Abstract
Here we describe a bioinformatic strategy for extracting and analyzing the list of variants revealed from an exome sequencing project to identify potential disease genes. This in silico method filters out the majority of common SNPs and extracts a list of potential candidate protein-coding and non-coding RNA (ncRNA) genes. The workflow employs Galaxy, a publically available Web-based software, to filter and sort sequence variants identified by capture-based target enrichment and sequencing from exomes including selected ncRNAs.
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References
McKusick, V. A. (2007) Mendelian inheritance in man and its online version, OMIM. Am J Hum Genet 80, 588–604.
Manolio, T. A., and Collins, F. S. (2009) The HapMap and genome-wide association studies in diagnosis and therapy. Annu Rev Med 60, 443–456.
Ashley, E. A., Butte, A. J., Wheeler, M. T., et al. (2010) Clinical assessment incorporating a personal genome. Lancet 375, 1525–1535.
Ng, S. B., Turner, E. H., Robertson, P. D., et al. (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272–276.
Choi, M., Scholl, U. I., Ji, W., et al. (2009) Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci USA 106, 19096–19101.
Hoischen, A., van Bon, B. W., Gilissen, C., et al. (2010) De novo mutations of SETBP1 cause Schinzel–Giedion syndrome. Nat Genet 42, 483–485.
Ng, S. B., Buckingham, K. J., Lee, C., et al. (2010) Exome sequencing identifies the cause of a Mendelian disorder. Nat Genet 42, 30–35.
Shoubridge, C., Tarpey, P. S., Abidi, F., et al. (2010) Mutations in the guanine nucleotide exchange factor gene IQSEC2 cause nonsyndromic intellectual disability. Nat Genet 42, 486–488.
Lupski, J. R., Reid, J. G., Gonzaga-Jauregui, C., et al. (2010) Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N Engl J Med 362, 1181–1191.
Lalonde, E., Albrecht, S., Ha, K. C., et al. (2010) Unexpected allelic heterogeneity and spectrum of mutations in Fowler syndrome revealed by next generation exome sequencing. Hum Mutat 31, 918–923.
Sobreira, N. L. M. (2010) Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene. PLOS Genetics 6, e1000991.
Herman, D. S., Hovingh, G. K., Iartchouk, O., et al. (2009) Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection. Nat Methods 6, 507–510.
Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigo, R., Gingeras, T. R., et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816.
Henikoff, S. (2007) ENCODE and our very busy genome. Nat Genet 39, 817–818.
Taft, R. J., Pang, K. C., Mercer, T. R., et al. (2010) Non-coding RNAs: regulators of disease. J Pathol 220, 126–139.
Agilent (2010) SureSelect Target Enrichment System Protocol. Agilent Technologies, Santa Clara, CA, USA.
Blankenberg, D., Von Kuster, G., Coraor, N., et al. (2010) Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol Chapter 19, Unit 19 10 11–21.
Giardine, B., Riemer, C., Hardison, R. C., et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res 15, 1451–1455.
AppliedBiosystems (2010) Bioscope Software for Scientists Guide. Applied Biosystems, Foster City, CA, USA.
Pelak, K., Shianna, K. V., Ge, D., Maia, J. M., et al. (2010) The characterization of twenty sequenced human genomes. PLoS Genet 6, e1001111.
Mitchell, A. A., Zwick, M. E., Chakravarti, A., and Cutler, D. J. (2004) Discrepancies in dbSNP confirmation rates and allele frequency distributions from varying genotyping error rates and patterns. Bioinformatics 20, 1022–1032.
Musumeci, L., Arthur, J. W., Cheung, F. S., et al. (2010) Single nucleotide differences (SNDs) in the dbSNP database may lead to errors in genotyping and haplotyping studies. Hum Mutat 31, 67–73.
NCBI. (2010) dbSNP summary for build 131 http://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi.
Ng, S. B., Bigham, A. W., Buckingham, K. J., et al. (2010) Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet 42, 790–793.
Wang, K., Li, M., and Hakonarson, H. (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38 , e164.
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Hinchcliffe, M., Webster, P. (2011). In Silico Analysis of the Exome for Gene Discovery. In: Yu, B., Hinchcliffe, M. (eds) In Silico Tools for Gene Discovery. Methods in Molecular Biology, vol 760. Humana Press. https://doi.org/10.1007/978-1-61779-176-5_7
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DOI: https://doi.org/10.1007/978-1-61779-176-5_7
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