BGRF announces OncoFinder algorithm for reducing errors in transcriptome analysis

Scientists from the Biogerontology Research Foundation (BGRF), a UK-based charity founded to support ageing research and address the challenges of a rapidly ageing population, propose a new concept for signalome-wide analysis of changes in intracellular pathways, called OncoFinder, which allows for accurate and robust cross-platform analysis of gene expression data. This new technique will allow scientists to derive useful information from and compare the hundreds of thousands of data sets obtained using legacy equipment as well as data sets obtained from biological samples preserved in paraffin blocks and partially-degraded samples.

The original research, published in the journal Frontiers in Molecular Biosciences, shows that the OncoFinder method significantly reduces errors introduced by transcriptome-wide experimental techniques. Scientists compared gene expression data for the same obtained by both next generation sequencing (NGS) and microarray methods, finding that these different techniques have almost no correlation between the gene expression values for all datasets analysed. In contrast, when the OncoFinder algorithm is applied to the data, a clear correlation between next generation sequencing and microarray gene expression datasets was seen.

"For several years the potential for the use of in research and clinical applications has been underappreciated due to the inconsistency of the data coming from the various types of equipment. There is just too much variation and complexity when comparing the massive number of individual genes. But when this complexity is reduced and the is mapped onto signalling pathways, we can evaluate the pathway activation drift and analyse the changes and transitions much more effectively. The OncoFinder algorithm enables scientists to characterise the functional states of transcriptomes more accurately than before and we hope that this will become a method of choice in genetics, physiology, biomedicine and molecular diagnostics," said Alex Zhavoronkov, PhD, director of the BGRF and co-author of the study.

More information: journal.frontiersin.org/Journa… .2014.00008/abstract

Related Stories

New bioinformatics tool to visualize transcriptomes

date Mar 09, 2014

ZENBU, a new, freely available bioinformatics tool developed at the RIKEN Center for Life Science Technology in Japan, enables researchers to quickly and easily integrate, visualize and compare large amounts of genomic information ...

Recommended for you

Genetic testing in kids is fraught with complications

date Jul 02, 2015

A woman coping with the burden of familial breast cancer can't help but wonder if her young daughter will suffer the same fate. Has she inherited the same disease-causing mutation? Is it best to be prepared ...

Cause of acute liver failure in young children discovered

date Jul 02, 2015

Acute liver failure is a rare yet life-threatening disease for young children. It often occurs extremely rapidly, for example, when a child has a fever. Yet in around 50 percent of cases it is unclear as to why this happens. ...

Genome sequencing illuminates rare Aicardi syndrome

date Jul 02, 2015

As my inbox fills with ever more updates on the number of human genomes sequenced and the plummeting time and cost of next next next generation sequencing, I find myself hitting delete more and more often. ...

User comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.