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1,000 Genomes Pilot Project Data Accounts for 95 Percent of Human Variation

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The 1,000 Genomes Project Consortium recently completed its pilot study, which involved sequencing 179 people at low coverage, deep-sequencing six people in two trios, and sequencing exons in 697 people. All told, the researchers found 15 million SNPs, 1 million short insertions and deletions, and 20,000 structural variants — which collectively account for 95 percent of all variation observed in humans. The team published its results in Nature and Science in October.

In a press teleconference, Richard Durbin — co-chair of the consortium and a group leader at the Wellcome Trust Sanger Institute — said the team had also found that each individual carries 250 to 300 loss-of-function gene variants — which account for about 1 percent of all genes — 50 to 100 of which have been implicated in various diseases and disorders.

For its participation in the pilot project, Evan Eichler's group at the University of Washington looked at copy-number variations in the "more difficult regions of the genome" — those that are difficult to assay because they contain multiple copies of various genes, Eichler said during the conference call. In a companion study published in Science, Eichler and his team describe their work, in which they analyzed the short-read mapping depth for 159 human genomes. In comparing these genomes to those of great apes, Eichler said his team was able to identify the genes and gene families that have continued to evolve and expand in the human lineage since its divergence from the chimpanzee and gorilla lines. "Even though the numbers are quite small, we find a particularly tantalizing set of genes that are important in terms of neural development — in terms of neuronal migration — and we want to focus on these going forward to determine some aspect of the human condition," Eichler said.

David Altshuler, consortium co-chair and deputy director of the Broad Institute, added that when it comes to applying the pilot study to medical research, the project itself has been a "laboratory" of sorts for researchers to work out new methods and standards of genomic study and add as many SNPs as possible to a shared database. "This project is not about any given model. It's about … a comprehensive approach [and] testing all the models," Altshuler said. Because the team made its results freely available, the data is already being used and is having an impact on research in both rare and common diseases, he added.

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