Abstract Number: OC 55.1
Meeting: ISTH 2022 Congress
Theme: Coagulation and Natural Anticoagulants » Coagulation Factors and Inhibitors
Background: Retrotransposons are repetitive mobile sequences of DNA spread throughout the genome. Retrotransposon insertions (RI) are important for genome evolution, but they can also trigger diseases. As current molecular technologies hardly detect RI, their localization in the genome is largely unknown, and their role in genetic diseases could be underestimated. Antithrombin deficiency (ATD) is a dominant monogenic disorder caused by defects in SERPINC1, although causes are not yet known in up to 20% of cases.
Aims: To use long-read whole genome nanopore sequencing (LR-WGS) to identify RI in the human genome, particularly in SERPINC1, as cause of ATD.
Methods: LR-WGS, done on the PromethION platform, was performed in 24 unrelated patients with ATD, 14 with gross SERPINC1 defects, and 10 with unknown defects. A bioinformatic pipeline was developed to detect, localize, and characterize RI in the genome. Validation of SERPINC1 RI was done by PCR and sequencing.
Results: An insertion of 2.4Kb in intron 6 of SERPINC1 not reported in GnomAD was identified in 2 ATD patients with unknown cause. De novo assembly of the inserted sequence revealed a new SVA retrotransposon, antisense oriented, with a tandem site duplication of 14bp. These data and phasing results supported a founder effect. Primers flanking the breakpoint did not amplify the insertion, which was only verified using SVA inner and SERPINC1 flanking primers. Pedigree studies confirmed the segregation of RI with ATD.
Whole genome analysis of RI, revealed a median of 396 polymorphic or novel RI/patient, mainly SINE. A median of 230 RI/patient directly affected genes, 12 of them in coding regions.
Conclusion(s): LR-WGS allowed the first detection and the complete characterization of a new SVA insertion in SERPINC1 causing ATD. A novel pipeline for localization, and characterization of RI in the genome has been developed which can potentially identify pathogenic elements.
PI21/00174, PMP21/00052 (ISCIII&FEDER).
To cite this abstract in AMA style:
de la Morena-Barrio B, Cuencia-Guardiola J, Garrido-Rodríguez P, Sanchis-juan A, de la Morena-Barrio M, Cifuentes-Riquelme R, Bravo-Pérez C, Padilla J, Miñano A, vidal F, Lozano M, Ouwehand W, fernández-breis J, Corral J. Retrotransposon insertions: a challenging detection and characterization solved by long-read nanopore sequencing. Relevance in antithrombin deficiency [abstract]. https://abstracts.isth.org/abstract/retrotransposon-insertions-a-challenging-detection-and-characterization-solved-by-long-read-nanopore-sequencing-relevance-in-antithrombin-deficiency/. Accessed March 21, 2024.« Back to ISTH 2022 Congress
ISTH Congress Abstracts - https://abstracts.isth.org/abstract/retrotransposon-insertions-a-challenging-detection-and-characterization-solved-by-long-read-nanopore-sequencing-relevance-in-antithrombin-deficiency/