One of the main features revealed by the completion of the human genome is the large amount of polymorphic sequence variation present in human populations, such that on average any two chromosomes differ every 600 - 800 base pairs. The majority of these sequence variants are Single Nucleotide Polymorphisms (SNPs), although other types of polymorphisms exist. So far around 5 million SNPs have been validated, and an international consortium has been set-up to characterize the main features of human variation in different populations (www.hapmap.org).
Although most of the sequence variation in the human genome is thought to be neutral, a fraction of it is known to have functional consequences, for instance, modifying the activity/function of a protein or affecting the spatio-temporal regulation of a gene. As such, functional sequence variants underlie a substantial proportion of phenotypic variability including quantitative traits, susceptibility to common disorders (for example Diabetes, Asthma), and differential response to drugs. One of the main challenges of modern genomics is to identify specific SNPs associated to phenotypic states (discrete or continuous). Over the last two years there have been remarkable advances in genotyping technology and conceptual frame-works that make it possible for the first time to perform truly genome-wide studies. However substantial challenges remain concerning how best to extract the information in view of problems such as multiple hypothesis testing and non-additive gene-gene and gene-environment interactions. Finding the genes in the genome and associating them with a particular disease.