Knome Assists Canadian Team Identify Parkinson’s Disease Gene

By Kevin Davies 

July 14, 2011 | An international consortium led by researchers at the University of British Columbia (UBC) in Canada, with a major assist from the genome analysis company Knome, have used exome sequencing to identify the sixth known inherited gene defect causing Parkinson’s disease (PD).  

The results identify the gene encoding vacuolar protein-sorting 35 (VPS35) as the cause of Parkinson’s in several families with late-onset inherited PD. Their findings were published today online in the American Journal of Human Genetics. 

The UBC team, led by Matthew Farrer and Carles Vilariño-Güell of the UBC Brain Research Center, contacted Knome some 18 months ago seeking help in the genome analysis of a large Swiss family with inherited PD, which the Canadians had been studying for a few years. 11 members of the extended family have developed PD. 

“Until now, we had five known PD genes, but there were no mutations in any of them in this family,” says Vilariño-Güell. Those genes include alpha-synuclein and LRRK2, a mutation carried by Google co-founder Sergey Brin. 

The affected patients in the Swiss family studied by the UBC group present with typical parkinsonism, with an average age of onset in the 50s, and treated with levadopa. As in other cases of inherited parkinsonism, however, the disease is not fully penetrant – some individuals are symptom-free in their 60s despite inheriting the putative gene mutation. 

18 Months Later 

Some 18 months ago, the UBC group sent DNA from two first cousins from the Swiss family to Knome, which in turn sent them to BGI for sequencing. “It’s taken a long time, because the technology doesn’t give you the answer straight away,” says Vilariño-Güell. “Knome thoroughly characterized both known and novel variants in these genomes. Their analysis helped clarify which variants were most important, greatly accelerating our discovery.” 

Vilariño-Güell says the choice to partner with Knome reflected the realities and costs of high-throughput genome analysis. “Knome had the contacts with BGI and the skills to do the analysis. By ourselves, the system would cost $1 million! Investing that much money on a developing technology, it was impossible for us. They had the skills to do the analysis, and they gave us the best price. We’re academics, we don’t have pockets full of money.”  

18 months ago, the cost was about $10,000/sample. “Now it’s $1,600/sample. Take the cost of reagents – at scale you can get better pricing. It makes sense to collaborate to do this through a factory,” says Farrer. 

The results that came back from Knome presented a list of 60 potentially pathogenic variants from the exome sequences. “We had to narrow it done,” says Vilariño-Güell. “We had to take these variants and study them in [other] families, to see which segregate with PD… That brought the list down to six variants. Then we had to see which of those six was the pathogenic mutation. We sequenced more than 4,300 patients… to find which one was the real one.” 

Searching for additional families with a PD mutation became “a major international consortium effort with many investigators involved,” says Farrer. 

Singling out the true culprit from the short list based on their putative biological function is not as easy as one might think. “I saw the list of six and said, ‘It is clear cut,’” recalls Vilariño-Güell. One of his colleagues reviewed the same list and also thought the answer was obvious. “We were talking about different genes!” Vilariño-Güell laughs. “It is easy to make stories. There are many pathways involved [in PD], and many genes expressed in the brain. You always have a candidate.” 

In the end, the genetic evidence proved overwhelming. The consortium found four different families from North America, the Middle East, Africa and Asia, in which VPS35 mutations segregated, affecting about a dozen individuals overall. (A German group independently found the same mutation in another family, which is reported in a companion paper.)  

The discovery is an exciting one for PD research. “VPS35 opens up some different biology,” says Vilariño-Güell. “It gels nicely with other avenues. This may be important for PD and neurodegeneration as a whole.”  

The VPS35 protein forms the central piece of the retromer complex, which helps nerve cells recycle membrane proteins. The retromer throws internalized receptors back into the membrane. The UCB team is collaborating with the Michael J. Fox Foundation to create genetically engineered mice to thoroughly study the biological role of the VPS35 gene in animal models of PD.  

Part of the delay in releasing these results is that the paper was initially turned down by a couple of Nature sister journal publications before being accepted by the American Journal of Human Genetics.