Navigation Links
New virtual tool may provide more accurate diagnosis of genetic mutations
Date:2/5/2012

Philadelphia, PA, February 6, 2012 DNA sequencing to detect genetic mutations can aid in the diagnosis and selection of treatment for cancer. Current methods of testing DNA samples, Sanger sequencing and pyrosequencing, occasionally produce complex results that can be difficult or impossible to interpret. Scientists at the Johns Hopkins University School of Medicine have developed a free software program, Pyromaker, that can more accurately identify such complex genetic mutations.

Pyromaker is a web-based application that produces simulated pyrograms based on user input including the percentage of tumor and normal cells, the wild-type sequence, the dispensation order, and any number of mutant sequences. Pyromaker calculates the relative mutant and wild-type allele percentages and then uses these to generate the expected signal at each point in the dispensation sequence. The final result is a virtual trace of the expected pyrogram.

The researchers validated Pyromaker against actual pyrograms containing common mutations in the KRAS gene, which plays an important role in the pathogenesis of a variety of tumors. The actual pyrograms and virtual pyrograms were quantitatively identical for all mutations tested.

They then demonstrated that all codon 12 and 13 single and complex mutations generate unique pyrograms. However, some complex mutations were indistinguishable from single base mutations, indicating that complex mutations may be underreported. Working with two complex pyrograms that were difficult to interpret initially, the researchers identified five approaches to resolve them: Sanger sequencing alone, hypothesis testing with Pyromaker, Pyromaker iterative mutation re-creation, melting curve analysis, and TA cloning with Sanger sequencing.

Senior author James R. Eshleman, MD, PhD, Professor of Pathology and Oncology, Associate Director, Molecular Diagnostics Laboratory, Johns Hopkins University School of Medicine, explains, "User-directed hypothesis testing allows for generating virtual traces that can be compared to the actual data to clarify ambiguous results from pyrosequencing and the Sanger method. Alternatively, Pyromaker can quickly and efficiently test the possibilities that can explain a complicated polysequencing result." Both strategies were able to successfully identify the complex mutations.

TA cloning and sequencing also provided unequivocal interpretation, but this method is labor intensive, risks plasmid contamination of the laboratory, may delay reporting, and is not routinely used in most clinical diagnostic laboratories.

"Although pyrosequencing and Sanger sequencing are both powerful tools to resolve most mutations, for certain complex cases, neither of them alone is enough to provide a definitive interpretation," notes Dr. Eshleman. "Additional methods, such as Pyromaker analysis or TA cloning and sequencing, allow one to definitively diagnose the variant allele. Pyromaker is available free online and can be accessed from any computer with internet access. Iterative Pyromaker analysis is the least expensive and fastest method to resolve these cases."


'/>"/>

Contact: David Sampson
jmdmedia@elsevier.com
215-239-3171
Elsevier Health Sciences
Source:Eurekalert

Related biology news :

1. £20 million to fight virtual crime and treat our ageing population
2. £20 million to fight virtual crime and treat our aging population
3. Virtual reality: Keyhole surgeons training could help meet European working time directives
4. A virtual physicians conference
5. ASCB wins NIH stimulus grant to build virtual library of cell images for researchers and public
6. CSI in a virtual world: New grant furthers NC States work in forensic science
7. A virtual liver, a better chance of life
8. Glencoe Software to Support the ASCB Stimulus Grant to Build Virtual Image Library of the Cell
9. Penn bioengineers create simulator to test blood platelets in virtual heart attacks
10. Designing touch-sensitive virtual reality tools to train and test tomorrows surgeons
11. Wiecha receives grant to study face-to-face vs. virtual health education for African-American women
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:3/27/2017)... CENTRE, N.Y. , March 27, 2017 /PRNewswire-USNewswire/ ... Healthcare Information and Management Systems Society (HIMSS) Analytics ... Outpatient EMR Adoption Model sm . In addition, ... 12% of U.S. hospitals using an electronic medical ... CHS for its high level of EMR usage ...
(Date:3/23/2017)... , March 23, 2017 The report "Gesture Recognition ... Biometric), Industry, and Geography - Global Forecast to 2022", published by MarketsandMarkets, the ... a CAGR of 29.63% between 2017 and 2022. ... ... ...
(Date:3/22/2017)... YORK , March 21, 2017 ... Marketing Cloud used by retailers such as 1-800-Flowers ... its platform — Product Recommendations and Replenishment. Using Optimove,s ... give more personalized product and replenishment recommendations to ... but also on predictions of customer intent drawn ...
Breaking Biology News(10 mins):
(Date:8/15/2017)... ... August 15, 2017 , ... JULABO USA ... responsive, the new website makes it easy to navigate through the site whether ... now find detailed product information, educational industry content and visit the company’s social ...
(Date:8/11/2017)... 2017  Market researcher Kalorama Information was ... regarding the telemedicine market.  The telemedicine market ...  The article, "Heart and Asthma Monitors? ... information from Kalorama Information,s Remote Patient Monitoring ...  (Sleep, Diabetes, Vital Signs /EKG and ...
(Date:8/10/2017)... Indiana (PRWEB) , ... August 09, 2017 , ... ... equipped to help the agriculture industry reach its ideal customers with the right ... the nation. , “As a Midwest company, we realize how crucial the agriculture ...
(Date:8/10/2017)... ... August 09, 2017 , ... Okyanos Center for Regenerative Medicine has ... Pelican Bay Hotel in Freeport, Grand Bahama on September 27, 2017. This daytime event ... With oversight from the Ministry of Health’s National Stem Cell Ethics Committee (NSCEC) and ...
Breaking Biology Technology: