Dear All, I need your help. I have a pedigree and seven individuals included and whole genomic SNPs' genotypes. Now, I'm trying to analyze the linkage and linkage peak within whole genome with this family.
However, it is a real challenge for me. I'm not sure which kind of method or software is suitable to make a whole genome linkage analysis.
So, I wondered, whether you can introduce some good methods, related softwares or suggestion to me about this issue.
Are you analyzing a binary or quantitative phenotype?
parametric or not parametric method? depending on if you want to specify model of segregation of the phenotype. You could test both.
And the software, there are plenty of them. I used Merlin, but there are a lot of them.
Have a look at this link http://lab.rockefeller.edu/ott/programs
Evelina
Hello,
Maybe the PLINK family-based association can be a good option.
http://pngu.mgh.harvard.edu/~purcell/plink/fanal.shtml
Are you analyzing a binary or quantitative phenotype?
parametric or not parametric method? depending on if you want to specify model of segregation of the phenotype. You could test both.
And the software, there are plenty of them. I used Merlin, but there are a lot of them.
Have a look at this link http://lab.rockefeller.edu/ott/programs
Evelina
Merlin is also a widely used program that allows you to specify inheritance models (or non parametric models) for the analysis. You usually use PLINK beforehand for doing quality control and LD pruning of SNPs prior to the analysis.
Thanks for all!
It seems that I still do not really understand the utility of PLINK completely, so far. How about the limit of maximum loci of its input files? More than 50K loci will be included. Whether a special computer is need?
PLINK is designed for whole genome data. 50K loci is considered a small dataset for PLINK. Please read the PLINK documentation carefully: http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-doc-1.07.pdf
Sebastian
PLINK is not designed for linkage analysis and association analysis of one pedigree would not be that informative. MERLIN was a better suggestion IMHO since it would help you localize regions of interest for further investigation. But as Daniel Gaston pointed out, you can't use all of the SNPs in the analysis since the LD (correlations) can induce false positive linkage signals. However, PLINK can be used to remove SNPs in LD prior to a MERLIN run.
You can also use the cluster option in Merlin which identifies sets of SNPs that are in strong LD and sets those up as extended haplotypes.
It is also reasonable to do as Chris above suggested first to remove pairwise LD first ( I would remove snps with LD r2>0.05 or even 0, since you don't need very many snps), and then you can still invoke the cluster option to be sure that results are valid (you will know if you have a problem if you get a lot of signals that are highly significant). If your pedigree is too large you will have to use Morgan or Gigi.
Yes, in agreement with the previous comments, use Merlin with pruning of SNPS in LD, optionally with PLINK first for the pruning step. Run the error detection and correction functions of Merlin prior to linkage analysis.
BTW, what do you mean about whole genome SNPs? A SNP chip or sequence data?
Use Merlin & prune with PLINK, or try our software LINKDATAGEN (bioinf.wehi.edu.au/software/linkdatagen) to prepare your files for input into MERLIN with a simple bin prune, rather than LD based. You need to figure out which genetic model is appropriate - dominant/recessive. Also have a look at the MERLIN website for further instructions on how to perform a linkage analysis.
Hello,
You may use SUPERLINK SNP online software, that works on cloud. You may analyse both SNP and STR data with that and the .DAT file that is uploaded specifies which programme will be used eg. genehunter etc.
You can please follow the links below to obtain certain interesting informations:-
1. https://books.google.co.in/books?id=BIlnAmfGIbEC&pg=PA47&lpg=PA47&dq=pedigree+individual+data+analysis&source=bl&ots=9oCeBKZmAw&sig=sklMGwFjYiZJKUlLG86O4FFf2to&hl=en&sa=X&ved=0CD0Q6AEwBWoVChMIq4bnrteUxwIVxKymCh1DdgAG#v=onepage&q=pedigree%20individual%20data%20analysis&f=false
2. http://www.progenygenetics.com/lab/analysis.html
3. http://www.ncbi.nlm.nih.gov/pubmed/15838848
4. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462645/
You can also download the pdf of the file attached herewith.
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