Molecular Dissection of Structural Variations Involved in Antithrombin Deficiency

• Published in: The Journal of molecular diagnostics : JMD Vol. 24; no. 5; pp. 462 - 475
• Main Authors: de la Morena-Barrio, Belén, Orlando, Christelle, Sanchis-Juan, Alba, García, Juan L., Padilla, José, de la Morena-Barrio, María E., Puruunen, Marija, Stouffs, Katrien, Cifuentes, Rosa, Borràs, Nina, Bravo-Pérez, Carlos, Benito, Rocio, Cuenca-Guardiola, Javier, Vicente, Vicente, Vidal, Francisco, Hernández-Rivas, Jesús M., Ouwehand, Willem, Jochmans, Kristin, Corral, Javier
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.05.2022
• ISSN: 1525-1578; 1943-7811; 1943-7811
• DOI: 10.1016/j.jmoldx.2022.01.009

Inherited antithrombin deficiency, the most severe form of thrombophilia, is predominantly caused by variants in SERPINC1. Few causal structural variants have been described, usually detected by multiplex ligation-dependent probe amplification or cytogenetic arrays, which only define the gain or loss and the approximate size and location. This study has done a complete dissection of the structural variants affecting SERPINC1 of 39 unrelated patients with antithrombin deficiency using multiplex ligation-dependent probe amplification, comparative genome hybridization array, long-range PCR, and whole genome nanopore sequencing. Structural variants, in all cases only affecting one allele, were deleterious and caused a severe type I deficiency. Most defects were deletions affecting exons of SERPINC1 (82.1%), but the whole cohort was heterogeneous, as tandem duplications, deletion of introns, or retrotransposon insertions were also detected. Their size was also variable, ranging from 193 bp to 8 Mb, and in 54% of the cases involved neighboring genes. All but two structural variants had repetitive elements and/or microhomologies in their breakpoints, suggesting a common mechanism of formation. This study also suggested regions recurrently involved in structural variants causing antithrombin deficiency and found three structural variants with a founder effect: the insertion of a retrotransposon, duplication of exon 6, and a 20-gene deletion. Finally, nanopore sequencing was determined to be the most appropriate method to identify and characterize all structural variants at nucleotide level, independently of their size or type.