genetic haplotypes

[pgoody]

Does anyone here understand haplotypes and how to determine your own haplotypes? As far as I know they're different from SNPs in that they are combinations of several genes rather than just a single SNP. Here's a simple example of what I am talking about

"A haplotype previously identified for association with OCD [Dickelnet al., 2006], including this SNP (rs301430–rs301979),was also significant under a recessive model. The T–G haplotype type was undertransmitted to individuals with autism."

What confuses me is that it doesn't seem to discuss the existence of two alleles. Does this mean that rs301430 "TT" and that rs301979 "GG" defines this haplotype and that the AA-CC would indicate not having this haplotype?

Also I am also wondering what "undertransmitted" means in this context.

 

[Valentijn]

Does anyone here understand haplotypes and how to determine your own haplotypes? As far as I know they're different from SNPs in that they are combinations of several genes rather than just a single SNP. Here's a simple example of what I am talking about

Haplotype is looking at a combination of alleles (from SNPs) on multiple genes. Usually these are SNPs on the same gene, but I don't suppose they'd have to be.

"A haplotype previously identified for association with OCD [Dickelnet al., 2006], including this SNP (rs301430–rs301979),was also significant under a recessive model. The T–G haplotype type was undertransmitted to individuals with autism."

What confuses me is that it doesn't seem to discuss the existence of two alleles. Does this mean that rs301430 "TT" and that rs301979 "GG" defines this haplotype and that the AA-CC would indicate not having this haplotype?

Sort of, except they're just looking at one allele for each SNP rather than both alleles for each SNP. So AA-CC wouldn't have the haplotype, but AT-CG would. Usually it's not just homozygous that matters - simply having one copy of the relevant allele is often significant, albeit on a small scale. Though it this case it says it's a "recessive" problem so only the homozygous genotypes would be relevant.

Also I am also wondering what "undertransmitted" means in this context.

I'm pretty sure this means, usually when looking at studies involving parents and their children, that an allele present in percentage of the parents is not showing up in a similar percentage of the children. It's a matter of chance, but in large populations the numbers should match up. I'm not sure if there's a good explanation for why this happens (maybe the undertransmitted allele creates a fatal recessive disease when it is transmitted, hence there's no live subjects in the study who have it).

 

[pgoody]

Sort of, except they're just looking at one allele for each SNP rather than both alleles for each SNP. So AA-CC wouldn't have the haplotype, but AT-CG would. Usually it's not just homozygous that matters - simply having one copy of the relevant allele is often significant, albeit on a small scale. Though it this case it says it's a "recessive" problem so only the homozygous genotypes would be relevant.

So in this circumstance would being AT-CG be similar to being "heterozygous" for the haplotype in the way people would say that being AG is heterozygous for some SNP, and TT-GG be homozygous in that it's a "double whammy" of the refrenced haplotype? Not to remove any significance of a single haplotype, I am just curious to know if they compound eachother.

 

[Valentijn]

So in this circumstance would being AT-CG be similar to being "heterozygous" for the haplotype in the way people would say that being AG is heterozygous for some SNP, and TT-GG be homozygous in that it's a "double whammy" of the refrenced haplotype? Not to remove any significance of a single haplotype, I am just curious to know if they compound eachother.

I think it can go either way. In some studies, just having one copy of the allele is enough to create a statistically significant difference, and having two copies might either have the same impact as just having one allele, or it might have a slightly bigger impact, or twice the impact, or a much bigger impact. You can't guess at these results - the study has to find and measure them.

But if they say it's only showing up as a recessive issue, than homozygosity is required - though it is possible that they might find a statistically significant heterozygous result if they conduct a larger study.