The most common genetic variations are single nucleotide polymorphisms (SNPs)—variation of a single base of the genome sequence among individuals—and it was estimated that the human genome has ~10 million SNPs [16]. However, the work of Gabriel in [17] provided the first evidence that, with the exception of hotspots of high recombination, the human genome is characterized by a block structure with sequences of SNPs that are highly correlated with each other in blocks of linkage disequilibrium (LD) (See Table I for technical definitions and Fig. 1). This structure implies that one can reconstruct the majority of variability of these blocks using a small subset of carefully selected tag-SNPs [18]. The International HapMap project was launched in 2003 to characterize common SNPs and to describe the block structure of the human genome that could be used to identify these tag-SNPs [19]. The first comprehensive catalog was published in 2005 and included more than 1 million common SNPs genotyped in 269 nuclear families of the three major ethnic groups [10]. This catalogue was useful to design the SNP microarrays produced by Illumina [12] and the latest SNP microarrays produced by Affymetrix [20].
