The Quality Sequencing Minimum (QSM): providing comprehensive, consistent, transparent next generation sequencing...

Area of Science:

• Clinical Genetics
• Bioinformatics
• Genomic Medicine

Background:

• Next-generation sequencing (NGS) is crucial for clinical genetic testing, demanding robust quality management.
• Current quality evaluation relies on metrics like depth of coverage, base quality, and mapping quality.
• A standardized approach is needed for consistent and transparent quality assessment.

Purpose of the Study:

• To introduce the Quality Sequencing Minimum (QSM), a novel metric for standardizing NGS quality evaluation.
• To demonstrate the utility of QSM in optimizing clinical genetic testing workflows.
• To facilitate consistent and transparent reporting of genetic test performance.

Main Methods:

• The QSM metric is defined as CX_BY(P_Y)_MZ(P_Z), specifying minimum thresholds for coverage (C), base quality (B), and mapping quality (M), along with the required percentage of reads.
• QSM is automatically calculable from standard BAM files within any NGS pipeline.
• The QSM was applied to optimize cancer predisposition gene testing using the TruSight Cancer Panel (TSCP) and assess genes with pseudogenes.

Main Results:

• Application of QSM (C50_B10(85)_M20(95)) to TSCP identified 100/1471 regions needing review, with subsequent probe addition improving performance in 85/100.
• Testing of genes with pseudogenes like PTEN and PMS2 showed 97% of regions passed QSM in 960 individuals.
• QSM effectively flagged regions for review and optimization, enhancing testing accuracy.

Conclusions:

• The QSM provides a consistent and transparent method for evaluating NGS quality in clinical genetic testing.
• Its adoption can improve the reliability and comparability of genetic test results across different laboratories.
• QSM facilitates succinct quality assurance reporting at the individual test level.