A mathematical discovery has extended the reach of a novel genome mapping method to humans, potentially giving cancer biology a faster and more cost-effective tool than traditional DNA sequencing.
A student-led group from the laboratory of Michael Waterman, USC University Professor in molecular and computational biology, has developed an algorithm to handle the massive amounts of data created by a restriction mapping technology known as "optical mapping." Restriction maps provide coordinates on chromosomes analogous to mile markers on freeways.
Lead author Anton Valouev, a recent graduate of Waterman's lab and now a postdoctoral fellow at Stanford University, said the algorithm makes it possible to optically map the human genome.
"It carries tremendous benefits for medical applications, specifically for finding genomic abnormalities," he said.
The algorithm appears in this week's PNAS Early Edition.
Optical mapping was developed at New York University in the late 1990s by David Schwartz, now a professor of chemistry and genetics at the University of Wisconsin-Madison. Schwartz and a collaborator at Wisconsin, Shiguo Zhou, co-authored the PNAS paper.
The power of optical mapping lies in its ability to reveal the size and large-scale structure of a genome. The method uses fluorescence microscopy to image individual DNA molecules that have been divided into orderly fragments by so-called restriction enzymes.
By imaging large numbers of an organism's DNA molecules, optical mapping can produce a map of its genome at a relatively low cost.
An optical map lacks the minute detail of a genetic sequence, but it makes up for that shortcoming in other ways, said Philip Green, a professor of genome sciences at the University of Washington who edited the PNAS paper.
Geneticists often say that humans have 99.9 percent of their DNA in common. But, Green said, "individuals occasionally have big differences in their chromosome structure. You sometimes find regions where there are larger changes."
Such changes could include wholesale deletions of chunks of the genome or additions of extra copies. Cancer genomes, in particular, mutate rapidly and contain frequent abnormalities.
"That's something that's very hard to detect" by conventional sequencing, Green said, adding that sequencing can simply miss part of a genome.
Optical mapping, by contrast, can estimate the absolute length of a genome and quickly detect differences in length and structure between two genomes. Comparing optical maps of healthy and diseased genomes can guide researchers to crucial mutations.
Though he called optical mapping "potentially very powerful," Green added that it requires such a high level of expertise that only a couple of laboratories in the world use the method.
The Waterman group's algorithm may encourage others to take a second look.
Carl Marziali | EurekAlert!
Scientists uncover the role of a protein in production & survival of myelin-forming cells
19.07.2018 | Advanced Science Research Center, GC/CUNY
NYSCF researchers develop novel bioengineering technique for personalized bone grafts
18.07.2018 | New York Stem Cell Foundation
A new manufacturing technique uses a process similar to newspaper printing to form smoother and more flexible metals for making ultrafast electronic devices.
The low-cost process, developed by Purdue University researchers, combines tools already used in industry for manufacturing metals on a large scale, but uses...
For the first time ever, scientists have determined the cosmic origin of highest-energy neutrinos. A research group led by IceCube scientist Elisa Resconi, spokesperson of the Collaborative Research Center SFB1258 at the Technical University of Munich (TUM), provides an important piece of evidence that the particles detected by the IceCube neutrino telescope at the South Pole originate from a galaxy four billion light-years away from Earth.
To rule out other origins with certainty, the team led by neutrino physicist Elisa Resconi from the Technical University of Munich and multi-wavelength...
For the first time a team of researchers have discovered two different phases of magnetic skyrmions in a single material. Physicists of the Technical Universities of Munich and Dresden and the University of Cologne can now better study and understand the properties of these magnetic structures, which are important for both basic research and applications.
Whirlpools are an everyday experience in a bath tub: When the water is drained a circular vortex is formed. Typically, such whirls are rather stable. Similar...
Physicists working with Roland Wester at the University of Innsbruck have investigated if and how chemical reactions can be influenced by targeted vibrational excitation of the reactants. They were able to demonstrate that excitation with a laser beam does not affect the efficiency of a chemical exchange reaction and that the excited molecular group acts only as a spectator in the reaction.
A frequently used reaction in organic chemistry is nucleophilic substitution. It plays, for example, an important role in in the synthesis of new chemical...
Optical spectroscopy allows investigating the energy structure and dynamic properties of complex quantum systems. Researchers from the University of Würzburg present two new approaches of coherent two-dimensional spectroscopy.
"Put an excitation into the system and observe how it evolves." According to physicist Professor Tobias Brixner, this is the credo of optical spectroscopy....
13.07.2018 | Event News
12.07.2018 | Event News
03.07.2018 | Event News
20.07.2018 | Power and Electrical Engineering
20.07.2018 | Information Technology
20.07.2018 | Materials Sciences