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UCSD, Brown release InvChecker microinversion software
SAN DIEGO—A project spearheaded at the University of California, San Diego (UCSD), and brought East to Brown University on the back of a post doctoral student whose study prompted the work, has yielded a new online software product called InvChecker, which provides a more accurate method of identifying genomic variations called microinversions.
A form of genetic mutation, microinversions occur when short DNA sequences break away from a chromosome and subsequently reattach in the reverse direction. Ranging from a few dozen to as many as a few thousand base pairs can result in a string of code that ought to read ATTAGCCG to be inverted and read GCCGATTA. These microinversions have been implicated as genetic causes of certain diseases including infertility and muscular dystrophy.
Ben Raphael, a co-author of the study which recently appeared online in the Proceedings of the National Academy of Sciences says the original work for his post-doctoral study began in a completely different area then shifted to the study of microinversions.
"What we were trying to do was come up with a fine-grained way of looking at genomic sequences," says Raphael, now an assistant professor of computer science at Brown. "Pavel [Pezner—a senior author of the study] and other collaborators had been involved in other whole-genome comparisons, and had seen that there are these chromosomal rearrangements that occur over evolutionary time." In so doing, Pezner and associates had found regions of "symphony" or regions of the genome that are indentical in different species and allow researchers to chart an evolutionary path.
But, Raphael notes, this work had been done on a much larger scale. What he—and lead author Mark Chaisson, a graduate student at UCSD's Jacobs School of engineering—sought to do, was create a software tool that would draw on the idea that microinversions are preserved over evolutionary time and are much easier to spot when comparing the genomes of three or more species.
From this work was born InvChecker, Raphael says, an important tool for researchers conducting comparative genomic studies to better understand how genomes evolved over time.
While the tool's main audience would be researchers conducting evolutionary studies, Raphael sees the potential for InvChecker to aid drug discovery researchers as well. He says that researchers are beginning to appreciate more that human are not "99.9 percent identical because of these larger scale [genomic] changes and duplicated pieces, deleted pieces and missing pieces. "This is a rich new source of genetic material for all kinds of disease association studies," he says. "All of these changes are related to disease, in a sporadic sense, and effect how gene are expressed. So it is a rich and more accurate source of information for people looking to study these much smaller inversions."