#apaperaday: Identifying inversions with breakpoints in the Dystrophin gene through long-read sequencing: report of two cases
In today’s #apaperaday, Prof. Aartsma-Rus reads and comments on the paper titled: Identifying inversions with breakpoints in the dystrophin gene through long-read sequencing: report of two cases
Today’s pick is from @BioMedCentral medical genetics by Chen et al on one of my favorite topics: complex mutations in the dystrophin gene – selected because I have teaching this week about also Duchenne genetics. DOI: 10.1186/s12920-024-01997-2
Duchenne and Becker are caused by mutations in the dystrophin gene, mainly deletions (2/3 cases). MLPA is usually the first technique to test and will find a deletion or duplication of one or more exons in 3/4 cases. Most of the other cases, will have small mutations.
Small mutations can be found by sanger sequencing or whole exome sequencing (WES). Authors here point out that in rare cases, complex mutations occur such as long inversions. These are missed by MLPA (all exons are there after all) and WES (there are no small mutations).
Long read sequencing is a new technique that can identify inversions. Oxford Nanopore and Pacific Biosciences both have systems for long read sequencing. Authors had best results with Pacific Bio to identify inversions for 2 cases, which they report in the paper.
Case 1 is a 10 year old patient, without a family history who showed symptoms of Duchenne (high CK, gait problems, weakness, Gowers sign etc), and also had learning difficulties and cognitive problems (authors identified this was part of the Duchenne spectrum!)
MLPA and WES did not reveal mutations, but long read sequencing identified an inversion in intron 47 of dystrophin and somewhere beyond the dystrophin gene. This means no functional dystrophin can be produced. Finding was confirmed with PCR of the breakpoints.
Case 2 was a 6 year old boy with muscle symptoms and high CK but no learning difficulties. He had a maternal uncle and cousin who had the same symptoms and both passed away before age 11 🙁 MLPA and WES again showed no mutations, but long read sequencing did!
There was an inversion between intron 41 and the RANBP1BP1 and MAGEB18 genes. Breakpoints were confirmed by sequencing. Authors discuss that inversions are rarely reported: only 14 cases for Duchenne so far. Likely there are more as they are difficult to pick up.
They argue that likely the first patient had cognitive problems because he cannot make Dp140, while the second patient could. They also looked into why there were inversions where they were: small microsatelite repeats were found (CATATA)n for each case.
Authors finish by stressing the importance of finding mutations. A confirmed genetic diagnosis allows care and counseling (for the second case, the mother was a carrier – as expected given the family history). Nice work and I appreciate the diligence of finding these variants
