Navigation Links
Powerful genome ID method extended to humans

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 di fferences 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.


'"/>

Source:University of Southern California


Related biology news :

1. Powerful new tool for studying brain development
2. Powerful technique for multiplying adult stem cells may aid therapies
3. Man and mouse share genome structures
4. Whole genome fine map of rice completed
5. Study finds more than one-third of human genome regulated by RNA
6. A bacterial genome reveals new targets to combat infectious disease
7. Scientists decipher genome of fungus that can cause life-threatening infections
8. Highly adaptable genome in gut bacterium key to intestinal health
9. Fleshing out the genome
10. Agilent Technologies new genome analysis technology set to accelerate Australia fight against mesothelioma
11. wFleaBase: the Daphnia genome database
Post Your Comments:
*Name:
*Comment:
*Email:


(Date:1/12/2017)... and PUNE, India , January 12, 2017 ... Forecasts, 2015 - 2022," projects that the global biometric technology market is expected to ... 2016 to 2022. Continue Reading ... ...      ...
(Date:1/6/2017)... JOLLA, Calif. , Jan. 6, 2017 /PRNewswire/ ... 1 safety studies in healthy volunteers of a ... intended to treat acute pancreatitis. ... is typically a mild disorder, but can be ... organ failure and sepsis, where extended hospital stays, ...
(Date:1/4/2017)... LAS VEGAS , Jan. 4, 2017  For the thousands of ... , a global leader in connected health and biometric measurement devices and ... pressure monitors. On display in A&D Medical,s special CES ... monitors represent the ongoing expansion of the company,s WellnessConnected product ... ...
Breaking Biology News(10 mins):
(Date:1/19/2017)... ... January 19, 2017 , ... FireflySci Inc. is a go-getter type of company ... is accounted to two main factors. The first is the amazing customer service ... supplying FireflySci products all around the world. , 2016 was a tremendous sales year ...
(Date:1/19/2017)... , Jan. 18, 2017 BD (Becton, Dickinson and Company) ... today that it will host a live webcast of its Annual ... (ET). The webcast can be accessed from the ... replay through Tuesday, January 31, 2017. ... About BD BD is a global ...
(Date:1/18/2017)... 18, 2017   Parent Project Muscular Dystrophy (PPMD) ... Duchenne muscular dystrophy (Duchenne) , today announced a ... Institute of Technology (NJIT) and Talem Technologies (Talem) as ... technology to assist people living with Duchenne. PPMD ... – an embedded computer, software, a force sensor and ...
(Date:1/18/2017)... ... 2017 , ... MYOLYN, which creates medical technology for people ... to the FDA, requesting clearance of the MyoCycle Home and the MyoCycle Pro ... , The submission marks a major milestone for the technology startup. MYOLYN spun ...
Breaking Biology Technology: