From jillian.maddox alumni.unimelb.edu.au Thu Mar 29 18:23:14 2012
From: Jill Maddox <jillian.maddoxalumni.unimelb.edu.au>
Subject: RE: sheep HD SNP array and MHC typing
To: Multiple Recipients of <SheepModelsanimalgenome.org>
Date: Thu, 29 Mar 2012 18:23:14 -0500
Hi Jon
Hopefully the whole genome sequences that the ISGC has obtained from
a diverse range of breeds will help expand the repertoire of MHC
genes from non European breeds. This presumes that the bioinformatics
is up to handling the MHC region sequences which is not a given, but
it should at least give information about some of the alternatives.
As you say in the long run the HD array is likely to be superseded by
WGS although it is possible that the HD array will always be cheaper
than WGS. I think the important thing is to work towards getting as
comprehensive a system as is possible now so that it can be used asap
and then update the information and develop something better later.
Regards
Jill
At 08:32 AM 30/03/2012, you wrote:
>Hi Jill
>
>Like you can't make it to ISAG for a discussion.
>
>I do wonder how difficult it might be to develop an array-based
>typing system that will be of value when we actually know so very
>little about sequence variation, especially outside of the common
>western World (or European) breeds. I suspect we might only be able
>to "find what we are looking for" and in the context of Class I
>especially, that might be very little! This stated, if we could get
>a system of any kind working for MHC typing, I could see its utility
>in analysing disease associations. So, yes I am having a "quid each way".
>
>I am also suspicious that by the time we could iron out a sensible
>array-based typing system, an alternative sequencing option may
>actually become available. The rate of change is such that a
>whole-genome sequence on any given sheep might only be US$200 within
>the decade. How we will handle all those data, especially if we
>have 40 columns of phenotypic data off say 5000 flock ewes is beyond me!
>
>Not against a discussion though!
>
>
>Jon
>
>
>Jon Hickford
>Associate-Professor
>
>Faculty of Agriculture and Life Sciences
>Department of Agricultural Sciences
>JBB020
>P O Box 84
>Lincoln University 7647
>Christchurch, New Zealand
>
>p +64 3 325 3838 extn: 8186 | m +64 27 280 1285 | f +64 3 325 3851
>e Jon.Hickfordlincoln.ac.nz | w http://www.lincoln.ac.nz
>
>Lincoln University, Te Whare Wanaka o Aoraki
>New Zealand's Specialist Land Based University
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Jill Maddox
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