Navigation Links
Taking the gamble out of DNA sequencing
Date:2/24/2013

Two USC scientists have developed an algorithm that could help make DNA sequencing affordable enough for clinics and could be useful to researchers of all stripes.

Andrew Smith, a computational biologist at the USC Dornsife College of Letters, Arts and Sciences, developed the algorithm along with USC graduate student Timothy Daley to help predict the value of sequencing more DNA, to be published in Nature Methods on February 24.

Extracting information from the DNA means deciding how much to sequence: sequencing too little and you may not get the answers you are looking for, but sequence too much and you will waste both time and money. That expensive gamble is a big part of what keeps DNA sequencing out of the hands of clinicians. But not for long, according to Smith.

"It seems likely that some clinical applications of DNA sequencing will become routine in the next five to 10 years," Smith said. "For example, diagnostic sequencing to understand the properties of a tumor will be much more effective if the right mathematical methods are in place."

The beauty of Smith and Daley's algorithm, which predicts the size and composition of an unseen population based on a small sample, lies in its broad applicability.

"This is one of those great instances where a specific challenge in our research led us to uncover a powerful algorithm that has surprisingly broad applications," Smith said.

Think of it: how often do scientists need to predict what they haven't seen based on what they have? Public health officials could use the algorithm to estimate the population of HIV positive individuals; astronomers could use it to determine how many exoplanets exist in our galaxy based on the ones they have already discovered; and biologists could use it to estimate the diversity of antibodies in an individual.

The mathematical underpinnings of the algorithm rely on a model of sampling from ecology known as capture-recapture. In this model, individuals are captured and tagged so that a recapture of the same individual will be known and the number of times each individual was captured can be used to make inferences about the population as a whole.

In this way scientists can estimate, for example, the number of gorillas remaining in the wild. In DNA sequencing, the individuals are the various different genomic molecules in a sample. However, the mathematical models used for counting gorillas don't work on the scale of DNA sequencing.

"The basic model has been known for decades, but the way it has been used makes it highly unstable in most applications. We took a different approach that depends on lots of computing power and seems to work best in large-scale applications like modern DNA sequencing," Daley said.

Scientists faced a similar problem in the early days of the human genome sequencing project. A mathematical solution was provided by Michael Waterman of USC, in 1988, which found widespread use. Recent advances in sequencing technology, however, require thinking differently about the mathematical properties of DNA sequencing data.

"Huge data sets required a novel approach. I'm very please it was developed here at USC," said Waterman.


'/>"/>

Contact: Robert Perkins
perkinsr@usc.edu
213-740-9226
University of Southern California
Source:Eurekalert

Related biology news :

1. Taking the pulse of volcanoes using satellite images
2. Taking a hit or 2
3. Taking Americas rarest snake back to the woods
4. Young researcher taking fight against global killer to the next level in Vietnam
5. An invasive Asian fly is taking over European fruit
6. Seals gamble with their pups futures
7. Sequencing hundreds of chloroplast genomes now possible
8. Researchers develop tool to evaluate genome sequencing method
9. Genetic sequencing breakthrough to aid treatment for congenital hyperinsulinism
10. Gene sequencing project identifies abnormal gene that launches rare childhood leukemia
11. Duke Medicine news -- Genome sequencing of Burkitt Lymphoma reveals unique mutation
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:11/30/2016)... CHICAGO , Nov. 30, 2016  higi ... a new partnership initiative targeting national brands, industry ... and reward their respective audiences for taking steps ... Since its inception in 2012, higi has built ... US, impacting over 38 million people who have ...
(Date:11/24/2016)... -- Cercacor today introduced Ember TM Sport Premium ... measure hemoglobin, Oxygen Content, Oxygen Saturation, Perfusion Index, ... approximately 30 seconds. Smaller than a smartphone, using only ... key data about their bodies to help monitor these ... Hemoglobin carries oxygen to muscles. When hemoglobin and ...
(Date:11/17/2016)... Nov. 17, 2016 Global Market Watch: ... (Disease-Based Banks, Population-Based Banks and Academics) market is to witness ... Private Biobanks shows the highest Compounded Annual Growth Rate (CAGR) ... region during the analysis period 2014-2020. North America ... 9.95% followed by Europe at 9.56% ...
Breaking Biology News(10 mins):
(Date:12/2/2016)... ... , ... DrugDev believes the only way to achieve real change ... three tenets were on display at the 2nd Annual DrugDev User Summit (hosted by ... and site organizations to discuss innovation and the future of clinical research. , ...
(Date:12/2/2016)... ... December 02, 2016 , ... Robots will storm the Prudential Center in Boston, ... The event, which is held on the United Nations International Day of Persons with ... into the workplace. Suitable Technologies is partnering with NTI to showcase how technology can ...
(Date:12/2/2016)... leader in rapid infectious disease tests, introduced the Company,s newest product, the INSTI HIV ... http://photos.prnewswire.com/prnh/20161201/444905 ) Continue Reading ... ... , bioLytical was invited by the Clinton Health ... Self Test to 350 pharmacy representatives in Nairobi and Mombasa, ...
(Date:11/30/2016)... , November 30, 2016 ... a few players hold a dominant share in the ... River Laboratories International, Inc., and Merck KGaA, held a ... 2015. Transparency Market Research observes that these companies are ... on development products that are do not require rabbit ...
Breaking Biology Technology: