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:4/19/2017)... , April 19, 2017 ... its vendor landscape is marked by the presence of ... is however held by five major players - 3M ... these companies accounted for nearly 61% of the global ... leading companies in the global military biometrics market boast ...
(Date:4/13/2017)... , April 13, 2017 According to a new ... Authentication, Identity Analytics, Identity Administration, and Authorization), Service, Authentication Type, Deployment Mode, ... IAM Market is expected to grow from USD 14.30 Billion in 2017 ... (CAGR) of 17.3%. ... MarketsandMarkets Logo ...
(Date:4/11/2017)... 2017 NXT-ID, Inc. (NASDAQ:   NXTD ... the appointment of independent Directors Mr. Robin D. Richards ... of Directors, furthering the company,s corporate governance and expertise. ... Gino Pereira , Chief ... to their guidance and benefiting from their considerable expertise as ...
Breaking Biology News(10 mins):
(Date:4/27/2017)... ... April 27, 2017 , ... Oncolinx, a spin-out of the ... has truly taken their cancer research out of this world. On April 22, ... Canaveral to the International Space Station’s (ISS) U.S. National Laboratory, managed by the ...
(Date:4/27/2017)... ... April 27, 2017 , ... Arrowhead Publishers ... http://www.paintherapeuticsummit.com ) is coming to San Diego, CA on September 27-28, 2017. Leaders ... about the latest advances in the treatment of various types of pain. There ...
(Date:4/27/2017)... ... April 27, 2017 , ... Volunteers supported by SPIE, ... and industry professionals in visiting U.S. Congressional offices in Washington, D.C., yesterday to ... photonics industry. , This year, National Photonics Initiative (NPI) Congressional Visits ...
(Date:4/26/2017)... ... April 26, 2017 , ... ... premiere team-building and cooking events company, offers one-of-a-kind gifts, ranging from gourmet cooking ... in California cuisine, and guests leave inspired with new cooking tips and techniques, ...
Breaking Biology Technology: