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Genotyping Rat Cancer Models

Analysis of the genomic DNA framework for an organism is called genotyping.  The official reference sequence for the rat genome from the Brown Norway (BN) strain can be used as a comparison to the model rats or the diseased tissue samples. Large scale projects to identify SNPs and CNVs have provided additional crucial information. Genotyping can also be performed on any control animals and their modified counterparts for comparison.  Primary or secondary metastatic tumors can also be evaluated.  The specific technique used to assess the genotype will vary by tissue, experimental design or available technology. The complexities of chromosomal instability in cancer situations require special attention for analytical techniques. For example, loss of heterozygosity (LOH) has been implicated in many cancers. Tissue and tumor heterogeneity, or mixtures of different cells types and stages, can be a factor in analysis. Improvements in genotyping methods and software over time will increase the rate, quality, and volume of these processes. 

Cytogenetics

As with mice, many of the same techniques and methods to assess genomic stability and aberrant recombination using cytogenetics provide informative leads.  Methods to use spectral karyotyping (SKY) have been developed for rats. This type of analysis is particularly useful for studies of myeloproliferative disorders in rats.

Array-based hybridization

Array-based hybridization technologies are used in the evaluation of rat genotypes.  As with other species, careful experimental design is required to ensure that the results can be interpreted correctly.  Protocols for the hybridization techniques will be quite similar to that of human and mouse samples, of course, and researchers can use the same strategies for rat samples. 

Sequencing methods

As technologies for rapid and large-scale genomic sequencing continue to progress (sometimes referred to as next-generation sequencing), increasingly there will be efforts to fully sequence normal and tumor samples as a means to identify mutations and to understand the mechanisms and pathologies of cancer. These strategies will certainly be employed for the study of rat cancer models. 

 

Other techniques

A variety of other techniques may be used for determining genomic content of cells. Many types of PCR strategies, fragment length polymorphism analysis, and other methods are performed in some laboratory settings.  The amount of sequence to be studied, the locally available equipment and tools, and the volume of the analysis to be performed will determine the choice of the appropriate method. The PhysGen project developed genotyping protocols for rat that may give guidance to researchers who which to employ the methods for cancer research. New strategies are being developed continually to improve the sensitivity and speed of these investigations.

Informatics resources

Once genotyping data is obtained, it will need to be processed, analyzed, and compared with other data sets to draw conclusions.  Although many bioinformatics resources with a focus on cancer will emphasize human genomics and human cancer (such as The Cancer Genome Atlas TCGA and the International Cancer Genome Consortium projects) and may assist in the explorations of comparisons with model animals, many of them will also provide data for other species.  Ratmine offers rat-centric data sets that include genomic features, SNPs, and more. Array-based hybridization data can be searched via the GEO and ArrayExpress repositories, which will offer links to relevant research publications and array providers.  Other resources may be more focused on rat cancer biology specifically, such as the Rat Genome Database (RGD) Cancer Portal.  Sequence repositories like the NCBI’s Sequence Read Archive are storing data from large-scale sequencing projects, with links to submitting labs and literature that can guide researchers to useful techniques and technologies. The CaBIG® project is also providing extensive protocols and informatics tools support with cross-species utility.  Explore many resources associated with CaBIG® to find resources such as CaArray, CaGWAS, geWorkbench for integrated genomics strategies, and tools for managing samples such as caTissue Suite.