Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions

Area of Science:

• Genomics
• Human Genetics
• Molecular Biology

Background:

• Bartter syndrome type 3 (BS 3) is a genetic disorder caused by variants in the CLCNKB gene, often large deletions.
• Current diagnostic methods may not fully characterize complex rearrangements in BS 3 patients.
• Structural variants, particularly in repetitive regions, can be challenging to detect and analyze.

Purpose of the Study:

• To investigate the precise breakpoint regions and genomic structures associated with CLCNKB deletions in Bartter syndrome type 3 patients.
• To identify novel genetic variants and structural rearrangements contributing to the disease.
• To explore the role of common genetic haplotypes in the occurrence of CLCNKB deletions.

Main Methods:

• Employed long-read sequencing, synthetic long-read sequencing, and targeted long-read sequencing.
• Analyzed structural variants in 32 BS 3 patients and one BS4b patient with CLCNKB deletions.
• Investigated precise breakpoint regions and genomic structures for detailed analysis.

Main Results:

• Identified a ~3 kb duplication of 3'-UTR CLCNKB material transposed to the CLCNKA gene, present in healthy controls and significantly enriched in patients.
• Characterized eight different CLCNKB deletion alleles, including complex rearrangements and CLCNKA/CLCNKB hybrid genes.
• Confirmed CLCNKB deletions in 32 BS 3 patients and one BS4b patient, with detailed breakpoint analysis.

Conclusions:

• A common sequence transposition haplotype is associated with and likely predisposes to CLCNKB deletions, expanding the known spectrum of disease-causing alleles.
• The findings suggest multiple independent recurrent genomic events at specific hotspots contribute to CLCNKB deletions.
• Propose a sensitive, cost-efficient method using indirect sequence capture and long-read sequencing for analyzing structural variant hotspots.