The creation of the SNP chip

John McEwan measuring chip results

Researchers used computer simulations to determine the best sequencing strategy. At the time, this was sequencing 6 animals to 0.5x depth each using Roche’s 454 FLX platform. The actual sequence data subsequently underwent quality control during which clonal reads were removed, for example.

The remaining sequence was mapped onto the bovine genome. This allowed us to remove reads that could not be positioned uniquely and therefore would not be interesting for SNPs. It also allowed the total dataset to be broken down into smaller units which were assembled individually without overloading the assembler. Reads that could be positioned uniquely were mapped back onto the newly created sheep genome.

Information about the read origin was tracked and used to improve SNP detection. Finally, SNPs were rated based on a variety of criteria. 50,000 of our best SNPs were selected for the SNP chip, making sure they are equally spaced across the sheep genome.

This work was undertaken under the framework of the International Sheep Genomics Consortium and was funded by Ovita (owned jointly by Beef + Lamb New Zealand and AgResearch).

For more information see the Sheep HapMap website or Ovita.