A population genetic approach to mapping neurological disorder genes using deep resequencing.

Autor: Rachel A Myers, Ferran Casals, Julie Gauthier, Fadi F Hamdan, Jon Keebler, Adam R Boyko, Carlos D Bustamante, Amelie M Piton, Dan Spiegelman, Edouard Henrion, Martine Zilversmit, Julie Hussin, Jacklyn Quinlan, Yan Yang, Ronald G Lafrenière, Alexander R Griffing, Eric A Stone, Guy A Rouleau, Philip Awadalla

Publikováno v: PLoS Genetics, Vol 7, Iss 2, p e1001318 (2011)

Deep resequencing of functional regions in human genomes is key to identifying potentially causal rare variants for complex disorders. Here, we present the results from a large-sample resequencing (n = 285 patients) study of candidate genes coupled w

Externí odkaz: https://doaj.org/article/7822770fc1324cd2be8ef97eeaaad035

Mapping copy number variation by population-scale genome sequencing

Autor: 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

Publikováno v: Nature, vol 470, iss 7332
Nature
Nature, 470(7332), 59-65
PMC

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 unk

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::269d6a83a9f2331dd1a0b27b4a0987d5
https://hdl.handle.net/1887/108472

A murine specific expansion of the Rhox cluster involved in embryonic stem cell biology is under natural selection

Autor: Philip Awadalla, Melany Jackson, Franck Prugnolle, Philippe Gautier, Jon Keebler, Derek S. Gilchrist, Alistair J. Watt, Johanna Driehaus, Gerard J. Graham, Lesley M. Forrester

Publikováno v: Jackson, M, Watt, A J, Gautier, P, Gilchrist, D, Driehaus, J, Graham, G J, Keebler, J, Prugnolle, F, Awadalla, P & Forrester, L M 2006, ' A murine specific expansion of the Rhox cluster involved in embryonic stem cell biology is under natural selection ', BMC Genomics, vol. 7, 212 . https://doi.org/10.1186/1471-2164-7-212
BMC Genomics
BMC Genomics, Vol 7, Iss 1, p 212 (2006)

Background The rodent specific reproductive homeobox (Rhox) gene cluster on the X chromosome has been reported to contain twelve homeobox-containing genes, Rhox1-12. Results We have identified a 40 kb genomic region within the Rhox cluster that is du

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::87eeca4e5b4e2bf0e7196d05722a4c33
https://www.pure.ed.ac.uk/ws/files/12435794/A_murine_specific_expansion_of_the_Rhox_cluster_involved_in_embryonic_stem_cell_biology_is_under_natural_selection..pdf

Selection shapes malaria genomes and drives divergence between pathogens infecting hominids versus rodents

Autor: Philip Awadalla, Franck Prugnolle, Kate M. McGee, Jon Keebler

Publikováno v: BMC Evolutionary Biology, Vol 8, Iss 1, p 223 (2008)
BMC Evolutionary Biology

Background Malaria kills more people worldwide than all inherited human genetic disorders combined. To characterize how the parasites causing this disease adapt to different host environments, we compared the evolutionary genomics of two distinct gro

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::851357ba3fb9d959d0d7e417a25d267c