Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency
De La Morena-Barrio, Belén (Universidad de Murcia)
Stephens, J. (Cambridge University Hospitals NHS Foundation Trust (Anglaterra))
De La Morena-Barrio, M.E. (Universidad de Murcia)
Stefanucci, L. (Addenbrookes Hospital (Cambridge, Regne Unit))
Padilla, J. (Universidad de Murcia)
Miñano, A. (Universidad de Murcia)
Gleadall, N. (Cambridge University Hospitals NHS Foundation Trust (Anglaterra))
García, J.L. (Hospital Universitario de Salamanca)
López-Fernández, M.F. (Complejo Hospitalario Universitario de A Coruña)
Morange, Pierre-Emmanuel (Aix-Marseille Université)
Puurunen, M. (Lung and Blood Institute)
Undas, A. (Jagiellonian University)
Vidal, Francisco (Vall d'Hebron Institut de Recerca (VHIR))
Raymond, F.L. (University of Cambridge)
Vicente, V. (Universidad de Murcia)
Ouwehand, W.H. (CCambridge University Hospitals NHS Foundation Trust (Regne Unit))
Corral, J. (Universidad de Murcia)
Sanchis-Juan, A. (Cambridge University Hospitals NHS Foundation Trust (Anglaterra))
Universitat Autònoma de Barcelona

Date:	2022
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.
Grants:	Instituto de Salud Carlos III PI18/00598 Instituto de Salud Carlos III PI21/00174 Instituto de Salud Carlos III PMP21/00052
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, i la comunicació pública de l'obra, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original. No es permet la creació d'obres derivades.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Published in:	Thrombosis and Haemostasis, Vol. 122 Núm. 8 (21 2022) , p. 1369-1378, ISSN 2567-689X

DOI: 10.1055/s-0042-1749345
PMID: 35764313

10 p, 3.2 MB

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