We expect that the continued deployment of these technologies will change how genotype imputation is used in many different ways. An example of these changes is given by the 1,000 Genome Project (see www.1000genomes.org). The 1,000 Genomes Project aims to deliver whole genome sequences for >1,000 individuals from several different populations in next 12-18 months. To deliver these sequences in a cost effective manner, the 1,000 Genomes Project is using a strategy that combines massively parallel shotgun sequencing technology with the same statistical machinery used to drive genotype imputation based analyses. Specifically, the project is collecting a relatively modest amount of shotgun sequence data for each of the individuals being sequenced: each of the target bases will be re-sequenced only 2-4x on average (statistical fluctuations around this average mean that many bases will not be covered even once), rather than the 10-20x used in previous applications of these technologies to whole genome resequencing. To accurately call polymorphisms in each genome, the Project will then use imputation based techniques to combine information across individuals who share a particular haplotype stretch. Using
