Iceland first nation with whole genome sequence

Researchers have sequenced the whole genomes of 2,500 people from Iceland. They have genotyped about 120,000 Icelanders with an Illumina chip. They can impute whole genome sequence down to variants with less than 0.1% frequency into about 370,000 Icelanders — there are only 320,000 living today.

“We basically have the whole genome sequence of an entire nation.” Kari-Stefansson of deCode said.

deCODE has formed a collaboration with the National Hospital of Iceland to impute the genome sequence of all patients over the past 3 years (~300,000) and ask: in what indication, in what disease would WGS have the biggest impact on the selection of treatment and outcome? “Rather than doing it on a priori assumptions, we’ll do it by data mining,” he says. “Rather than doing it on a handful of people, we’ll do it on the basis of the whole nation. That shouldn’t take more than a year. We’re in a privileged position.”

deCODE has been studying the genetics of longevity since the company was founded in the 1990s. Indeed, in the company’s first major publication, Stefansson’s team showed that Icelanders who reach 90 years of age are much more related to each other than control groups, suggesting there is a genetic component to becoming a nonagenarian.

“This is important,” says Stefansson. “You’re asking the genetic effect to rise above 90 years of environmental influences. This is the biggest stress test you can put on genetics. So what is it? What are you inheriting for this ability to live to 90? Are you ducking disease genes or inheriting a positive asset?”

Over the years, deCODE has gathered strong evidence for the existence of one or a few “positive assets” in the Icelandic population to promote longevity. “So this is a genetic asset conferred to you by a relatively simple genetic mechanism, probably via one gene,” he says.

Importantly, Stefansson says the new APP discovery was not hypothesis driven. Rather, it fell out of a systematic analysis of every new DNA variant discovered by whole-genome sequencing in 1,800 Icelanders (at the time) scanned against 1,500 phenotypes. (deCODE has currently amassed some 41 million SNPs in the Icelandic population.)

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