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Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer
Wigard P Kloosterman, Marlous Hoogstraat, Oscar Paling, Masoumeh Tavakoli-Yaraki, Ivo Renkens, Joost S Vermaat, Markus J van Roosmalen, Stef van Lieshout, Isaac J Nijman, Wijnand Roessingh, Ruben van 't Slot, José van de Belt, Victor Guryev, Marco Koudijs, Emile Voest, Edwin Cuppen Genome Biology 2011, 12:R103 (19 October 2011)
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Editor’s summary
Chromothripsis is found to be a common mechanism driving structural rearrangement in primary colorectal cancer and metastases
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SpeCond: a method to detect condition-specific gene expression
Florence MG Cavalli, Richard Bourgon, Wolfgang Huber, Juan M Vaquerizas, Nicholas M Luscombe Genome Biology 2011, 12:R101 (18 October 2011)
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Editor’s summary
A method to detect condition-specific gene expression from microarray data
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Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control
Robert S Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B Hostetler, Daniel Brami, Vinita S Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H Badger, Ujjwal Kumar, Milton Saier, Yufeng Wang, Hong Cai, Jianying Gu, Michael W Mather, Akhil B Vaidya, David E Wilkes, Vidyalakshmi Rajagopalan, David J Asai, Chad G Pearson, Robert C Findly, Harry W Dickerson, Martin Wu, Cindy Martens, Yves Van de Peer, David S Roos, Donna M Cassidy-Hanley, Theodore G Clark Genome Biology 2011, 12:R100 (17 October 2011)
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Editor’s summary
The genome of the pathogenic ciliate Ichthyophthirius multifiliis, which causes white spot disease in fish, is presented
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Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium
Lara Rajeev, Eric G Luning, Paramvir S Dehal, Morgan N Price, Adam P Arkin, Aindrila Mukhopadhyay Genome Biology 2011, 12:R99 (12 October 2011)
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All response regulators in the genome of Desulfovibrius vulgaris are identified, as are all their target genes
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The transcriptional landscape of Chlamydia pneumoniae
Marco Albrecht, Cynthia M Sharma, Marcus T Dittrich, Tobias Müller, Richard Reinhardt, Jörg Vogel, Thomas Rudel Genome Biology 2011, 12:R98 (11 October 2011)
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Editor’s summary
The life cycle of the obligate intracellular human pathogen C. pneumoniae has a dynamic transcriptional landscape
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A comparative analysis of exome capture
Jennifer S Parla, Ivan Iossifov, Ian Grabill, Mona S Spector, Melissa Kramer, W Richard McCombie Genome Biology 2011, 12:R97 (29 September 2011)
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The coverage of two solution exome capture kits is compared
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The one new journal we might actually need
Gregory A Petsko Genome Biology 2011, 12:129 (29 September 2011)
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Editor’s summary
The one thing that I actually do want for Christmas: another scientific journal
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First somatic mutation of E2F1 in a critical DNA binding residue discovered in well-differentiated papillary mesothelioma of the peritoneum
Willie Yu, Waraporn Chan-On, Melissa Teo, Choon Ong, Ioana Cutcutache, George E Allen, Bernice Wong, Swe Myint, Kiat Lim, P Mathijs Voorhoeve, Steve Rozen, Khee Soo, Patrick Tan, Bin Teh Genome Biology 2011, 12:R96 (28 September 2011)
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An E2F1 somatic mutation is discovered in a rare form of cancer by exome sequencing
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Comprehensive comparison of three commercial human whole-exome capture platforms
Asan, Yu Xu, Hui Jiang, Chris Tyler-Smith, Yali Xue, Tao Jiang, Jiawei Wang, Mingzhi Wu, Xiao Liu, Geng Tian, Jun Wang, Jian Wang, Huangming Yang, Xiuqing Zhang Genome Biology 2011, 12:R95 (28 September 2011)
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A comparison of three human exome-capture platforms shows that NimbleGen's SeqCap EZ gives the best efficacy of exome capture and SNP detection
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Comparison of solution-based exome capture methods for next generation sequencing
Anna-Maija Sulonen, Pekka Ellonen, Henrikki Almusa, Maija Lepistö, Samuli Eldfors, Sari Hannula, Timo Miettinen, Henna Tyynismaa, Perttu Salo, Caroline Heckman, Heikki Joensuu, Taneli Raivio, Anu Suomalainen, Janna Saarela Genome Biology 2011, 12:R94 (28 September 2011)
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Roche NimbleGen and Agilent solution-based exome capture kits are compared. NimbleGen kits give more accurate alignments to target regions
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Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis
Tejasvi S Niranjan, Abby Adamczyk, Héctor Bravo, Margaret A Taub, Sarah J Wheelan, Rafael Irizarry, Tao Wang Genome Biology 2011, 12:R93 (28 September 2011)
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Two methods are presented, SRFIM and SERVIC4E, for detecting rare variants in pooled exome samples
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Exome sequencing identifies a novel missense variant in RRM2B associated with autosomal recessive progressive external ophthalmoplegia
Atsushi Takata, Maiko Kato, Masayuki Nakamura, Takeo Yoshikawa, Shigenobu Kanba, Akira Sano, Tadafumi Kato Genome Biology 2011, 12:R92 (28 September 2011)
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Exome sequencing in a single recessive case of progressive external ophthalmoplegia identifies a novel missense variant in RRM2B as a potential causative mutation
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SHROOM3 is a novel candidate for heterotaxy identified by whole exome sequencing
Muhammad Tariq, John W Belmont, Seema Lalani, Teresa Smolarek, Stephanie M Ware Genome Biology 2011, 12:R91 (21 September 2011)
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A recessive missense mutation in SHROOM3, which is associated with heterotaxy is identified using exome sequencing
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Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice
Jennifer M Hilton, Morag A Lewis, M'hamed Grati, Neil Ingham, Selina Pearson, Roman A Laskowski, David J Adams, Karen P Steel Genome Biology 2011, 12:R90 (21 September 2011)
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Exome sequencing was used to identify a potentially causative mutation in the Dearish mouse, a model for otitis media
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Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in middle eastern families
Zippora Brownstein, Lilach M Friedman, Hashem Shahin, Varda Oron-Karni, Nitzan Kol, Amal Rayyan, Thomas Parzefall, Dorit Lev, Stavit Shalev, Moshe Frydman, Bella Davidov, Mordechai Shohat, Michele Rahile, Sari Lieberman, Ephrat Levy-Lahad, Ming K Lee, Noam Shomron, Mary-Claire King, Tom Walsh, Moien Kanaan, Karen B Avraham Genome Biology 2011, 12:R89 (14 September 2011)
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Targeted capture and sequencing of genomic DNA from subjects with inherited hearing loss offers an effective screen for mutations
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Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome
Cyrille Saintenac, Dayou Jiang, Eduard D Akhunov Genome Biology 2011, 12:R88 (14 September 2011)
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Capture tools for 3.5 Mb exon regions of allotetraploid wheat are developed and applied to identify coding differences in wild and cultivated wheat
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Expanding whole exome resequencing into non-human primates
Eric J Vallender Genome Biology 2011, 12:R87 (14 September 2011)
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Human DNA capture tools are used to capture and sequence non-human primate DNA
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Mutation discovery in mice by whole exome sequencing
Heather Fairfield, Griffith J Gilbert, Mary Barter, Rebecca R Corrigan, Michelle Curtain, Yueming Ding, Mark D'Ascenzo, Daniel J Gerhardt, Chao He, Wenhui Huang, Todd Richmond, Lucy Rowe, Frank J Probst, David E Bergstrom, Stephen A Murray, Carol Bult, Joel Richardson, Benjamin T Kile, Ivo Gut, Jorg Hager, Snaevar Sigurdsson, Evan Mauceli, Federica Di Palma, Kerstin Lindblad-Toh, Michael L Cunningham, Timothy C Cox, Monica J Justice, Mona S Spector, Scott W Lowe, Thomas Albert, Leah Donahue, Jeffrey Jeddeloh, Jay Shendure, Laura G Reinholdt et al.
Genome Biology 2011, 12:R86 (14 September 2011)
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| F1000 Biology
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In solution capture reagents are developed for the mouse exome and demonstrated in multiple inbred strains and novel mutant strains
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Reducing the exome search space for Mendelian diseases using genetic linkage analysis of exome genotypes
Katherine R Smith, Catherine J Bromhead, Michael S Hildebrand, A Eliot Shearer, Paul J Lockhart, Hossein Najmabadi, Richard J Leventer, George McGillivray, David J Amor, Richard J Smith, Melanie Bahlo Genome Biology 2011, 12:R85 (14 September 2011)
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A method for performing linkage analysis from exome sequencing variant data is presented
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Next-generation human genetics
Jay Shendure Genome Biology 2011, 12:408 (14 September 2011)
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Exome and genome sequencing are reshaping the landscape of human genetics; Jay Shendure discusses the lessons learnt and opportunities opened
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The exome factor
Hannah Stower Genome Biology 2011, 12:407 (14 September 2011)
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Special Issues Editor, Hannah Stower, introduces Genome Biology's issue on exome sequencing
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Unlocking Mendelian disease using exome sequencing
Christian Gilissen, Alexander Hoischen, Han G Brunner, Joris A Veltman Genome Biology 2011, 12:228 (14 September 2011)
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Editor’s summary
In the past 2 years, exome sequencing has provided significant new insights into the causes of both Mendelian and sporadic genetic diseases
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Computational and statistical approaches to analyzing variants identified by exome sequencing
Nathan O Stitziel, Adam Kiezun, Shamil Sunyaev Genome Biology 2011, 12:227 (14 September 2011)
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Editor’s summary
Many computational and statistical methods are now available to narrow down causal variants in exome sequencing data, for both Mendelian and complex diseases
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Exome sequencing: the expert view
Leslie G Biesecker, Kevin V Shianna, Jim C Mullikin Genome Biology 2011, 12:128 (14 September 2011)
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Editor’s summary
Three leaders in the field of exome sequencing discuss why the approach is so popular and how it is contributing to genomics
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The promise and limitations of population exomics for human evolution studies
Jacob A Tennessen, Timothy D O'Connor, Michael J Bamshad, Joshua M Akey Genome Biology 2011, 12:127 (14 September 2011)
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Editor’s summary
Exome sequencing is poised to yield substantial insights into human genetic variation and evolutionary history, but there are significant challenges to overcome before this becomes a reality
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