Sunday, March 16, 2008

First Take by Mailund

The first blog response comes From Dr Mailund of Denmark. Thomas is an Associate Professor at the Bioinformatics Research Center (BiRC), University of Aarhus, Denmark.

His response is telling and it essentially says what is true....we would initially be "Lost" but not for too long

My goal is to figure out ways to analyse full sequence data for disease mapping. With full sequences, a few things change compared to SNP chip data.

First, of course, there is the matter of scale. Now you get 6 billion nucleotides per individual instead of 2×500K or 2×1M as with SNP chips. (This is a huge Point!!! This doesn't include methylation and other epigenetic phenomena either)

Second, you are no longer looking for indirect signals, so there are no tagging and multi-marker methods will not be needed to boost the power of indirect signals. You have all the variation observed (but the types of variation is much more complicated).

Third (and perhaps most interesting), the kind of signals we are looking for will change. With SNP chips and tagging SNPs, we are looking for high-frequent variants with modest effect. High frequent variants is all we are tagging (and these have a modest effect if we are still looking for it, if they didn’t we would have found them ages ago). With full sequencing, we will be able to look for low frequency variants as well.

The Sherpa Says:
We would still need more research.......But I am certain it would come in a hurry! Who's next with their take?

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