Confusion over terms related to genetics

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Jamus
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Confusion over terms related to genetics

Post by Jamus » Wed Jan 07, 2009 4:34 am

Greetings all,
I’m experiencing slight confusion over the difference and meaning of these terms:

1. Mutation
2. Polymorphism
3. Variants

On top of these, how do we know when to use the prefix “disease associated…” with the above terms? For instance, “disease associated polymorphism”.

Besides this, I’m having trouble understanding the term “wild-type”. Consider this scenario: If African-Americans have a greater prevalence of nucleotide “A” on an arbitrary position, while the Chinese and the Europeans tend to have the nucleotide “C” instead, how should one consider the meaning of wild-type?

I apologize in advance if similar topics have already been made and discussed. Thank you for your time :)

wbla3335
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Re: Confusion over terms related to genetics

Post by wbla3335 » Wed Jan 07, 2009 7:45 am

Hi Jamus,

Similar discussions have occurred, but the literature is still full of confusing usage of terms. Things weren't so bad when it was just the scientists doing the science.

Mutation just means change. But, as you say, which is the change and which is the "wild type"? We'll need to be sequencing a lot more genomes from many individuals of many species to be able to determine what is ancestral and what is derived, or what is common in a population and what is rare. Polymorphism means "many forms", whether molecular or morphological. So mutation creates polymorphism. The different polymorphic forms are variants, so "polymorphism" and "variant" are essentially synonymous. It is my opinion that much of the confusion stems from the misuse of the word "mutation". Medical people love using this word, and will do so at any opportunity. The first sequence of a gene had an A at position X. Someone else comes along and finds a G at this position and proceeds to claim that A has mutated to G in their sample. Such a claim is, of course, nonsense. Position X, though, is polymorphic with two known variants (or polymorphisms), A and G. Whether A mutated to G or G mutated to A is unknown in most cases. Both A and G may have been in the population for thousands of years, and both may even have mutated from an ancestral T for all we know.

If one polymorphism at position X of gene Y is found in individuals with a particular disease significantly more often than another polymorphism at position X in gene Y, then the first polymorphism is said to be associated with the disease. This is the basis of association studies where there are two groups of test subjects, those with a disease (or some other phenotype) and those without. DNAs of both groups are then compared at various loci or the entire genome to look for polymorphisms that tend to be more common in one group than in the other. These polymorphisms need not necessarily cause the disease (or other phenotype), but are located sufficiently close to the polymorphisms that do cause the disease for them to be physically linked on the same chromosome and therefore co-inherited until a crossover event separates them. This close physical association is why the polymorphism is called "disease associated". They can be used as markers for the disease if the cause of the disease is unknown.

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whizzbee
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Post by whizzbee » Wed Jan 07, 2009 2:36 pm

nice :D
always aim for the sky, for if you fail, at least you can reach the clouds..

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