West Hannah D, Nellist Mark, Brouwer Rutger W W, van den Hout-van Vroonhoven Mirjam C G N, de Almeida Luiz Gustavo Dufner, Hendriks Femke, Elfferich Peter, Raja Meera, Giles Peter, Alfano Rosa M, Peron Angela, Sznajer Yves, De Waele Liesbeth, Jansen Anna, Koopmans Marije, Kievit Anneke, Farach Laura S, Northrup Hope, Sampson Julian R, Thomas Laura E, van IJcken Wilfred F J
Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University, School of Medicine, Cardiff, UK.
Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, Netherlands.
Hum Mutat. 2023 Jul 13;2023:4899372. doi: 10.1155/2023/4899372. eCollection 2023.
Tuberous sclerosis complex (TSC) is caused by inactivating variants in and . Somatic mosaicism, as well as the size and complexity of the and loci, makes variant identification challenging. Indeed, in some individuals with a clinical diagnosis of TSC, diagnostic testing fails to identify an inactivating variant. To improve and variant detection, we screened the and genomic regions using targeted HaloPlex custom capture and next-generation sequencing (NGS) in genomic DNA isolated from peripheral blood of individuals with definite, possible or suspected TSC in whom no disease-associated variant had been identified by previous diagnostic genetic testing. We obtained >95% target region coverage at a read depth of 20 and >50% coverage at a read depth of 300 and identified inactivating or variants in 83/155 individuals (54%); 65/113 (58%) with clinically definite TSC and 18/42 (43%) with possible or suspected TSC. These included 19 individuals with deep intronic variants and 54 likely cases of mosaicism (variant allele frequency 1-28%; median 7%). In 13 cases (8%), we identified a variant of uncertain significance (VUS). Targeted genomic NGS of and increases the yield of inactivating variants found in individuals with suspected TSC.
结节性硬化症复合体（TSC）由 和 的失活变异引起。体细胞镶嵌现象以及 和 基因座的大小与复杂性使得变异鉴定具有挑战性。实际上，在一些临床诊断为TSC的个体中，诊断性检测未能鉴定出失活变异。为了提高 和 变异的检测率，我们使用靶向HaloPlex定制捕获和新一代测序（NGS）技术，对从明确、可能或疑似患有TSC且先前诊断性基因检测未鉴定出疾病相关变异的个体外周血中分离出的基因组DNA中的 和 基因组区域进行了筛选。我们在20的读取深度下获得了>95%的目标区域覆盖率，在300的读取深度下获得了>50%的覆盖率，并在83/155名个体（54%）中鉴定出失活的 或 变异；在临床确诊的113名TSC患者中有65名（58%），在可能或疑似TSC的42名患者中有18名（43%）。这些包括19名具有内含子深处变异的个体和54例可能的镶嵌现象（变异等位基因频率为1 - 28%；中位数为7%）。在13例（8%）中，我们鉴定出意义未明的变异（VUS）。对 和 进行靶向基因组NGS可提高疑似TSC个体中发现的失活变异的检出率。
