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Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency
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 stru...
Autores principales: | , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Georg Thieme Verlag KG
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9393088/ https://www.ncbi.nlm.nih.gov/pubmed/35764313 http://dx.doi.org/10.1055/s-0042-1749345 |
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author | de la Morena-Barrio, Belén Stephens, Jonathan de la Morena-Barrio, María Eugenia Stefanucci, Luca Padilla, José Miñano, Antonia Gleadall, Nicholas García, Juan Luis López-Fernández, María Fernanda Morange, Pierre-Emmanuel Puurunen, Marja Undas, Anetta Vidal, Francisco Raymond, Frances Lucy Vicente, Vicente Ouwehand, Willem H. Corral, Javier Sanchis-Juan, Alba |
author_facet | de la Morena-Barrio, Belén Stephens, Jonathan de la Morena-Barrio, María Eugenia Stefanucci, Luca Padilla, José Miñano, Antonia Gleadall, Nicholas García, Juan Luis López-Fernández, María Fernanda Morange, Pierre-Emmanuel Puurunen, Marja Undas, Anetta Vidal, Francisco Raymond, Frances Lucy Vicente, Vicente Ouwehand, Willem H. Corral, Javier Sanchis-Juan, Alba |
author_sort | de la Morena-Barrio, Belén |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-9393088 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Georg Thieme Verlag KG |
record_format | MEDLINE/PubMed |
spelling | pubmed-93930882022-08-22 Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency de la Morena-Barrio, Belén Stephens, Jonathan de la Morena-Barrio, María Eugenia Stefanucci, Luca Padilla, José Miñano, Antonia Gleadall, Nicholas García, Juan Luis López-Fernández, María Fernanda Morange, Pierre-Emmanuel Puurunen, Marja Undas, Anetta Vidal, Francisco Raymond, Frances Lucy Vicente, Vicente Ouwehand, Willem H. Corral, Javier Sanchis-Juan, Alba Thromb Haemost 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. Georg Thieme Verlag KG 2022-06-28 /pmc/articles/PMC9393088/ /pubmed/35764313 http://dx.doi.org/10.1055/s-0042-1749345 Text en The Author(s). This is an open access article published by Thieme under the terms of the Creative Commons Attribution-NonDerivative-NonCommercial License, permitting copying and reproduction so long as the original work is given appropriate credit. Contents may not be used for commercial purposes, or adapted, remixed, transformed or built upon. ( https://creativecommons.org/licenses/by-nc-nd/4.0/ ) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License, which permits unrestricted reproduction and distribution, for non-commercial purposes only; and use and reproduction, but not distribution, of adapted material for non-commercial purposes only, provided the original work is properly cited. |
spellingShingle | de la Morena-Barrio, Belén Stephens, Jonathan de la Morena-Barrio, María Eugenia Stefanucci, Luca Padilla, José Miñano, Antonia Gleadall, Nicholas García, Juan Luis López-Fernández, María Fernanda Morange, Pierre-Emmanuel Puurunen, Marja Undas, Anetta Vidal, Francisco Raymond, Frances Lucy Vicente, Vicente Ouwehand, Willem H. Corral, Javier Sanchis-Juan, Alba Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency |
title | Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency |
title_full | Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency |
title_fullStr | Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency |
title_full_unstemmed | Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency |
title_short | Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing Antithrombin Deficiency |
title_sort | long-read sequencing identifies the first retrotransposon insertion and resolves structural variants causing antithrombin deficiency |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9393088/ https://www.ncbi.nlm.nih.gov/pubmed/35764313 http://dx.doi.org/10.1055/s-0042-1749345 |
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