Genome Biology | Volume 12 Issue 9

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	Volume 12 Issue 9 Exome sequencing special issue 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.
	Comment
	Editorial The exome factor Hannah Stower Genome Biology 2011, 12:407 (14 September 2011) Abstract \| Full text \| PDF \| Editor’s summary Special Issues Editor, Hannah Stower, introduces Genome Biology's issue on exome sequencing
	Editorial Next-generation human genetics Jay Shendure Genome Biology 2011, 12:408 (14 September 2011) Abstract \| Full text \| PDF \| Editor’s summary Exome and genome sequencing are reshaping the landscape of human genetics; Jay Shendure discusses the lessons learnt and opportunities opened
	Comment The one new journal we might actually need Gregory A Petsko Genome Biology 2011, 12:129 (29 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The one thing that I actually do want for Christmas: another scientific journal
	Review
	Review 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 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
	Review Unlocking Mendelian disease using exome sequencing Christian Gilissen, Alexander Hoischen, Han G Brunner, Joris A Veltman Genome Biology 2011, 12:228 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 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
	Opinion 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 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
	Opinion Exome sequencing: the expert view Leslie G Biesecker, Kevin V Shianna, Jim C Mullikin Genome Biology 2011, 12:128 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 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
	Research
	Research The functional spectrum of low-frequency coding variation Gabor T Marth, Fuli Yu, Amit R Indap, Kiran Garimella, Simon Gravel, Wen 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, Bob Fulton, Chris Hartl, Dan Koboldt, Donna Muzny, Richard Smith, Carrie Sougnez, Chip Stewart, Alistair Ward, Jin Yu, Yali Xue, David Altshuler, Carlos D Bustamante, Andrew G Clark, Mark Daly, Mark DePristo, Paul Flicek, Stacey Gabriel, Elaine Mardis, Aarno Palotie, Richard Gibbs, the 1000 Genomes Project et al. Genome Biology 2011, 12:R84 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The 1000 Genomes Project presents exome sequence data for 1000 genes from 700 individuals, better defining low frequency variants
	Research Expanding whole exome resequencing into non-human primates Eric J Vallender Genome Biology 2011, 12:R87 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Human DNA capture tools are used to capture and sequence non-human primate DNA
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Capture tools for 3.5 Mb exon regions of allotetraploid wheat are developed and applied to identify coding differences in wild and cultivated wheat
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Targeted capture and sequencing of genomic DNA from subjects with inherited hearing loss offers an effective screen for mutations
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Exome sequencing was used to identify a potentially causative mutation in the Dearish mouse, a model for otitis media
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recessive missense mutation in SHROOM3, which is associated with heterotaxy is identified using exome sequencing
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Exome sequencing in a single recessive case of progressive external ophthalmoplegia identifies a novel missense variant in RRM2B as a potential causative mutation
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Roche NimbleGen and Agilent solution-based exome capture kits are compared. NimbleGen kits give more accurate alignments to target regions
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparison of three human exome-capture platforms shows that NimbleGen's SeqCap EZ gives the best efficacy of exome capture and SNP detection
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An E2F1 somatic mutation is discovered in a rare form of cancer by exome sequencing
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The coverage of two solution exome capture kits is compared
	Method 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for performing linkage analysis from exome sequencing variant data is presented
	Method 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary In solution capture reagents are developed for the mouse exome and demonstrated in multiple inbred strains and novel mutant strains
	Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two methods are presented, SRFIM and SERVIC4E, for detecting rare variants in pooled exome samples

	Volume 12 Issue 9 Exome sequencing special issue 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.
	Comment
	Editorial The exome factor Hannah Stower Genome Biology 2011, 12:407 (14 September 2011) Abstract \| Full text \| PDF \| Editor’s summary Special Issues Editor, Hannah Stower, introduces Genome Biology's issue on exome sequencing
	Editorial Next-generation human genetics Jay Shendure Genome Biology 2011, 12:408 (14 September 2011) Abstract \| Full text \| PDF \| Editor’s summary Exome and genome sequencing are reshaping the landscape of human genetics; Jay Shendure discusses the lessons learnt and opportunities opened
	Comment The one new journal we might actually need Gregory A Petsko Genome Biology 2011, 12:129 (29 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The one thing that I actually do want for Christmas: another scientific journal
	Review
	Review 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 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
	Review Unlocking Mendelian disease using exome sequencing Christian Gilissen, Alexander Hoischen, Han G Brunner, Joris A Veltman Genome Biology 2011, 12:228 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 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
	Opinion 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 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
	Opinion Exome sequencing: the expert view Leslie G Biesecker, Kevin V Shianna, Jim C Mullikin Genome Biology 2011, 12:128 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 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
	Research
	Research The functional spectrum of low-frequency coding variation Gabor T Marth, Fuli Yu, Amit R Indap, Kiran Garimella, Simon Gravel, Wen 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, Bob Fulton, Chris Hartl, Dan Koboldt, Donna Muzny, Richard Smith, Carrie Sougnez, Chip Stewart, Alistair Ward, Jin Yu, Yali Xue, David Altshuler, Carlos D Bustamante, Andrew G Clark, Mark Daly, Mark DePristo, Paul Flicek, Stacey Gabriel, Elaine Mardis, Aarno Palotie, Richard Gibbs, the 1000 Genomes Project et al. Genome Biology 2011, 12:R84 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The 1000 Genomes Project presents exome sequence data for 1000 genes from 700 individuals, better defining low frequency variants
	Research Expanding whole exome resequencing into non-human primates Eric J Vallender Genome Biology 2011, 12:R87 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Human DNA capture tools are used to capture and sequence non-human primate DNA
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Capture tools for 3.5 Mb exon regions of allotetraploid wheat are developed and applied to identify coding differences in wild and cultivated wheat
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Targeted capture and sequencing of genomic DNA from subjects with inherited hearing loss offers an effective screen for mutations
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Exome sequencing was used to identify a potentially causative mutation in the Dearish mouse, a model for otitis media
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A recessive missense mutation in SHROOM3, which is associated with heterotaxy is identified using exome sequencing
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Exome sequencing in a single recessive case of progressive external ophthalmoplegia identifies a novel missense variant in RRM2B as a potential causative mutation
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Roche NimbleGen and Agilent solution-based exome capture kits are compared. NimbleGen kits give more accurate alignments to target regions
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparison of three human exome-capture platforms shows that NimbleGen's SeqCap EZ gives the best efficacy of exome capture and SNP detection
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An E2F1 somatic mutation is discovered in a rare form of cancer by exome sequencing
	Research 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The coverage of two solution exome capture kits is compared
	Method 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A method for performing linkage analysis from exome sequencing variant data is presented
	Method 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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary In solution capture reagents are developed for the mouse exome and demonstrated in multiple inbred strains and novel mutant strains
	Method 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) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Two methods are presented, SRFIM and SERVIC4E, for detecting rare variants in pooled exome samples

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Volume 12 Issue 9

Exome sequencing special issue

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