Bioinformatics Core Launches High-Resolution Copy Number Variation Analysis Service


The Stokes Bioinformatics Core recently launched its newest service — genome-wide copy number variation (CNV) analysis. The service is available to all members of the Hospital's research community.

A major source of human diversity, CNVs contribute to the cause of many diseases and mediate phenotypic changes that may or may not be the result of a chromosomal deletion. A rapid and high-resolution method for detecting genomic CNVs and determining their role in disease becomes critical as the role of variations becomes better understood.

To address this need, the Bioinformatic Core's designed its CNV analysis service to allow investigators to break through some of the principal barriers in analyzing this type of data. The Core provides access to both the algorithm that identifies such CNVs and interactive annotations to interpret the chromosomal regions affected. Both analysis and interpretation are driven by a highly intuitive, Web-based platform tentatively named CHOPPY.

The algorithm for the new service was developed in collaboration with the Center for Applied Genomics by using thousands of available baseline microarray samples that represent a healthy pediatric population. Investigators can then combine this robust baseline with the algorithm to quickly identify CNVs for experimental samples.
The Bioinformatics Core has incorporated publicly available genomics resources into the results from CHOPPYto automatically annotate CNV chromosomal locales with information like gene name, ontology information, and reported disease labels. In addition, the platform is fully integrated with the UCSC Genome Browser. Researchers can navigate freely through the list of CNVs using the default list of annotations and can easily click through to publicly hosted Web sites that offer more in-depth information on individual genes of interest.

The Core has also developed advanced capabilities and knowledge in the more general CNV arena. Core members are available for consultation, grant preparation support and general collaboration for CNV projects and will work individually with researchers to provide additional interpretation of results or to develop more customized solutions for CNV problems.

The Bioinformatics Core and the Center for Applied Genomics are collaborating with Stokes investigators on several different CNV studies that focus on pediatric diseases. To date, the Core has processed approximately 7,750 different samples. The Core can process results for up to 1,000 samples in a few days.

Under the supervision of interim director, Xiaowu Gai, Ph.D., and faculty advisor, Peter White, Ph.D., the Bioinformatics Core plans to further develop CNV analysis to establish statistical significance of variation signals and to optimize the use of metadata to better prioritize results.

The new service expands the current capabilities of the group, who also offer support in the areas of gene expression microarray analysis, nucleotide and protein sequence informatics, advanced computing platforms, and bioinformatics software training and implementation.

To learn more or to contact the Bioinformatics Core for this or other services, please visit the Core's Web site at: or contact Dr. Gai at