Tag Archives: linkage disequilibrium

What’s the Answer? Haploview and LD plots?

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question is….

 Is Haploview the best method for defining LD blocks?

The answer to this question is, not necessarily, but it’s good.

The answer given goes into some detail as to what methods one might want to consider:

I would look at the methods used by Gil McVean and others in determining recombination hotspots across the human genome. I would also read papers by DW Bowden on MYH9 as I know that they narrowed the susceptibility region (end-stage renal disease) with LD and recombination hotspots.

It may be that all three methods are more or less equally informative for your region, thereby giving “fuzzy” boundaries. Recall that LD boundaries are not as precise as a single SNP coordinate – although results from Haploview, HelixTree and others often give that impression.

Mentioned here:

Haploview (a publicly available analysis tool)
HelixTree (for fee analysis tool)
Might also want to check analysis tools listed here or here.

“What’s the Answer” Thread

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday* we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

BioStar Question of the Week:

What’s the difference between GWAS and genome wide linkage studies?
I don’t understand the difference between a GWA (genome wide association study) and a GWLS (genome wide linkage study). I’m a computer scientist having to brush up biology!

Highlighted Answer:
The accepted, and well detailed answer is from David Quigley. Of course, if you are deep into GWAS and similar studies the answer is obvious :D, but for those who are new to the field or interesting in it…

…Linkage studies are performed when you have pedigrees of related individals and a phenotype (such as breast cancer) that is present in some but not all of the family members. These individuals could be humans or animals; linkage in humans is studied using existing families, so no breeding is involved. For each locus, you tabulate cases where parents and children who do or don’t show the phenotype also have the same allele. Linkage studies are the most powerful approach when studying highly penetrant phenotypes, which means that if you have the allele you have a strong probability of exhibiting the phenotype. They can identiy rare alleles that are present in small numbers of families, usualy due to a founder mutation. Linkage is how you find an allele such as the mutations in BRCA1 associated with breast cancer.

Association studies are used when you don’t have pedigrees; here the statistical test is a logistic regression or a related test for trends. They work when the phenotype has much lower penetrance; they are in fact more powerful than linkage analysis in those cases, provided you have enough informative cases and matched controls. Association studies are how you find common, low penetrance alleles such as the variations in FGFR2 that confer small increases in breast cancer susceptibility…

Go here for the rest of the answer

Tip of the Week: Genome Variation Tour III


Today’s tip is the continuation of researching a single SNP in an individual genome. Trey will use a dbSNP RS ID to find linkage disequilibrium information between a SNP of interest and SNPs in the region easily and quickly. GVS, the Genome Variation Server at the University of Washington to analyze a dbSNP rs ID of your choice. This 3 minute screencast will show you how to use the GVS tool to quickly get this information for a wide range of populations.

Tip of the Week: HapMap data in Haploview

HapMap has had a few minor updates to their browser, and importantly, new phase 3 data was released early last year (drafts of that data were released in 2008). Haploview, the downloaded software that allows the user to perform in depth LD and haplotype analysis, has been recently updated from version 4.1 to version 4.2. Haploview can be used with user data or data downloaded from the HapMap project. Though, version 4.1 did not work for phase III HapMap project data, so the user had to use phase I and II data if they wanted to use version 4.1. Haploview has now been updated to version 4.2, allowing the user to use HapMap phase III data.

That’s a lot of versions and phases :). The short of it is, if you use Haploview 4.2, you can view and analyze data from any phase of the HapMap project.

Today’s tip briefly shows you how to download data from the HapMap project and view it in Haploview.