Human Genetics - Agency Nixes deCODE's New Data-Mining Plan

[FarCenter]

Led by founder and CEO Kári Stefánsson, deCODE set out in 2006 to combine Iceland's extensive genealogical records, which it put into a database, with genetic data and also health records for all citizens. Unless individuals explicitly asked to opt out, all Icelanders would be included, making it one of the largest such biobanks in the world. The company would collect DNA from consenting individuals and mine this information to find disease genes.

After Iceland's Supreme Court said that deCODE could not use the health records without consent, deCODE instead built a research database using DNA and clinical data for more than 120,000 research volunteers and analyzed their DNA for a selection of subtle genetic variations called single-nucleotide polymorphisms (SNPs). The company has published a slew of papers in top journals tying specific genetic mutations to risks of diseases such as heart disease, diabetes, and cancer. deCODE's drug discovery efforts were less successful, and it filed for bankruptcy 4 years ago. Last December, however, Amgen purchased the company for $415 million; it is now an Amgen subsidiary.

The current dispute involves a relatively new approach in which geneticists calculate the odds of whether an individual carries a particular genetic variant without directly sequencing their DNA. deCODE has done costly whole genome sequencing on DNA from only about 2500 research participants, but using the approach it has extended that data's reach to many more. When it finds a variant of interest among the whole genomes, the company can use the more limited SNP data that it has on tens of thousands of volunteers to impute, or infer, with 99% accuracy whether these individuals also carry the mutation. In this way, researchers can see if a disease risk variant found by fully sequencing the DNA of a small group holds up in a larger population.

deCODE is taking this technique a step further than others have, however. Combining the known and estimated genotypes for its research participants with its genealogical database, the company is also estimating what it calls in silico genotypes of close relatives of the SNP-chipped volunteers. That encompasses about 200,000 living and 80,000 dead Icelanders, who have not consented to participate in deCODE's studies, and would essentially give the company genotypes for the entire population. The firm then uses these estimated genotypes for individuals as controls in its studies and also combines them with health records for patients who are part of a disease study in Iceland but whose DNA has not been sampled.

But when deCODE last November asked DPA if it could continue this strategy as part of a new study—it now wanted to impute the genotypes of close relatives of the SNP-chipped volunteers and then collaborate with researchers at Iceland's National Hospital to link them to certain hospital records for individuals, such as surgery codes and prescriptions—the oversight agency turned the company down. If deCODE wants to impute genotypes for these 280,000 living and dead relatives and link to their hospital data, it must obtain their informed consent, the DPA decision says. It gives the company until 1 November to present "documents on how the company has complied with the instructions."

http://www.sciencemag.org/content/340/6139/1388.full