Molecular Dissection of Structural Variations Involved in Antithrombin Deficiency

Area of Science:

• Genetics
• Molecular Biology
• Hematology

Background:

• Inherited antithrombin deficiency is a severe form of thrombophilia, primarily linked to variations in the SERPINC1 gene.
• Previous detection of structural variants in SERPINC1 was limited, often only indicating gain/loss and approximate size/location.

Purpose of the Study:

• To comprehensively analyze and characterize structural variants within the SERPINC1 gene in patients with antithrombin deficiency.
• To identify the mechanisms and common formation pathways of these structural variants.
• To evaluate nanopore sequencing as a method for identifying and characterizing SERPINC1 structural variants.

Main Methods:

• Employed multiplex ligation-dependent probe amplification, comparative genome hybridization array, long-range PCR, and whole genome nanopore sequencing.
• Analyzed 39 unrelated patients with antithrombin deficiency.
• Focused on nucleotide-level characterization of structural variants.

Main Results:

• Identified diverse structural variants in SERPINC1, predominantly deletions (82.1%) affecting exons, but also including duplications, intron deletions, and retrotransposon insertions.
• Variants ranged from 193 bp to 8 Mb, often involved neighboring genes (54%), and typically occurred in regions with repetitive elements or microhomologies.
• Discovered three structural variants with a founder effect and confirmed nanopore sequencing's efficacy in comprehensive variant characterization.

Conclusions:

• Structural variants in SERPINC1 are heterogeneous and a significant cause of severe type I antithrombin deficiency.
• Repetitive elements and microhomologies likely drive the formation of these variants.
• Nanopore sequencing is the optimal method for complete identification and characterization of SERPINC1 structural variants.