Use of long-read nanopore sequencing and short-read whole genome sequencing to resolve individuals with antithrombin deficiency, a rare disease which increase the risk of thrombosis, with unknown molecular base.

Study code

Lead researcher
Dr Belén de la Morena-Barrio

Study type
Data only

Institution or company
University of Murcia (Department of Medicine), Spain

Researcher type

Speciality area
Genomics and Rare Diseases, Haematology

Recruitment Site
N/A (data only)


This project aims to resolve by nanopore sequencing patients with antithrombin deficiency, a rare disease which significantly increase the risk of thrombosis, in patients with no mutation detected to date in order to fully characterise them.


de la Morena-Barrio, B., Stephens, J., de la Morena-Barrio, M., Stefanucci, L., Padilla, J., Miñano, A., et al. (2022). 'Long-read sequencing identifies the first retrotransposon insertion and resolves structural variants causing antithrombin deficiency.' Thromb Haemost, 122(08): 1369-1378. (link)


The identification of inherited antithrombin deficiency (ATD) is critical to prevent potentially life-threatening thrombotic events. Causal variants in SERPINC1 are identified for up to 70% of cases, the majority being single-nucleotide variants and indels. The detection and characterization of structural variants (SVs) in ATD remain challenging due to the high number of repetitive elements in SERPINC1. Here, we performed long-read whole-genome sequencing on 10 familial and 9 singleton cases with type I ATD proven by functional and antigen assays, who were selected from a cohort of 340 patients with this rare disorder because genetic analyses were either negative, ambiguous, or not fully characterized. We developed an analysis workflow to identify disease-associated SVs. This approach resolved, independently of its size or type, all eight SVs detected by multiple ligation-dependent probe amplification, and identified for the first time a complex rearrangement previously misclassified as a deletion. Remarkably, we identified the mechanism explaining ATD in 2 out of 11 cases with previous unknown defect: the insertion of a novel 2.4 kb SINE-VNTR-Alu retroelement, which was characterized by de novo assembly and verified by specific polymerase chain
reaction amplification and sequencing in the probands and affected relatives. The nucleotide-level resolution achieved for all SVs allowed breakpoint analysis, which revealed repetitive elements and microhomologies supporting a common replication based mechanism for all the SVs.

Our study underscores the utility of long-read sequencing technology as a complementary method to identify, characterize, and unveil the molecular mechanism of disease-causing SVs involved in ATD, and enlarges the catalogue of genetic disorders caused by retrotransposon insertions.

Morena-Barrio et al 2022