DNA microarrays are small, solid supports containing thousands of gene sequences that are immobilized or attached at fixed locations. This technologic advance has revolutionized the basic approach to research as hundreds to thousands of genes can be analyzed simultaneously under identical conditions to assess various biological models, including disease, therapy, or experimental manipulation.
Genetic research for better horse health
A public nucleotide sequence database maintained at the National Center for Biotechnology Information (NCBI) contains around 20,000 equine related sequences, which are sufficient for the generation of the first equine DNA microarray.
Mammalian commercial microarrays currently exist for human, mouse, and rat, but not for the horse.
Sequence selection and probe design are crucial for the reliability, sensitivity, and specificity of DNA microarrays. The completed human genome consists of 3,000 mega-bases and 35,000 genes distributed across 23 chromosomes. The mouse genome is in similar size and gene number, except with 3 fewer chromosomes.
These genetic data are good templates in comparative analysis to annotate gene information of other organisms. However, huge computation is involved in sequence similarity comparisons.
Currently, a public nucleotide sequence database maintained at the National Center for Biotechnology Information (NCBI) contains around 20,000 equine related sequences, which are sufficient for the generation of the first equine DNA microarray. However, several challenges exist for the equine DNA microarray design:
- No public algorithm and software available for DNA microarray design;
- Not all available equine sequence data are suitable for DNA microarray;
- There is significant data redundancy and replication in the equine public database. Hence, the data need to be pruned;
- Significant equine gene data with unknown function need to be annotated by comparative analysis against the annotated human and mouse data.
In addition, researchers at Ohio State University have created the first DNA gene chip that contains thousands of the genes for a horse and one of the first gene chips for a domestic animal.
The new chip houses more than 3,200 expressed horse genes on a sliver of glass about the size of a postage stamp. When the researchers began developing this chip two years ago, only 200 horse genes were known.
This new chip will allow researchers to scan an individual horses genes at once to see which ones are active in a certain situation. For example, drug companies might use a gene chip to predict how a particular drug will affect an animal.
Since their invention nearly a decade ago, gene chips have revolutionized some basic approaches to research. Having a representative gene chip for a large animal could lead to better accuracy in studying human disease.