From salamon.d_at_gmail.com Tue Jun 8 09:14:00 2010 From: "Dragica Salamon" Postmaster: submitted from web posting form To: Multiple Recipients of AnGenMap Subject: sheep small SNPchip development Date: Tue, 08 Jun 2010 09:14:00 -0500 Hello, everyone! As I am new in this discusion/information group, I was wondering if this would be a good place to talk about the development of SNP chips... (If not, could you, please, direct me to some discussion groups) The thing is, I am in progress of preparing a study on (10-15 indigenous) eastern Adriatic sheep breeds (diversity, distances, population stuff...) and I am interested in adopting the new SNP marker methods instead of microsatellite ones in case I can make my financial frame to fit. Do you think using 100 SNPs in order to exchange for 30 microsatellites and using the additional 30SNPs more (of some production and functional traits) would make an interesting chip construction to share among researh teams? I would be happy if to hear back from you... Dragica, Croatia

From Paul.Boettcher_at_fao.org Tue Jun 8 09:29:13 2010 From: "Boettcher, Paul (AGAG)" To: Multiple Recipients of AnGenMap Subject: RE: sheep small SNPchip development Date: Tue, 08 Jun 2010 09:29:13 -0500 Dear Dr. Salamon The FAO is also interested to migrate from microsatellites to SNP for population characterization. However, we foresee the need for some prior research in SNP selection to obtain a representative measure of diversity. Paul Boettcher

From taylorjerr_at_missouri.edu Tue Jun 8 13:20:06 2010 From: "Taylor, Jerry F." To: Multiple Recipients of AnGenMap Subject: RE: sheep small SNPchip development Date: Tue, 08 Jun 2010 13:20:06 -0500 The Illumina SNP50 assays has been used for phylogenetic work and I suspect that the existing sheep and swine 50K assays are being used for the same purpose. See for example: Decker JE, JC Pires, GC Conant, SD McKay, MP Heaton, K Chen, A Cooper, J Vilkki, CM Seabury, AR Caetano, GS Johnson, RA Brenneman, O Hanotte, LS Eggert, P Wiener, JJ Kim, KS Kim, TS Sonstegard, CP Van Tassell, HL Neibergs, JC McEwan, R Brauning, LL Coutinho, ME Babar, GA Wilson, MC McClure, MM Rolf, JW Kim, RD Schnabel, JF Taylor. 2009. Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proc. Natl. Acad. Sci. U S A. 106:18644-9. MacEachern S, McEwan J, Goddard M. 2009. Phylogenetic reconstruction and the identification of ancient polymorphism in the Bovini tribe (Bovidae, Bovinae). BMC Genomics. 2009 Apr 24;10:177. 100 SNPs is probably too few for what you want to do. If you can't afford to use the 50K sheep assay you could develop a 3,072 Goldengate assay that would cost about $30 per sample if you could afford to genotype 1000 samples. There are likely others out there using the sheep chip for this purpose and so a great advantage of using this assay is that the data sets become integrable and extendable. SNP ascertainment is going to be a problem for estimating genetic distances probably no matter what assay you use. See the Decker paper about for a discussion on this. Good luck, Jerry

From salamon.d_at_gmail.com Tue Jun 8 16:00:31 2010 From: =?UTF-8?Q?Dragica_=C5=A0alamon?= To: Multiple Recipients of AnGenMap Subject: Re: sheep small SNPchip development Date: Tue, 08 Jun 2010 16:00:31 -0500 thank you all on very useful inputs and guidelines in your replys today! now I have a thing or two to think about for a few days :) like the size of a chip... the ascertainment bias... and also to "tame" my somewhat idealistic ideas into, hopefully, start of a nice and useful project... :)

From jillm_at_rubens.its.unimelb.edu.au Tue Jun 8 19:02:53 2010 From: Jill Maddox To: Multiple Recipients of AnGenMap Subject: Re: sheep small SNPchip development Date: Tue, 08 Jun 2010 19:02:53 -0500 Hi Dragica and others interested in sheep SNPs The International Sheep Genomics Consortium (http://www.sheephapmap.org/) is currently developing an Illumina Infinium 5K chip with SNPs being selected from the 50K chip based on their informativeness for multiple breeds. This chip may be suitable for your needs and given that large numbers of it will be produced should be relatively affordable. The contact person for the 5K SNP chip this is John McEwan . Sheep parentage SNP tests are also being developed by a couple of organisations (I know of AgResearch/Ovita New Zealand and Meat and Livestock Australia but there may be others) based on this information. As far as I am aware the MLA SNP parentage test will be public domain in terms of what SNPs are being used. I think the AgResearch SNP list will be private - but John would know more about this. Regards Jill Maddox

From hillel_at_agri.huji.ac.il Wed Jun 9 06:47:25 2010 From: "Jossi Hillel" To: Multiple Recipients of AnGenMap Subject: RE: sheep small SNPchip development Date: Wed, 09 Jun 2010 06:47:25 -0500 Based on our analysis of ten chicken populations (10 birds each) using STRUCTURE software, microsatellites discriminate between populations far better than any other marker type. I’d stay with microsatellites for this kind of need, given the budget is limited. Jossi Hillel

From Martien.Groenen_at_wur.nl Wed Jun 9 07:52:14 2010 From: "Groenen, Martien" To: Multiple Recipients of AnGenMap Subject: RE: sheep small SNPchip development Date: Wed, 09 Jun 2010 07:52:14 -0500 In the past we have used microsatellites and in recent years moved completely to SNPs. I would strongly advice to use SNPs rather than micros. SNPs are more cost effective, allele calling is the same between different labs and although you need 3-4 times the number of markers, overall the costs are lower than using micros. Martien Groenen

From taylorjerr_at_missouri.edu Wed Jun 9 07:56:08 2010 From: "Taylor, Jerry F." To: Multiple Recipients of AnGenMap Subject: RE: sheep small SNPchip development Date: Wed, 09 Jun 2010 07:56:08 -0500 This depends on the objectives of the study. If you want to discriminate between recently diverged populations then running a few microsatellites and observing 5-6 alleles per locus will do a decent job. There is still likely to be an issue of ascertainment depending on how the microsats were discovered and chosen to be run in the populations. If you are dealing with populations that have much older divergence times then homoplasy becomes an issue due to the much higher mutation rates of microsatellites. That is, when you see a specific allele within two populations can you conclude that they are identical by descent or has recurrent mutation produced the alleles from parent alleles that were evolutionarily distinct? Finally, the logistics of scoring 30-40 microsats is a bit of a pain. Even if you have these nicely multiplexed you need to process your DNAs 5-6 times which makes them costly and allows opportunity for error (sample swapping). Simply running one sample one time and producing 50,000 genotypes makes the genotyping part of the project very simple. The issue of informativeness is simply the sum of the effective number of alleles at each locus summed across all loci. If you run 30 SNPs the informativeness is going to be less than if you run 30 microsats. But if you run 3,000 or 5,000 or 50,000 SNPs you will produce topologies that effectively have 100% bootstrap support. Jerry

From hsimian_at_gwdg.de Wed Jun 9 08:01:44 2010 From: "Simianer, Henner" To: Multiple Recipients of AnGenMap Subject: RE: sheep small SNPchip development Date: Wed, 09 Jun 2010 08:01:44 -0500 We did a study in eight chicken breeds (8 animals each) to compare microsatellites and SNPs using STRUCTURE software and principal component analysis (PCA). For the same number of markers you cannot see any difference in the PCA-Plot of the first two components or for the differentiation in the distruct-plot. We also calculated the euclidean distance and from that a statistic that describes the level of differentiation. These values show that the differentiation surprisingly is much better for the SNPs compared to microsatellites even with the same number of markers. These results will be presented at the WCGALP in Leipzig in August 2010. Christian Gaerke and Henner Simianer

From hillel@agri.huji.ac.il Wed Jun 9 10:58:35 2010 From: "Jossi Hillel" To: Multiple Recipients of AnGenMap Subject: RE: sheep small SNPchip development Date: Wed, 09 Jun 2010 10:58:35 -0500 Hi again, In my previous message I pasted a figure into the mail and it turned out that many of the recepients did not get it. Here I attach that figure from which one can see informative results. From this figure you can see that 29 microsatellites did much better job than 152 SNPs. If these results are not in full agreement with those mentioned in previous messages by Martien and Henner, it is possible that apart from the microsatellites and intergenic loci in the attached figure, all others SNP markers are within genes or related to genes. I wonder where the SNPs mentioned by Henner and Martien are located. These results will be submitted for publication very soon. Jossi Hillel

From john.mcewan@agresearch.co.nz Wed Jun 9 14:31:13 2010 From: "McEwan, John" To: Multiple Recipients of Subject: RE: sheep small SNPchip development Date: Wed, 09 Jun 2010 14:31:13 -0500 Dear all The "rule of thumb" for mammalian species is 1 microsatellite has the discrimination power of about 5 SNPs for a variety of typical tasks 29*5 ~ 152 However, SNPs and microsatellites have different utility depending on the task. Microsatellites have a higher mutation rate and even with the problem of recurrent mutations this means they are somewhat better on a blow by blow comparison of recent fine scale differences on the Y chromosome for instance. However, please be realistic here. The cost of a SNP on a 50K chip at ~US$100 for consumables is the equivalent cost of genotyping say 30-50 microsatellites (with multiplexing) but the power of the results is way way better for almost all tasks and the information that can be extracted just cannot be compared sensibly. In addition the technology costs are much more scalable. John McEwan

From lipkin@ginegar.net Wed Jun 9 22:30:06 2010 From: "Udi Lipkin" To: Multiple Recipients of Subject: RE: sheep small SNPchip development Date: Wed, 09 Jun 2010 22:30:06 -0500 The problem is that you can't have each "low cost" SNP alone. You must take the entire array, and the cost of this array is sharply limiting your population size. Thus, with SNPs you have far many more markers per individuals, but far fewer individuals per marker. As a result, in many studies the population dimension is lost. Ehud Lipkin

From Peter.Hunt@csiro.au Wed Jun 9 22:38:54 2010 From: To: Multiple Recipients of Subject: RE: sheep small SNPchip development Date: Wed, 09 Jun 2010 22:38:54 -0500 Dear all, Have been following this email trail with interest. Homoplasy was raised earlier in the discussion regarding differences between SNP and Msats. I have noticed that there seems to be little discrimination between Ts and Tv SNPs in chip design (at least for the sheep one). Has anyone considered the higher potential for homoplasic mutations in Ts compare to Tv SNP? For some investigations a Tv only SNP chip might be preferable? Has anyone studied Tv data separate to Ts data to see if there is any divergence of results? Are there enough Tv on the current chip to make a fair comparison anyway? I'd be interested in any comments or information on these points, Peter --------------------------------------------------------------- Dr Peter Hunt Research Scientist, CSIRO McMaster laboratory, Locked Mail Bag 1, Armidale, NSW, 2350 Australia Phone +61 2 6776 1300 Fax +61 2 6776 1333 email peter.hunt@csiro.au ---------------------------------------------------------------

From taylorjerr@missouri.edu Wed Jun 9 23:54:43 2010 From: "Taylor, Jerry F." To: Multiple Recipients of Subject: Re: sheep small SNPchip development Date: Wed, 09 Jun 2010 23:54:43 -0500 Yes, we have. We found no difference in the cattle tree in the decker et al paper, but there is a big difference in the numbers of Ts vs Tv SNPs on the BovineSNP50. Jerry Sent from my iPhone

From salamon.d@gmail.com Thu Jun 10 09:49:05 2010 From: =?UTF-8?Q?Dragica_=C5=A0alamon?= To: Multiple Recipients of Subject: Re: sheep small SNPchip development Date: Thu, 10 Jun 2010 09:49:05 -0500 Looks like the SNP discussion has a few new questions and directions :) as far as my first question from a few days ago is concerned, I found all of your replies to be very helpful! (both on topic and in priv. mailbox) Thank you. I'm more or less decided how to address my research ideas now, ... however I still have questions on this diversity use issue with the ascertainment bias... How do you think this problem could be addressed in analysis of the 5K chip data, or the Goldengate assay data... Would it be better maybe, or could this problem somehow be be taken care of by different selection of the SNPs for the chip construction? Or is the size of the chip, also in this case, the alleviating factor? Regards, Dragica

From taylorjerr@missouri.edu Thu Jun 10 10:05:44 2010 From: "Taylor, Jerry F." To: Multiple Recipients of Subject: RE: sheep small SNPchip development Date: Thu, 10 Jun 2010 10:05:44 -0500 Dragica: To overcome the problem, the SNPs need to be considered to be a random sample of the SNPs (in terms of their minor allele frequencies) from each of the assayed populations. This is clearly a technically difficult problem since it would require independent SNP discovery projects which were not biased toward finding the common SNPs within each population (highly non trivial and would require a lot of deep sequencing). It also runs highly counter to the design philosophy of most genotyping assays in which we deliberately bias the content towards SNPs with high MAF in all populations. I have discussed this with several heavy-hitting mathematical geneticists and am trying to put some collaborations together to see if a mathematical "fix" might be possible. But for now, all the things I tried (see Decker paper) were fruitless. Jerry

From gianola@ansci.wisc.edu Thu Jun 10 10:21:14 2010 From: Daniel Gianola To: Multiple Recipients of Subject: RE: sheep small SNPchip development Date: Thu, 10 Jun 2010 10:21:14 -0500 And probably the sheep are not a random sample either, so there are two sources of non-ignorable missingness. A better name for would be nonrandom sheep small nonrandomSNP chip. Please make it cheap too. Dan

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