Sunday, January 26, 2014

“We basically have the whole genome sequence of an entire nation.”

Interesting comments from Kari Stefansson of deCODE (2012). See also this earlier video; Kong notes that multiple common variants can be used to tag rare variants ...
Bio-IT World: “We have fully sequenced now about 2,500 Icelanders, and publishing paper after paper about discoveries coming out of sequencing. As in everything, the proof is in the eating. We’re managing and mining these data effectively. There’s nothing miraculous about it, but it hasn’t constituted any destructive discovery in IT. We have reasonable software system to gather, store, and manage these data. We’re making a lot of discoveries out of them.”

“A lot has been written of late about the difficulty of managing manage all the data from whole genome sequencing. Analysts at big banks such as Goldman Sachs have been making bold statements about how important informatics inventions will be in biology because they will constitute the next disruptive discoveries coming out of biology, giving the impression that for the moment, this is an insurmountable difficulty in medicine. And that is just a crock of s—t!”

Stefansson says there are about 20 recently formed companies trying to develop software for genome sequencing interpretation, which he says deCODE has already achieved.

“We’re going from genotypes to phenotypes, not from a disease and looking for a variant. There are many companies trying to sell the scientific community methods to manage WGS data to make discoveries, and other companies trying to market software systems to manage clinical systems. And we have this all in place.”

Stefansson also says that deCODE plans to begin marketing later this year its system for managing sequence data, both for discovery and clinical sequencing – as well as release diagnostic tests in areas such as developmental disorders, prenatal testing, and cancer. Some of this may be done through spin-out companies.

deCODE’s principal sources of revenue comes from collaboration with big pharma, diagnostics tests, and scientific grants. ”Future growth will come from projects that will help integrate genetics into healthcare: software systems, diagnostic tests, and the way in which we help the pharma industry to use genetics.”

We have sequenced the whole genomes of 2,500 people. We have genotyped about 120,000 Icelanders with an Illumina chip. We 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.”

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.”


Richard Seiter said...

This is very interesting: "We can impute whole genome sequence down to variants with less than 0.1% frequency..." I wonder what the accuracy is like and how it scales to smaller/larger populations? For example, how many individuals are needed in a 3 generation family tree to accurately infer WGS from SNPs? It seems to me we might see a persistent difference in SNP/WGS cost due to differing levels of technological complexity (at what absolute level is unclear, if low enough a relative difference may not matter). Can anyone with more knowledge of the sequencing industry comment on that speculation?

deCODE is using much additional publicly available data for sequence imputation:

As an aside, this bit on CNVs looked interesting:

5371 said...

So in a couple of years, we should be able to test the hypothesis that gene-based medicine can contribute to a rise in life expectancy. I know which way I would bet.

Richard Seiter said...

I'd settle for an increase in quality of life (e.g. number of healthy years). Do you think that unlikely as well?

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