Exome Sequencing: Capture and Sequencing of All Human Coding Regions for Disease Gene Discovery

  • Rinki Ratna Priya
  • Harsha Karur Rajasimha
  • Matthew J. Brooks
  • Anand SwaroopEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 884)


In humans, protein-coding exons constitute 1.5–1.7% of the human genome. Targeted sequencing of all coding exons is termed as exome sequencing. This method enriches for coding sequences at a genome-wide scale from 3 μg of DNA in a hybridization capture. Exome analysis provides an excellent opportunity for high-throughput identification of disease-causing variations without the prior knowledge of linkage or association. A comprehensive landscape of coding variants could also offer valuable mechanistic insights into phenotypic heterogeneity and genetic epistasis.

Key words

Targeted sequencing Next-generation sequencing Massively parallel sequencing Genetic variation Mutation Inherited retinal disease Neurodegeneration 



The authors are supported by Intramural Research Program of the National Eye Institute, National Institutes of Health, Bethesda, MD, USA.


  1. 1.
    Stenson PD et al (2009) The human gene mutation database: 2008 update. Genome Med 1:13PubMedCrossRefGoogle Scholar
  2. 2.
    Ng SB et al (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461:272–276PubMedCrossRefGoogle Scholar
  3. 3.
    Ku CS, Naidoo N, Pawitan Y (2010) Revisiting Mendelian disorders through exome sequencing. Hum Genet 129:351–370CrossRefGoogle Scholar
  4. 4.
    O’Roak BJ et al (2011) Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat Genet 43:585–589PubMedCrossRefGoogle Scholar
  5. 5.
    Züchner S et al (2011) Whole-exome sequencing links a variant in DHDDS to retinitis pigmentosa. Am J Hum Genet 88:201–206PubMedCrossRefGoogle Scholar
  6. 6.
    Bainbridge MN et al (2010) Whole exome capture in solution with 3 Gbp of data. Genome Biol 11:R62PubMedCrossRefGoogle Scholar
  7. 7.
    Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760PubMedCrossRefGoogle Scholar
  8. 8.
    Langmead B et al (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25PubMedCrossRefGoogle Scholar
  9. 9.
    Cox AJ (2007) ELAND: efficient large-scale alignment of nucleotide databases. Illumina, San DiegoGoogle Scholar
  10. 10.
    Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842PubMedCrossRefGoogle Scholar
  11. 11.
    Li H et al (2009) The sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25:2078–2079PubMedCrossRefGoogle Scholar
  12. 12.
    Li Y et al (2011) Low-coverage sequencing: implications for design of complex trait association studies. Genome Res 21:940–951PubMedCrossRefGoogle Scholar
  13. 13.
    McKenna A et al (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303PubMedCrossRefGoogle Scholar
  14. 14.
    DePristo M et al (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Na Genet 43:491–498CrossRefGoogle Scholar
  15. 15.
    Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851–1858PubMedCrossRefGoogle Scholar
  16. 16.
    Wang K, Li M, Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from next-generation sequencing data. Nucleic Acids Res 38:e164PubMedCrossRefGoogle Scholar
  17. 17.
    Robinson JT et al (2011) Integrative genomics viewer. Nat Biotechnol 29:24–26PubMedCrossRefGoogle Scholar
  18. 18.
    Fujita PA et al (2011) The UCSC genome browser database: update 2011. Nucleic Acids Res 39:D876–D882PubMedCrossRefGoogle Scholar
  19. 19.
    Bentley DR et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Rinki Ratna Priya
    • 1
  • Harsha Karur Rajasimha
    • 1
  • Matthew J. Brooks
    • 1
  • Anand Swaroop
    • 1
    Email author
  1. 1.Neurobiology Neurodegeneration and Repair LaboratoryNational Eye Institute, National Institutes of HealthBethesdaUSA

Personalised recommendations