Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2005 Sep;77(3):337-45.
doi: 10.1086/432962. Epub 2005 Aug 1.

Recent developments in genomewide association scans: a workshop summary and review

Duncan C Thomas  1 , Robert W Haile, David Duggan
Affiliations
Review

Recent developments in genomewide association scans: a workshop summary and review

Duncan C Thomas et al. Am J Hum Genet. 2005 Sep.

Abstract

With the imminent availability of ultra-high-volume genotyping platforms (on the order of 100,000-1,000,000 genotypes per sample) at a manageable cost, there is growing interest in the possibility of conducting genomewide association studies for a variety of diseases but, so far, little consensus on methods to design and analyze them. In April 2005, an international group of >100 investigators convened at the University of Southern California over the course of 2 days to compare notes on planned or ongoing studies and to debate alternative technologies, study designs, and statistical methods. This report summarizes these discussions in the context of the relevant literature. A broad consensus emerged that the time was now ripe for launching such studies, and several common themes were identified--most notably the considerable efficiency gains of multistage sampling design, specifically those made by testing only a portion of the subjects with a high-density genomewide technology, followed by testing additional subjects and/or additional SNPs at regions identified by this initial scan.

PubMed Disclaimer

References

Supplemental References

    1. Akey JM, Eberle MA, Rieder MJ, Carlson CS, Shriver MD, Nickerson DA, Kruglyak L (2004) Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol 2:e286 - PMC - PubMed
    1. Antoniou AC, Easton DF (2003) Polygenic inheritance of breast cancer: implications for design of association studies. Genet Epidemiol 25:190–202 - PubMed
    1. Bortolini MC, Salzano FM, Thomas MG, Stuart S, Nasanen SP, Bau CH, Hutz MH, Layrisse Z, Petzl-Erler ML, Tsuneto LT, Hill K, Hurtado AM, Castro-de-Guerra D, Torres MM, Groot H, Michalski R, Nymadawa P, Bedoya G, Bradman N, Labuda D, Ruiz-Linares A (2003) Y-chromosome evidence for differing ancient demographic histories in the Americas. Am J Hum Genet 73:524–539 - PMC - PubMed
    1. Carlson CS, Eberle MA, Rieder MJ, Smith JD, Kruglyak L, Nickerson DA (2003) Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat Genet 33:518–521 - PubMed
    1. Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA (2004) Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 74:106–120 - PMC - PubMed

Web Resources

    1. Affymetrix, http://www.affymetrix.com/index.affx
    1. Epicenter Software, http://www.epicentersoftware.com/genetrix.php (for Genetrix)
    1. Illumina, http://www.illumina.com
    1. ParAllele BioScience, http://www.parallelebio.com (for 100K panel)
    1. Sequenom, http://www.sequenom.com (for 75K and 100K panels)

References

    1. Bansal A, van den Boom D, Kammerer S, Honisch C, Adam G, Cantor CR, Kleyn P, Braun A (2002) Association testing by DNA pooling: an effective initial screen. Proc Natl Acad Sci USA 99:16871–16874 - PMC - PubMed
    1. Barratt BJ, Payne F, Rance HE, Nutland S, Todd JA, Clayton DG (2002) Identification of the sources of error in allele frequency estimations from pooled DNA indicates an optimal experimental design. Ann Hum Genet 66:393–405 - PubMed
    1. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D (2004) Ultraconserved elements in the human genome. Science 304:1321–1325 - PubMed
    1. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300
    1. Boehnke M (1994) Limits of resolution of genetic linkage studies: implications for the positional cloning of human disease genes. Am J Hum Genet 55:379–390 - PMC - PubMed

Publication types

Substances