Smart Nonuniformity for Calibrating Sequencing Depth of a Targeted Gene Panel to Simultaneously Detect Somatic and...

Area of Science:

• Genomics
• Molecular Diagnostics
• Bioinformatics

Background:

• Targeted gene panel sequencing offers diagnostic potential for genomic variations.
• Clonal hematopoiesis of indeterminate potential (CHIP) involves somatic variants requiring high sequencing depth (>500×).
• Germline variants require lower sequencing depth (≥50×).

Purpose of the Study:

• To develop and validate a targeted gene panel for detecting both CHIP-associated somatic variants and germline variants.
• To optimize sequencing depth ratios for different variant types within a single panel.
• To confirm the accuracy and reliability of the developed panel for variant detection.

Main Methods:

• Designed a dual-depth targeted gene panel (panel 1) adjusting probe ratios for CHIP and germline regions.
• Manufactured a custom CHIP-specific panel (panel 2) for validation.
• Sequenced 150 diverse blood-derived DNA samples using both panels.
• Analyzed sequencing data for variant calling and depth ratios.

Main Results:

• The median depth ratio between CHIP and germline regions was 4.7:1.
• Fourteen CHIP-associated variants were accurately identified by both panels.
• All known germline variants were successfully detected.
• Smart nonuniformity sequencing demonstrated reliable detection of variants with allele frequencies from 0.01 to 1.

Conclusions:

• The developed targeted gene panel effectively detects both CHIP-associated somatic and germline variants in a single workflow.
• Optimized sequencing depths and probe ratios enable accurate variant identification for different genomic applications.
• This approach provides a reliable and efficient tool for molecular diagnostics.