Long-read DNA and RNA sequencing reveal an intronic retrotransposon insertion in TCOF1 causing Treacher Collins syndrome

Treacher Collins syndrome (TCS) is a craniofacial genetic disorder caused by loss of function variants in TCOF1, POLR1B, POLR1C or POLR1D . Here we describe two previously undiagnosed half-siblings affected with clinical TCS, and their apparently unaffected parent. Diagnostic short-read RNA-Sequencing identified aberrant expression of TCOF1 and optical genome mapping detected a large genomic insertion therein. Long-read genome sequencing (LR-GS) resolved a deep intronic 3.5 kb SINE-VNTR-Alu (SVA) retrotransposon insertion in intron 17 of TCOF1 . Long read RNA-Seq demonstrated that the insertion was partially exonized inducing isoform switch to the shorter non-canonical TCOF1 isoform c. SVA-insertion was confirmed in both half-siblings and we detected mosaicism one paarent. This is the first description of a retrotransposon causing TCS, and the first intronic SVA causing isoform switch as a disease mechanism. This work demonstrates the potential of LR-RNA-Seq and LR-GS, to identify pathogenic variants in unexplained genetic disorders.