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Exome sequencing

Guest Editor: Jay Shendure

In this issue of Genome Biology we present a special collection of articles focusing on exome capture sequencing, a technique that has recently expanded in popularity owing to the sequencing focus of targeted regions only. The research, review and opinion articles provide an overview of developments in the exome sequencing field and future directions from leaders in the field.

Support for the production of this special issue has been provided by Roche NimbleGen.

  1. Human exome resequencing using commercial target capture kits has been and is being used for sequencing large numbers of individuals to search for variants associated with various human diseases. We rigorously...

    Authors: Jennifer S Parla, Ivan Iossifov, Ian Grabill, Mona S Spector, Melissa Kramer and W Richard McCombie

    Citation: Genome Biology 2011 12:R97

    Content type: Research

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  2. Well differentiated papillary mesothelioma of the peritoneum (WDPMP) is a rare variant of epithelial mesothelioma of low malignancy potential, usually found in women with no history of asbestos exposure. In th...

    Authors: Willie Yu, Waraporn Chan-On, Melissa Teo, Choon Kiat Ong, Ioana Cutcutache, George E Allen, Bernice Wong, Swe Swe Myint, Kiat Hon Lim, P Mathijs Voorhoeve, Steve Rozen, Khee Chee Soo, Patrick Tan and Bin Tean Teh

    Citation: Genome Biology 2011 12:R96

    Content type: Research

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  3. Exome sequencing, which allows the global analysis of protein coding sequences in the human genome, has become an effective and affordable approach to detecting causative genetic mutations in diseases. Current...

    Authors: 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 and Xiuqing Zhang

    Citation: Genome Biology 2011 12:R95

    Content type: Research

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  4. Techniques enabling targeted re-sequencing of the protein coding sequences of the human genome on next generation sequencing instruments are of great interest. We conducted a systematic comparison of the solut...

    Authors: 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 and Janna Saarela

    Citation: Genome Biology 2011 12:R94

    Content type: Research

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  5. Sequencing targeted DNA regions in large samples is necessary to discover the full spectrum of rare variants. We report an effective Illumina sequencing strategy utilizing pooled samples with novel quality (Sr...

    Authors: Tejasvi S Niranjan, Abby Adamczyk, Héctor Corrada Bravo, Margaret A Taub, Sarah J Wheelan, Rafael Irizarry and Tao Wang

    Citation: Genome Biology 2011 12:R93

    Content type: Method

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  6. Whole-exome sequencing using next-generation technologies has been previously demonstrated to be able to detect rare disease-causing variants. Progressive external ophthalmoplegia (PEO) is an inherited mitocho...

    Authors: Atsushi Takata, Maiko Kato, Masayuki Nakamura, Takeo Yoshikawa, Shigenobu Kanba, Akira Sano and Tadafumi Kato

    Citation: Genome Biology 2011 12:R92

    Content type: Research

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  7. Heterotaxy-spectrum cardiovascular disorders are challenging for traditional genetic analyses because of clinical and genetic heterogeneity, variable expressivity, and non-penetrance. In this study, high-resol...

    Authors: Muhammad Tariq, John W Belmont, Seema Lalani, Teresa Smolarek and Stephanie M Ware

    Citation: Genome Biology 2011 12:R91

    Content type: Research

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  8. Inflammation of the middle ear (otitis media) is very common and can lead to serious complications if not resolved. Genetic studies suggest an inherited component, but few of the genes that contribute to this ...

    Authors: Jennifer M Hilton, Morag A Lewis, M'hamed Grati, Neil Ingham, Selina Pearson, Roman A Laskowski, David J Adams and Karen P Steel

    Citation: Genome Biology 2011 12:R90

    Content type: Research

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  9. The field of human genetics is being reshaped by exome and genome sequencing. Several lessons are evident from observing the rapid development of this area over the past 2 years, and these may be instructive w...

    Authors: Jay Shendure

    Citation: Genome Biology 2011 12:408

    Content type: Editorial

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  10. Exome sequencing is rapidly expanding both as a technique and in its biological applications.

    Authors: Hannah Stower

    Citation: Genome Biology 2011 12:407

    Content type: Editorial

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  11. Exome sequencing is revolutionizing Mendelian disease gene identification. This results in improved clinical diagnosis, more accurate genotype-phenotype correlations and new insights into the role of rare geno...

    Authors: Christian Gilissen, Alexander Hoischen, Han G Brunner and Joris A Veltman

    Citation: Genome Biology 2011 12:228

    Content type: Review

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  12. To complement our special issue on exome sequencing, Genome Biology asked several leaders in the field for their views on this new approach. Leslie G Biesecker (LGB), Jim C Mullikin (JM) and Kevin V Shianna (KVS)...

    Authors: Leslie G Biesecker, Kevin V Shianna and Jim C Mullikin

    Citation: Genome Biology 2011 12:128

    Content type: Opinion

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  13. Identification of genes responsible for medically important traits is a major challenge in human genetics. Due to the genetic heterogeneity of hearing loss, targeted DNA capture and massively parallel sequenci...

    Authors: Zippora Brownstein, Lilach M Friedman, Hashem Shahin, Varda Oron-Karni, Nitzan Kol, Amal Abu Rayyan, Thomas Parzefall, Dorit Lev, Stavit Shalev, Moshe Frydman, Bella Davidov, Mordechai Shohat, Michele Rahile, Sari Lieberman, Ephrat Levy-Lahad, Ming K Lee…

    Citation: Genome Biology 2011 12:R89

    Content type: Research

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  14. We report the development and optimization of reagents for in-solution, hybridization-based capture of the mouse exome. By validating this approach in a multiple inbred strains and in novel mutant strains, we ...

    Authors: 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…

    Citation: Genome Biology 2011 12:R86

    Content type: Method

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  15. Many exome sequencing studies of Mendelian disorders fail to optimally exploit family information. Classical genetic linkage analysis is an effective method for eliminating a large fraction of the candidate ca...

    Authors: 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 and Melanie Bahlo

    Citation: Genome Biology 2011 12:R85

    Content type: Method

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  16. Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants alteri...

    Authors: Gabor T Marth, Fuli Yu, Amit R Indap, Kiran Garimella, Simon Gravel, Wen Fung Leong, Chris Tyler-Smith, Matthew Bainbridge, Tom Blackwell, Xiangqun Zheng-Bradley, Yuan Chen, Danny Challis, Laura Clarke, Edward V Ball, Kristian Cibulskis, David N Cooper…

    Citation: Genome Biology 2011 12:R84

    Content type: Research

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