Analysis of Human Genetic Variations Using DNA Sequencing

作者: Gregory A. Hawkins

DOI: 10.1016/B978-0-12-803077-6.00005-9

关键词: GenomicsBiologyMassive parallel sequencingShotgun sequencingDNA sequencingGeneticsExome sequencingWhole genome sequencingCancer genome sequencingDeep sequencing

摘要: Abstract Genetic mutations, also termed genetic variations or polymorphisms, alter protein production and are the primary drivers of diseases. DNA sequencing is gold standard for identifying variations, has more recently become a tool that allows rapid analysis whole genomes targeted small portion human genome contains genes. This chapter will focus on use two methods to identify in genome: Sanger next-generation sequencing.

参考文章(10)
Sing Yu Moorcraft, David Gonzalez, Brian A. Walker, Understanding next generation sequencing in oncology: A guide for oncologists Critical Reviews in Oncology Hematology. ,vol. 96, pp. 463- 474 ,(2015) , 10.1016/J.CRITREVONC.2015.06.007
Kary B. Mullis, Fred A. Faloona, Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods in Enzymology. ,vol. 155, pp. 335- 350 ,(1987) , 10.1016/0076-6879(87)55023-6
Gregory A. Hawkins, David J. Friedman, Lingyi Lu, David R. McWilliams, Jeff W. Chou, Satria Sajuthi, Jasmin Divers, Rulan S. Parekh, Man Li, Giulio Genovese, Martin R. Pollack, Pamela J. Hicks, Donald W. Bowden, Lijun Ma, Barry I. Freedman, Carl D. Langefeld, Re-Sequencing of the APOL1-APOL4 and MYH9 Gene Regions in African Americans Does Not Identify Additional Risks for CKD Progression. American Journal of Nephrology. ,vol. 42, pp. 99- 106 ,(2015) , 10.1159/000439448
Barry I. Freedman, Carl D. Langefeld, JoLyn Turner, Marina Núñez, Kevin P. High, Mitzie Spainhour, Pamela J. Hicks, Donald W. Bowden, Amber M. Reeves-Daniel, Mariana Murea, Michael V. Rocco, Jasmin Divers, Association of APOL1 variants with mild kidney disease in the first-degree relatives of African American patients with non-diabetic end-stage renal disease Kidney International. ,vol. 82, pp. 805- 811 ,(2012) , 10.1038/KI.2012.217
F. Sanger, A.R. Coulson, A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase Journal of Molecular Biology. ,vol. 94, pp. 441- 448 ,(1975) , 10.1016/0022-2836(75)90213-2
Stephen B. Liggett, The pharmacogenetics of β2-adrenergic receptors: Relevance to asthma ☆ ☆☆ ★ The Journal of Allergy and Clinical Immunology. ,vol. 105, ,(2000) , 10.1016/S0091-6749(00)90048-4
Victor E Ortega, Gregory A Hawkins, Wendy C Moore, Annette T Hastie, Elizabeth J Ampleford, William W Busse, Mario Castro, Domingo Chardon, Serpil C Erzurum, Elliot Israel, Federico Montealegre, Sally E Wenzel, Stephen P Peters, Deborah A Meyers, Eugene R Bleecker, Effect of rare variants in ADRB2 on risk of severe exacerbations and symptom control during longacting β agonist treatment in a multiethnic asthma population: a genetic study The Lancet Respiratory Medicine. ,vol. 2, pp. 204- 213 ,(2014) , 10.1016/S2213-2600(13)70289-3
J Craig Venter, Mark D Adams, Eugene W Myers, Peter W Li, Richard J Mural, Granger G Sutton, Hamilton O Smith, Mark Yandell, Cheryl A Evans, Robert A Holt, Jeannine D Gocayne, Peter Amanatides, Richard M Ballew, Daniel H Huson, Jennifer Russo Wortman, Qing Zhang, Chinnappa D Kodira, Xiangqun H Zheng, Lin Chen, Marian Skupski, Gangadharan Subramanian, Paul D Thomas, Jinghui Zhang, George L Gabor Miklos, Catherine Nelson, Samuel Broder, Andrew G Clark, Joe Nadeau, Victor A McKusick, Norton Zinder, Arnold J Levine, Richard J Roberts, Mel Simon, Carolyn Slayman, Michael Hunkapiller, Randall Bolanos, Arthur Delcher, Ian Dew, Daniel Fasulo, Michael Flanigan, Liliana Florea, Aaron Halpern, Sridhar Hannenhalli, Saul Kravitz, Samuel Levy, Clark Mobarry, Knut Reinert, Karin Remington, Jane Abu-Threideh, Ellen Beasley, Kendra Biddick, Vivien Bonazzi, Rhonda Brandon, Michele Cargill, Ishwar Chandramouliswaran, Rosane Charlab, Kabir Chaturvedi, Zuoming Deng, Valentina Di Francesco, Patrick Dunn, Karen Eilbeck, Carlos Evangelista, Andrei E Gabrielian, Weiniu Gan, Wangmao Ge, Fangcheng Gong, Zhiping Gu, Ping Guan, Thomas J Heiman, Maureen E Higgins, Rui-Ru Ji, Zhaoxi Ke, Karen A Ketchum, Zhongwu Lai, Yiding Lei, Zhenya Li, Jiayin Li, Yong Liang, Xiaoying Lin, Fu Lu, Gennady V Merkulov, Natalia Milshina, Helen M Moore, Ashwinikumar K Naik, Vaibhav A Narayan, Beena Neelam, Deborah Nusskern, Douglas B Rusch, Steven Salzberg, Wei Shao, Bixiong Shue, Jingtao Sun, Zhen Yuan Wang, Aihui Wang, Xin Wang, Jian Wang, Ming-Hui Wei, Ron Wides, Chunlin Xiao, Chunhua Yan, Alison Yao, Jane Ye, Ming Zhan, Weiqing Zhang, Hongyu Zhang, Qi Zhao, Liansheng Zheng, Fei Zhong, Wenyan Zhong, Shiaoping C Zhu, Shaying Zhao, Dennis Gilbert, Suzanna Baumhueter, Gene Spier, Christine Carter, Anibal Cravchik, Trevor Woodage, Feroze Ali, Huijin An, Aderonke Awe, Danita Baldwin, Holly Baden, Mary Barnstead, Ian Barrow, Karen Beeson, Dana Busam, Amy Carver, Angela Center, Ming Lai Cheng, Liz Curry, Steve Danaher, Lionel Davenport, Raymond Desilets, Susanne Dietz, Kristina Dodson, Lisa Doup, Steven Ferriera, Neha Garg, Andres Gluecksmann, Brit Hart, Jason Haynes, Charles Haynes, Cheryl Heiner, Suzanne Hladun, Damon Hostin, Jarrett Houck, Timothy Howland, Chinyere Ibegwam, Jeffery Johnson, Francis Kalush, The Sequence of the Human Genome Science. ,vol. 291, pp. 1304- 1351 ,(2001) , 10.1126/SCIENCE.1058040
Gregory A. Hawkins, Kelan Tantisira, Deborah A. Meyers, Elizabeth J. Ampleford, Wendy C. Moore, Barbara Klanderman, Stephen B. Liggett, Stephen P. Peters, Scott T. Weiss, Eugene R. Bleecker, Sequence, Haplotype, and Association Analysis of ADRβ2 in a Multiethnic Asthma Case-Control Study American Journal of Respiratory and Critical Care Medicine. ,vol. 174, pp. 1101- 1109 ,(2006) , 10.1164/RCCM.200509-1405OC
US DOE Joint Genome Institute: Hawkins Trevor 4 Branscomb Elbert 4 Predki Paul 4 Richardson Paul 4 Wenning Sarah 4 Slezak Tom 4 Doggett Norman 4 Cheng Jan-Fang 4 Olsen Anne 4 Lucas Susan 4 Elkin Christopher 4 Uberbacher Edward 4 Frazier Marvin 4, RIKEN Genomic Sciences Center: Sakaki Yoshiyuki 9 Fujiyama Asao 9 Hattori Masahira 9 Yada Tetsushi 9 Toyoda Atsushi 9 Itoh Takehiko 9 Kawagoe Chiharu 9 Watanabe Hidemi 9 Totoki Yasushi 9 Taylor Todd 9, Genoscope and CNRS UMR-8030: Weissenbach Jean 10 Heilig Roland 10 Saurin William 10 Artiguenave Francois 10 Brottier Philippe 10 Bruls Thomas 10 Pelletier Eric 10 Robert Catherine 10 Wincker Patrick 10, Department of Genome Analysis, Institute of Molecular Biotechnology: Rosenthal André 12 Platzer Matthias 12 Nyakatura Gerald 12 Taudien Stefan 12 Rump Andreas 12, GTC Sequencing Center: Smith Douglas R. 11 Doucette-Stamm Lynn 11 Rubenfield Marc 11 Weinstock Keith 11 Lee Hong Mei 11 Dubois JoAnn 11, Beijing Genomics Institute/Human Genome Center: Yang Huanming 13 Yu Jun 13 Wang Jian 13 Huang Guyang 14 Gu Jun 15, Multimegabase Sequencing Center, The Institute for Systems Biology: Hood Leroy 16 Rowen Lee 16 Madan Anup 16 Qin Shizen 16, Stanford Genome Technology Center: Davis Ronald W. 17 Federspiel Nancy A. 17 Abola A. Pia 17 Proctor Michael J. 17, University of Oklahoma's Advanced Center for Genome Technology: Roe Bruce A. 22 Chen Feng 22 Pan Huaqin 22, Max Planck Institute for Molecular Genetics: Ramser Juliane 23 Lehrach Hans 23 Reinhardt Richard 23, Cold Spring Harbor Laboratory, Lita Annenberg Hazen Genome Center: McCombie W. Richard 24 de la Bastide Melissa 24 Dedhia Neilay 24, GBF—German Research Centre for Biotechnology: Blöcker Helmut 25 Hornischer Klaus 25 Nordsiek Gabriele 25, Scientific management: National Human Genome Research Institute, US National Institutes of Health: Collins Francis fc23a@ nih. gov 46 b Guyer Mark S. 46 Peterson Jane 46 Felsenfeld Adam 46 Wetterstrand Kris A. 46, Stanford Human Genome Center: Myers Richard M. 18 Schmutz Jeremy 18 Dickson Mark 18 Grimwood Jane 18 Cox David R. 18, University of Washington Genome Center: Olson Maynard V. 19 Kaul Rajinder 19 Raymond Christopher 19, Department of Molecular Biology, Keio University School of Medicine: Shimizu Nobuyoshi 20 Kawasaki Kazuhiko 20 Minoshima Shinsei 20, University of Texas Southwestern Medical Center at Dallas: Evans Glen A. 21 49 50 49 Athanasiou Maria 21 Schultz Roger 21, Office of Science, US Department of Energy: Patrinos Aristides 47, Wellcome Trust: Morgan Michael J. 48, None, Initial sequencing and analysis of the human genome. Nature. ,vol. 409, pp. 860- 921 ,(2001) , 10.1038/35057062