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Human Variome Project Developing Strategies for Cataloguing Disease-Related Genetic Variation

NEW YORK (GenomeWeb News) – The Australian-led Human Variome Project is taking strides toward creating a resource housing information on genetic polymorphisms known or suspected of influencing disease risk, according to a policy paper published online today in Science.
“We’ve now got a way of going forward and making [the project] possible,” lead author Richard Cotton, a researcher at the Howard Florey Institute’s Genomic Disorders Research Centre in Melbourne, Australia, told GenomeWeb Daily News.
The first genetic variation was linked to human disease some 60 years ago, Cotton said. But, he added, scientists have only recently realized that they need a better way to compile information on these mutations. And with variation information available for just 3,000 or so of the more than 20,000 genes in the human genome, researchers have a ways to go to understand the role of genetic variation in human disease — and catalogue it completely and accurately, the authors argued.
The Human Variome Project was officially established in 2006. Now, the project is coming into its own, with pilot projects, a new scheme for funding part of the effort, and planning committees aimed at creating information pipelines.
The project was conceived because of a need to catalogue information on variation or changes across the human genome and to make it accessible clinically, co-author Finlay Macrae, a cancer researcher at the Royal Melbourne Hospital, told GenomeWeb Daily News.
In the absence of such a resource for compiling data on mutations and their known or suspected links to specific phenotypes, Cotton said, physicians are often left scratching their heads and trawling numerous databases trying to determine whether a genetic mutation they see in a patient has been previously tied to a disease or not.
To address this, variome participants are working to encourage the development and adoption of standards, define and reach consensus on ethical guidelines, develop automated data submission systems, support curation, promote participation in developing countries, and more.
Ultimately, Macrae explained, the team hopes to be able to “develop systems whereby diagnostic lab DNA information is fed into the Human Variome Project to provide a much more comprehensive database.” That requires methods for capturing both legacy data — disease-related mutations that have been published or are sitting in lab books — and new data from the literature and diagnostic labs, he said.
Collecting information from around the world regarding mutations in tens of thousands of genes is no small task, Cotton emphasized. Toward that goal, the Human Variome Project members have held a series of meetings and have set up eight committees so far.
Several pilot projects are also being organized or are underway, the authors noted. For instance, the International Society for Gastrointestinal Hereditary Tumours, or InSIGHT, started a project in early 2007 to create a database of mutations associated with colon cancer. That project involves creating a pipeline for collecting new and old data and compiling it on the Leiden Open Variation Database.
An InSIGHT pilot project is also aimed at compiling worldwide information on mutations in four genes of interest and their relationship to colon cancer.
“Strategies need to be developed and appropriate software created and put in place in the next three years that will enable the seamless, effortless, and low-cost collection of data from laboratories, clinics, and hospital records and their delivery to appropriate databases,” Cotton and his colleagues wrote.
On a broader scale, those spearheading the Human Variome Project are currently developing strategies and resources to help researchers set up variome projects around the world. “We’re now developing a protocol which people need to follow to collect mutations in their individual countries,” Cotton said.
In addition, the team has also come up with a new scheme to help pay for such massive collection and curation efforts. The “Adopt-a-Gene Program” is intended to give industry and patient support groups the opportunity to sponsor data collection on mutations in specific genes of interest.
The researchers noted that they see the variome project as complementary to resequencing projects such as the 1000 Genomes Project. But, Cotton said, “There is still a lot of other data to be collected.” “What we’re dealing with is mutations with a phenotype,” he added.

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