Tag Archives: clinical studies

Guest Post: CHOP’s new tool, CNV Workshop – Xiaowu Gai

This next post in our continuing semi-regular Guest Post series is from Xiaowu Gai, the Bioinformatics Core Director at CHOP . If you are a provider of a free, publicly available genomics tool, database or resource and would like to convey something to users on our guest post feature, please feel free to contact us at wlathe AT openhelix DOT com.

Thanks to Mary for running a Tip of the Week – “CHOP CNV database” a couple of months back. CHOP CNV database is a high-resolution genome-wide survey of copy number variations of a large number (2,026) of apparently healthy individuals. It is publicly accessible and has been widely used by a large number of research groups world-wide. I am now pleased to announce the public release of our software system behind it: CNV Workshop. CNV Workshop is a suite of software tools that we have developed over the last a few years. It provides a comprehensive workflow for analyzing, managing, and visualizing genome copy number variation (CNV) data.

It can be used for almost any CNV research or clinical project by offering the following capabilities for both individual samples and cohort studies:

CNV identification
Implements a modified circular binary segmentation algorithm that reduces false positives
Fully configurable parameters for sensitivity/specificity management
Annotation
Individual locus-specific annotations such as position, type of variation, call metrics, and overlap with CNVs of other data sets, including the Database of Genomic Variants.
Functional gene annotations such as genes affected and known disease associations
Accepts user-provided annotations
Presentation
GBrowse-enabled visuals for querying, browsing, interpreting, and reporting CNVs
Export of results into Excel, XML, CSV, and BED files
Direct links to public resources such as the UCSC Genome Browser, NCBI Entrez, Entrez Gene, and FABLE
Project and Account Management
Authentication and permission scheme that is especially useful for clinical diagnostic settings
Analysis result sharing within and between projects
Simple Web-based administrative interface
Remote access and administration enabled

CNV Workshop currently accepts genotyping array data from Illumina’s 550k, 610- and 660-Quad, and Omni arrays, along with Affymetrix’s 5.0 and 6.0 arrays, and can be easily configured to accept data from other platforms. The package comes preloaded with publicly available reference data from more than 2,000 healthy control subjects (the CHOP CNV Database). CNV Workshop also allows the user to upload already processed CNV calls for annotation and presentation.

The software package is freely available at http://sourceforge.net/projects/cnv/. It is also described in more detailed in our recent paper on BMC Bioinformatics.

-Xiaowu Gai

Tip of the Week: Phenotypic Data from the PhysioNet

PhysioNet TipOne of the things I’ve been thinking about lately are connections between genotype and phenotype – it is a topic in the news & I have been working on tutorials for the genotype-to-phenotype resources PhenomicDB & NCI’s dbGaP. Recently a friend notified of an article in Science featuring the PhysioNet – a resource intended to stimulate current research and new investigations in the study of complex biomedical and physiologic signals. The article was interesting & so I checked out this nice resource. In this short video I introduce you to a few of the features and data types available from the PhysioNet. You can read more about the PhysioNet, or see their mission statment by following the ‘continue reading’ link.

Continue reading