Copy number variants in the genetic landscape of Hereditary Thoracic Aortic Disease (HTAD)

Background/Introduction Heritable Thoracic Aortic Diseases (HTAD) can be divided in non-syndromic (ns-HTAD), and syndromic (s-HTAD), which mainly includes Marfan syndrome, Ehlers-Danlos syndrome, and Loeys-Dietz syndrome. The diagnostic yield of genetic testing globally ranges between 20% and 30%, with variants identified in over 20 HTAD-associated genes; the vast majority are point mutations (missense, nonsense, or frameshift), although copy number variations (CNVs) have been described in haploinsufficiency-intolerant genes. However, their contribution to HTAD etiology has not yet been well established. Purpose This study aims to determine the contribution of CNVs to the etiology of HTAD in a large cohort of probands with the disease. Methods This retrospective study analyzed the presence of CNVs in a cohort of patients referred for next-generation sequencing (NGS) due to suspected HTAD. CNVs were detected using a proprietary read-depth comparison method. Positive cases were confirmed through orthogonal molecular techniques, including Sanger sequencing, MLPA, or digital PCR (dPCR). Results A total of 2,414 independent correlative probands with suspected HTAD underwent NGS at our center; CNV analysis was feasible in 90% of the studies. Non-syndromic HTAD represented 58.6% of the cohort (n=1,416), and a P/LP variant was identified in 10.9% (154/1,416); the contribution of P/LP CNVs to these positive cases was 5.1% (7), being the genes involved FBN1 (3), FLNA (2), COL3A1(1), and SMAD3 (1). Of the 998 probands (41.4%) with s-HTAD, a P/LP variant was found in 334 (diagnostic-yield=33.5%). A CNV contributed to 3.9% of the positive cases (12). Genes detected were FBN1 (9), COL5A1 (1), BGN (1), and SKI (1). Conclusions In our cohort of suspected HTAD patients, CNVs accounted for 3.9% of s-HTAD positive cases and 5.1% of ns-HTAD positive cases, with FBN1 being the most frequently affected gene in both groups. Our findings highlight the importance of systematic CNV analysis in NGS studies to enhance the diagnostic yield for this broad spectrum of aortic diseases.