SeqReporter: automating next-generation sequencing result interpretation and reporting workflow in a clinical...

Area of Science:

• Bioinformatics
• Clinical Molecular Diagnostics
• Next-Generation Sequencing (NGS) Data Analysis

Background:

• Bioinformatics tools for next-generation sequencing (NGS) data analysis often fall short of clinical molecular laboratory requirements.
• Key limitations include comprehensive report generation, laboratory information system (LIS) compatibility, knowledgebase development, quality management, and data security.

Purpose of the Study:

• To develop and evaluate SeqReporter, a web-based application designed to overcome the limitations of existing bioinformatics tools in clinical settings.
• To automate and optimize the downstream analysis of clinical NGS data, ensuring comprehensive reporting and LIS compatibility.

Main Methods:

• SeqReporter was developed using ASP.NET framework (version 4.0) with a VB.NET server-side and a customized SQL server 2008 R2 database.
• Client-side technologies included HTML5, CSS3, and Javascript.
• The application analyzed 104 cases (1062 variant calls), classifying each into five report levels.

Main Results:

• SeqReporter achieved 99.9% accuracy in annotating and classifying sequence variants (859 out of 860).
• Classifications included known clinical significance, uncertain significance, pending review, synonymous/intronic, and errors.
• Automated generation of LIS-compatible clinical reports and facilitation of quality management activities were demonstrated.

Conclusions:

• SeqReporter is a customized informatics solution that effectively optimizes and automates clinical NGS data analysis.
• It serves as a model for developing comprehensive clinical informatics solutions addressing laboratory-specific needs.