Tag Archives: LD

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.

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.