Replies to post #142326 on Biotech Values

[vinmantoo]

genisi,

You can cite all the old references you want, but you still keep missing the point. All single base changes from the ancestral human genomes are mutations and represent SNPs. Calling something a SNP as opposed to a mutation is a somewhat arbitrary division as the parameter used to made that division can change. Sequence variant is a more neutral term for the base change, and then one can ascribe additional nomenclature to reflect phenotypic function. I guess I should have said the ApoA1-Milano allele represents a "rare sequence variant" rather than a "rare SNP", but my usage is far better than yours. As far as insults, rest assure you insult yourself more than me when you cling to an arbitrary delineation as if is were some absolute distinction.


http://www.hgvs.org/mutnomen/recs.html

"In some disciplines the term "mutation" is used to indicate "a change" while in other disciplines it is used to indicate "a disease-causing change". Similarly, the term "polymorphism" is used both to indicate "a non disease-causing change" or "a change found at a frequency of 1% or higher in the population". To prevent this confusion we do not use the terms mutation and polymorphism (including SNP or Single Nucleotide Polymorphism) but use neutral terms like "sequence variant", "alteration" and "allelic variant". Human Mutation (Vol. 19 ( 1) of 2002) contains several contributions discussing these issues as well as the fact that the term "mutation" has developed a negative connotation (see Cotton RGH - p.2, Condit CM et al. - p.69 and Marshall JH - p.76).

General recommendations

(suggestions extending the published recommendations in italics)

The most important rule is that all variants should be described at the most basic level, i.e. the DNA level. Descriptions should always be in relation to a reference sequence, either a genomic or a coding DNA reference sequence. Discussions on which type of reference sequence to prefer, genomic or coding DNA, have been lively. Although theoretically a genomic reference sequence seems best, in practice a coding DNA reference sequence is preferred (see Reference Sequence discussions)."