From michael.deveer monash.edu Thu Mar 29 20:23:03 2012
Subject: Re: sheep HD SNP array and MHC typing
From: Michael De Veer <michael.deveermonash.edu>
To: Multiple Recipients of <SheepModelsanimalgenome.org>
Date: Thu, 29 Mar 2012 20:23:03 -0500
Hi All,
We are looking at transcriptomic data in sheep immune cells following
vaccination. We have used next generation sequencing and will continue to
use it as we generated alot of data. On an information per $ basis it
outcompetes array based technology quite easily.
I guess a question becomes where resources would be better spent,
development of a snp array or better sheep/livestock specific bioinformatic
tools for next gen data. Personally I would like to see better tools
available to analyse, store, collate and compare next generation sequencing
data within livestock species as that is going to be the more flexible
platform over the long term.
Thanks,
Mike de Veer
Monash University, Australia
On 30 March 2012 11:59, Thomson, Jennifer <Jennifer.Thomsonales.ualberta.ca
> wrote:
>
> Excuse my inexperience please, I'm starting as a new prof at Montana State
> this year. In shopping for a sequencer for my new lab I am looking at the
> Ion
> Proton machine from LT. It is in early release and can do about 2 whole
> genomes at 5x coverage in a single run 10GB of data for $1000- rough
> estimate
> because I don't have the numbers in front of me. They say the next chip
> will
> do 100GB also for $1000. That would be about 6 genomes for $1000 in a
> single
> day run. I think it is a real viable alternative if you have the ability to
> process that amount of data.
>
> Jennifer Thomson
> Future Asst Professor
> Montana State University
>
> Sent from my iPhone
>
> On Mar 29, 2012, at 5:45 PM, "Imke Tammen" <imke.tammensydney.edu.au>
> wrote:
>
> > Will be at Isag and think a discussion would be good - agree that whole
> genome
> > sequencing needs to be considered as an alternative....
> > -----Original Message-----
> > .From: Hickford, Jonathan [mailto:Jonathan.Hickfordlincoln.ac.nz]
> > .Sent: Friday, 30 March 2012 8:32 AM
> > .To: Multiple Recipients of <SheepModelsanimalgenome.org>
> > .Subject: RE: sheep HD SNP array and MHC typing
> > 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 www.lincoln.ac.nz
> > Lincoln University, Te Whare Wanaka o Aoraki
> > New Zealand's Specialist Land
> > Based University
> > -----Original Message-----
> > .From: Jill
> > Maddox [mailto:jillian.maddoxalumni.unimelb.edu.au]
> > .Sent: Thursday, 29
> > March 2012 1:29 p.m.
> > .To: Multiple Recipients of <SheepModelsanimalgenome.org>
> > .Subject: sheep HD SNP array
> > and MHC typing
> > [ sheepmodels Discussion Mailing List - Mail distributed to
> > ]
> > 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
> >> ***************************************************************
> > ***************************************************************
> > Jill Maddox
> > 16 Park Square Port Melbourne, 3207 Australia phone: 03 9646
> > 0428 E-mail:
> > jillian.maddoxalumni.unimelb.edu.au
> > ***************************************************************
> > -o
> > -o
> > http://www.animalgenome.org Help desk: bioinfo-teamanimalgenome.org
> > -o
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>>>>
>
>
--
Michael de Veer
Dept. Physiology,
Monash University,
Wellington Rd, Vic, 3800
Australia.
PH: (613) 99055132
|
