The completion of the Human Geneome Project in 2003 ushered in a new era of genomics. Equipt with a reference genome new initiatives could explore uncharted waters. The International HapMap Project (HapMap), launched in 2003, genotyped 1.6 millions single nucleotide polymorphisms (SNPs) in 1184 samples from 11 different ethnic populations, with the aim of understanding genetic variability between individuels [http://hapmap.ncbi.nlm.nih.gov] \cite{20811451}. For the first time it was possible to map the haplotype structure of the human genome and calculate linkage disequalibrium (LD) between SNPs. Using this information, the genetic variability within a ’gene of interest’ could now be captured with a smaller number of ’tag-SNPs’, vastly reducing experiment cost and time.
Octobre 2015 saw completion of the 1000 Genomes Project (1KP) which, like HapMap, sought to catalogued human genetic variability, albeit on a much finer scale \cite{26432245}. The combination of whole-genome (7.4x) and deep whole-exome (65.7x) sequencing in over 2500 samples has enabled a comprehensive catalogue of over 88 million variant sites to be discovered, including rare and structural changes. This has has several important applications, including designing arrays of rarer coding changes (’exome chips’) and providing a reference set of haplotypes for genotype imputation.
Genome-wide association studies (GWAS) became a reality when commercial microarray providers (Affymetrix and Illumina) began to use produce ’SNP chips’ containing hundreds of thousands of non-redundant, informative polymorphisms based on HapMap data (Figure 1). The seminal GWAS was published in 2007 by the Wellcome Trust Case Control Consortium (WTCCC) \cite{17554300}. With a series of 3,000 healthy controls and 14,000 combined cases across seven common human disease, the consortium identified 24 novel genetic associations with complex diseases using the Affymetric 500K GeneChip. Realising that large sample large sample sizes were key, research groups in other fields began to form larger consortia in order to pool their resources. The era of GWAS had arrived.