Haplotype analysis - How? - (May/30/2005 )

hi every one, i'm a newcomer and any help will be appreciated.

i'v sequenced some PCR products. Now I want to analyze the haplotypes, but how? i don't konw, especially the heterozygotes. although there are many combinations in heterozygote, but only 2 haplotypes in each heterozygote. so how can i find them?

Hello,
I am in the same situation as yours. I have multiple SNPs in the same gene which give haplotypes. I dont know how to analyze them statistically? :unsure:If you have found out a way to do that, I would appreciate if you could let me know. I really need the information.

For your query if you have one SNP per gene you can use a chi square test to analyze the heterozygotes. Just follow the steps in the Chi square analysis. Hope this helps you.

Hello,
          I am in the same situation as yours. I have multiple SNPs in the same gene which give haplotypes. I dont know how to analyze them statistically? :unsure:If you have found out a way to do that, I would appreciate if you could let me know. I really need the information.

For your query if you have  one SNP per gene you can use a chi square test to analyze the heterozygotes. Just follow the steps in the Chi square analysis. Hope this helps you.

For haplotype analysis, as far as I know, once you have genotyped the SNPs. You can use a program to infer the haplotypes. The program will give the inferred haplotypes and also their frequencies in the population.
Further work, may be something like identifying the haplotype blocks and tagging the SNPs.

I don't think that you can know the exact two haplotypes for your PCR product (or maybe it's out of my knowledge) except that you sequenced the whole very long sequence (is it possible?) which is expensive and time consuming.

I have a gene D. I found 2 SNPs in this gene, say 1a/1b and the 2nd change was 2a/2b. The possible types of haplotypes would be 1a/2a, 1a/2b, 1b/2a etc... I have 2 different populations. I have calculated the haplotype frequencies for each haplotype in the 2 populations but dont know how to prove that if the frequencies are differnt in the 2 populations how are they statistically significant using JMP (statistical software) (I dont have SAS) or which statistical test to use?
Hope this clarifies my question. Someone mentioned about the software that can be used, I would appreciate if you could tell me what software.
Thanks

QUOTE (Solution @ Jul 10 2005, 07:04 AM)

Hello,
          I am in the same situation as yours. I have multiple SNPs in the same gene which give haplotypes. I dont know how to analyze them statistically? :unsure:If you have found out a way to do that, I would appreciate if you could let me know. I really need the information.

For your query if you have  one SNP per gene you can use a chi square test to analyze the heterozygotes. Just follow the steps in the Chi square analysis. Hope this helps you.

"analyze" is too broad a question, maybe you can elaborate on the question you are trying to answer more specifically.

I am using DNASP. It pretty great but without know exactly what you want to measure I can't comment further.

thanks for the website info! it really helped.

Solution

Another free software for haplotype analysis is PHASE at

http://www.stat.washington.edu/stephens/software.html

Hi,

If you only want to estimate your haplotypes, then I can recommend powermarker, http://statgen.ncsu.edu/powermarker/ this really works well and is easy to use.

If you would like to see what the haplotypes really are, the clone them and do your SNP tests again on each clone to see how the world actually looks like