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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. Research

    A comparative analysis of exome capture

    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...

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

    Genome Biology 2011 12:R97

    Published on: 29 September 2011

  2. Research

    Comprehensive comparison of three commercial human whole-exome capture platforms

    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...

    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

    Genome Biology 2011 12:R95

    Published on: 28 September 2011

  3. Method

    Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis

    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...

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

    Genome Biology 2011 12:R93

    Published on: 28 September 2011

  4. Research

    First somatic mutation of E2F1 in a critical DNA binding residue discovered in well-differentiated papillary mesothelioma of the peritoneum

    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...

    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

    Genome Biology 2011 12:R96

    Published on: 28 September 2011

  5. Research

    Comparison of solution-based exome capture methods for next generation sequencing

    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...

    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

    Genome Biology 2011 12:R94

    Published on: 28 September 2011

  6. Research

    Exome sequencing identifies a novel missense variant in RRM2B associated with autosomal recessive progressive external ophthalmoplegia

    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...

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

    Genome Biology 2011 12:R92

    Published on: 28 September 2011

  7. Research

    SHROOM3 is a novel candidate for heterotaxy identified by whole exome sequencing

    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...

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

    Genome Biology 2011 12:R91

    Published on: 21 September 2011

  8. Research

    Exome sequencing identifies a missense mutation in Isl1associated with low penetrance otitis media in dearisch mice

    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 ...

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

    Genome Biology 2011 12:R90

    Published on: 21 September 2011

  9. Research

    Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in middle eastern families

    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...

    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…

    Genome Biology 2011 12:R89

    Published on: 14 September 2011

  10. Research

    Expanding whole exome resequencing into non-human primates

    Complete exome resequencing has the power to greatly expand our understanding of non-human primate genomes. This includes both a better appreciation of the variation that exists in non-human primate model spec...

    Eric J Vallender

    Genome Biology 2011 12:R87

    Published on: 14 September 2011

  11. Method

    Reducing the exome search space for Mendelian diseases using genetic linkage analysis of exome genotypes

    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...

    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

    Genome Biology 2011 12:R85

    Published on: 14 September 2011

  12. Method

    Mutation discovery in mice by whole exome sequencing

    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 ...

    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…

    Genome Biology 2011 12:R86

    Published on: 14 September 2011

  13. Research

    The functional spectrum of low-frequency coding variation

    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...

    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…

    Genome Biology 2011 12:R84

    Published on: 14 September 2011

  14. Review

    Unlocking Mendelian disease using exome sequencing

    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...

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

    Genome Biology 2011 12:228

    Published on: 14 September 2011

  15. Editorial

    Next-generation human genetics

    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...

    Jay Shendure

    Genome Biology 2011 12:408

    Published on: 14 September 2011

  16. Opinion

    Exome sequencing: the expert view

    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)...

    Leslie G Biesecker, Kevin V Shianna and Jim C Mullikin

    Genome Biology 2011 12:128

    Published on: 14 September 2011

  17. Editorial

    The exome factor

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

    Hannah Stower

    Genome Biology 2011 12:407

    Published on: 14 September 2011