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  • Jon_Keats
    replied
    Originally posted by BaCh View Post
    You sure about that ".com" ending?

    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.
    Opps my bad I've updated the link... thanks for the heads up

    Leave a comment:


  • BaCh
    replied
    Originally posted by Jon_Keats View Post
    This thread shows a common problem of lack of international standards and referencing. Last time I checked hgvs (www.hgvs.com) is a standards group ...
    You sure about that ".com" ending?

    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.

    Leave a comment:


  • Joann
    replied
    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?

    Leave a comment:


  • laura
    replied
    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

    Leave a comment:


  • Jon_Keats
    replied
    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.

    Leave a comment:


  • bioinfosm
    replied
    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

    Leave a comment:


  • laura
    replied
    The Sequence Ontology group are defining a standard ontology for variant consequences

    You can browse their resource here



    stop lost seems to be their term for this

    Leave a comment:


  • Jon_Keats
    replied
    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
    This thread shows a common problem of lack of international standards and referencing. Last time I checked hgvs (www.hgvs.org) is a standards group that most follow or should follow. What you, your facility, your boss thinks is correct or even others follow is not a standard that deserves an exclamation mark in a public form!!

    Thus "No-Stop"
    Last edited by Jon_Keats; 12-01-2010, 11:26 AM. Reason: Fixed URL error noted by other participant

    Leave a comment:


  • bioinfosm
    replied
    '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

    Leave a comment:


  • laura
    replied
    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

    Leave a comment:


  • mard
    replied
    Originally posted by yuanzhi View Post
    From 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
    Just to let you know Ensembl class those mutations as "Stop lost".

    Leave a comment:


  • ntremblay
    replied
    I would say it is a non-synonymous mutation as it cause a change in the translated amino acid sequence ...!

    Leave a comment:


  • yuanzhi
    replied
    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?

    Leave a comment:


  • yuanzhi
    replied
    awesome! Many thanks to both of you.

    Happy Holiday~

    Leave a comment:


  • Jon_Keats
    replied
    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.

    Leave a comment:

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