Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency - Archive ouverte HAL Access content directly
Journal Articles Thrombosis and Haemostasis Year : 2022

Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency

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1
Belén de la Morena-Barrio
Jonathan Stephens
  • Function : Author
María Eugenia de la Morena-Barrio
Luca Stefanucci
  • Function : Author
José Padilla
  • Function : Author
Antonia Miñano
  • Function : Author
Nicholas Gleadall
  • Function : Author
Juan Luis García
  • Function : Author
Marja Puurunen
  • Function : Author
Anetta Undas
  • Function : Author
Francisco Vidal
Frances Lucy Raymond
  • Function : Author
Vicente Vicente
  • Function : Author
Willem Ouwehand
  • Function : Author
Javier Corral
  • Function : Author
Alba Sanchis-Juan
  • Function : Author

Abstract

Abstract 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.

Dates and versions

hal-03813959 , version 1 (13-10-2022)

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Belén de la Morena-Barrio, Jonathan Stephens, María Eugenia de la Morena-Barrio, Luca Stefanucci, José Padilla, et al.. Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency. Thrombosis and Haemostasis, 2022, 122 (08), pp.1369-1378. ⟨10.1055/s-0042-1749345⟩. ⟨hal-03813959⟩
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