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1. Mutation discovery in the mouse using genetically guided array capture and resequencing

Author

James R. Knight, Todd Richmond, Jeffrey A. Jeddeloh, Laura G. Reinholdt, Jacob O. Kitzman, Jason P. Affourtit, Mark D'Ascenzo, Leah Rae Donahue, Roger Winer, Miroslav Kukricar, Christina M. Middle, Anne Czechanski, Carl Meacham, and Thomas J. Albert

Subjects
Male, Nonsynonymous substitution, Positional cloning, DNA Mutational Analysis, Molecular Sequence Data, Locus (genetics), Biology, Genome, Article, Mice, Gene mapping, Genotype, Genetics, Animals, Amino Acid Sequence, Alleles, Oligonucleotide Array Sequence Analysis, Base Sequence, Forward genetics, Human genetics, Mice, Inbred C57BL, Mice, Inbred DBA, Mutation, Female, Sequence Alignment
Abstract

Forward genetics (phenotype-driven approaches) remain the primary source for allelic variants in the mouse. Unfortunately, the gap between observable phenotype and causative genotype limits the widespread use of spontaneous and induced mouse mutants. As alternatives to traditional positional cloning and mutation detection approaches, sequence capture and next-generation sequencing technologies can be used to rapidly sequence subsets of the genome. Application of these technologies to mutation detection efforts in the mouse has the potential to significantly reduce the time and resources required for mutation identification by abrogating the need for high-resolution genetic mapping, long-range PCR, and sequencing of individual PCR amplimers. As proof of principle, we used array-based sequence capture and pyrosequencing to sequence an allelic series from the classically defined Kit locus (approximately 200 kb) from each of five noncomplementing Kit mutants (one known allele and four unknown alleles) and have successfully identified and validated a nonsynonymous coding mutation for each allele. These data represent the first documentation and validation that these new technologies can be used to efficiently discover causative mutations. Importantly, these data also provide a specific methodological foundation for the development of large-scale mutation detection efforts in the laboratory mouse.

Published
2009

2. The bonobo genome compared with the chimpanzee and human genomes

Author

Nick Patterson, Mario Ventura, Roger Winer, Brian P. Walenz, Michael Lachmann, Lawrence Mugisha, Claudia Rita Catacchio, Asger Hobolth, Kasper Munch, Gerton Lunter, Saneyuki Higashino, Anne Fischer, Chris P. Ponting, Thomas Mailund, Can Alkan, Jörg Junhold, Jason R. Miller, Svante Pääbo, James C. Mullikin, Kay Prüfer, Emre Karakoc, Mikkel H. Schierup, Keiko Akagi, Tomas Marques-Bonet, Granger G. Sutton, Claudine André, Susan E. Ptak, Rebeca Atencia, Stephen Meader, Jeffrey M. Good, Michael Siebauer, Ines Hellmann, James R. Knight, Aida M. Andrés, Sergey Koren, David E. Symer, Chinnappa D. Kodira, Evan E. Eichler, Saba Sajjadian, Julien Y. Dutheil, and Janet Kelso

Subjects
transposon, life history trait, primate, Genome, 0302 clinical medicine, Gene Duplication, Phylogeny, genome analysis, Genetics, 0303 health sciences, Multidisciplinary, biology, Bonobo, allele, article, chromosome analysis, Pan paniscus, Phenotype, priority journal, Genotype, Pan troglodytes, phenotype, species comparison, Molecular Sequence Data, gene sequence, Article, Chimpanzee genome project, Evolution, Molecular, 03 medical and health sciences, sexual behavior, Species Specificity, Molecular evolution, chimpanzee, geographic distribution, human genome, Animals, Humans, controlled study, human, Gene, genome, 030304 developmental biology, Whole genome sequencing, nonhuman, molecular evolution, Genome, Human, ancestry, evolutionary biology, Genetic Variation, biology.organism_classification, Pan, Evolutionary biology, DNA Transposable Elements, Human genome, 030217 neurology & neurosurgery
Abstract

Prüfer, K. et al.-- This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence, Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other. © 2012 Macmillan Publishers Limited. All rights reserved.

Published
2012

3. Mapping copy number variation by population-scale genome sequencing

Author

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

Subjects
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.

Published
2011

4. The genome sequence of Atlantic cod reveals a unique immune system

Author

Mari Espelund, Christopher Previti, Roger Winer, Sigbjørn Lien, Martin Malmstrøm, Ola F. Wetten, Truls Moum, Bronwen Aken, Richard Reinhardt, Trine B. Rounge, Steinar Johansen, Tor Gjøen, Anders Lanzén, Karin Lagesen, Jonas Paulsen, Jim Thorsen, Kirubakaran G. Tina, Chirag Nepal, Kjetill S. Jakobsen, Øivind Andersen, Jan-Hinnerk Vogel, Alexander J. Nederbragt, Morten Skage, James D.R. Knight, Lei Du, Inge Jonassen, Nils Christian Stenseth, Sissel Jentoft, Monica Hongrø Solbakken, Paul R. Berg, Ave Tooming-Klunderud, Ketil Malde, Unni Grimholt, Stig W. Omholt, Tone F. Gregers, Frank Nilsen, Bastiaan Star, Heiner Kuhl, Bård Ove Karlsen, Steve Searle, Rolf B. Edvardsen, and Animesh Sharma

Subjects
0106 biological sciences, Male, Molecular biology, 01 natural sciences, Genome, Matematikk og naturvitenskap: 400::Basale biofag: 470::Genetikk og genomikk: 474 [VDP], Major Histocompatibility Complex, Hemoglobins, VDP::Matematikk og naturvitenskap: 400::Basale biofag: 470::Genetikk og genomikk: 474, Gadus, atlantic cod, genetics, VDP::Mathematics and natural science: 400::Basic biosciences: 470::General immunology: 478, Genetics, 0303 health sciences, Multidisciplinary, biology, atlantisk torsk, Toll-Like Receptors, genetikk, Genomics, Acquired immune system, Gadus morhua, Evolution, Immunology, chemical and pharmacologic phenomena, VDP::Mathematics and natural science: 400::Basic biosciences: 470::Genetics and genomics: 474, Major histocompatibility complex, 010603 evolutionary biology, Synteny, Evolution, Molecular, 03 medical and health sciences, Immune system, MHC class I, Animals, 14. Life underwater, Mathematics and natural scienses: 400::Basic biosciences: 470::Genetics and genomics: 474 [VDP], 030304 developmental biology, Innate immune system, Polymorphism, Genetic, VDP::Mathematics and natural science: 400::Basic biosciences: 470::Molecular biology: 473, Immunity, biology.organism_classification, VDP::Mathematics and natural scienses: 400::Basic biosciences: 470::Genetics and genomics: 474, Genetics and genomics, Evolutionary biology, Immune System, biology.protein, Atlantic cod
Abstract

The genome of the Atlantic cod has been sequenced, and genomic analysis reveals an immune system that differs significantly from that in other vertebrates. The major histocompatibility complex (MHC) II has been lost, as have some other genes that are essential for MHC II function. But there is an expansion in the number of MHC I genes and a unique composition for its toll-like receptor family. These compensatory changes in both adaptive and innate immunity mean that cod is no more susceptible to disease than most other vertebrates. These findings challenge current models of vertebrate immune evolution, and may facilitate the development of targeted vaccines for disease management in aquaculture. Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture1,2. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC) II is a conserved feature of the adaptive immune system of jawed vertebrates3,4, but we show that Atlantic cod has lost the genes for MHC II, CD4 and invariant chain (Ii) that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions5. We find a highly expanded number of MHC I genes and a unique composition of its Toll-like receptor (TLR) families. This indicates how the Atlantic cod immune system has evolved compensatory mechanisms in both adaptive and innate immunity in the absence of MHC II. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.

Published
2011

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