A new paper by Thomas et al. reviews a meeting that was held in April to discuss genome-wide association analysis.
Thomas DC, Haile RW, Duggan D. Recent developments in genomewide association scans: a workshop summary and review. Am J Hum Genet. 2005 Sep;77(3):337-45. [PubMed
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.
Detecting epistasis in genome-wide association studies will be a particularly difficult challenge. See our paper from last year on this topic:
Moore JH, Ritchie MD. The challenges of whole-genome approaches to common diseases. JAMA. 2004 Apr 7;291(13):1642-3. [PubMed