VIP

VIP analyzes 454/Roche GS-FLX amplicon resequencing data to detect and report genetic variants for diagnostic and research applications.

Key Features:

• Integrated Database-Oriented Pipeline: Uses Perl scripting and a relational database to manage and analyze 454/Roche GS-FLX amplicon resequencing experiments.
• Variation Detection and Validation: Identifies genetic variants and includes mechanisms for validating variant calls.
• Advanced Data Analysis: Performs analyses that inform PCR efficiency optimization using traditional analytical methods.
• Modular Design: Modular architecture supports customization and integration with variant interpretation modules and Laboratory Information Management Systems (LIMS).
• Standard Reporting Scripts: Includes scripts that generate standardized reports of variant calls and analyses.

Scientific Applications:

• High-Throughput Genetic Diagnostics: Enables simultaneous sequencing of multiple genes across many patients in a single 454/Roche GS-FLX run to increase diagnostic throughput.
• PCR Optimization: Provides analytical outputs to evaluate and refine PCR reaction efficiency.
• Customizable Analysis Pipelines: Allows researchers to tailor analysis workflows to specific project requirements.

Methodology:

Perl scripts execute SQL statements against a relational database to manage and analyze 454/Roche GS-FLX amplicon resequencing data and to generate standardized reports.