A Pipeline for Faecal Host DNA Analysis by Absolute Quantification of LINE-1 and Mitochondrial Genomic Elements Using ddPCR.
作者： Kuang He , Hideaki Fujiwara , Cynthia Zajac , Erin Sandford , Pavan Reddy
DOI: 10.1038/S41598-019-41753-6
关键词:
摘要: Stool contains DNA shed from cells of the gastrointestinal (GI) tract and has great potential as a bio-specimen for non-invasive, nucleic acid-based detection GI diseases. Whereas methods studying faecal microbiome are plentiful, there is lack well-characterised procedures stabilisation, isolation, quantitative analysis host DNA. We report an optimised pipeline point-of-collection to droplet digital PCR (ddPCR) absolute quantification host-specific gene targets. evaluated multiple preservation isolation stool identify highest performing methods. To quantify even if present in partially degraded form, we developed sensitive, human-specific short-amplicon ddPCR assays targeting repetitive nuclear genomic elements (LINE-1) mitochondrial genes. validated ability these perform 200 extracts samples that were serially collected three healthy individuals hospitalised patients. These specimens allowed assessment day-to-day variability with widely varying physical characteristics (i.e., Bristol scores). further extended this approach mouse analysis, enable studies animal disease models well.
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W. J. Kent, C. W. Sugnet, T. S. Furey, K. M. Roskin, T. H. Pringle, A. M. Zahler, a. D. Haussler, The Human Genome Browser at UCSC Genome Research. ,vol. 12, pp. 996- 1006 ,(2002) , 10.1101/GR.229102
Barbara A Methé, Karen E Nelson, Mihai Pop, Heather H Creasy, Michelle G Giglio, Curtis Huttenhower, Dirk Gevers, Joseph F Petrosino, Sahar Abubucker, Jonathan H Badger, Asif T Chinwalla, Ashlee M Earl, Michael G Fitzgerald, Robert S Fulton, Kymberlie Hallsworth-Pepin, Elizabeth A Lobos, Ramana Madupu, Vincent Magrini, John C Martin, Makedonka Mitreva, Donna M Muzny, Erica J Sodergren, James Versalovic, Aye M Wollam, Kim C Worley, Jennifer R Wortman, Sarah K Young, Qiandong Zeng, Kjersti M Aagaard, Olukemi O Abolude, Emma Allen-Vercoe, Eric J Alm, Lucia Alvarado, Gary L Andersen, Scott Anderson, Elizabeth Appelbaum, Harindra M Arachchi, Gary Armitage, Cesar A Arze, Tulin Ayvaz, Carl C Baker, Lisa Begg, Tsegahiwot Belachew, Veena Bhonagiri, Monika Bihan, Martin J Blaser, Toby Bloom, Vivien R Bonazzi, Paul Brooks, Gregory A Buck, Christian J Buhay, Dana A Busam, Joseph L Campbell, Shane R Canon, Brandi L Cantarel, Patrick S Chain, I Chen, A Min, Lei Chen, Shaila Chhibba, Ken Chu, Dawn M Ciulla, Jose C Clemente, Sandra W Clifton, Sean Conlan, Jonathan Crabtree, Mary A Cutting, Noam J Davidovics, Catherine C Davis, Todd Z Desantis, Carolyn Deal, Kimberley D Delehaunty, Floyd E Dewhirst, Elena Deych, Yan Ding, David J Dooling, Shannon P Dugan, W Michael Dunne, A Scott Durkin, Robert C Edgar, Rachel L Erlich, Candace N Farmer, Ruth M Farrell, Karoline Faust, Michael Feldgarden, Victor M Felix, Sheila Fisher, Anthony A Fodor, Larry Forney, Leslie Foster, Valentina di Francesco, Jonathan Friedman, Dennis C Friedrich, Catrina C Fronick, Lucinda L Fulton, Hongyu Gao, Nathalia Garcia, Georgia Giannoukos, Christina Giblin, Maria Y Giovanni, Jonathan M Goldberg, Johannes Goll, Antonio Gonzalez, Allison Griggs, Sharvari Gujja, Brian J Haas, Holli A Hamilton, Emily L Harris, Theresa A Hepburn, Brandi Herter, Diane E Hoffmann, Michael E Holder, Clinton Howarth, Katherine H Huang, Susan M Huse, Jacques Izard, Janet K Jansson, Huaiyang Jiang, Catherine Jordan, Vandita Joshi, James A Katancik, Wendy A Keitel, Scott T Kelley, Cristyn Kells, Susan Kinder-Haake, Nicholas B King, Rob Knight, Dan Knights, Heidi H Kong, Omry Koren, Sergey Koren, Karthik C Kota, Christie L Kovar, Nikos C Kyrpides, Patricio S La Rosa, Sandra L Lee, Katherine P Lemon, Niall Lennon, Cecil M Lewis, Lora Lewis, Ruth E Ley, Kelvin Li, Konstantinos Liolios, Bo Liu, Yue Liu, Chien-Chi Lo, Catherine A Lozupone, R Dwayne Lunsford, Tessa Madden, Anup A Mahurkar, A framework for human microbiome research Nature. ,vol. 486, pp. 215- 221 ,(2012) , 10.1038/NATURE11209
Shan Chen, Zongchang Li, Ying He, Fengyu Zhang, Hong Li, Yanhui Liao, Zhen Wei, Guobin Wan, Xi Xiang, Maolin Hu, Kun Xia, Xiaogang Chen, Jinsong Tang, Elevated mitochondrial DNA copy number in peripheral blood cells is associated with childhood autism BMC Psychiatry. ,vol. 15, pp. 50- 50 ,(2015) , 10.1186/S12888-015-0432-Y
Maria Eugenia Delgado, Thomas Grabinger, Thomas Brunner, Cell death at the intestinal epithelial front line. FEBS Journal. ,vol. 283, pp. 2701- 2719 ,(2016) , 10.1111/FEBS.13575
Robert W. Taylor, Doug M. Turnbull, MITOCHONDRIAL DNA MUTATIONS IN HUMAN DISEASE Nature Reviews Genetics. ,vol. 6, pp. 389- 402 ,(2005) , 10.1038/NRG1606
Anthony P. Shuber, Stanley N. Lapidus, Gail E. Radcliffe, Methods for stool sample preparation ,(1998)
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
Marcelino T Suzuki, Oded Beja, Lance T Taylor, Edward F DeLong, None, Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton Environmental Microbiology. ,vol. 3, pp. 323- 331 ,(2001) , 10.1046/J.1462-2920.2001.00198.X
Xiwei He, Huimei Chen, Wei Shi, Yibin Cui, Xu-Xiang Zhang, Persistence of mitochondrial DNA markers as fecal indicators in water environments. Science of The Total Environment. ,vol. 533, pp. 383- 390 ,(2015) , 10.1016/J.SCITOTENV.2015.06.119
Liu ShiRong Liu ShiRong, AP da Cunha, RM Rezende, R Cialic, Wei ZhiYun Wei ZhiYun, L Bry, LE Comstock, R Gandhi, HL Weiner, The Host Shapes the Gut Microbiota via Fecal MicroRNA Cell Host & Microbe. ,vol. 19, pp. 32- 43 ,(2016) , 10.1016/J.CHOM.2015.12.005