellenberg, Adam Felsenfeld, Alison Goate, Eric Boerwinkle, Alan E. Renton, Eduardo Marcora, Margaret A. Pericak-Vance, Mugdha Khaladkar, Badri N. Vardarajan, Yiyi Ma, Keoni Kauwe, Sudha Seshadri, Laura B. Cantwell, Amanda Partch, Rebecca Cweibel, Dan Kobolt, Carlos Cruchaga, and Lindsay A. Farrer
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Apolipoprotein E ,Genetics ,Epidemiology ,Health Policy ,Disease ,Biology ,Psychiatry and Mental health ,Cellular and Molecular Neuroscience ,Disease susceptibility ,Developmental Neuroscience ,Genotype ,Neurology (clinical) ,Geriatrics and Gerontology ,Resilience (network) ,Gene - Published
- 2016
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5. P2‐077: Alzheimer's Disease Sequencing Project: Search for Alzheimer's Disease Resilience Genes That May Modify Disease Susceptibility in Specific Apoe Genotype Backgrounds
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Eduardo Marcora, Alan E. Renton, Gary W. Beecham, Eric Boerwinkle, Laura Cantwell, Carlos Cruchaga, Rebecca Cweibel, Adam Felsenfeld, Myriam Fornage, Manav Kapoor, Keoni Kauwe, Mugdha Khaladkar, Dan Kobolt, Yiyi Ma, Richard Mayeux, Marilyn Miller, Adam C. Naj, Amanda B. Partch, Margaret A. Pericak-Vance, Gerard D. Schellenberg, Sudha Seshadri, Badri N. Vardarajan, Li-San Wang, Joshua C. Bis, Lindsay A. Farrer, and Alison M. Goate
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Psychiatry and Mental health ,Cellular and Molecular Neuroscience ,Developmental Neuroscience ,Epidemiology ,Health Policy ,Neurology (clinical) ,Geriatrics and Gerontology - Published
- 2016
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6. Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species
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Stephan C. Schuster, Richard E. Green, Leo Joseph, Michele Clamp, Cibele R. Bonvicino, Philippe Gaubert, David Haussler, Steve Turner, Joanna Sumner, Robert Hanner, Shannon J. Hackett, Héctor N. Seuánez, David M. Kingsley, Andrew J. Crawford, Olivier Hanotte, Mark S. Springer, Ya-Ping Zhang, Wesley C. Warren, Eldredge Bermingham, F. Keith Barker, Ngan Nguyen, Nathan D. Wolfe, Aaron M. Bauer, David M. Rawson, Jennifer A. Marshall Graves, Robert W. Murphy, Mark Diekhans, Guillermo Ortí, Robert C. Vrijenhoek, Stephen J. O'Brien, William J. Murphy, Terrie M. Williams, Jon Fjelsda, Paola Martelli, Harris A. Lewin, Frederick H. Sheldon, Joel Cracraft, Bailey Kessing, Emma C. Teeling, Per G. P. Ericson, Terry Burke, George Amato, Warren E. Johnson, Brian L. Pike, Sydney Brenner, Oliver A. Ryder, Giacomo Bernardi, C. Scott Baker, Fred W. Allendorf, Gordon Luikart, Byrappa Venkatesh, Webb Miller, Albano Beja-Pereira, Robert K. Wayne, James A. Estes, Miguel A. M. Moreira, Nate Flesness, Erik D. Green, Adam Felsenfeld, Barry Sinervo, Kristofer M. Helgen, Edward O. Wiley, Robert D. Ward, H. Bradley Shaffer, Scott V. Edwards, Tony Gamble, Jimmy A. McGuire, Paul D. N. Hebert, Alexander S. Graphodatsky, and Joshua M. Stuart
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Comparative genomics ,Whole genome sequencing ,Genome ,Genomics ,Original Articles ,Biology ,Vertebrate Biology ,DNA sequencing ,Species Specificity ,Evolutionary biology ,Vertebrates ,Genetics ,Animals ,Gene sequence ,Molecular Biology ,Biological sciences ,Genetics (clinical) ,Biological Specimen Banks ,Biotechnology ,Genetic association - Abstract
The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10 000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16 203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60 000 living species). In this proposal, we present precise counts for these 16 203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.
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- 2009
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7. Assessing the Quality of the DNA Sequence from The Human Genome Project
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Adam Felsenfeld, Jane Peterson, Jeffery A. Schloss, and Mark S. Guyer
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Genetics ,Whole genome sequencing ,Contig ,Human genome ,Genome project ,Computational biology ,Biology ,ENCODE ,Genome ,Genetics (clinical) ,DNA sequencing ,Sequence (medicine) - Abstract
It is sometimes hard to remember that the first DNA sequence of the entire genome of a free-living organism, Hemophilus influenzae, was reported 17 other prokaryotes (http://linkage.rockefeller. edu/wli/seq/), a unicellular eukaryote, Saccharomyces cerevisiae (Nature 1996), and a multicellular organism, Caenorhabditis elegans (The C. elegans Sequencing Consortium 1998), have been completely sequenced. Progress toward determination of the human DNA sequence has also become more rapid; at the time of this writing, the public databases contain 227.2 Mb of nonredundant, finished sequence available in contigs of >30 kb (and another 152.7 Mb of unfinished sequence) (http:// www.ncbi.nlm.nih.gov/genome/seq/ weekly_report.html). In comparison, there was 84.4 Mb of finished data (http://www.ebi.ac.uk/∼sterk/genomeMOT/) in February 1998. It is increasingly likely that the human sequence will be complete by 2003, and a working draft will be in hand even sooner (Collins et al. 1998; Venter et al. 1998). One consequence of our increased sequencing capacity is that within the next couple of years, we expect the rate of deposition of sequence data to increase from the current ∼3 Mb per week, to an average of well over 10 Mb per week worldwide. Very few scientific fields can measure progress as easily as can be done for large-scale genomic sequencing, quantifiable as it is into base pairs per unit time. However, mere numbers can be deceptive—the essential ‘‘production’’ nature of large-scale genomic sequencing leaves it susceptible to errors in ways other scientific endeavors are not. Because of the rapid accumulation of human genomic sequence data, there is little opportunity for, or even possibility of, direct peer review of data prior to publication. The major venue for primary publication of genomic data is not the peer-reviewed literature at all, but public databases. This is appropriate: Current peer-reviewed biological journals could not handle this much primary data, nor would they want to, nor would the community be likely to entrust this resource only to the printed medium. But more critically, the community has made the important decision that these data must be accessible very rapidly. For publicly funded laboratories throughout the world, genome sequence data are supposed to be released into a public database within 24 hr of being generated (Collins et al. 1998), a standard that is, as far as we are aware, unmatched by any other scientific discipline. This rapid release is in many ways at odds with what is normally understood to be peer review. Finally, the bulk of the work will probably not be directly replicated, especially for the human sequence and that of other large genomes. There is little doubt, however, that the data will be heavily relied on. For all of these reasons, it is important that the Human Genome Project (HGP) devise a way of measuring and reporting the quality of sequence data deposited in the public databases.
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- 1999
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8. Painting a moving picture: large-scale proteomics efforts and their potential for changing patient care
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Daniel C. Liebler, Andrew N. Hoofnagle, Adam Felsenfeld, Ruedi Aebersold, and N. Leigh Anderson
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Proteomics ,Biomedical Research ,Point (typography) ,Proteome ,business.industry ,media_common.quotation_subject ,Biochemistry (medical) ,Clinical Biochemistry ,Medical laboratory ,Genomics ,Biology ,Bioinformatics ,Data science ,Variety (cybernetics) ,Reading (process) ,Human proteome project ,Humans ,business ,Databases, Protein ,media_common - Abstract
Many investigators have used proteomic methodologies to investigate specific questions in basic biology and medical science. Indeed, many millions of dollars have been spent around the world on the generation of extensive lists of proteins that reside in a particular organelle, cell type, tissue, or body fluid. These lists represent the proteomes of those specific systems. Many studies attempt to go one step further and compare proteomes via a variety of approaches, in most cases with methods that are much too imprecise to be considered for clinical use. Some argue that it is difficult to point to the clinical application of these lists and crude comparisons, but at least 2 organizations are aiming to lead or synthesize expanded efforts to characterize the human proteome (see the suggested reading in the Data Supplement that accompanies the online version of this Q&A at http://www.clinchem.org/content/vol57/issue10). What does this mean for clinical laboratory medicine? Can the results of these efforts possibly lead to important discoveries that will change how we care for our patients? We compiled the opinions of 4 experts in proteomics and genomics to provide a perspective from individual leading investigators and the National Human Genome Research Institute. Their views provide cautious optimism and important insights on how to move forward. In general, have experiments aimed at cataloguing human proteomes made important advances? N. Leigh Anderson: Yes. I would point to 3 significant results as examples: (1) the reliable detection of almost 2000 proteins in human plasma by numerous groups; (2) passing the halfway point in the Human Proteome Resource effort to use antibodies to map locations of the human proteins by Matthias Uhlen et al. (see suggested reading in the online Data Supplement); and (3) the recent synthesis and characterization of nearly all human tryptic proteotypic peptides by Robert Moritz, Ruedi …
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- 2011
9. Mapping copy number variation by population-scale genome sequencing
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L. McDade, Eric D. Green, Aravinda Chakravarti, Susan Lindsay, Justin Paschall, Aylwyn Scally, Deborah A. Nickerson, Chip Stewart, Stephen T. Sherry, Chunlin Xiao, Alex Reynolds, Carol Scott, H. M. Khouri, Pardis C. Sabeti, Xinmeng Jasmine Mu, Stephen B. Montgomery, Eric Banks, Gabor T. Marth, A. Caprio, Xiaole Zheng, Philip Awadalla, Qunyuan Zhang, Wei Chen, Matthew N. Bainbridge, Donna Muzny, Steven A. McCarroll, Jeffrey M. Kidd, Honglong Wu, Audrey Duncanson, Vladimir Makarov, Lilia M. Iakoucheva, Mark Gerstein, Han-Jun Jin, Can Alkan, Iman Hajirasouliha, T. J. Fennell, C. R. Juenger, J. Kidd, Chris Tyler-Smith, Qasim Ayub, D. Ashworth, Kristian Cibulskis, Yutao Fu, William M. McLaren, Sol Katzman, Yujun Zhang, Rajini R Haraksingh, A. Kebbel, Stuart L. Schreiber, Manual Rivas, Onur Sakarya, Tobias Rausch, Yuan Chen, M. Bachorski, Matthew E. Hurles, N. C. Clemm, Wei Wang, Xiangqun Zheng-Bradley, Adrian M. Sütz, Thomas M. Keane, E. Bank, Stephen F. McLaughlin, Javier Herrero, Jon Keebler, Simon Myers, Aleksandr Morgulis, James Nemesh, Jing Leng, Molly Przeworski, Alon Keinan, Lorraine Toji, Ilya Shlyakhter, Joshua M. Korn, Martine Zilversmit, Luke Jostins, Jun Wang, Jared Maguire, J. M. Korn, Ryan E. Mills, Seungtai Yoon, Bo Wang, F. M. De La Vega, Heng Li, L. Guccione, Laura Clarke, Huisong Zheng, Jeffrey K. Ichikawa, K. Kao, Kirill Rotmistrovsky, L. Gu, David B. Jaffe, David Haussler, Toby Bloom, Tara Skelly, S. Yoon, Gil McVean, Carrie Sougnez, Mark A. Batzer, A. De Witte, Ralf Herwig, Jane Wilkinson, Min Hu, K. Pareja, John V. Pearson, Robert E. Handsaker, Jerilyn A. Walker, Fuli Yu, Anthony A. Philippakis, Aniko Sabo, Jonathan Marchini, Ryan D. Hernandez, Guoqing Li, Peter Donnelly, Eric S. Lander, David J. Dooling, Jun Ding, Lukas Habegger, Pilar N. Ossorio, Andreas Dahl, Wilfried Nietfeld, Miriam F. Moffatt, Alexej Abyzov, Sebastian Zöllner, Ekta Khurana, Jean E. McEwen, Robert S. Fulton, Alexey Soldatov, Fiona Hyland, Philippe Lacroute, Richa Agarwala, Paul Flicek, Weichun Huang, Alison J. Coffey, Tony Cox, John W. Wallis, Robert Sanders, David Neil Cooper, Jason P. Affourtit, Mark A. DePristo, D Wheeler, Christopher Celone, Eugene Kulesha, Craig Elder Mealmaker, B. Desany, Zhengdong D. Zhang, Jonathan M. Manning, Cynthia L. Turcotte, Lisa D Brooks, Xiuqing Zhang, C. Coafra, Rajesh Radhakrishnan, Alan J. Schafer, Jonathan Sebat, Ken Chen, Andrew G. Clark, Alexis Christoforides, Edward V. Ball, Mark S. Guyer, Sharon R. Grossman, Philip Rosenstiel, J. Knowlton, Gonçalo R. Abecasis, Min Jian, James O. Burton, S. Wang, Lucinda Murray, George M. Weinstock, Mark Lathrop, Harold Swerdlow, Michael L. Metzker, Xiaowei Zhan, Yeyang Su, Ruibang Luo, Charles Lee, Huanming Yang, P. Marquardt, Charles N. Rotimi, Lynne V. Nazareth, Michael Snyder, Faheem Niazi, Quan Long, Jane Kaye, Michael Strömberg, Adam Auton, Michael Bauer, Cheng-Sheng Lee, S. Gabriel, Jim Stalker, Heather E. Peckham, D. Conners, Raffaella Smith, Yingrui Li, Niall Anthony Gormley, Megan Hanna, Jinchuan Xing, Hugo Y. K. Lam, S. Giles, Evan E. Eichler, Justin Jee, Loukas Moutsianas, Jiang Du, Hyun Min Kang, Eric F. Tsung, Ni Huang, Kai Ye, Stephen F. Schaffner, Suleyman Cenk Sahinalp, Xinghua Shi, Sean Humphray, Ahmet Kurdoglu, Amy L. McGuire, Sandra J. Lee, Linnea Fulton, Francis S. Collins, Huiqing Liang, S. C. Melton, A. Nawrocki, Aaron R. Quinlan, Tatjana Borodina, Lynn B. Jorde, Leopold Parts, Michael D. McLellan, Adrian M. Stütz, Paul Scheet, Amit Indap, Vyacheslav Amstislavskiy, Waibhav Tembe, S. Attiya, Jin Yu, Dmitri Parkhomchuk, Si Quang Le, Fabian Grubert, E. Buglione, Ruiqiang Li, Yan Zhou, Fiona Cunningham, Gilean McVean, Wan-Ping Lee, W. Song, Richard Durbin, Andrew Kernytsky, Stephen M. Beckstrom-Sternberg, Xin Ma, J. Jeng, Lauren Ambrogio, Carol Churcher, Ryan Poplin, William O.C.M. Cookson, Rasko Leinonen, Alexey N. Davydov, Kenny Ye, Paige Anderson, Alexander E. Urban, Adam Felsenfeld, Jeffrey S. Reid, Cornelis A. Albers, Jan O. Korbel, Senduran Balasubramaniam, Elaine R. Mardis, Gozde Aksay, Peter H. Sudmant, Aaron McKenna, M. Labrecque, Amanda J. Price, Vadim Zalunin, Donald F. Conrad, Florian Mertes, Christie Kovar, Danny Challis, A. D. Ball, Petr Danecek, Kiran V. Garimella, Bryan Howie, Scott Kahn, Shuaishuai Tai, E. P. Garrison, Robert D. Bjornson, Shankar Balasubramanian, Fereydoun Hormozdiari, Geng Tian, S. Clark, Joanna L. Kelley, Asif T. Chinwalla, Ramenani Ravi K, Ralf Sudbrak, Mark Kaganovich, Jeffrey C. Barrett, David Rio Deiros, Jeremiah D. Degenhardt, A. Palotie, Alistair Ward, Gianna Costa, Huyen Dinh, M. Minderman, R. Keira Cheetham, Jingxiang Li, Michael A. Quail, P. Koko-Gonzales, Alastair Kent, Martin Shumway, David R. Bentley, Ferran Casals, Leena Peltonen, Klaudia Walter, Christopher Hartl, Erica Shefler, Zhaolei Zhang, Hans Lehrach, Jessica L. Peterson, Roger Winer, Daniel C. Koboldt, D. Riches, Terena James, Wen Fung Leong, Michael Egholm, Thomas W. Blackwell, Peter D. Stenson, Anthony J. Cox, Andrew D. Kern, David M. Carter, M. Tolzmann, Daniel G. MacArthur, Jiantao Wu, Jennifer Stone, Angie S. Hinrichs, M. Albrecht, Jo Knight, Chang-Yun Lin, Adam R. Boyko, Dan Turner, Xiaodong Fang, Youssef Idaghdour, Liming Liang, Ryan N. Gutenkunst, David Craig, Mark J. Daly, Xiaosen Guo, Neda Gharani, Gerton Lunter, Shuli Kang, A. Burke, Shripad Sinari, Yongming A. Sun, Zoya Kingsbury, Robert M. Kuhn, Miriam K. Konkel, T. Li, Kevin McKernan, Simon Gravel, Brian L. Browning, C Sidore, Zamin Iqbal, Matthew Mort, Afidalina Tumian, Michael C. Wendl, Adam Phillips, Bernd Timmermann, Carlos Bustamante, H. Y. Lam, Deniz Kural, Richard A. Gibbs, Bartha Maria Knoppers, Emmanouil T. Dermitzakis, Lon Phan, Richard K. Wilson, D. L. Altshuler, S. Keenen, Assya Abdallah, Eric A. Stone, Michael A. Eberle, Li Ding, and Broad Institute of MIT and Harvard
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DNA Copy Number Variations ,Genotype ,Population ,Genomic Structural Variation ,Genomics ,Computational biology ,Biology ,Genome ,Article ,DNA sequencing ,structural variation segmental duplications short-read rearrangements disorders disease common schizophrenia polymorphism insertions ,03 medical and health sciences ,0302 clinical medicine ,Gene Duplication ,Insertional ,Genetics ,Humans ,Genetic Predisposition to Disease ,Copy-number variation ,1000 Genomes Project ,education ,Sequence Deletion ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,Multidisciplinary ,Genome, Human ,Reproducibility of Results ,Sequence Analysis, DNA ,DNA ,Mutagenesis, Insertional ,Genetics, Population ,Mutagenesis ,Human genome ,Sequence Analysis ,030217 neurology & neurosurgery ,Human - Abstract
Summary Genomic structural variants (SVs) are abundant in humans, differing from other variation classes in extent, origin, and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (i.e., copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analyzing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.
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- 2011
10. Completing the map of human genetic variation
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Anne M. Bowcock, Douglas Smith, James C. Mullikin, Deborah A. Nickerson, Stephen T. Sherry, Jonathan Sebat, Deanna M. Church, Mark S. Guyer, Nigel P. Carter, David Valle, James R. Lupski, Robert H. Waterston, Adam Felsenfeld, David Altshuler, Charles Lee, Jonathan K. Pritchard, Evan E. Eichler, and Lisa D. Brooks
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Genetics ,Multidisciplinary ,Genome, Human ,Genetic Variation ,Genomics ,Human genetic variation ,Biology ,Physical Chromosome Mapping ,Genome ,Polymorphism, Single Nucleotide ,Human genetics ,Article ,Phenotype ,Evolutionary biology ,Genetic variation ,Humans ,Human genome ,Disease ,Copy-number variation ,1000 Genomes Project - Abstract
Large-scale studies of human genetic variation have focused largely on understanding the pattern and nature of single-nucleotide differences within the human genome. Recent studies that have identified larger polymorphisms, such as insertions, deletions and inversions, emphasize the value of investing in more comprehensive and systematic studies of human structural genetic variation. We describe a community resource project recently launched by the National Human Genome Research Institute (NHGRI) to sequence large-insert clones from many individuals, systematically discovering and resolving these complex variants at the DNA sequence level. The project includes the discovery of variants through development of clone resources, sequence resolution of variants, and accurate typing of variants in individuals of African, European or Asian ancestry. Sequence resolution of both single-nucleotide and larger-scale genomic variants will improve our picture of natural variation in human populations and will enhance our ability to link genetics and human health.
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- 2007
11. Insights into social insects from the genome of the honeybee Apis mellifera
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George M. Weinstock, Andrew K. Jones, Katherine A Aronstein, Irene Gattermeier, Kiyoshi Kimura, Susan E. Fahrbach, Laura I. Decanini, Christina M. Grozinger, Evgeny M. Zdobnov, Susan J. Brown, Jonathan V. Sweedler, Kazutoyo Osoegawa, Christian A. Ross, Joseph J. Gillespie, Ngoc Nguyen, Geert Baggerman, Frank Hauser, Dan Graur, Michelle M. Elekonich, Alison R. Mercer, Amanda F. Svatek, Jean Marie Cornuet, Cornelis J. P. Grimmelikhuijzen, Aleksandar Milosavljevic, Anand Venkatraman, Andrew J. Schroeder, Huaiyang Jiang, Michael R. Kanost, Justin T. Reese, Margaret Morgan, Tomoko Fujiyuki, Kim C. Worley, Susanta K. Behura, Jun Kawai, Robert Kucharski, Gildardo Aquino-Perez, Miguel Corona, Diana E. Wheeler, Kathryn S. Campbell, William M. Gelbart, Amy L. Toth, Yanping Chen, Mira Cohen, Noam Kaplan, Michihira Tagami, Miguel A. Peinado, Peter K. Dearden, Glenford Savery, Liliane Schoofs, Takeo Kubo, Giuseppe Cazzamali, Sylvain Forêt, Thomas C. Newman, Ross Overbeek, Piero Carninci, Ryszard Maleszka, Barbara J. Ruef, Michal Linial, Alexandre S. Cristino, Mary A. Schuler, Huyen Dinh, J. Troy Littleton, Manoj P. Samanta, Waraporn Tongprasit, L. Sian Grametes, Eran Elhaik, Jean-Luc Imler, Zhen Zou, Rodrigo A. Velarde, Tanja Gempe, Dorothea Eisenhardt, Juan Manuel Anzola, Graham J. Thompson, Aaron J. Mackey, René Feyereisen, Mrcia M.G. Bitondi, Lora Lewis, Guy Bloch, Richard A. Gibbs, Jane Peterson, Jay D. Evans, Robert E. Page, Amanda B. Hummon, Viktor Stolc, Donna M. Muzny, Yair Shemesh, Francis M. F. Nunes, Dawn Lopez, Judith H. Willis, Martin Hasselmann, Mark S. Guyer, John G. Oakeshott, Pinglei Zhou, Eriko Kage, Dominique Vautrin, Kevin J. Hackett, Sandra L. Lee, Clay Davis, Christine Emore, Gene E. Robinson, Alexandre Souvorov, T.A. Richmond, Rachel Thorn, Jurgen Huybrechts, Elad B. Rubin, Craig Mizzen, Deborah R. Smith, Walter S. Sheppard, Takekazu Kunieda, Adam Felsenfeld, Bingshan Li, Jeffrey G. Reid, La Ronda Jackson, Jamie J. Cannone, Robin R. Gutell, Jireh Santibanez, Megan J. Wilson, David B. Sattelle, Azusa Kamikouchi, George Miner, Hideaki Takeuchi, Geoffrey Okwuonu, Jennifer Hume, Jonathan Miller, Kazuaki Ohashi, Angela Jovilet, Yoshihide Hayashizaki, Joseph Chacko, Paul Kitts, Erica Sodergren, Charles Hetru, Andrew V. Suarez, Brian P. Lazzaro, Susan E. St. Pierre, Evy Vierstraete, Haobo Jiang, Sandra Hines, Teresa D. Shippy, Greg J. Hunt, Peter Kosarev, Dan Hultmark, Stefan Albert, Susan M. Russo, Chung Li Shu, Michel Solignac, H. Michael G. Lattorff, Xu Ling, Grard Leboulle, Miklós Csürös, Neil D. Tsutsui, Lynne V. Nazareth, Ying Wang, Florence Mougel, Beverly B. Matthews, Kevin L. Childs, Rita A. Wright, Hugh M. Robertson, Lan Zhang, Peter Verleyen, Daniel B. Weaver, Christie Kovar, Chikatoshi Kai, Charles W. Whitfield, Madeline A. Crosby, Natalia V. Milshina, Reed M. Johnson, Michael A. Ewing, Peter L. Jones, Sandra L. Rodriguez-Zas, Michael B. Eisen, Klaus Hartfelder, Karl H.J. Gordon, W. Augustine Dunn, Ling Ling Pu, M. Monnerot, Stephen Richards, Richa Agarwala, Judith Hernandez, Pieter J. de Jong, Michael Williamson, Marcé D. Lorenzen, Zilá Luz Paulino Simões, Mark D. Drapeau, Donna Villasana, Katarína Bíliková, J. Spencer Johnston, David I. Schlipalius, Xuehong Wei, Laurent Duret, Venky N. Iyer, Andrew G. Clark, Christine G. Elsik, Hilary Ranson, Kyle T. Beggs, Mireia Jordà, Shiro Fukuda, Seth A. Ament, Vivek Iyer, Jozef Šimúth, Stewart H. Berlocher, May R. Berenbaum, Robin F. A. Moritz, Tatsuhiko Kadowaki, Charles Claudianos, Gro V. Amdam, Yue Liu, Naoko Sakazume, Morten Schioett, Paul Havlak, Anita M. Collins, Dirk C. de Graaf, Derek Collinge, Ivica Letunic, Carlos H. Lobo, Mizue Morioka, Martin Beye, Rachel Gill, C. Michael Dickens, Daisuke Sasaki, Victor V. Solovyev, Peer Bork, Sunita Biswas, David A. Wheeler, Heidi Paul, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Evolution, Génomes et Spéciation (LEGS), Centre National de la Recherche Scientifique (CNRS), and Physical and genetic mapping
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Male ,0106 biological sciences ,Transposable element ,[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT] ,Proteome ,Genome, Insect ,Molecular Sequence Data ,Genes, Insect ,Genomics ,Biology ,010603 evolutionary biology ,01 natural sciences ,Genome ,Article ,Evolution, Molecular ,03 medical and health sciences ,Molecular evolution ,Phylogenetics ,Animals ,Gene ,Phylogeny ,abeille domestique ,030304 developmental biology ,Whole genome sequencing ,Genetics ,Base Composition ,0303 health sciences ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,Multidisciplinary ,Behavior, Animal ,Reproduction ,SOCIAL BEHAVIOR ,[SDV.BA]Life Sciences [q-bio]/Animal biology ,Immunity ,APIS MELLIFERA ,food and beverages ,Bees ,Telomere ,Physical Chromosome Mapping ,INSECTE ,Gene Expression Regulation ,DNA methylation ,DNA Transposable Elements ,Female ,GENETIQUE DES POPULATIONS ,Signal Transduction - Abstract
Ce travail résulte de la collaboration de très nombreux chercheurs. Seuls les auteurs de la rubrique Physical and Genetic Mapping sont cités explicitement.; Here we report the genome sequence of the honeybee Apis mellifera, a key model for social behaviour and essential to global ecology through pollination. Compared with other sequenced insect genomes, the A. mellifera genome has high A1T and CpG contents, lacks major transposon families, evolves more slowly, and is more similar to vertebrates for circadian rhythm, RNA interference and DNA methylation genes, among others. Furthermore, A.mellifera has fewer genes for innate immunity, detoxification enzymes, cuticle-forming proteins and gustatory receptors, more genes for odorant receptors, and novel genes for nectar and pollen utilization, consistent with its ecology and social organization. Compared to Drosophila, genes in early developmental pathways differ in Apis, whereas similarities exist for functions that differ markedly, such as sex determination, brain function and behaviour. Population genetics suggests a novel African origin for the species A.mellifera and insights into whether Africanized bees spread throughout the New World via hybridization or displacement
- Published
- 2006
- Full Text
- View/download PDF
12. Genome sequence of the Brown Norway rat yields insights into mammalian evolution
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Rui Chen, George M. Weinstock, Cynthia Pfannkoch, Chris P. Ponting, Mark S. Guyer, Manuel L. Gonzalez-Garay, James Taylor, Yixin Chen, Eric D. Green, Simon Cawley, Jo Gullings-Handley, Granger G. Sutton, Jose M. Duarte, Stephen M. J. Searle, Laura Elnitski, Aleksandar Milosavljevic, Alicia Hawes, Stephen C. Mockrin, Oliver Delgado, Shannon Dugan-Rocha, Christine Deramo, Dean Pasko, Marina Alexandersson, Eitan E. Winter, Robert W. Blakesley, Donna Karolchik, Huajun Wang, David Shteynberg, Diane M. Dunn, Carlos López-Otín, Abel Ureta-Vidal, Jia Qian Wu, A. Glodek, Shan Yang, Natasja Wye, Sue Daniels, Keita Geer, Arian F.A. Smit, Jozef Lazar, Pallavi Eswara, Carl Fosler, Douglas Smith, Martin Krzywinski, Uma Mudunuri, George Miner, Herbert Schulz, Angie S. Hinrichs, Manimozhiyan Arumugam, Josep F. Abril, Ursula Vitt, Andrei Volkov, Peter J. Tonellato, Von Bing Yap, Bingshan Li, Jyoti Shetty, Ian Bosdet, Evgeny M. Zdobnov, San Diego Glenn Tesler, Chris Fjell, Yi Zhang, Francis S. Collins, Serafim Batzoglou, Robert Baertsch, Laura Clarke, David Neil Cooper, Carrie Mathewson, Diana L. Kolbe, Kate R. Rosenbloom, Valerie Curwen, Bret A. Payseur, Gerard G. Bouffard, Michael R. Brent, Barbara J. Trask, Scott A. Beatson, Sourav Chatterji, Francisco Camara, Detlev Ganten, Andrew R. Jackson, Claire M. Fraser, Klaus Lindpaintner, Yue Liu, Mark Raymond Adams, Robert A. Holt, Erik Gustafson, Hiram Clawson, Michael L. Metzker, John Douglas Mcpherson, Gregory M. Cooper, Martin S. Taylor, Scott Schwartz, Hui Huang, Darryl Gietzen, Patrick Cahill, Geoffrey Okwuonu, Sandra Hines, J. Craig Venter, Jan Monti, David Steffen, Marco A. Marra, Arnold Kana, Richard D. Emes, Asim Sarosh Siddiqui, Erica Sodergren, Mario Caccamo, Jim Wingrove, Richard R. Copley, Leo Goodstadt, Francesca Chiaromonte, Davinder Virk, Kirt Martin, Colin N. Dewey, Xiang Qin, T. Dan Andrews, K. James Durbin, Michael P. McLeod, Susan Bromberg, Pavel A. Pevzner, Petra Brandt, Austin J. Cooney, Don Jennings, Baoli Zhu, Lynn Doucette-Stamm, Heather Trumbower, Eray Tüzün, Kristian Stevens, Norbert Hubner, Young-Ae Lee, Zhiping Gu, Harold Riethman, Xose S. Puente, Cynthia Sitter, Michael Brudno, Gerald Nyakatura, Oliver Hummel, Caleb Webber, Olivier Couronne, Kim Fechtel, W. J. Kent, Zhengdong D. Zhang, Xing Zhi Song, Matt Weirauch, Ewan Birney, Richard A. Gibbs, William C. Nierman, Anne E. Kwitek, Alexander Poliakov, Mary Barnstead, Jeanette Schmidt, Yanru Ren, Howard J. Jacob, Kateryna D. Makova, Edward M. Rubin, Susan Old, Trixie Nguyen, Arend Sidow, Nicolas Bray, Hong Mei Lee, Lisa M. D'Souza, Heinz Himmelbauer, Cara Woodwark, Peter G. Amanatides, Paul Havlak, Janet M. Young, Eduardo Eyras, Thomas Kreitler, Heming Xing, Sofiya Shatsman, Kushal Chakrabarti, Stephen Rice, Cheryl A. Evans, Kim C. Worley, Peter D. Stenson, Rachel Gill, Pieter J. de Jong, Jacqueline E. Schein, Lior Pachter, Steve Ferriera, Santa Cruz David Haussler, Ross C. Hardison, Holly Baden-Tillson, Margaret Adetobi, Krishna M. Roskin, Guillaume Bourque, Eric A. Stone, Emmanuel Mongin, Michele Clamp, Margaret Morgan, Richard Durbin, Cathy Riemer, Anton Nekrutenko, Mikita Suyama, Soo H. Chin, Kenneth J. Kalafus, Anat Caspi, Donna M. Muzny, Inna Dubchak, Shaying Zhao, Sofyia Abramzon, Michael I. Jensen-Seaman, Steven E. Scherer, Lora Lewis, M. Mar Albà, Terrence S. Furey, Peer Bork, Trevor Woodage, David A. Wheeler, Hans Lehrach, Graham R. Scott, Bin Ma, Paula E. Burch, Robert B. Weiss, Kazutoyo Osoegawa, Evan E. Eichler, Amy Egan, Webb Miller, Cheryl L. Kraft, Steven J.M. Jones, Jeffrey A. Bailey, Roderic Guigó, David Torrents, Heike Zimdahl, Adam Felsenfeld, Jane Peterson, Simon N. Twigger, Claudia Goesele, Keith Weinstock, Minmei Hou, and Zdobnov, Evgeny
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Male ,Models, Molecular ,Mammalian Genetics ,RNA, Untranslated ,Retroelements ,Sequence analysis ,Gene prediction ,Centromere ,Genomics ,Biology ,Regulatory Sequences, Nucleic Acid ,Genome ,DNA, Mitochondrial ,Polymorphism, Single Nucleotide ,Rat Genome Database ,Evolution, Molecular ,Mice ,Gene Duplication ,Rats, Inbred BN ,Animals ,Humans ,ddc:576.5 ,Gene ,Whole genome sequencing ,Genetics ,Base Composition ,Multidisciplinary ,Sequence Analysis, DNA ,Telomere ,Chromosomes, Mammalian ,Introns ,Rats ,Evolutionary biology ,Mutagenesis ,DNA Transposable Elements ,CpG Islands ,RNA Splice Sites - Abstract
The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
- Published
- 2003
13. Initial sequencing and comparative analysis of the mouse genome
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Laura Elnitski, David B. Jaffe, Jia Li, Marina Alexandersson, Michael J. Morgan, Shiaw Pyng Yang, Robert Baertsch, Claire M. Wade, John Tromp, Michael C. Zody, Terrence S. Furey, Emma Overton-Larty, Stephen D. Brown, Scott Schwartz, Diane M. Dunn, J. P. Leger, Kris A. Wetterstrand, David Torrents, Ratna Shownkeen, Brian Schultz, Kim C. Worley, Richard D. Emes, John Mayer, Tom Landers, Beverley Meredith, Carol Scott, R. J. Weber, Sean R. Eddy, David Kulp, Jun Kawai, J Bailey, Fan Hsu, Diana L. Kolbe, Kirsten McLay, Marc Botcherby, Richard Mott, Tracie L. Miner, Jill P. Mesirov, Cristyn Kells, Michael A. Quail, Melanie M. Wall, Alistair G. Rust, Josep F. Abril, Ian F Korf, Peter An, Roderic Guigó, Abel Ureta-Vidal, Evan Mauceli, L. Steven Johnson, Arian F.A. Smit, Arkadiusz Kasprzyk, Michael C. Wendl, Deanna M. Church, Francis S. Collins, Wayne N. Frankel, Pallavi Eswara, Bin Ma, Robert H. Waterston, Stylianos E. Antonarakis, Edward M. Rubin, John Douglas Mcpherson, Andrew Sheridan, Megan McCarthy, Ming Li, Colin N. Dewey, Justin Deri, Rosie Levine, Matthew Jones, Sheila Dodge, Richard R. Copley, Leo Goodstadt, Shan Yang, Donna Maglott, Jamey Wierzbowski, Nick Goldman, Evgeny M. Zdobnov, Simon G. Gregory, C M Clee, Steven Leonard, Elaine R. Mardis, Simon C. Potter, Sarah Sims, Richard A. Gibbs, Mark S. Guyer, Francesca Chiaromonte, Susan Lucas, Mark Diekhans, Steve Searle, Rachel Ainscough, Jane Peterson, Emmanouil T. Dermitzakis, Robert Nicol, Lucy Matthews, Guy Slater, Adam Felsenfeld, Karen Foley, Lucinda Fulton, Tim Hubbard, Richard K. Wilson, Deana W. LaHillier, W. Richard McCombie, Johanna Thompson, Robert David, John Attwood, Anthony P. West, Jane Rogers, Evan Keibler, Lisa Cook, Raju Kucherlapati, Steven Seaman, William E. Nash, Ian J. Jackson, Jonathan Singer, Axin Hua, Tina Graves, Ted Sharpe, Dudley Wyman, Bruce W. Birren, Stuart McLaren, David Willey, A Joy, Douglas Smith, Alexandre Reymond, Paul Flicek, Simon Cawley, Richa Agarwala, Diane Gage, Evanne Trevaskis, Ginger A. Fewell, Michael R. Brent, Tracy C. Ponce, W. James Kent, Timothy Holzer, Eduardo Eyras, Michael J. O’Connor, Webb Miller, Donna M. Muzny, Andrew von Niederhausern, Inna Dubchak, Eitan E. Winter, Catherine Ucla, Arne Stabenau, Michael N. Nhan, Piero Carninci, Michele Clamp, Pavel A. Pevzner, James Meldrim, Tim Cutts, R. D. Campbell, Joy Davies, Wratko Hlavina, Elinor K. Karlsson, David Haussler, John Burton, Peer Bork, Nicole Stange-Thomann, Mikita Suyama, Mark J. Daly, Ewan Birney, Edward J. Kulbokas, Craig Pohl, James C. Mullikin, Chad Nusbaum, Genís Parra, Jade P. Vinson, Yoshihide Hayashizaki, Sante Gnerre, Eric Berry, Daniel G. Brown, Asif T. Chinwalla, Emmanuel Mongin, Robert B. Weiss, Raymond Wheeler, Andrew Kirby, Yasushi Okazaki, Lior Pachter, Ross C. Hardison, Brian Spencer, Carol J. Bult, Joanne O. Nelson, Pankaj K. Agarwal, Darren Grafham, Gustavo Glusman, Thomas A. Jones, Glenn Tesler, Simon Whelan, James Cuff, Robert S. Fulton, K F Barlow, Jörg Schultz, Matthias S. Schwartz, Alex Poliakov, Jonathan Butler, Bruce A. Roe, Angela S. Hinrichs, Alan Coulson, Kate Montgomery, Eric D. Green, Stephan Beck, Val Curwen, Krishna M. Roskin, Robert W. Plumb, Chris P. Ponting, Ralph Santos, Victor Sapojnikov, Nicolas Bray, Kymberlie H. Pepin, Charles W. Sugnet, Olivier Couronne, Ivica Letunic, Sophie Williams, Kimberly D. Delehaunty, Kerstin Lindblad-Toh, Zemin Ning, Karen Oliver, Toby Bloom, Michael Kamal, Nicholas J. Dickens, Eric S. Lander, Christine Lloyd, Donna Karolchik, Adrienne Hunt, Antonarakis, Stylianos, Couronne, Olivier, Dermitzakis, Emmanouil, and Zdobnov, Evgeny
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RNA, Untranslated ,Proteome ,Untranslated/genetics ,Genome ,Transgenic ,Repetitive Sequences ,Mice ,Models ,Neoplasms ,Conserved Sequence ,ddc:616 ,Genetics ,Mice, Knockout ,Base Composition ,Multidisciplinary ,Sex Chromosomes ,Pseudogenes/genetics ,Genomics ,Multigene Family/genetics ,Physical Chromosome Mapping ,Neoplasms/genetics ,CpG Islands/genetics ,Proteome/genetics ,Genetic Variation/genetics ,Multigene Family ,Mice/classification/ genetics ,Models, Animal ,Conserved Sequence/genetics ,Sequence Analysis ,Pseudogenes ,Human ,Genome evolution ,Evolution ,Sequence analysis ,Knockout ,Quantitative Trait Loci ,Mice, Transgenic ,Sex Chromosomes/genetics ,Computational biology ,Biology ,Synteny ,Chromosomes ,Evolution, Molecular ,Nucleic Acid/genetics ,Genetic ,Species Specificity ,Mammalian/ genetics ,Animals ,Humans ,Genes/genetics ,Selection, Genetic ,Selection ,Repetitive Sequences, Nucleic Acid ,Comparative genomics ,Animal ,Genome, Human ,Molecular ,Genetic Variation ,DNA ,Sequence Analysis, DNA ,Chromosomes, Mammalian ,Gene Expression Regulation ,Genes ,Mutagenesis ,RNA ,Human genome ,CpG Islands ,Quantitative Trait Loci/genetics ,Reference genome - Abstract
The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.
- Published
- 2002
14. Correction: Initial sequencing and analysis of the human genome
- Author
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Paul Predki, John Sulston, William Morris, Sarah Wenning, Jun Gu, Danielle Thierry-Mieg, Roger A. Schultz, Michael J. Morgan, Michael Doyle, Joseph Szustakowki, Lorenzo Cerutti, A. Coulson, Alex Bateman, Patrick Wincker, Michael C. Zody, Mark T. Ross, Paul G. Richardson, Keri Devon, Yasushi Totoki, Karsten Hokamp, George M. Weinstock, John Howland, Arek Kaspryzk, James G. R. Gilbert, Cher Miranda, Aristides Patrinos, William Saurin, A. Pia Abola, Kazuhiko Kawasaki, John Bouck, Marvin Frazier, Wonhee Jang, Jan Fang Cheng, Stephanie L. Chissoe, Matthew C. Jones, Glen A. Evans, Huanming Yang, Daniel G. Brown, Richard Durbin, Jennifer Baldwin, Tracie L. Miner, Asif T. Chinwalla, Arian F.A. Smit, C M Clee, Elaine R. Mardis, Henning Hermjakob, Nicole Stange-Thomann, Maynard V. Olson, Jian Wang, Cyrus L. Harmon, Shiaw Pyng Yang, André Rosenthal, Catherine Robert, Masahira Hattori, Jane Peterson, Ratna Shownkeen, Maria Athanasiou, Christopher B. Burge, Erica Sodergren, Carrie Sougnez, Lynn Doucette-Stamm, Hidemi Watanabe, Ronald W. Davis, Tarjei S. Mikkelsen, Mark Rosetti, Christopher J. Elkin, Todd M. Lowe, LaDeana W. Hillier, Jane Grimwood, Kazutoyo Osoegawa, Richard R. Copley, Simon Kasif, Joseph J. Catanese, Keith Weinstock, Lee Rowen, Roel Funke, Paul Kitts, Lukas Wagner, Guy Slater, Anne S. Olsen, Edward Uberbacher, Lucinda Fulton, Andrew Dunham, Andrew Heaford, David Kulp, Elbert Branscomb, William Fitzhugh, Eugene V. Koonin, Leroy Hood, Anup Madan, Jean Thierry-Mieg, Richard Reinhardt, Kim C. Worley, Richard M. Myers, Dudley Wyman, Jean Weissenbach, David R. Bentley, Panos Deloukas, Philippe Brottier, H. Blöcker, Stephan Beck, Marc Rubenfield, Terrence S. Furey, Ken Dewar, Michael L. Metzker, Rajinder Kaul, Guyang Huang, Hsiu Chuan Chen, Ewan Birney, Warren Gish, John Douglas Mcpherson, Asao Fujiyama, Aoife McLysaght, Shinsei Minoshima, Sandra W. Clifton, Lisa Kann, R Ainscough, K. Hornischer, Simon G. Gregory, Lauren Linton, Kim D. Delehaunty, James C. Mullikin, Neilay Dedhia, Matthias Platzer, Gerald Nyakatura, John V. Moran, Andrew J. Mungall, Chiharu Kawagoe, François Artiguenave, Deanna M. Church, Elia Stupka, Jun Yu, Peer Bork, Evan E. Eichler, L. Aravind, James H. Gorrell, Bruce A. Roe, Raymond Wheeler, Norman A. Doggett, Douglas R. Smith, Yu Juin Chen, David Haussler, Todd D. Taylor, Stefan Taudien, Susan Lucas, Rebecca Deadman, Hans Lehrach, Hiroaki Shizuya, Doron Lancet, Greg Schuler, Nigel P. Carter, John Burton, Huaqin Pan, Eric S. Lander, Andreas Rump, Nikola Stojanovic, Victor J. Pollara, Alan Williams, Melissa De La Bastide, W. James Kent, Mark S. Guyer, Nicola Mulder, Sarah Milne, Bruce W. Birren, John W. Wallis, Joann Dubois, Tom Slezak, Lisa Cook, Raju Kucherlapati, Andrew Delehaunty, Lucy Matthews, Ian Dunham, L. Steven Johnson, Robert H. Waterston, Andrew Sheridan, Jörg Schultz, Nancy A. Federspiel, Jason B. Kramer, Tim Hubbard, Ru Fang Yeh, Steven E. Scherer, Francis S. Collins, David L. Nelson, Sean Humphray, Tobias Doerks, Chad Nusbaum, Darren Grafham, Mei Lee Hong, Michael Proctor, Christopher K. Raymond, Diane Gage, Kris A. Wetterstrand, Feng Chen, Simon Mercer, Thomas A. Jones, Trevor Hawkins, Aravind Subramanian, Jeffrey A. Bailey, Amanda McMurray, Serafim Batzoglou, Jeremy Schmutz, Jill P. Mesirov, Shizen Qin, Rosie Levine, Adam Felsenfeld, Thomas Brüls, Kevin McKernan, Michele E. Clamp, Christine Lloyd, Susan L. Naylor, Gabriele Nordsiek, Jessica A. Lehoczky, Adrienne Hunt, Marco A. Marra, David R. Cox, Mark Dickson, Michael C. Wendl, Yuri I. Wolf, Jane Rogers, Ian F Korf, Eric Pelletier, Takehiko Itoh, Juliane Ramser, Robert S. Fulton, Sarah Sims, Richard A. Gibbs, Lisa French, Katrina Harris, Richa Agarwala, Christina Raymond, James Meldrim, Sangdun Choi, Richard K. Wilson, Patrick Minx, Douglas L. Johnson, Yoshiyuki Sakaki, Scot Kennedy, Pieter J. de Jong, Yoshihide Hayashizaki, W. Richard McCombie, Sean R. Eddy, Donna M. Muzny, Jerome Naylor, Paul A. McEwan, Atsushi Toyoda, Tetsushi Yada, Nobuyoshi Shimizu, Robert W. Plumb, Catherine M. Rives, Chris P. Ponting, Ralph Santos, Kenneth H. Wolfe, Kymberlie H. Pepin, Roland Heilig, and James E. Galagan
- Subjects
Multidisciplinary ,Correction ,Human genome ,Computational biology ,Biology - Published
- 2001
- Full Text
- View/download PDF
15. Mouse beta 2-microglobulin cDNA clones: a screening procedure for cDNA clones corresponding to rare mRNAs
- Author
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Jonathan G. Seidman, Ettore Appella, Adam Felsenfeld, Umberto Ferrini, Lata Ramanathan, Baruch Velan, and Jane R. Parnes
- Subjects
Beta-Globulins ,DNA, Recombinant ,Biology ,Beta globulins ,law.invention ,Mice ,law ,Complementary DNA ,Animals ,Amino Acid Sequence ,RNA, Messenger ,Cloning, Molecular ,Peptide sequence ,Gene ,Messenger RNA ,Multidisciplinary ,Base Sequence ,cDNA library ,Nucleic acid sequence ,Molecular biology ,Genes ,Liver ,Recombinant DNA ,beta 2-Microglobulin ,Plasmids ,Research Article - Abstract
We have isolated three cDNA clones for beta 2-microglobulin, the small subunit of the major histocompatibility antigens. beta 2-Microglobulin makes up less than 0.1% of mouse liver protein, and its mRNA is approximately 0.03% of liver poly(A)+ mRNA. The cDNA clones were identified by screening 1400 cDNA clones made from 9--10S mouse liver poly(A)+ mRNA. The procedure for screening the cDNA clones involved binding pooled plasmid DNA to nitrocellulose filters and testing the ability of each filter to select beta 2-microglobulin mRNA. The filter-selected mRNAs were assayed for their ability to direct the synthesis of beta 2-microglobulin in translation reactions in vitro. The isolated clones were shown by nucleotide sequence analysis to encode beta 2-microglobulin. The positive-selection--hybridization assay has been modified to facilitate the screening of large numbers of cDNA clones, and the modified assay should allow the isolation of cDNAs corresponding to any mRNA whose in vitro translation products can be immunoprecipitated. These modifications are of particular value in the isolation of cDNA clones corresponding to rare species of mRNA.
- Published
- 1981
- Full Text
- View/download PDF
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