Exome sequencing analysis: a guide to disease variant detection.
作者： Ofer Isakov , Marie Perrone , Noam Shomron
DOI: 10.1007/978-1-62703-514-9_8
关键词: Genetic variation 、 Exome sequencing 、 Sequence analysis 、 Gene Annotation 、 Allele frequency 、 Genome 、 Gene 、 Exome 、 Computational biology 、 Biology
摘要: Whole exome sequencing presents a powerful tool to study rare genetic disorders. The most challenging part of using for the purpose disease-causing variant detection is analyzing, interpreting, and filtering large number detected variants. In this chapter we provide comprehensive description various steps required such an analysis. We address strategies in selecting samples sequence, technical considerations involved sequencing. then discuss how identify variants, methods first annotating variants characteristics as allele frequency, location genome, predicted severity, classifying prioritizing based on those annotations. Finally, review possible gene annotations that may help establish relationship between genes carrying high-priority phenotype question, order likely causative mutations.
springer.com
sci-hub.se 参考文章(67)
Hsiang-Fu Kung, Ming-Liang He, Yaqing He, Ying Chen, Jun Wang, Quan Chen, Huanming Yang, Jing Zhao, Multiple gene dysfunctions lead to high cancer-susceptibility: evidences from a whole-exome sequencing study. American Journal of Cancer Research. ,vol. 1, pp. 562- 573 ,(2011)
Christian Gilissen, Alexander Hoischen, Han G Brunner, Joris A Veltman, Disease gene identification strategies for exome sequencing European Journal of Human Genetics. ,vol. 20, pp. 490- 497 ,(2012) , 10.1038/EJHG.2011.258
Holly K. Tabor, Neil J. Risch, Richard M. Myers, Candidate-gene approaches for studying complex genetic traits: practical considerations. Nature Reviews Genetics. ,vol. 3, pp. 391- 397 ,(2002) , 10.1038/NRG796
Sarah B. Ng, Emily H. Turner, Peggy D. Robertson, Steven D. Flygare, Abigail W. Bigham, Choli Lee, Tristan Shaffer, Michelle Wong, Arindam Bhattacharjee, Evan E. Eichler, Michael Bamshad, Deborah A. Nickerson, Jay Shendure, Targeted capture and massively parallel sequencing of 12 human exomes Nature. ,vol. 461, pp. 272- 276 ,(2009) , 10.1038/NATURE08250
R. Drmanac, A. B. Sparks, M. J. Callow, A. L. Halpern, N. L. Burns, B. G. Kermani, P. Carnevali, I. Nazarenko, G. B. Nilsen, G. Yeung, F. Dahl, A. Fernandez, B. Staker, K. P. Pant, J. Baccash, A. P. Borcherding, A. Brownley, R. Cedeno, L. Chen, D. Chernikoff, A. Cheung, R. Chirita, B. Curson, J. C. Ebert, C. R. Hacker, R. Hartlage, B. Hauser, S. Huang, Y. Jiang, V. Karpinchyk, M. Koenig, C. Kong, T. Landers, C. Le, J. Liu, C. E. McBride, M. Morenzoni, R. E. Morey, K. Mutch, H. Perazich, K. Perry, B. A. Peters, J. Peterson, C. L. Pethiyagoda, K. Pothuraju, C. Richter, A. M. Rosenbaum, S. Roy, J. Shafto, U. Sharanhovich, K. W. Shannon, C. G. Sheppy, M. Sun, J. V. Thakuria, A. Tran, D. Vu, A. W. Zaranek, X. Wu, S. Drmanac, A. R. Oliphant, W. C. Banyai, B. Martin, D. G. Ballinger, G. M. Church, C. A. Reid, Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays Science. ,vol. 327, pp. 78- 81 ,(2010) , 10.1126/SCIENCE.1181498
P. P. Gardner, J. Daub, J. G. Tate, E. P. Nawrocki, D. L. Kolbe, S. Lindgreen, A. C. Wilkinson, R. D. Finn, S. Griffiths-Jones, S. R. Eddy, A. Bateman, Rfam: updates to the RNA families database Nucleic Acids Research. ,vol. 37, pp. 136- 140 ,(2009) , 10.1093/NAR/GKN766
K. D. Pruitt, T. Tatusova, W. Klimke, D. R. Maglott, NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Research. ,vol. 37, pp. 32- 36 ,(2009) , 10.1093/NAR/GKN721
K. Wang, M. Li, H. Hakonarson, ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data Nucleic Acids Research. ,vol. 38, ,(2010) , 10.1093/NAR/GKQ603
Zippora Brownstein, Yoni Bhonker, Karen B Avraham, High-throughput sequencing to decipher the genetic heterogeneity of deafness. Genome Biology. ,vol. 13, pp. 245- 245 ,(2012) , 10.1186/GB-2012-13-5-245
S. A. Forbes, N. Bindal, S. Bamford, C. Cole, C. Y. Kok, D. Beare, M. Jia, R. Shepherd, K. Leung, A. Menzies, J. W. Teague, P. J. Campbell, M. R. Stratton, P. A. Futreal, COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Research. ,vol. 39, pp. 945- 950 ,(2011) , 10.1093/NAR/GKQ929