From Keith.Ballingall moredun.ac.uk Thu Mar 29 11:04:12 2012
From: Keith Ballingall <Keith.Ballingallmoredun.ac.uk>
Subject: RE: sheep HD SNP array and MHC typing
To: Multiple Recipients of <SheepModelsanimalgenome.org>
Date: Thu, 29 Mar 2012 11:04:12 -0500
Hi Jill and others, I would be happy to be involved in such a working
group. Sorry you can't make it to ISAG. Although time is limited at the
ISAG MHC workshop, if there is demand for such a discussion I can certainly
schedule a discussion on this topic and post the results on this site. Let
me know if there is interest. Regards Keith
Dr Keith Ballingall
Moredun Research Institute
Pentlands Science Park
Bush Loan,
Penicuik Midlothian,
EH26 0PZ
Scotland,
UK.
Tel + 44 (0)131 445 5111
e-mail keith.ballingallmoredun.ac.uk
-----Original Message-----
.From: Jill Maddox [mailto:jillian.maddoxalumni.unimelb.edu.au]
.Sent: 29 March 2012 01:29
.To: Multiple Recipients of
.Subject: sheep HD SNP array and MHC typing
Hi Keith and others
Given that the HD SNP array will be able to hold lots of functional SNPs I
think it is worth trying to come up with a typing system, but I agree that
we may not know enough especially for class I for it to be comprehensive.
We can at least aim for it to include all currently known alleles. Given
that there are lots of segmental exchanges that contribute to allelic
diversity, it may be a situation whereby if we make the set of
discriminating SNPs that go
on the HD array as comprehensive as possible (assuming assay design permits
this) that we may end up sorting out many haplotypes and MHC types after the
array has been used for a bit rather than beforehand. The ISGC has whole
genome sequence information from at least 80 animals and there are lots of
groups that have MHC information that hasn't yet made it into GenBank and it
would be good if these groups could also contribute their sequences to the MHC
SNP allele/haplotype resolving process too. In terms of which MHC SNPs to
include on the chip they will probably have to be restricted to those that
cause amino acid changes or have other functional properties such as affecting
expression levels, premature stop codons etc. Given the sheep MHC is extremely
complex we will probably need to set up a working group to handle making
recommendations re which SNPs to include on the chip. If this was to happen we
would be looking for volunteers to belong to the working group - please let me
know if you would be interested in belonging to such a group? Yes, I think it
would be good to have a discussion at ISAG about this.
Unfortunately I'm unlikely to be able to attend (funding constraints).
Best wishes from
Jill
At 07:13 PM 28/03/2012, you wrote:
>Hi Jill,
>This is a really interesting point; can a SNP chip be used to
>accurately type the MHC region of sheep or cattle given what we already
>know about the exceptional diversity at individual class II loci both
>in terms of allelic and structural diversity and the limited
>information we have regarding allelic and haplotype diversity within
>the class I region. Obviously we can cover every informative SNP
>within every allele of every gene identified so far but will that tell
>us anything about the combinations of SNP's that make up each allele
>within each gene within the two haplotypes of a heterozygous animals.
>I don't know enough about high density SNP chip design to answer this
>but I suppose it depend on what you need to know about the MHC in you
>study population. The sequence based approaches we are currently using
>at least for class II are time consuming and relatively expensive but
>the data are good. It would be really good to have a discussion on this
>possibly at the ISAG meeting in July. I am trying to put together the
>Comparative MHC workshop which may be a good place for this discussion.
>
>Regards
>Keith
>
>
>
>Dr Keith Ballingall
>Moredun Research Institute
>Pentlands Science Park
>Bush Loan, Penicuik
>Midlothian, EH26 0PZ
>Scotland, UK.
>Tel + 44 (0)131 445 5111
>e-mail keith.ballingallmoredun.ac.uk
>
>
>-----Original Message-----
>From: Jill Maddox [mailto:jillian.maddoxalumni.unimelb.edu.au]
>Sent: 28 March 2012 00:09
>To: j.pembertoned.ac.uk; j.slatesheffield.ac.uk;
>JGreeffagric.wa.gov.au; jhcalvoaragon.es; Yu.Jiangcsiro.au;
>jillmrubens.its.unimelb.edu.au; jjarrsunileon.es; jmm1ualberta.ca;
>John.Daniasdownstate.edu; john.mcewanagresearch.co.nz;
>juha.kantanenmtt.fi; julius.vanderwerfune.edu.au;
>K.Marshallcgiar.org; Keith Ballingall; kgietzenillumina.com;
>lherrmanvetmed.wsu.edu; Yutao.Licsiro.au; Lutz.Bungersac.ac.uk;
>M.Garcia-Podestaiaea.org; magali.san-cristobaltoulouse.inra.fr;
>martykardosgmail.com; massoud.malekiaea.org;
>matthew.peter.kentumb.no; Sean.Mcwilliamcsiro.au;
>mike.heatonars.usda.gov; mohammadvetsci.usyd.edu.au;
>msalyayahoo.com; msanderyillumina.com; neelamgnbagrgmail.com;
>neil.gemmellotago.ac.nz; ocobanoglunku.edu.tr;
>Ottmar.Distltiho-hannover.de; paolo.ajmoneunicatt.it;
>PAScheetmdanderson.org; Paul.Boettcherfao.org;
>Paul.Goodingagrf.org.au; pillaunimol.it; pradeepaspdn.ac.lk;
>raadsmacamden.usyd.edu.au; rgodfreuvi.edu;
>riccardo.negriniunicatt.it; richard.talbotroslin.ed.ac.uk;
>Rudiger.Brauningagresearch.co.nz; samuelcenargen.embrapa.br;
>Shannon.Clarkeagresearch.co.nz; simon.boitardtoulouse.inra.fr;
>sqanbargwdg.de; stefan.hiendlederadelaide.edu.au;
>stephen.bishopbbsrc.ac.uk; s.moore3uq.edu.au; swhitevetmed.wsu.edu;
>Ross.Tellamcsiro.au; Thomas.Farauttoulouse.inra.fr;
>tizianasechigmail.com; tlonghurstmla.com.au; vs.guptancl.res.in;
>wangjgenomics.org.cn; kworleyBCM.EDU; wwangmail.kiz.ac.cn;
>xuxungenomics.org.cn; zhuiastate.edu; hans.daetwylerdpi.vic.gov.au;
>lmatukumallinifa.usda.gov
>Subject: Re: Minutes from Sheep Genomics Consortium Call #99
>
>Hi All
>
>Re the discussion of functional SNPs on the proposed sheep SNP HD chip
>I think we need to discuss whether we can put sufficient MHC SNPs on
>the chip to enable accurate MHC typing of sheep.
>
>I think it would be really useful for sheep groups conducting
>immunology research to be able to have an accurate way of doing MHC typing.
>However given the diversity of the MHC region in sheep this might mean
>devoting a couple of hundred of the functional SNPs to the MHC region
>and would require development of a SNP based system for such typing.
>
>What do others think about one of the uses of the HD chip being to do
>MHC typing?
>
>Regards
>
>
>Jill
>At 03:47 PM 27/03/2012, James.Kijascsiro.au wrote:
> >2. Parameters for an HD Chip
> >Chip demand: community wide demand now stands at approximately 15,000
> >samples in an initial commitment, with at least another 10,000 to
> >follow after 18 months. Concerning the relative merit of an HD array
> >(800 K 1M SNP) versus application of emerging genotyping by
> >sequencing
> >(GBS) approaches, John put the view from AgResearch experimentation
> >that at present HD arrays are more cost competitive. This may not be
> >the case where lower density SNP genotyping applications are required.
> >Group discussed design criteria. This can be summarized as:
> >- functional content: inclusion of 100K SNP from classes such as
> >non-synonymous SNP, mis-sense, loss of function, intronic and SNP
> >within promoters etc that have an inferred functional impact.
> >- spacing: remains essential
> >- LD structure: tag SNP that efficiently capture haplotypes
> >- rare SNP: inclusion of SNP that have low MAF to tag rare haplotypes
> >in key breeds. Assisting in genomic selection.
> >- back compatibility: include all 50K SNP from existing SNP50
> >beadchip
>
>
>***************************************************************
>
>Jill Maddox
>16 Park Square
>Port Melbourne, 3207
>Australia
>phone: 03 9646 0428
>E-mail: jillian.maddoxalumni.unimelb.edu.au
>
>***************************************************************
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