A report on the British Atherosclerosis Society autumn meeting 'Genetics of Complex Diseases', Cambridge, UK, 17-18 Septem ber 2009.
IntroductionComplex disease genetics is at a critical turning point. Genome-wide association studies (GWASs) have generated an abundance of data, resulting in the use of advanced analytic methods and raising many questions. This common platform has brought together various scientific disciplines, including genetics, epidemiology, bioinformatics, statistics and medicine, reflected in the diverse backgrounds of speakers and delegates at this meeting. Here, we summarize two principal themes that emerged in the meeting: first, the success of GWASs in the discovery of novel disease loci using emerging new analytical methodologies, and second, the current and future translational applications of GWASs.
Genome-wide association studiesdiscoveries, limitations and future directionsGWASs enable a hypothesis-free approach to finding novel genes associated with diseases and traits. Facilitated by the HapMap project (http://www.hapmap.org), chips with probes for up to one million single nucleotide polymorphisms (SNPs) can be used to capture variation across the entire human genome. Mark Caulfield (Barts and The London School of Medicine, London, UK), Sekar Kathiresan (Massachusetts General Hospital and Broad Institute, Boston, USA) and Nilesh Samani (University of Leicester, UK) communicated results on novel loci arising from recent GWASs conducted on cardiovascular diseases (CVDs). They also highlighted the importance of collaborative analyses in reliably identifying signals that might otherwise be missed owing to small sample sizes. This was exemplified by the finding of novel genes associated with blood pressure and the discovery of SNPs on chromosome 1 associated with CVD that alter lowdensity lipoprotein (LDL)-cholesterol.Generation of large volumes of data brings with it analytical challenges, resulting in methodological development. Bayesian approaches that enable direct comparison among SNPs both within and between studies were described by David Balding (Imperial College, London, UK). These methods are in contrast to classical ('frequentist') methods, which compute a P-value as evidence for association without incorporating any information about minor allele frequency (MAF) and study size, both factors that affect the power of the test. Hence, the same P-value computed at different SNPs or in different studies may not provide the same level of confidence for true association. To partly avoid this issue, it has become the norm to discard low-MAF SNPs when using classical methods, but this may result in detectable association being discarded. In Bayesian analysis prior knowledge is incorporated into the model. The outcome is the posterior probability of association, which can be directly compared between SNPs and studies and also avoids the problem of multiple testing.John Whittaker (London School of Hygiene and Tropical Medicine, London, UK) further described how the Bayesian ap...