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Animal Breeding, Genetics, & Genomics

High density porcine SNP chip

The Swine Genome Sequencing Consortium (SGSC), which is developing a high density(~50K) SNP chip for pigs, is seeking collaboration with, and information from, researchers interested in the technology.

SNP stands for single nucleotide polymorphism. An SNP chip is a microscope slide on which DNA sequences are immobilized and is used by researchers to detect the presence of SNPs. It helps detect variation in DNA components between different individuals.

It is envisioned that the chip will be employed widely by the porcine research community to drive gene discovery and associated analyses and eventually whole genome selection. The SNPs included for this project was selected from those in public databases on February 1, 2008.

The consortium encourages researchers interested in access to the technology to join their group. In addition, investigators possessing SNP information that has not been placed in public databases are encouraged to submit their information as soon as possible so that the most useful set of SNPs can be included in the final product.

In September 2008 Illumina and the International Porcine SNP Chip Consortium announced that they will soon have a preliminary 60K SNP panel and additional content information available for anyone interested. Based on total current known order commitments worldwide, they 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.

Researchers should contact either Mohammad Koohmaraie, Max Rothschild or Larry Schook if their research program/institution would consider purchasing and employing the 60K pig SNP chip. They should indicate the approximate number of chips required initially and per year, so that they can be included in the mailing list concerning chip production and supply. The consortium aims to achieve the maximum economy of scale across the pig genomic community and in turn achieve the lowest unit cost per chip.

The Swine Genome Sequencing Consortium involves NIFA, the USDA’s Agricultural Research Service, the University of Illinois, Iowa State University, and the National Pork Board. Sequencing of the pig genome continues on schedule with completion expected in 2009. As of August 2008,  sequencing is at 71% sequence coverage and 92% tile path coverage.

The contacts above can provide additional information to interested parties.

 

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