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
Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Instituto Murciano de Investigación Biosanitaria, Centro de Investigación Biomédica en Red de Enfermedades Raras, Murcia, Spain.
Department of Haematology, Vrije Universiteit Brussel, Universitair Ziekenhuis Brussel, Brussels, Belgium.
J Mol Diagn. 2022 May;24(5):462-475. doi: 10.1016/j.jmoldx.2022.01.009. Epub 2022 Feb 23.
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.
遗传性抗凝血酶缺乏症是最严重的一种易栓症，主要由SERPINC1基因的变异引起。很少有因果性结构变异被描述，通常通过多重连接依赖探针扩增或细胞遗传学阵列检测，这些方法只能确定增减情况以及大致的大小和位置。本研究使用多重连接依赖探针扩增、比较基因组杂交阵列、长程PCR和全基因组纳米孔测序，对39例无亲缘关系的抗凝血酶缺乏症患者中影响SERPINC1的结构变异进行了全面剖析。结构变异在所有病例中仅影响一个等位基因，具有有害性并导致严重的I型缺乏症。大多数缺陷是影响SERPINC1外显子的缺失（82.1%），但整个队列具有异质性，因为也检测到了串联重复、内含子缺失或逆转座子插入。它们的大小也各不相同，范围从193 bp到8 Mb，并且在54%的病例中涉及相邻基因。除两个结构变异外，所有变异在其断点处都有重复元件和/或微同源性，提示存在共同的形成机制。本研究还指出了在导致抗凝血酶缺乏症的结构变异中反复涉及的区域，并发现了三个具有奠基者效应的结构变异：一个逆转座子的插入、外显子6的重复和一个20个基因的缺失。最后，确定纳米孔测序是在核苷酸水平上识别和表征所有结构变异的最合适方法，无论其大小或类型如何。
