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The 1000 Genomes Project is a major international research project that aims to map all the common genetic variations (those present in 1% or more of the population) in the human genome. The initial pilot phase sought to develop and assess different approaches for rapid whole genome sequencing (WGS).

The newly released first phase results comprise low coverage genome sequences of 179 humans from four populations, high coverage genome sequences from two family trios (mother–father–child), and exome sequences of 697 humans from seven populations.

Using the sequence data, researchers have identified around 15 million single nucleotide polymorphisms (SNPs), 1 million short insertions and deletions, and 20,000 structural variants, most of which had not been described before. Collectively, the catalogue of common human genetic variation is said to be largely complete, including over 95% of the common variants present in any individual.

The researchers calculate that on average each person will have 250-300 variants within genes linked to a loss of function and 50-100 variants implicated in inherited disorders. They estimate (on the basis of the two family trios) that minor new mutations arise at a rate of around10⁻⁸ per base pair of DNA per generation. They also set out methods by which this new reference set of common variants can be used to improve genome-wide association studies (GWAS) by allowing genotype imputation (inferring absent data from incomplete genome sequences by comparison with reliable reference sequences).

Although it has produced some interesting findings about human genetic variation, the true value of this work is in the capacity to improve future research into human genomics, health and disease via GWAS and other large-scale genomic analysis projects. With respect to the health of individuals with serious diseases, exome sequencing (facilitated by the advent of rapid whole genome sequencing technologies) to identify rare variants is likely to be of more use.