1. Pathogenic variants detected by RNA sequencing in Cornelia de Lange syndrome
- Author
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Rie Seyama, Yuri Uchiyama, José Ricard Magliocco Ceroni, Veronica Eun Hue Kim, Isabel Furquim, Rachel Sayuri Honjo, Matheus Augusto Araujo Castro, Lucas Vieira Lacerda Pires, Hiromi Aoi, Kazuhiro Iwama, Kohei Hamanaka, Atsushi Fujita, Naomi Tsuchida, Eriko Koshimizu, Kazuharu Misawa, Satoko Miyatake, Takeshi Mizuguchi, Shintaro Makino, Atsuo Itakura, Débora R. Bertola, Chong Ae Kim, and Naomichi Matsumoto
- Subjects
Epstein-Barr Virus Infections ,Herpesvirus 4, Human ,Phenotype ,Nucleotides ,Sequence Analysis, RNA ,De Lange Syndrome ,Genetics ,Humans ,Protein Isoforms ,Cell Cycle Proteins - Abstract
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.
- Published
- 2022