SFU behind genetic leap
Cenk Sahinalp, 778.782.5415; firstname.lastname@example.org
Iman Hajirasouliha, 778.782.7040; email@example.com
Fereydoun Hormozdiari, 778.782.7040; firstname.lastname@example.org
Carol Thorbes, PAMR, 778.782.3035; email@example.com
Two new international studies, involving five Simon Fraser University faculty, students and alumni, hold the keys to understanding how genomic differences between individuals dictate their medical fate. Nature and Science have just published the studies in their latest issues.
The Nature article reveals results from the pilot phase of the 1,000 Genomes Project, a three-year effort to sequence all of the millions of genetic variations between people’s DNA. Ultimately, the completed project will illuminate the genetic roots of diseases, such as cancer; focus the search for treatments and shed light on human evolution.
This latest leap in genomic analysis is the most complete inventory yet of variations between people’s DNA. It catalogues 4.9 trillion letters of human DNA code — enough to fill 300,000 copies of War and Peace.
The project has identified 95 per cent of the variation found across the human genome and isolated differences that occur in only one per cent of the world’s population.
In addition to eight million previously unknown variants that affect single nucleotides (units of RNA and DNA sequences) the researchers also found one million structural variants, such as repeated or deleted DNA sequences.
That means each of us could have 250 or 300 genes that have defective copies.
“The difference between you and me or any pair of individuals is very small. However, those differences make us look, function and live differently,” explains SFU computing science professor, Cenk Sahinalp. He is one of more than 100 international co-authors of the new Nature and Science papers.
“Between just two individual genomes there can be whole segments that are different. A block of several thousand letters can be totally missing in one individual and multiplied several times over in another. These structural differences not only determine how we differ from each other, but also are key to understanding how genome-based diseases originate and progress.”
Sahinalp notes that understanding what a healthy genome looks like is key to identifying a diseased one. But this analysis is comparable to looking for several needles in several haystacks because there are many different types of healthy genomes, not just one.
In a Science paper, which is a companion piece to the Nature paper, four of Sahinalp’s graduate students describe how their invention of new computational tools helps identify mutant DNA needles in genomic haystacks.
The grad students have developed mrsFAST and VariationHunter. mrsFAST is a tool for mapping information from an individual genome to the human reference genome. VariationHunter is a new algorithm for identifying structural variation among genomes throughout the world.
The tools have helped scientists discover that differences in multiple copies of genes in humans and great apes affects brain development. This discovery will help scientists uncover missing links in the evolution of the human species.
Iman Hajirasouliha and Fereydoun Hormozdiari work in Sahinalp’s Lab for Computational Biology, the only Canadian and computing science oriented research group to analyze the genomic sequences in this project. Farhad Hormozdiari is studying at the University of California Los Angeles and Can Alkan is a research scientist at the University of Washington.
“Structural variations are perhaps the main cause of genomic diseases, such as autism, mental retardation, alzheimer’s disease, crohn’s disease, and many types of cancers,” says Hajirasouliha. “Our tools will help identify risk factors associated with these diseases and will enable early diagnosis.”
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