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

## TL;DR

Long-read DNA and RNA sequencing identified a retrotransposon insertion in TCOF1 causing Treacher Collins syndrome in two siblings.

## Contribution

Demonstrates the utility of long-read sequencing to identify and characterize deep intronic pathogenic variants in genetic disorders.

## Key findings

- A 3.5 kb SINE-VNTR-Alu retrotransposon insertion in intron 17 of TCOF1 was identified as the cause of Treacher Collins syndrome.
- The insertion partially exonized, leading to an isoform switch to a shorter non-canonical TCOF1 isoform.
- Mosaicism in the father was detected, confirming the origin of the insertion.

## Abstract

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 paternal half-siblings affected with clinical TCS, and their apparently unaffected father. Diagnostic short-read RNA sequencing) identified aberrant expression of TCOF1 and optical genome mapping detected a large genomic insertion therein. Long-read genome sequencing (lrGS) resolved a deep intronic 3.5 kb SINE-VNTR-Alu (SVA) retrotransposon insertion in intron 17 of TCOF1. Long-read RNA sequencing (lrRNA-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 in the father. This work demonstrates the potential of lrRNA-seq and lrGS, to identify pathogenic variants in unexplained genetic disorders.

We report two paternal half-siblings affected by Treacher Collins syndrome, caused by a pathogenic retrotransposon insertion in TCOF1. We show the utility of short-read RNA sequencing to prioritize the affected gene, long-read genome sequencing to resolve the event, and long-read RNA sequencing to characterize the functional impact of the insertion.