Test development, optimization and validation of a WGS pipeline for genetic disorders.

Area of Science:

• Genomics
• Clinical Diagnostics
• Bioinformatics

Background:

• Whole-genome sequencing (WGS) is increasingly vital for diagnosing genetic disorders.
• Clinical deployment and pipeline validation for WGS are currently limited.
• Advances in massive parallel sequencing (MPS) drive WGS adoption.

Purpose of the Study:

• To introduce and validate a comprehensive WGS pipeline for genetic disorder diagnostics.
• To establish best practices for clinical WGS implementation.
• To provide a benchmark dataset for WGS pipeline evaluation.

Main Methods:

• Developed a complete WGS pipeline from sample acquisition to clinical reporting.
• Utilized PCR-free library preparation and MGISEQ-2000 sequencing.
• Implemented bioinformatics tools for simultaneous detection of SNVs, indels, CNVs, balanced rearrangements, MT variants, and complex variants.
• Validated the pipeline using 45 samples with known variants.

Main Results:

• Successfully developed and optimized a WGS pipeline for genetic disorders.
• The pipeline demonstrated effectiveness in detecting diverse variants, including SNVs, indels, CNVs, balanced rearrangements, MT variants, repeat expansions, and AOHs.
• Validation confirmed the pipeline's capability across various known genetic variants.

Conclusions:

• The developed WGS pipeline is effective for genetic disorder diagnostics.
• Recommended best practices for pipeline usage and provided a positive sample dataset for benchmarking.
• The study contributes to the standardization and validation of clinical WGS.