Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


Novel gene-searching software improves accuracy in disease studies

Children's Hospital of Philadelphia scientist develops versatile tool for finding disease-causing CNVs

A novel software tool, developed at The Children's Hospital of Philadelphia, streamlines the detection of disease-causing genetic changes through more sensitive detection methods and by automatically correcting for variations that reduce the accuracy of results in conventional software.

The software, called ParseCNV, is freely available to the scientific-academic community, and significantly advances the identification of gene variants associated with genetic diseases.

"The algorithm we developed detects copy number variation associations with a higher level of accuracy than that available in existing software," said the lead inventor of ParseCNV, Joseph T. Glessner, of the Center for Applied Genomics at The Children's Hospital of Philadelphia. "By automatically correcting for variations in the length of deleted or duplicated DNA sequences from one individual to another, ParseCNV produces high-quality, highly replicable results for researchers studying genetic contributions to disease."

Glessner is the lead author of a study describing ParseCNV, published Jan. 4 in Nucleic Acids Research.

Copy number variations (CNVs) are particular sequences of DNA, ranging in length from 1000 to millions of nucleotide bases, which may be deleted or duplicated. While in any given region of a person's DNA, CNVs are very rare, everyone's genome has CNVs, many of which play important roles in causing or influencing disease.

In searching for associations between CNVs and diseases, researchers typically perform case-control studies, comparing DNA samples from patients to DNA from healthy individuals, looking for telltale differences in how CNVs are overrepresented or underrepresented.

CNVs, however, occur in multiple types among individuals, said senior author Hakon Hakonarson, M.D., Ph.D., director of the Center for Applied Genomics at The Children's Hospital of Philadelphia. "One person may have a 60-kilobase deletion, while another may have a 100-kilobase deletion; that may determine the difference between a healthy state versus disease. Many CNV detection softwares may misread the boundary of a CNV region, which could lead to a misclassification and result in false-positive or false-negative associations."

ParseCNV is designed with built-in corrections to adjust for these size variations and other red flags that confound results. Using polymerase chain reaction testing to validate the initial findings, the study team determined that the software had called 90 percent of the CNVs accurately—a better rate than conventional CNV association softwares, which typically produce validation rates that are notably lower.

The authors say the program's comprehensive design, statistical capabilities, and quality-control features lend it versatility, applicable not just to case-control studies, but also to family studies, and quantitative analyses of continuous traits, such as obesity or height.

Glessner says the Center for Applied Genomics team will continue to refine ParseCNV's features as CNV research progresses. Hakonarson adds that the ParseCNV algorithm will advance genomic diagnostics: "It is likely to play a future key role as a research tool in improving detection of CNV association in individual patients enrolled in disease studies—perhaps through an initial diagnostic screen, to be followed up with a CLIA-certified laboratory test."

An Institutional Development Award from The Children's Hospital of Philadelphia supported this research, along with the Cotswold Foundation and a donation from Adele and Daniel Kubert. The third co-author, also from the Children's Hospital genome center, was Jin Li.

"ParseCNV integrative copy number variation association software with quality tracking," Nucleic Acids Research, published online Jan. 4, 2013.

About The Children's Hospital of Philadelphia: The Children's Hospital of Philadelphia was founded in 1855 as the nation's first pediatric hospital. Through its long-standing commitment to providing exceptional patient care, training new generations of pediatric healthcare professionals and pioneering major research initiatives, Children's Hospital has fostered many discoveries that have benefited children worldwide. Its pediatric research program is among the largest in the country, ranking third in National Institutes of Health funding. In addition, its unique family-centered care and public service programs have brought the 516-bed hospital recognition as a leading advocate for children and adolescents. For more information, visit

John Ascenzi | EurekAlert!
Further information:

More articles from Life Sciences:

nachricht Two decades of training students and experts in tracking infectious disease
27.11.2015 | Hochschule für Angewandte Wissenschaften Hamburg

nachricht Increased carbon dioxide enhances plankton growth, opposite of what was expected
27.11.2015 | Bigelow Laboratory for Ocean Sciences

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Climate study finds evidence of global shift in the 1980s

Planet Earth experienced a global climate shift in the late 1980s on an unprecedented scale, fuelled by anthropogenic warming and a volcanic eruption, according to new research published this week.

Scientists say that a major step change, or ‘regime shift’, in the Earth’s biophysical systems, from the upper atmosphere to the depths of the ocean and from...

Im Focus: Innovative Photovoltaics – from the Lab to the Façade

Fraunhofer ISE Demonstrates New Cell and Module Technologies on its Outer Building Façade

The Fraunhofer Institute for Solar Energy Systems ISE has installed 70 photovoltaic modules on the outer façade of one of its lab buildings. The modules were...

Im Focus: Lactate for Brain Energy

Nerve cells cover their high energy demand with glucose and lactate. Scientists of the University of Zurich now provide new support for this. They show for the first time in the intact mouse brain evidence for an exchange of lactate between different brain cells. With this study they were able to confirm a 20-year old hypothesis.

In comparison to other organs, the human brain has the highest energy requirements. The supply of energy for nerve cells and the particular role of lactic acid...

Im Focus: Laser process simulation available as app for first time

In laser material processing, the simulation of processes has made great strides over the past few years. Today, the software can predict relatively well what will happen on the workpiece. Unfortunately, it is also highly complex and requires a lot of computing time. Thanks to clever simplification, experts from Fraunhofer ILT are now able to offer the first-ever simulation software that calculates processes in real time and also runs on tablet computers and smartphones. The fast software enables users to do without expensive experiments and to find optimum process parameters even more effectively.

Before now, the reliable simulation of laser processes was a job for experts. Armed with sophisticated software packages and after many hours on computer...

Im Focus: Quantum Simulation: A Better Understanding of Magnetism

Heidelberg physicists use ultracold atoms to imitate the behaviour of electrons in a solid

Researchers at Heidelberg University have devised a new way to study the phenomenon of magnetism. Using ultracold atoms at near absolute zero, they prepared a...

All Focus news of the innovation-report >>>



Event News

Fraunhofer’s Urban Futures Conference: 2 days in the city of the future

25.11.2015 | Event News

Gluten oder nicht Gluten? Überempfindlichkeit auf Weizen kann unterschiedliche Ursachen haben

17.11.2015 | Event News

Art Collection Deutsche Börse zeigt Ausstellung „Traces of Disorder“

21.10.2015 | Event News

Latest News

Siemens to supply 126 megawatts to onshore wind power plants in Scotland

27.11.2015 | Press release

Two decades of training students and experts in tracking infectious disease

27.11.2015 | Life Sciences

Coming to a monitor near you: A defect-free, molecule-thick film

27.11.2015 | Materials Sciences

More VideoLinks >>>