Novel approach results in first-ever rhesus macaque whole-genome array
Robert B. Norgren, PhD
Rob Norgren of The University of Nebraska Medical Center and Katja Nowick of Lawrence Livermore National Laboratory discuss the innovation behind the development of the Affymetrix GeneChip® Rhesus Macaque Genome Array
Researchers at the University of Nebraska Medical Center (UNMC), in collaboration with scientists at Affymetrix, have discovered a novel way to derive sequences for microarrays, resulting in the first ever commercially available whole-genome rhesus macaque microarray. This advance in primate genome research may help researchers to better understand the evolutionary relationship between humans and other primates, and will increase the utility of rhesus macaque as a model organism for disease research.
We are just starting to explore the similarities in gene expression between rhesus and humans. When we compare the same tissues from humans on the human chip and rhesus samples on the rhesus chip, we get a very high degree of similarity in expression. The same genes are expressed.
Rob Norgren and his collaborators used human transcript annotation to design primers to amplify and sequence rhesus genes. In collaboration with Affymetrix, this strategy was extended to an in silico approach using information from the Baylor Rhesus Genome Project. This project resulted in a set of probes representing 18,296 rhesus/human orthologs, including transcript variants and more than 17,000 genes for the GeneChip® Rhesus Macaque Genome Array. The resulting human genome-derived macaque array was the first whole-genome rhesus expression array. The array design was published in the January 23, 2007, issue of BMC Genomics. Experiments illustrating the reliability and validity of the array were published in the February 28, 2007, issue of BMC Genomics.
"The normal way a microarray is developed, you have to wait until you have a complete genome project and then you cluster the ESTs [expressed sequence tags] and come up with a consensus sequence to align with the genome project. By using our method, we were able to get the orthologous rhesus macaque sequence using human sequences to design primers," said Norgren. "It was a nice shortcut. As far as I know, this is the only Affymetrix microarray that has been made in this way."
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