Martin Godbout, president of Genome Canada, said his organization had been expecting about $120 million from the federal government to help fund new international research projects. (CBC)

The head of the not-for-profit agency responsible for funding large-scale science and genetics projects is perplexed after the foundation was shut out of the federal budget.

Genome Canada president Martin Godbout said his organization was expecting about $120 million from the government to help fund new international research projects, including those led by Canadian scientists. That number would be in line with the $140 million the group received in the 2008 budget and the $100 million it got in 2007.

Instead, Genome Canada received no mention in this year's budget, presented Tuesday.

"It's like we fell between the chairs," said Godbout. "This was an infrastructure budget, and so money went into that, but we got nothing."

The organization, established nine years ago with a mandate to develop and support large-scale genomics and proteomics research projects, has become a key funding partner for a host of medical and genetic researchers across the country, supporting 33 major research projects with operating grants of $10 million a year.

Genome Canada research aims to improve forests, crops, the environment, health and new technology development.

Since its creation in 2000, it has received $840 million from the federal government and raised another $1 billion through partner co-funding and interest earnings.

'It's like we fell between the chairs.'— Martin Godbout

Godbout said the lack of funding won't affect projects already underway and funded through previous budgets, but it will limit Canada's ability to contribute to new, large-scale genetics research projects.

For a government-run funding agency like the Natural Sciences and Engineering Research Council, no mention in a budget would mean a continuation of existing annual budgets, but for Genome Canada, which operates outside the government, a lack of funding effectively stalls any new research initiatives, said Godbout.

Liberal party science and technology critic Marc Garneau told CBC News the funding of Genome Canada would be an issue the party would address with the government when it discusses amendments to the budget.

It will also raise cuts in the budget to Canada's three research councils. The cuts total close to $150 million and peak in 2011-12 at $87.2 million, Garneau said.

But he stopped short of saying these issues would be deal-breakers in ongoing budget talks.

"What we're going to do is continue to remind the government that they are not doing enough in that particular area," said Garneau. "I won't tell you whether or not this is a show-stopper because I'm not making those decisions, but I think our party will continue to point out the lack of real support in science by this government."

The lack of funding for Genome Canada in the budget was "devastating," said Ken Dewar, an associate professor in human genetics at Montreal's McGill University.

"If we sit in a brand new building with brand new equipment and have scholarships for students, what are they going to do when there's no money to actually do an experiment?" he said.

The research funding is mainly used to train and maintain highly qualified personnel and to buy supplies for experiments, added Dewar.

Dewar is working on sequencing strains of C. difficile bacteria that have been plaguing hospitals.

The federal budget contrasts with that of the U.S., where funding appears to be more balanced between infrastructure upgrades and support for leading-edge research, said Dewar, who is also the acting scientific director of the McGill University and Génome Québec Innovation Centre.

Minister disputes funding cut

It isn't the first time Genome Canada received nothing in a federal budget. In 2006, the agency also received no mention, but Godbout said it was understood at the time that the $165 million the group received in 2005 would have to last for two years.

During question period on Thursday, Garneau questioned the government on whether the lack of funds was an oversight.

Minister of State for Science and Technology Gary Goodyear disputed that funding was cut, saying Genome Canada was still receiving funds from the two previous budget announcements, and that these funds amounted to $106 million this year and $108 million next year.

"This government has in place two five-year contracts with Genome Canada retaining almost a quarter of a billion dollars for science research," said Goodyear. "We're doing that, Mr. Speaker, because we know Genome Canada is good for Canada and the good work they do is good for Canadians' health."

But Garneau disputed that claim, arguing the government was counting money that was previously committed in its calculations.

"Canadian scientists can only contribute to new discoveries and create the jobs of tomorrow if we give them the support they urgently need," said Garneau. "Is this government deliberately undermining Canada's scientists or [has it] simply forgotten to fund their future work?"

Godbout said that while money from last year's budget was allocated over the next four years to fund ongoing projects, there was no indication that they would receive nothing this year for new initiatives.

He pointed to a project to sequence the genomes of 50 different types of cancer, led by Ontario Institute of Cancer Research scientific director Tom Hudson, as one project that would be short of funding without further federal support.

Hudson is participating in a worldwide effort to study the genetics of cancer. The Ontario government is funding a $25 million project on pancreatic cancer, and researchers were hoping the federal government would commit to studying other forms of cancer, said Rhea Cohen, a spokeswoman for the Ontario institute.

Godbout said he has expressed his concerns to the federal opposition parties but has yet to speak with the government on the issue.