UCSD, Brown release InvChecker microinversion software
February 2007
SHARING OPTIONS:
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.” Code: E020708
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