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linkage disequlibrium, haplotypes, SNPs

Genetics as it applies to evolution, molecular biology, and medical aspects.

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linkage disequlibrium, haplotypes, SNPs

Postby tou » Thu Apr 21, 2011 12:11 am

hello

I am a little bit confused about the relationship between LD, haplotypes and SNPs.

Is that correct?
SNPs act as markers, they may be in LD with the susceptibility alleles for a disease. Generally, SNPs together with other genetic variants (like disease alleles) can be inherited in/as haplotypes, which means they are in LD. The HapMap project identifies common haplotype blocks and the specific SNPs that uniquely identify them (tag SNPs). Genes are inherited together as haplotypes because of LD, i.e. the non random association of alleles at different loci (they form a block of DNA that is inherited together). When there is a preferential association between a specific marker allele (SNPs) and disease allele in a population, this forms a haplotye. So the idea of the HapMap Project is to identify haplotypes and tag SNPs. Using tag SNPs, one can find chromosome regions that have different haplotype distributions in two groups of people (one with disease, one control). So the differences tell you which haplotypes to investigate? That only works because of LD between the marker (tag SNPs?) and the susceptibility alleles...? And how do you know which tag SNPs to look for?

Sorry, I know it's repetitive, I just want to check if my thoughts are correct? Thanks!
tou
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Postby tou » Mon May 16, 2011 9:34 am

nobody can help me?
tou
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