Difference between revisions of "Exome Capture"
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Exome capture is a method used to extract and sequence the exome (collection of all exons) in a genome and compare this variation across a sample of individual organisms. This allows studies to quickly focus in on the small percent of the genome that is most likely to contain variation that strongly affects phenotypes of interest. | Exome capture is a method used to extract and sequence the exome (collection of all exons) in a genome and compare this variation across a sample of individual organisms. This allows studies to quickly focus in on the small percent of the genome that is most likely to contain variation that strongly affects phenotypes of interest. | ||
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| + | Only a small fraction of many eukaryote genomes are protein coding exon sequences, e.g., in humans this is approximately 1%--2% of the genome spread over 180,000 exons in approximately 20,000-21,000 genes<ref>Elizabeth Pennisi (2012). "ENCODE Project Writes Eulogy For Junk DNA". Science 337 (6099): 1159–1160. doi:10.1126/science.337.6099.1159</ref>. The average human exon is only 145bp in length and the average gene contains 8.8 exons<ref>Table 21 of International Human Genome Sequencing Consortium (2001). "Initial sequencing and analysis of the human genome". Nature 409 (6822): 860–921. doi:10.1038/35057062</ref>. | ||
Bamshad, M. J., Ng, S. B., Bigham, A. W., Tabor, H. K., Emond, M. J., Nickerson, D. A., & Shendure, J. (2011). Exome sequencing as a tool for Mendelian disease gene discovery. Nature Reviews Genetics, 12(11), 745-755.[http://scholar.google.com/scholar?cluster=43169713721993051] | Bamshad, M. J., Ng, S. B., Bigham, A. W., Tabor, H. K., Emond, M. J., Nickerson, D. A., & Shendure, J. (2011). Exome sequencing as a tool for Mendelian disease gene discovery. Nature Reviews Genetics, 12(11), 745-755.[http://scholar.google.com/scholar?cluster=43169713721993051] | ||
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Teer, J. K., & Mullikin, J. C. (2010). Exome sequencing: the sweet spot before whole genomes. Human molecular genetics, ddq333.[http://scholar.google.com/scholar?cluster=1842772192214990382] | Teer, J. K., & Mullikin, J. C. (2010). Exome sequencing: the sweet spot before whole genomes. Human molecular genetics, ddq333.[http://scholar.google.com/scholar?cluster=1842772192214990382] | ||
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Revision as of 19:56, 15 July 2014
Exome capture is a method used to extract and sequence the exome (collection of all exons) in a genome and compare this variation across a sample of individual organisms. This allows studies to quickly focus in on the small percent of the genome that is most likely to contain variation that strongly affects phenotypes of interest.
Only a small fraction of many eukaryote genomes are protein coding exon sequences, e.g., in humans this is approximately 1%--2% of the genome spread over 180,000 exons in approximately 20,000-21,000 genes[1]. The average human exon is only 145bp in length and the average gene contains 8.8 exons[2].
Bamshad, M. J., Ng, S. B., Bigham, A. W., Tabor, H. K., Emond, M. J., Nickerson, D. A., & Shendure, J. (2011). Exome sequencing as a tool for Mendelian disease gene discovery. Nature Reviews Genetics, 12(11), 745-755.[1]
Bi, K., Vanderpool, D., Singhal, S., Linderoth, T., Moritz, C., & Good, J. M. (2012). Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales. BMC genomics, 13(1), 403.[2]
Choi, M., Scholl, U. I., Ji, W., Liu, T., Tikhonova, I. R., Zumbo, P., ... & Lifton, R. P. (2009). Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proceedings of the National Academy of Sciences, 106(45), 19096-19101.[3]
Ng, S. B., Turner, E. H., Robertson, P. D., Flygare, S. D., Bigham, A. W., Lee, C., ... & Shendure, J. (2009). Targeted capture and massively parallel sequencing of 12 human exomes. Nature, 461(7261), 272-276.[4]
Teer, J. K., & Mullikin, J. C. (2010). Exome sequencing: the sweet spot before whole genomes. Human molecular genetics, ddq333.[5]
References
<reference/>- ↑ Elizabeth Pennisi (2012). "ENCODE Project Writes Eulogy For Junk DNA". Science 337 (6099): 1159–1160. doi:10.1126/science.337.6099.1159
- ↑ Table 21 of International Human Genome Sequencing Consortium (2001). "Initial sequencing and analysis of the human genome". Nature 409 (6822): 860–921. doi:10.1038/35057062
