"Our role in the collaboration was to apply a technique that we developed a couple years ago for predicting variants where the sequencer failed to make a prediction," said Eskin, who holds a joint appointment in the department of human genetics at the David Geffen School of Medicine at UCLA. "Our technique, called imputation, uses the complete data to try to fill in some of these entries. The method, called EMINIM, was specifically designed for mouse data. Our contribution was to apply this technique to the data, which led to an increase in the number of variants identified."
With the full set of genetic information, researchers can now accurately predict the phylogeny similar in concept to the family tree of how the various mouse strains are related. The new study confirms that mice have a complex evolutionary history.
In addition, the study has some applications for the new genetic map, which were impossible before the development of this resource. One application involves identifying "allele specific expression." This expression describes the activity level of a gene. Each individual has two chromosomes, one from the mother and one from the father. For this reason, there are two copies of each gene.
Previous methods that would measure expression levels or activity levels of genes would measure the combined activity level of both copies of the genes. The genetic map generated by this study now allows researchers to measure the activity level of each copy individually.
"What the study confirms," Eskin said, "is that for many genes, these expression levels differ quite dramatically. This type of analysis was very difficult to perform before such a study."
|Contact: Wileen Wong Kromhout|
University of California - Los Angeles