Wednesday, April 18, 2007

Perl scripts & LaTeX

Not really related to any news, but I've written a couple of perl scripts for formatting the output from two tagging programs. In both cases the scripts take the standard output and generate LaTeX formatted tables for subsequent use.

Tagger (de Bakker et al 2005) is implemented in the program Haploview, and uses pair-wise LD to tag regions. The script for re-formatting the output is written in perl and is available here.

ldSelect (Carlson et al 2004) is an alternative method of tagging SNPs, but also based on LD. The output format from this is (in my opinion) a little awkward as the output uses the base-pair positions (mainly because the input file format is Prettybase). Thus in addition to the output file this script requires the user to provide a tab-delimited text file of the markers and their base-pair positions and will convert the base-pair positions of markers to their rs numbers in the resulting latex table. The script is again written in perl and is available here.


References



Carlson, C. S., Eberle, M. A., Rieder, M. J., Yi, Q., Kruglyak, L., Nickerson, D. A. (2004) Selecting a maximally informative set of single- nucleotide polymorphisms for association analyses using linkage disequilibrium American Journal of Human Genetics 74:106-120 PDF on PubMed

de Bakker, P. I. Yelensky, R. Pe'er, I. Gabriel, S. B. Daly, M. J., Altshuler, D. (2005) Efficiency and power in genetic association studies. Nature Genetics 37:1217-1223

2 Comments:

Blogger nates12 said...

Sorry to contact you by leaving a comment on an unrelated post, but I didn't know how to contact you directly.

I heard about this New Line Genetics company that's supposedly paying people for their DNA in order to gather stem cells and grow replacement organs.

I was wondering if you had heard of it, and what your thoughts were...

7:24 AM  
Blogger slack---line said...

Hi,

Not a problem leaving a message here, I get enough spam anyway, so don't list my email address.

I've never heard of the company before, but I had a look at the web-site, there are to me several inconsistencies with what they are claiming to do.

To start with you can not grow stem cells from DNA. DNA is a molecule pure and simple. This molecule contains all of the information required for an organism to develop (viz. a fertalised egg developing int a mature adult). However, you can not (as far as I'm aware anyway), take DNA and grow stem-cells from it. Its exceptionally hard to produce even the simplest cells such as bacteria from scratch. To date all that has been done is using the components of different bacteria and combining them to make a "new" bacteria from them, rather like building blocks. Thus the claim that they can use the DNA in stem-cell research is rather misleading in my opinion.

What is more likely is that they need to cross-match the anti-bodies of "organs that they are going to grow" with the recipients, thus they need to have a wide-range of samples (i.e. stem-cells, expressing the genetic make up from different people) from which to produce their organs. This is no different to the current situation whereby donors need to have very similar matches in anti-bodies/immune system.

Another problem with the site's claims is that it is exceptionally difficult to "grow an organ" in vitro. Thats not to say that research towards this goal isn't going on, at present there are various efforts working towards this, but at best they can grow organ specific cells in membranes, although last year it was announced that scientists had grown a bladder in the lab and transplanted it to a patient succesfully. As far as organs go the bladder is very simple in that it simply collects urea that is excreted from the body.

Anyway, with regards to a company paying people for access to their DNA, this is a lot more of an ethical problem. There are a number of problems when allowing people, be that companies or government bodies or resarch organisations, access to your DNA. The primary concern to the individual should be "What are they going to do with it?". In this instance the claim is that they will put it to use for something that will benefit humanity. However, I'd be very cautious of this company, there is no indication of how they are funded, although the number of adverts on their site suggests that they may be lacking in funding. Presonally I wouldn't trust them.

If at all interested in the legal, ethical and social implications of research into human genetics you may be interested to know that as part of the human genome project there was specific research done into the consequences of such research. A good place to start would be here.

There are also regular articles in various journals if you are interested I can let you know some of the references (Nature Reviews Genetics has regular articles).

Hope that helps,

slack---line

8:46 AM  

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