Skip to main content

Genome Variation: A Review of Web Resources

  • Protocol
  • First Online:
Genetic Epidemiology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 713))

Abstract

An enormous number of high-quality Web-based resources are now available to facilitate research into genome variation. Although identification of the most appropriate and informative resources can be challenging, a number of key sites provide links to more specialized resources that may be useful to follow up. Given ongoing research, focussing on the sequencing of many different genomes, we can expect sequence databases and their associated polymorphism-based resources to greatly increase in depth and complexity in a relatively short period of time. However, databases and tools developed to date, and described here, provide a sound basis for accommodating this next generation of genomic data. As well as sequence-oriented resources this review presents databases providing genotypic and common disease phenotype data, copy number variation, genetic maps, cytogenetic data, and gives an overview of key software tools, with the emphasis on analysis of the genetic basis of common disease.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC et al (2001) Initial sequencing and analysis of the human genome. Nature 409(6822):860–921.

    Article  PubMed  CAS  Google Scholar 

  2. The International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851–861.

    Article  Google Scholar 

  3. Scheet P, Stephens M (2006) A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78(4):629–644.

    Article  PubMed  CAS  Google Scholar 

  4. Botstein D, Risch N (2003) Discovering genotypes underlying human phenotypes: past successes for Mendelian disease, future approaches for complex disease. Nat Genet 33(Suppl):228–237.

    Article  PubMed  CAS  Google Scholar 

  5. Thomas DJ, Trumbower H, Kern AD, Rhead BL, Kuhn RM et al (2007) Variation resources at UC Santa Cruz. Nucleic Acids Res 35:D716–D720.

    Article  PubMed  CAS  Google Scholar 

  6. The ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816.

    Article  Google Scholar 

  7. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM et al (2005) Fine-scale structural variation of the human genome. Nat Genet 37:727–732.

    Article  PubMed  CAS  Google Scholar 

  8. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N et al (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453:56–64.

    Article  PubMed  CAS  Google Scholar 

  9. Matise TC, Chen F, Chen W, De La Vega F, Hansen M et al (2007) A second-generation combined linkage physical map of the human genome. Genome Res 17:1783–1786.

    Article  PubMed  CAS  Google Scholar 

  10. Dausset J, Cann H, Cohen D, Lathrop M, Lalouel JM et al (1990). Centre d’Etude du polymorphisme humain (CEPH): collaborative genetic mapping of the human genome. Genomics 6(3):575–577.

    Article  PubMed  CAS  Google Scholar 

  11. Tapper W, Gibson J, Morton NE, Collins A (2008) A comparison of methods to detect recombination hotspots. Hum Hered 66(3):157–169.

    Article  PubMed  Google Scholar 

  12. Maniatis N, Collins A, Xu CF, McCarthy LC, Hewett DR et al (2002) The first linkage disequilibrium (LD) maps: delineation of hot and cold blocks by diplotype analysis. Proc Natl Acad Sci USA 99:2228–2233.

    Article  PubMed  CAS  Google Scholar 

  13. Service S, DeYoung J, Karayiogou M, Roos JL, Pretorious H et al (2006). Magnitude and distribution of linkage disequilibrium in ­population isolates and implications for genome-wide association studies. Nat Genet 38(5):556–560.

    Article  PubMed  CAS  Google Scholar 

  14. Collins A, Lau W (2008) CHROMSCAN: genome-wide association using a linkage disequilibrium map. J Hum Genet 53(2):121–126.

    Article  PubMed  CAS  Google Scholar 

  15. Barber JCK (2005). Directly transmitted unbalanced chromosome abnormalities and euchromatic variants. J Med Genet 42(8):609–629.

    Article  PubMed  CAS  Google Scholar 

  16. Burton PR, Clayton DG, Cardon LR, Craddock N, Deloukas P et al (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447:661–678.

    Article  CAS  Google Scholar 

  17. Easton DF, Pooley KA, Dunning AM, Pharoah PDP, Thompson D et al (2007) Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447:1087–1093.

    Article  PubMed  CAS  Google Scholar 

  18. Purcell S, Cherny SS, Sham PC (2003) Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits. Bioinformatics 19(1):149–150.

    Article  PubMed  CAS  Google Scholar 

  19. Skol AD, Scott LJ, Abecasis GR, Boehnke M (2006) Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nat Genet 38:209–213.

    Article  PubMed  CAS  Google Scholar 

  20. Stephens M, Donnelly P (2003) A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73:1162–1169.

    Article  PubMed  CAS  Google Scholar 

  21. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR et al (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81(3):559–575.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Collins, A., Tapper, W.J. (2011). Genome Variation: A Review of Web Resources. In: Teare, M. (eds) Genetic Epidemiology. Methods in Molecular Biology, vol 713. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-416-6_10

Download citation

  • DOI: https://doi.org/10.1007/978-1-60327-416-6_10

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60327-415-9

  • Online ISBN: 978-1-60327-416-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics