VarBen: Generating in Silico Reference Data Sets for Clinical Next-Generation Sequencing Bioinformatics Pipeline...

Area of Science:

• Genomics
• Bioinformatics
• Clinical Oncology

Background:

• Next-generation sequencing (NGS) is crucial for detecting somatic variants in clinical oncology.
• Current bioinformatics pipelines lack robustness and standardization for clinical variant detection.
• A shortage of appropriate reference datasets hinders pipeline development and validation.

Purpose of the Study:

• To introduce Variant Benchmark (VarBen), an open-source software for variant simulation.
• To generate customized reference datasets by directly editing sequencing reads.
• To address the need for reliable tools in clinical bioinformatics.

Main Methods:

• VarBen simulates various variants (SNVs, indels, SVs) in targeted, exome, and whole-genome sequencing data.
• The tool supports Illumina and Ion Torrent sequencing platforms.
• Variant simulation was performed on diverse datasets and compared with real-world data.

Main Results:

• Simulated data generated by VarBen are highly comparable to real-world sequencing data.
• VarBen demonstrated reliability and feasibility in variant simulation.
• A collaborative study highlighted the necessity of customized reference datasets for pipeline evaluation.

Conclusions:

• VarBen is a reliable tool for generating customized reference datasets for variant simulation.
• The software facilitates the development and validation of bioinformatics pipelines.
• VarBen can enhance the standardization and robustness of somatic variant detection in clinical practice.