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:1/22/2016)... , January 22, 2016 ... the addition of the  "Global Behavioral ... offering. --> http://www.researchandmarkets.com/research/4lmf2s/global_behavioral ) ... "Global Behavioral Biometric Market 2016-2020"  report ... Research and Markets ( http://www.researchandmarkets.com/research/4lmf2s/global_behavioral ) has ...
(Date:1/20/2016)... --  MedNet Solutions , an innovative SaaS-based eClinical technology ... is pleased to announce the attainment of record-setting corporate ... of the company,s laser focus on (and growing international ... comprehensive, easy-to-use and highly affordable cloud-based technology platform. ... growth achievements in 2015 include: , Record ...
(Date:1/13/2016)... New York , January 13, 2016 ... Market Research has published a new market report titled ... Growth, Trends, and Forecast, 2015 - 2023. According to the ... in 2014 and is anticipated to reach US$1,625.8 mn ... 2015 to 2023. In terms of volume, the biometric ...
Breaking Biology News(10 mins):
(Date:2/9/2016)... PA (PRWEB) , ... February 09, 2016 , ... Tunnell ... Europe. Based in Paris, he will focus on acquiring new accounts and work ... met. , “Fred brings to our European clients more than 15 ...
(Date:2/9/2016)... , Feb. 9, 2016  DNAtrix, a ... for cancer, announced that its lead product, ... Commission as an orphan medicinal product for ... form of glioma, strikes approximately 25,000 people ... http://photos.prnewswire.com/prnh/20160208/330986LOGO --> ...
(Date:2/9/2016)... , Feb. 9, 2016 BERG, a ... biological research approach, has announced the appointment of ... and Chief Operating Officer. Haddock brings to BERG ... including 12 years in senior financial functions at ... in business organizational management. Niven ...
(Date:2/8/2016)... , Feb. 8, 2016  CytRx Corporation ... development company specializing in oncology, today announced that ... security agreement with Hercules Technology Growth Capital, Inc. ... $40 million in financing. --> ... first $25 million of financing under the loan ...
Breaking Biology Technology: