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Linking Variation to Disease

  • Title: Research Associate, Center for Applied Genomics, Hospital for Sick Children
  • Education: PhD, Karolinska Institute, 2002
  • Recommended by: Steve Scherer

As a research associate in Steve Scherer’s lab for the past four years, Lars Feuk knows a little bit about structural variation. Scherer’s lab may be best known for hosting the Toronto Database of Genomic Variants at the Center for Applied Genomics, which is part of Toronto’s Hospital for Sick Children. The source of that database was the 2004 Nature paper that first catalogued large-scale insertions and deletions in the human genome (“Detection of large-scale variation in the human genome”).

After completing a PhD at the Karolinska Institute in Stockholm, where Feuk worked with Anthony Brookes on SNPs and the genetics of Alzheimer’s disease, he knew he had to head west — to Toronto, that is. While his doctorate focused on the smallest known variants, SNPs, he wanted to expand his research into larger genetic alterations. “I felt that I wanted to study other types of variation in the genome, so I went from the single nucleotide level up to larger variations that were just being described for the first time at that stage,” he says. “When I started out there were just a few thousand SNPs known in the human genome, and at the end of my PhD, there were a few million SNPs known in the human genome. So that shows the pace at which that field was moving forward at the time. It was a very exciting time to work with that type of variation.”

Some of the challenges facing the community, he says, are making sense of all the data being generated, incorporating sequence data into current microarray data, and linking variation to disease. He sees the latter two as something that will come about in the next several years. “I think the hard thing is actually not going to be to generate the data; it’s going to be to make sense of that data,” he says. “To assemble all the sequences correctly and to interpret correctly what it is we see — I think that’s going to be the major challenge, and is mainly, I guess, a bioinformatics challenge.”

Another challenge for Feuk isn’t scientific as much as managerial.  Being a good teacher, problem solver, communicator, and writer is necessary to be a successful researcher, he says. “As you evolve as a PI, if you’re not good at it you’re not going to survive [because] it’s quite a competitive field.”

Looking ahead

The future, Feuk believes, lies with cheap whole-genome sequencing methods, not with microarray-based methods. “We can find very large variants using the current technologies, but I think with the next-generation sequencing that has come out now, we’re going to see many, many genomes sequenced over the next few years and we’re going to get a much better understanding of the full complement of variation,” he says. “It’s going to be much easier to be able to link the variants to specific phenotypes.”

Publications of note

Feuk’s current research focuses on trying to find links to the genetic causes of autism. He helped author the Autism Genome Project Consortium, published in March 2007 in Nature Genetics (“Mapping autism risk loci using genetic linkage and chromosomal rearrangements”). Over the last two years, Feuk’s focus has been on finding basic variation, but the next step, he says, is to “link it to disease. We can ask much smarter questions now that we have this basic understanding that we couldn’t do just a couple of years ago.”

And the Nobel goes to ....

Feuk would like to win the Nobel Prize for, ultimately, preventing human disease. “I think Nobel prizes are hard to predict because often the discoveries are a bit serendipitous,” he says. “I would like to find some as yet unknown fundamental mechanism that makes us understand our human genome better, which will in the long run … help us both understand [and] also prevent human disease.”

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