Originally posted by BaCh
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Originally posted by Jon_Keats View PostThis thread shows a common problem of lack of international standards and referencing. Last time I checked hgvs (www.hgvs.com) is a standards group ...
My company filter blocked me saying it was a gambling site. A quick search on Google gave www.hgvs.org as most probable address.
B.
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harmonization
Nomenclature groups should strive for harmonization and cite the earliest published convention assembled by an authoritative group--for use in naming an identical concept/event, that is. Nuances and hierarchical relationships should be explored and articulated as part of gaining consensus. There is nothing like using exactly the right word in annotating sequence data, no?
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The Sequence Ontology consortium being the people who define ontologies in genomics/bioinformatics are trying to solve this problem by providing a standard ontology and being open to suggestions about additions or changes
Ensembl is certainly adopting the SO consequence ontology so lets hope others follow suit
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Agreed, hopefully there can be a clear winner in the very near future. This thread started with a very junior question that has a definite unequivocal answer, as the definition of a nonsense change is well established and an accepted nomenclature for the type of event. Hopefully a standard can be reached soon, as the number of genome papers and data sharing will only increase and standardized nomenclature will becomes ever so important.
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2 standards already then = "No-Stop" and "Stop lost"
I think the key is, enforce a standard locally, but be aware of the synonyms, because bioinformatics standardization is not present yet
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Originally posted by bioinfosm View Post'Read through' are what they are called then!
We also recently saw quite a few 'loss of stop codon' mutations in exome data.. and was not sure how to interpret/annotate/log them
Thus "No-Stop"
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'Read through' are what they are called then!
We also recently saw quite a few 'loss of stop codon' mutations in exome data.. and was not sure how to interpret/annotate/log them
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The ensembl database is a good place to look for what the different sort of consequences
This documentation lists them
For a consequence which is non synonymous it means the base change results in an amino acid change in the protein sequence
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Originally posted by yuanzhi View PostFrom several genetics books I have read, nonsense mutations change a codon for an amino acid to a stop codon.
then how to define a mutation change a stop codon to a codon for an amino acid? still nonsense mutation?
Thanks
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I would say it is a non-synonymous mutation as it cause a change in the translated amino acid sequence ...!
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I just thought of another question. Can we call this readthrough mutation or non-stop extension as nonsynonymous mutation? Or, nonsynonymous mutation includes missense and nonsense?
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Not a nonsense change for sure as that exclusively means the creation of a stop codon.
These changes that eliminate the proper stop codon and allow translation to continue on into the 3'UTR finally have an official nomenclature (http://www.hgvs.org/mutnomen/recs-prot.html) of "NO-STOP" changes. Though others (http://www.sanger.ac.uk/perl/genetic...ummary&id=5333) use "non-stop extension" which seems a bit more descriptive and I've also see them listed as "missense-stopcodon".
This is definately one of two special mutation classes, that being mutations of the initiating methionine and stop codon.
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