It has been suggested that a great advance in the study of human diseases could be made through genetic studies. The study of genes is relatively new in animal species other than man. The dog is a useful subject for the genetic study of complex traits. Dogs have been used as models for studying physiological and pathophysiological processes, including cancer, diabetes, obesity, cardiovascular and psychiatric disorders. Genetics is a key element in understanding disease susceptibility, severity, and pharmacology in order to achieve the greatest benefits of companion animal models. Advances in the sequencing of the dog genome (Lindblad-Toh et al., 2004) will facilitate the mapping and identification of genes associated with disease in dogs. Furthermore, the dog genome has now been studied, and many genes of interest have been localized (Lindblad-Toh et al., 2004;Parker et al., 2003;Dubcovsky et al., 2003).
There are approximately 800 recognized dog breeds worldwide, and it is estimated that there are over 50 million dogs in the United States alone (American Kennel Club, 2006; http://www.akc.org). The large number of dog breeds, together with its popularity in the United States, makes it feasible to breed individuals that are predisposed to a disease that can be identified and then identified dogs could be bred in the future to produce unaffected progeny. This type of study would greatly speed the process of determining genes involved in disease susceptibility in a species other than the human. Furthermore, these affected dogs are also a valuable resource for studying the environmental factors that are involved in disease expression (McCarthy et al., 2005; Sutter et al., 2005).
Genetic studies in other species are dependent on markers with which polymorphisms can be reliably and reproducibly ascertained. Therefore, there is a need to identify and map gene loci that have polymorphisms between dog breeds, but not among breeds. Such polymorphic loci can be used as markers in the genetic analysis of dog breeds.
The advent of sequencing technology has enabled the investigation of genome variation in many species, including dog breeds, by making it possible to sequence genomes in multiple individuals to detect small sequence differences that are indicative of genetic variation. Variation in the number of repeat sequences across dogs may be responsible for breed-specific traits. For example, if some repeat sequences are involved in the process of spermatogenesis, then the number of repeats that a dog has could cause abnormalities in the process of producing viable sperm, and this in turn would result in a reduced fertility rate. Polymorphic repeats can be used to rapidly screen hundreds or thousands of dogs. These variations are expected to be a valuable tool in investigating the genetic basis of a number of traits, including but not limited to growth rate, developmental timing, and disease susceptibility.
Microsatellite markers, which are also called simple sequence repeat (SSR) markers or short tandem repeats (STR), have been widely used in genetic linkage mapping and in population genetics. Microsatellite markers are typically 1-6 bases in length, and can be located anywhere on the genome. Microsatellite markers provide a means of studying the polymorphisms between individuals in a random population, mapping genes and studying kinships. These markers can be scored by automated methods, and are amenable to high-throughput genotyping (Monsalve et al., 2005; Chagnon, et al., 2003). Furthermore, many microsatellite markers have already been discovered in dog breeds through simple, fast, automated sequencing of genome fragments, and these markers have already been studied for their usefulness in genetic studies (Lindblad-Toh et al., 2004). Thus, a large collection of dog breeds will enable the identification of polymorphic microsatellite loci that are useful as genetic markers for pedigree-based mapping.
Despite the advances made in molecular genetics, many aspects of the genetic basis of complex diseases remain unknown. A particularly useful model for understanding complex diseases is the dog, which has a history of extensive interbreeding to produce hundreds of distinct breeds with unique phenotypes. By using naturally occurring populations, the canine genome can be investigated for the genetic basis of phenotypic variability, including inherited diseases. Furthermore, through selective breeding, these models allow researchers to identify chromosomal regions that are associated with specific traits. This process of mapping chromosomal regions can be used to identify the gene within each region that is responsible for the observed trait. The identification of genes within specific chromosomal regions involved in disease pathogenesis will lead to insights about the genetics of the disease process.
A large number of polymorphic markers have been identified in dogs, and their polymorphic nature provides genetic markers that are especially suitable for pedigree studies. Genomic approaches involving genome-wide scans and single-nucleotide polymorphism (SNP) typing technologies have been successful in identifying genes for a variety of inherited traits in dogs (see, e.g., U.S. Pat. No. 6,664,079; U.S. Patent Application No. 2005/0186551; U.S. Patent Application No. 2007/0121784; U.S. Patent Application No. 2007/0121787; U.S. Patent Application No. 2007/0265886; U.S. Patent Application No. 2008/0176945; and U.S. Patent Application No. 2008/0176854). Genetic markers are of interest for a wide variety of purposes, including the mapping and identification of genes involved in diseases and disorders, the study of genetic diversity, the testing of relationships among individuals and populations, the mapping of quantitative trait loci (QTL) (e.g., genes involved in growth, development, disease resistance), marker-assisted selection and breeding value estimation.
In an attempt to identify genes involved in human health and disease, researchers have studied the genetic basis of inherited disease in animal species that are naturally prone to develop these diseases, such as dogs and horses. However, the study of naturally occurring disease mutations that occur naturally in a population makes it very difficult to identify the gene involved in the disorder. In these cases, researchers can make mutations within the genomes of the individuals and study the effect of these genetic changes. However, the creation and study of each new mutation requires considerable time and effort, and once the mutation has been studied, it is difficult to identify the exact gene that is responsible for causing the disease. Thus, there remains a need to study the molecular basis of genetic disorders and diseases in order to identify genes that contribute to certain phenotypes.
In the present invention, the identification and mapping of chromosomal regions associated with disease phenotypes, such as disease genes, is performed using a disease-targeted canine SNP array. The SNP marker data is used to identify linkage disequilibrium blocks and to identify haplotypes within them. The location of disease genes within the canine genome can be predicted by identifying linkage disequilibrium blocks in which the disease gene resides, and then selecting the haplotype (or haplotypes) that best explain the association between the disease phenotype and the disease gene. In the case of a disease that is known to affect humans, a human genome array is used to search for the homologous dog chromosome (or chromosomes) that the disease gene is located in.
Polymorphic markers are useful for association mapping for identifying genes that contribute to traits under study. Association studies rely on allele frequency differences between cases and controls, and so the number of cases and controls that are available is important. However, the success of a study depends on the extent to which the study cases and controls are matched for ascertainment purposes. For example, a small sample of dogs that are related by common ancestry may be used, such as dogs that belong to families or breeds that are well known for being related. If there is a family history of a certain disease in dogs, then many members of that family may be affected. However, if there is not a known family history of disease, then finding families with affected members may be more difficult. In this case, it may be beneficial to
