Pig Genome Update No. 92

September 1, 2008

  1. Illumina and the International Porcine SNP Chip Consortium are pleased to announce that we will soon have a preliminary 60K SNP panel
  2. Sequencing progress continues on schedule
  3. The 31st ISAG meetings were a huge success
  4. Nominations of new USDA Genome Coordinators due
  5. Planning for PAG XVII, January 10-15, 2009, is already underway
  6. The pig oligo arrays can be ordered
  7. Upcoming meetings (4 items)

Illumina and the International Porcine SNP Chip Consortium are pleased to announce that we will soon have a preliminary 60K SNP panel and additional content information available for anyone interested. If you are interested in receiving this list and/or additional content information, please contact Martien Groenen and Marylinn Munson mmunson@illumina.com and Martien.Groenen@wur.nl. Again, the deadline to participate in the early access and pricing discounts to 5 pm Pacific Time September 5, 2008. After 5th Sept, early access and pricing will not be available. Don't miss out on this opportunity!! Based on total current known order commitments worldwide, we estimate the price of the final array will be Tier B. However if all committed orders come in + another 1, 000 samples, the consortium will likely achieve Tier C pricing. The prices per sample for tier B are as product $120 (USD) and as service $192 (USD) and for Tier C $99.99 as product and $160 as service. These includes arrays and Illumina related reagents. Pricing does not include shipping, taxes, insurance or duties. To achieve Tier B or C pricing, all Qualifying Orders must be received by Illumina before 5th September and meet minimum required orders. If those individuals who do not have a system, Illumina provides Genotyping Services known as FastTrack Services. Additionally, there are many service providers that can provide Infinium genotyping services. Service Providers must meet the September deadline for placing orders. Some of these providers are able to provide Infinium services for fewer samples than Illumina's 282 sample minimum. Illumina Certified Service Providers (with Infinium Genotyping certification) can be found at (http://www.illumina.com/pagesnrn.ilmn?ID=69). Illumina would also be happy to provide additional names upon request.Please do not hesitate to contact Illumina for further information or questions at (http://www.illumina.com/contactMe.ilmn?CS=1). (kindly provided by Marylinn Munson Illumina).


Sequencing progress continues on schedule. Sequencing of the pig genome continues on schedule with completion expected in 2009. To date (August 27, 2008) sequencing is at 71% sequence coverage and 92% tile path coverage (kindly provided by Richard Clark, Sanger).


The 31st ISAG meetings were a huge success. Good weather, great talks and a beautiful venue all contributed to the excellent ISAG meetings. Excellent plenary talks and many exciting workshops were available to the attendees. On the swine side we had excellent talks in the swine sequencing workshop and a number of other pig workshop talks. Abstracts are available. A special thank you to our hosts who helped organize and made it a great meeting.


Nominations of new USDA Genome Coordinators due. While scientists are waiting on approval for our NRSP8 project renewal for the next five years nominations for the species coordinators for the next five years (2009 - 2013) are needed. To nominate an individual for the Swine, Horse, Poultry, Cattle/Sheep, Aquaculture and Bioinformatics Coordinators positions. Please make sure that your nominee has agreed to the nomination before you submit one. Please forward your nominee's name and complete contact information to me via email to mqureshi@csrees.usda.gov by September 15, 2008. Feel free to contact Dr. Muquarrab Qureshi, mqureshi@csrees.usda.gov if you may have any questions.


Planning for PAG XVII, January 10-15, 2009, is already underway. The new chairs of the swine genome section are Melissa Ashwell and Cathy Ernst. Ideas for speakers are gladly being taken by Max Rothschild or Hans Cheng for plenary talks. Some reorganization of the species workshops on Saturday and Sunday is likely to take place to avoid overlap and increase attendance to the NRSP8 meetings. Stay tuned for developments.


The pig oligo arrays can be ordered. Swine oligo arrays can now be ordered at(http://www.pigoligoarray.org/) . A validation experiment, funded in part by the participants and the USDA Pig Genome Coordinator, was reported on at PAG 2008.


Upcoming meetings (see: (http://www.animalgenome.org/pigs/community/meetings.html))

Items for Pig Genome Update 93 can be sent to me by no later than October 15 please.

                    Max Rothschild
                    U.S. Pig Genome Coordinator
                    2255 Kildee Hall, Department of Animal Science
                    Iowa State University
                    Ames, Iowa 50011
                    Phone: 515-294-6202, Fax: 515-294-2401

cc: Muquarrab Qureshi, CSREES and Caird Rexroad II, ARS

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