Mapping DNA structural variation in dogs.

作者: W.-K. Chen , J. D. Swartz , L. J. Rush , C. E. Alvarez

DOI: 10.1101/GR.083741.108

关键词: GeneStructural variationGenetic variationBiologyGenetic diversityGeneticsGenomeGene mappingLinkage disequilibriumBreed

摘要: DNA structural variation (SV) comprises a major portion of genetic diversity, but its biological impact is unclear. We propose that the history and extraordinary phenotypic dogs make them an ideal mammal in which to study effects SV on biology disease. The hundreds existing dog breeds were created by selection extreme morphological behavioral traits. And along with those traits, each breed carries increased risk for different diseases. used array CGH create first map copy number (CNV) or dogs. extent this variation, some gene classes affected, are similar mice humans. Most canine CNVs affect genes, including disease candidate thus likely be functional. identified many may class specific. Cluster analysis CNV regions showed tend group according classes. Our combined findings suggest (1) linkage disequilibrium flanking sequence, (2) associated breed-specific discuss how catalog will accelerate identification basis traits diseases, beginning use whole genome association candidate-CNV/gene approaches.

参考文章(63)
Jesse F Abelson, Kenneth Y Kwan, Brian J O'Roak, Danielle Y Baek, Althea A Stillman, Thomas M Morgan, Carol A Mathews, David L Pauls, Mladen-Roko Rašin, Murat Gunel, Nicole R Davis, A Gulhan Ercan-Sencicek, Danielle H Guez, John A Spertus, James F Leckman, Leon S Dure IV, Roger Kurlan, Harvey S Singer, Donald L Gilbert, Anita Farhi, Angeliki Louvi, Richard P Lifton, Nenad Sestan, Matthew W State, Sequence Variants in SLITRK1 Are Associated with Tourette's Syndrome Science. ,vol. 310, pp. 317- 320 ,(2005) , 10.1126/SCIENCE.1116502
Kerstin Lindblad-Toh, Claire M Wade, Tarjei S Mikkelsen, Elinor K Karlsson, David B Jaffe, Michael Kamal, Michele Clamp, Jean L Chang, Edward J Kulbokas III, Michael C Zody, Evan Mauceli, Xiaohui Xie, Matthew Breen, Robert K Wayne, Elaine A Ostrander, Chris P Ponting, Francis Galibert, Douglas R Smith, Pieter J DeJong, Ewen Kirkness, Pablo Alvarez, Tara Biagi, William Brockman, Jonathan Butler, Chee-Wye Chin, April Cook, James Cuff, Mark J Daly, David DeCaprio, Sante Gnerre, Manfred Grabherr, Manolis Kellis, Michael Kleber, Carolyne Bardeleben, Leo Goodstadt, Andreas Heger, Christophe Hitte, Lisa Kim, Klaus-Peter Koepfli, Heidi G Parker, John P Pollinger, Stephen MJ Searle, Nathan B Sutter, Rachael Thomas, Caleb Webber, Eric S Lander, None, Genome sequence, comparative analysis and haplotype structure of the domestic dog Nature. ,vol. 438, pp. 803- 819 ,(2005) , 10.1038/NATURE04338
Manuela Fanciulli, Penny J Norsworthy, Enrico Petretto, Rong Dong, Lorraine Harper, Lavanya Kamesh, Joanne M Heward, Stephen C L Gough, Adam de Smith, Alexandra I F Blakemore, Philippe Froguel, Catherine J Owen, Simon H S Pearce, Luis Teixeira, Loic Guillevin, Deborah S Cunninghame Graham, Charles D Pusey, H Terence Cook, Timothy J Vyse, Timothy J Aitman, FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity Nature Genetics. ,vol. 39, pp. 721- 723 ,(2007) , 10.1038/NG2046
Klaus Fellermann, Daniel E. Stange, Elke Schaeffeler, Hartmut Schmalzl, Jan Wehkamp, Charles L. Bevins, Walter Reinisch, Alexander Teml, Matthias Schwab, Peter Lichter, Bernhard Radlwimmer, Eduard F. Stange, A chromosome 8 gene-cluster polymorphism with low human beta-defensin 2 gene copy number predisposes to Crohn disease of the colon. American Journal of Human Genetics. ,vol. 79, pp. 439- 448 ,(2006) , 10.1086/505915
A John Iafrate, Lars Feuk, Miguel N Rivera, Marc L Listewnik, Patricia K Donahoe, Ying Qi, Stephen W Scherer, Charles Lee, Detection of large-scale variation in the human genome. Nature Genetics. ,vol. 36, pp. 949- 951 ,(2004) , 10.1038/NG1416
Julie A. Kerns, Edward J. Cargill, Leigh Anne Clark, Sophie I. Candille, Tom G. Berryere, Michael Olivier, George Lust, Rory J. Todhunter, Sheila M. Schmutz, Keith E. Murphy, Gregory S. Barsh, Linkage and Segregation Analysis of Black and Brindle Coat Color in Domestic Dogs Genetics. ,vol. 176, pp. 1679- 1689 ,(2007) , 10.1534/GENETICS.107.074237
A. B. Olshen, E. S. Venkatraman, R. Lucito, M. Wigler, Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics. ,vol. 5, pp. 557- 572 ,(2004) , 10.1093/BIOSTATISTICS/KXH008
S. I. Candille, C. B. Kaelin, B. M. Cattanach, B. Yu, D. A. Thompson, M. A. Nix, J. A. Kerns, S. M. Schmutz, G. L. Millhauser, G. S. Barsh, A β-Defensin Mutation Causes Black Coat Color in Domestic Dogs Science. ,vol. 318, pp. 1418- 1423 ,(2007) , 10.1126/SCIENCE.1147880
J. O. Korbel, A. E. Urban, J. P. Affourtit, B. Godwin, F. Grubert, J. F. Simons, P. M. Kim, D. Palejev, N. J. Carriero, L. Du, B. E. Taillon, Z. Chen, A. Tanzer, A. C. E. Saunders, J. Chi, F. Yang, N. P. Carter, M. E. Hurles, S. M. Weissman, T. T. Harkins, M. B. Gerstein, M. Egholm, M. Snyder, Paired-end mapping reveals extensive structural variation in the human genome. Science. ,vol. 318, pp. 420- 426 ,(2007) , 10.1126/SCIENCE.1149504