Genome Biology | Tags | #exomesequencing

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#exomesequencing

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	1.	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
	2.	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
	3.	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
	4.	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
	5.	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
	6.	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
	7.	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
	8.	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
	9.	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
	10.	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
	11.	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
	12.	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
	13.	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
	14.	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
	15.	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
	16.	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
	17.	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
	18.	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
	19.	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
	20.	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, 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