Navigation Links
Novel gene-searching software improves accuracy in disease studies
Date:1/22/2013

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 accuratelya 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 studiesperhaps through an initial diagnostic screen, to be followed up with a CLIA-certified laboratory test."


'/>"/>

Contact: John Ascenzi
ascenzi@email.chop.edu
267-426-6055
Children's Hospital of Philadelphia
Source:Eurekalert

Related medicine news :

1. Novel compound demonstrates anti-leukemic effect in zebrafish, shows promise for human treatment
2. Rutgers team discovers novel approach to stimulate immune cells
3. Novel drug candidates offer new route to controlling inflammation
4. Researchers present new findings for novel pancreatic cancer vaccine
5. Novel biomarkers reveal evidence of radiation exposure
6. VCU Massey Cancer Center sees potential in novel leukemia treatment
7. Study supports urate protection against Parkinsons disease, hints at novel mechanism
8. Novel Natural Sciences Repository Opens Web Portal
9. Novel Anti-Inflammatories May Offer a New Approach for the Treatment of Stroke
10. LA BioMed investigators, Drs. Kevin Bruhn and Noah Craft, develop novel treatment for melanoma
11. Novel radiation therapy safely treats prostate cancer and lowers the risk of recurrence
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:6/25/2016)... ... ... On Friday, June 10, Van Mitchell, Secretary of the Maryland Department of Health and ... their exemplary accomplishments in worksite health promotion. , The Wellness at Work Awards took ... the BWI Marriott in Linthicum Heights. iHire was one of 42 businesses to receive ...
(Date:6/24/2016)... ... June 24, 2016 , ... June 19, 2016 is World ... with chronic pain and the benefits of holistic treatments, Serenity Recovery Center ... with Sickle Cell Disease. , Sickle Cell Disease (SCD) is a disorder of the ...
(Date:6/24/2016)... Francisco, CA (PRWEB) , ... June 24, 2016 ... ... CitiDent, is now offering micro-osteoperforation for accelerated orthodontic treatment. Dr. Cheng has extensive ... self-ligating Damon brackets , AcceleDent, and accelerated osteogenic orthodontics. , Micro-osteoperforation ...
(Date:6/24/2016)... ... June 24, 2016 , ... ... the Clinical Decision Making in Emergency Medicine conference in Ponte Vedra Beach, FL. ... articles published in Emergency Medicine Practice and Pediatric Emergency Medicine Practice. ...
(Date:6/24/2016)... ... 2016 , ... National recruitment firm Slone Partners is pleased to ... genomics experience, as Vice President of North American Capital Sales at HTG Molecular ... the sales team in the commercialization of the HTG EdgeSeq system and associated reagents ...
Breaking Medicine News(10 mins):
(Date:6/26/2016)... , June 27, 2016  VMS Rehab Systems, Inc. ... will take whatever measures required to build a strong ... which is currently listed on the OTC Markets-pink current ... Chairman and CEO, "We are seeing an anomaly in ... understand, not only by the Company, but shareholders and ...
(Date:6/24/2016)... 24, 2016   Bay Area Lyme Foundation ... Dean Center for Tick Borne Illness , Harvard ... MIT Hacking Medicine, University of California, Berkeley, and ... the five finalists of Lyme Innovation , ... than 100 scientists, clinicians, researchers, entrepreneurs, and investors ...
(Date:6/24/2016)... and SAN CLEMENTE, Calif. , June 24, 2016 ... mobile pulmonary function testing company, is now able to perform sophisticated ... by ndd Medical Technologies , Inc. Patients ... hospital-based labs.  Thanks to ndd,s EasyOne PRO ® , ARL patients ... get any needed testing done in the comfort of her own ...
Breaking Medicine Technology: