Hi,
I have a question for those who has been recently involved in EMNQ schemes for the diseases that included large (whole exons) gene deletions/duplications.
Do you used official nomenclature of HGVS or some other nomenclature to describe it?
How can you check if the formula is right?
Can you give some example, perhaps?
Thank you in advance.
Dear Dr.Sanja,
I dont have any experience in this field, Iam adding a couple of papers which i think useful to you.
1.Best practice guidelines on molecular diagnostics in Duchenne/Becker muscular dystrophies by S Abbs, S Tuffery-Giraud, E Bakker, A Ferlini...2010 - Elsevier
2. Clonal expansion of secondary mitochondrial DNA deletions associated with spinocerebellar ataxia type 28
GS Gorman, G Pfeffer, H Griffin, EL Blakely… - JAMA …, 2015 - archneur.jamanetwork.com.sci-hub.org
Good luck!
Thanks, I am aware of these articles, a 5-7 years ago our lab was involved in EMNQ schemes for CF, DMD, SMA..., and passed these tests (we are in such diagnostics for 10-15 years and more)...
But, I wanted to know some of the latest experiences about using HGVS nomenclature in the result report.
Hi,
The HGVS guidelines are a bit tricky to figure out sometimes. Do you mean large deletions for which you do not know the breakpoints, found by arrayCGH, MLPA etc?
For these, you should use c.(first deleted exon, first nucleotide)-?_(last deleted exon, last nucleotide)+?del
This is because the breakpoint could be anywhere in those two introns flanking the deleted exon(s)
Does that help?
All the best,
Gavin
Hi Gavin,
It's about MLPA results. There are at least three kinds of results that we are getting (for the kits we used):
1. deletion/duplication of chromosome region, designated as: rsa "chromosome region"("name of the MLPA kit")x"number of copies"
2. copy number of the exons in the specific gene (all exons are analyzed)
3. copy number of the exon/exons (not all exons of the gene are analyzed).
The first case is simple and is officially recommended by ISCN 2013.
The other two cases are problematic.
According to https://mutalyzer.nl/ and HGVS sites (A+1_B-1)_(C+1_D-1) designation for exon del/dup is still a proposal, not recommendation of HGVS.
I suppose that the traditional designation is still officially recommended and in the use.
I just wanted to hear more about it from the "clinical lab" people and their experience.
Best regards,
Sanja
- Badges
- Science topic
- Similar topics
- Filing