Corporate Banner
Satellite Banner
Stem Cells, Cellular Therapy & Biobanking
>
Scientific Community
 
Become a Member | Sign in
Home>News>This Article
  News
Return

Georgia Tech Develops Computational Algorithm

Published: Tuesday, February 14, 2012
Last Updated: Tuesday, February 14, 2012
Bookmark and Share
High-throughput DNA sequencing technologies are leading to a revolution in how clinicians diagnose and treat cancer. The molecular profiles of individual tumors are beginning to be used in the design of chemotherapeutic programs optimized for the treatment of individual patients.

The real revolution, however, is coming with the emerging capability to inexpensively and accurately sequence the entire genome of cancers, allowing for the identification of specific mutations responsible for the disease in individual patients.

There is only one downside. Those sequencing technologies provide massive amounts of data that are not easily processed and translated by scientists. That’s why Georgia Tech has created a new data analysis algorithm that quickly transforms complex RNA sequence data into usable content for biologists and clinicians. The RNA-Seq analysis pipeline (R-SAP) was developed by School of Biology Professor John McDonald and Ph.D. Bioinformatics candidate Vinay Mittal. Details of the pipeline are published in the journal Nucleic Acids Research.

“A major bottleneck in the realization of the dream of personalized medicine is no longer technological. It’s computational,” said McDonald, director of Georgia Tech’s newly created Integrated Cancer Research Center. “R-SAP follows a hierarchical decision-making procedure to accurately characterize various classes of gene transcripts in cancer samples.”

There are at least 23,000 pieces of RNA in the human genome that encode the sequence of proteins. Millions of other pieces help regulate the production of proteins. R-SAP is able to quickly determine every gene’s level of RNA expression and provide information about splice variants, biomarkers and chimeric RNAs. Biologists and clinicians will be able to more readily use this data to compare the RNA profiles or “transcriptomes” of normal cells with those of individual cancers and thereby be in a better position to develop optimized personal therapies.

Personalized approaches to cancer medicine are already in widespread use for a few “cancer biomarkers” including variants of the BRAC 1 gene that can be used to identify women with a high risk of developing breast and ovarian cancer.

“Our goal was to design a pipeline that is easily installable with parallel processing capabilities,” said Mittal. “R-SAP can make 100 million reads in just 90 minutes. Running the program simultaneously on multiple CPUs can further decrease that time.”

R-SAP is open source software, freely accessible at the McDonald Lab website.

“This is another example of Georgia Tech’s ability to merge computer technology with science to create an essential feature of next-generation bioinformatics tools,” said McDonald. “We hope that R-SAP will be a useful and user-friendly instrument for scientists and clinicians in the field of cancer biology.”


Further Information

Join For Free

Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 4,000+ scientific posters on ePosters
  • More than 5,300+ scientific videos on LabTube
  • 35 community eNewsletters


Sign In



Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into TechnologyNetworks.com you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

Microparticles Create Localized Control of Stem Cell Differentiation; Reduce Growth Factor Use
Scientists report advances in the growth of 3D cellular structures.
Friday, July 12, 2013
Study Shows that Delivering Stem Cells Improves Repair of Major Bone Injuries in Rats
The study reinforces the potential value of stem cells in repairing major injuries involving the loss of bone structure.
Thursday, January 21, 2010
Scientific News
Stem Cells in Drug Discovery
Potential Source of Unlimited Human Test Cells, but Roadblocks Remain.
Designer Cell Fate Switches Could Streamline Stem Cell Biology
Researchers develop new method of reprogramming cells between cell types in a more efficient way than before.
Allen Institute Releases Gene Edited Human Stem Cell Lines
The Allen Cell Collection, a publicly available collection of gene edited pluripotent stem cells, has been made available by the Allen Institute.
Improving Drug Production with Computer Model
A model has been developed that can be used to improve and accelerate the production of biotherapeutics, cancer drugs, and vaccines.
Defining Immortality of Stem Cells
Researchers defined the mechanisms underlying increased protein quality control of pluripotent stem cells.
BioCision Forms MedCision
The new company will focus on technologies for the management and automation of vital clinical processes.
Enhancing CRISPR to Explore Further
Researchers have developed sOPTiKO, a more efficient and controllable CRISPR genome editing platform.
Stem Cells Police Themselves to Reduce Scarring
Scientists have discovered stem cells in muscle fibers change gene expressions to respond to injury.
Regenerating Diseased Hearts
Researchers from the University of Otago have probed the potential of adult stem cell types to repair diseased hearts.
Bright Red Fluorescent Protein Created
Scientists have created a bright red, fluorescent protein that could be used to track essential cellular processes.
Skyscraper Banner

SELECTBIO Market Reports
Go to LabTube
Go to eposters
 
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
4,000+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
5,300+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FOR FREE!