A clinically validated whole genome pipeline for structural variant detection and analysis

Area of Science:

• Genomics
• Clinical Diagnostics

Background:

• Whole genome sequencing (WGS) costs are decreasing, making it economically feasible for broader clinical application.
• WGS offers unique opportunities for structural variant detection, but its clinical use is limited.
• Structural variant analysis is crucial for diagnosing genetic disorders.

Purpose of the Study:

• To develop and validate a clinical pipeline for accurate structural variant detection using PCR-free WGS.
• To enable routine clinical application of structural variant analysis.
• To improve diagnostic yield for genetic disorders.

Main Methods:

• Development of a clinically validated pipeline using 30X PCR-free WGS.
• Combination of breakpoint analysis (split/discordant reads) and read depth analysis.
• Minimization of false positives using loss of heterozygosity and bi-modal heterozygous variant allele frequencies.
• Automatic detection of compound structural variants and small sequence changes.
• Annotation with phenotype (HGMD Professional) and population allele frequencies.

Main Results:

• Highly specific and sensitive detection of structural variants down to single base pair resolution.
• Enhanced detection of heterozygous deletions and duplications.
• Validated analytical and clinical sensitivity and specificity using reference genomes and orthogonal technologies.
• Facilitated clinical interpretation through comprehensive annotation.

Conclusions:

• Consistent read depth in PCR-free WGS enables reliable detection of structural variants of all sizes.
• Gene and variant level annotation aids clinicians in matching phenotypes to variants.
• The pipeline confidently identifies causative findings for clinical reporting.