Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan.
Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan; Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan.
Genomics. 2022 Sep;114(5):110468. doi: 10.1016/j.ygeno.2022.110468. Epub 2022 Aug 27.
Recent studies suggest that transcript isoforms significantly overlap (approximately 60%) between brain tissue and Epstein-Barr virus-transformed lymphoblastoid cell lines (LCLs). Interestingly, 14 cohesion-related genes with variants that cause Cornelia de Lange Syndrome (CdLS) are highly expressed in the brain and LCLs. In this context, we first performed RNA sequencing of LCLs from 22 solved (with pathogenic variants) and 19 unsolved (with no confirmed variants) CdLS cases. Next, an RNA sequencing pipeline was developed using solved cases with two different methods: short variant analysis (for single-nucleotide and indel variants) and aberrant splicing detection analysis. Then, 19 unsolved cases were subsequently applied to our pipeline, and four pathogenic variants in NIPBL (one inframe deletion and three intronic variants) were newly identified. Two of three intronic variants were located at Alu elements in deep-intronic regions, creating cryptic exons. RNA sequencing with LCLs was useful for identifying hidden variants in exome-negative cases.
最近的研究表明，脑组织和 Epstein-Barr 病毒转化的淋巴母细胞系（LCL）之间的转录本异构体有很大的重叠（约 60%）。有趣的是，14 个与 Cornelia de Lange 综合征（CdLS）相关的基因在大脑和 LCL 中高度表达，这些基因的变体导致 CdLS。在这种情况下，我们首先对 22 个已解决（有致病性变体）和 19 个未解决（无确认变体）的 CdLS 病例的 LCL 进行了 RNA 测序。接下来，我们使用两种不同的方法（单核苷酸和插入缺失变体的短变体分析和异常剪接检测分析）开发了一个 RNA 测序管道。然后，我们将 19 个未解决的病例应用于我们的管道，并在 NIPBL 中发现了四个致病性变体（一个框内缺失和三个内含子变体）。三个内含子变体中有两个位于深内含子区域的 Alu 元件中，产生了隐蔽外显子。使用 LCL 的 RNA 测序有助于鉴定外显子阴性病例中的隐藏变体。
