Skip to main content
SpringerLink
Log in
Book cover

Scan Statistics pp 195–202Cite as

Scan Statistics in Genome-Wide Scan for Complex Trait Loci

  • Chapter
  • First Online:

Part of the book series: Statistics for Industry and Technology ((SIT))

Abstract

In genome-wide genetic scans for disease susceptibility loci, true peaks have been shown to be wider than false peaks. We describe scan statistics to make use of this extra information, which is not generally taken into account otherwise. Our methods are applied to four disease datasets.

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

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
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

Learn about institutional subscriptions

References

  1. Cox, N. J., Frigge, M., Nicolae, D. L., Concannon, P., Hanis, C. L., Bell, G. I., and Kong, A. (1999). Loci on chromosomes 2 (NIDDM1) and 15 interact to increase susceptibility to diabetes in Mexican Americans, Nature Genetics, 21, 213–215.

    Article  Google Scholar 

  2. Dewan, A., Liu, M., Hartman, S., Zhang, S. S., Liu, D. T., Zhao, C., Tam, P. O., Chan, W. M., Lam, D. S., Snyder, M., Barnstable, C., Pang, C. P., and Hoh, J. (2006). HTRA1 promoter polymorphism in wet age-related macular degeneration, Science, 314, 989–992.

    Article  Google Scholar 

  3. Dewan, A., and Ott, J. (2004). Reanalysis of a genome scan for schizophrenia loci using multigenic methods, Human Heredity, 57, 191–194.

    Article  Google Scholar 

  4. Efron, B., and Tibshirani, R. (1991). Statistical data analysis in the computer age, Science 253, 390–395.

    Google Scholar 

  5. Faraone, S. V., Matise, T., Svrakic, D., Pepple, J., Malaspina, D., Suarez, B., Hampe, C., Zambuto, C. T., Schmitt, K., Meyer, J., Markel, P., Lee, H., Harkavy Friedman, J., Kaufmann, C., Cloninger, C. R., and Tsuang, M. T. (1998). Genome scan of European-American schizophrenia pedigrees: results of the NIMH Genetics Initiative and Millennium Consortium, American Journal of Medical Genetics, 81, 290–295.

    Article  Google Scholar 

  6. Friddle, C., Koskela, R., Ranade, K., Hebert, J., Cargill, M., Clark, C. D., McInnis, M., Simpson, S., McMahon, F., Stine, O. C., Meyers, D., Xu, J., MacKinnon, D., Swift-Scanlan, T., Jamison, K., Folstein, S., Daly, M., Kruglyak, L., Marr, T., DePaulo, J. R., and Botstein, D. (2000). Full-genome scan for linkage in 50 families segregating the bipolar affective disease phenotype, American Journal of Human Genetics, 66, 205–215.

    Article  Google Scholar 

  7. Fung, H. C., Scholz, S., Matarin, M., Simon-Sanchez, J., Hernandez, D., Britton, A., Gibbs, J. R., Langefeld, C., Stiegert, M. L., Schymick, J., Okun, M. S., Mandel, R. J., Fernandez, H. H., Foote, K. D., Rodriguez, R. L., Peckham, E., De Vrieze, F. W., Gwinn-Hardy, K., Hardy, J. A., and Singleton, A. (2006). Genome-wide genotyping in Parkinson’s disease and neurologically normal controls: first stage analysis and public release of data, Lancet Neurology, 5, 911–916.

    Article  Google Scholar 

  8. Glaz, J., and Balakrishnan, N. (1999). Introduction to scan statistics, in Scan Statistics and Applications, Editors: Glaz, J., Balakrishnan, N., 3–26, Birkhäuser, Boston, MA.

    Google Scholar 

  9. Goldin, L. R., and Chase, G. A. (1997). Improvement of the power to detect complex disease genes by regional inference procedures, Genetic Epidemiology, 14, 785–789.

    Article  Google Scholar 

  10. Goldin, L. R., Chase, G. A., and Wilson, A. F. (1999). Regional inference with averaged P values increases the power to detect linkage, Genetic Epidemiology, 17, 157–164.

    Article  Google Scholar 

  11. Gudbjartsson, D. F., Jonasson, K., Frigge, M. L., and Kong, A. (2000). Allegro, a new computer program for multipoint linkage analysis, Nature Genetics, 25, 12–13.

    Article  Google Scholar 

  12. Hernandez, S., Siegmund, D. O., and de Gunst, M. (2005) On the power for linkage detection using a test based on scan statistics, Biostatistics, 6, 259–269.

    Article  MATH  Google Scholar 

  13. Hoh, J., and Ott, J. (2000). Scan statistics to scan markers for susceptibility genes, Proceedings of the National Academy of Sciences USA, 97, 9615–9617.

    Article  Google Scholar 

  14. Hoh, J., and Ott, J. (2003). Mathematical multi-locus approaches to localizing complex human trait genes, Nature Reviews Genetics 4, 701–709.

    Google Scholar 

  15. Karlin, S., and Brendel, V. (1992). Chance and statistical significance in protein and DNA sequence analysis, Science, 257, 39–49.

    Article  Google Scholar 

  16. Klein, R. J., Zeiss, C., Chew, E. Y., Tsai, J. Y., Sackler, R. S., Haynes, C., Henning, A. K., SanGiovanni, J. P., Mane, S. M., Mayne, S. T., Bracken, M. B., Ferris, F. L., Ott, J., Barnstable, C., and Hoh, J. (2005). Complement factor H polymorphism in age-related macular degeneration, Science, 308, 385–389.

    Article  Google Scholar 

  17. Kruglyak, L., Daly, M. J., Reeve-Daly, M. P., and Lander, E. S. (1996). Parametric and nonparametric linkage analysis: a unified multipoint approach, American Journal of Human Genetics, 58, 1347–1363.

    Google Scholar 

  18. Lander, E., and Kruglyak, L. (1995). Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results, Nature Genetics, 11, 241–247.

    Article  Google Scholar 

  19. Liu, J., Nyholt, D. R., Magnussen, P., Parano, E., Pavone, P., Geschwind, D., Lord, C., Iversen, P., Hoh, J., Ott, J., and Gilliam, T. C. (2001). A genome-wide screen for autism susceptibility loci, American Journal of Human Genetics, 69, 327–340.

    Article  Google Scholar 

  20. MacLean, C. J., Sham, P. C., and Kendler, K. S. (1993). Joint linkage of multiple loci for a complex disorder, American Journal of Human Genetics 53, 353–366.

    Google Scholar 

  21. Manly, Bryan F. J. (2006). Randomization, Bootstrap and Monte Carlo Methods in Biology, Chapman & Hall/CRC, New York.

    Google Scholar 

  22. Schwab, S. G., Albus, M., Hallmayer, J., Honig, S., Borrmann, M., Lichtermann, D., Ebstein, R. P., Ackenheil, M., Lerer, B., Risch, N., Maier, W., and Wildenauer, W.B. (1995). Evaluation of a susceptibility gene for schizophrenia on chromosome 6p by multipoint affected sib-pair linkage analysis, Nature Genetics, 11, 325–327.

    Article  Google Scholar 

  23. Siegmund, D. (2001) Is peak height sufficient? Genetic Epidemiology, 20, 403–408.

    Article  Google Scholar 

  24. Simon-Sanchez, J., Scholz, S., Del Mar Matarin, M., Fung, H. C., Hernandez, D., Gibbs, J. R., Britton, A., Hardy, J., and Singleton, A. (2007). Genome-wide SNP assay reveals mutations underlying Parkinson disease, Human Mutation, 9, 9.

    Google Scholar 

  25. Terwilliger, J. D., Shannon, W. D., Lathrop, G. M., Nolan, J. P., Goldin, L. R., Chase, G. A., and Weeks, D. E. (1997). True and false positive peaks in genome-wide scans: applications of length-biased sampling to linkage mapping, American Journal of Human Genetics, 61, 430–438.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Epidemiology and Public Health, Yale University, New Haven, CT, USA

    Josephine Hoh

  2. Beijing Institute of Genomics, Beijing, China

    Jurg Ott

Authors
  1. Josephine Hoh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jurg Ott
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Dept. Statistics, University of Connecticut, Glenbrook Rd. 215, Storrs, 06269-3120, U.S.A.

    Joseph Glaz

  2. Dept. Statistics, University of Connecticut, Glenbrook Road 215, Storrs, 06269-4120, U.S.A.

    Vladimir Pozdnyakov

  3. Center for Biomathematical Sciences, Mount Sinai School of Medicine, Gustave L Levy Place 1, New York, 10029, U.S.A.

    Sylvan Wallenstein

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Birkhäuser Boston, a part of Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Hoh, J., Ott, J. (2009). Scan Statistics in Genome-Wide Scan for Complex Trait Loci. In: Glaz, J., Pozdnyakov, V., Wallenstein, S. (eds) Scan Statistics. Statistics for Industry and Technology. Birkhäuser Boston. https://doi.org/10.1007/978-0-8176-4749-0_9

Download citation

Publish with us

Policies and ethics

Search

Navigation