Methods and materials for canine breed identification

• US 20060235625A1
• Filed: 12/15/2004
• Published: 10/19/2006
• Est. Priority Date: 12/17/2003
• Status: Active Grant

• Current Assignee: Fred Hutchinson Cancer Center
• Original Assignee: Fred Hutchinson Cancer Research Center (Fred Hutchinson Cancer Research Center|Argus Genetics|Mars)
• Inventors: Malek, Tiffany B., Kim, Lisa V., Sutter, Nathan B, Stephens, Mathew, Carlson, Scott, Kruglyak, Leonid, Ostrander, Elaine, Parker, Heidi G.
• Granted Patent: US 7,729,863 B2
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: C12Q 1/6888 for detection or identification of organisms
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/40 Population genetics; Linkage disequilibrium

Abstract

In one aspect, the invention provides methods for determining the contributions of canid populations to a canid genome. The methods comprise the steps of: (a) obtaining the identity of one or both alleles in a test canid genome for each of a set of markers; and (b) determining the contributions of canid populations to the test canid genome by comparing the alleles in the test canid genome to a database comprising canid population profiles, wherein each canid population profile comprises genotype information for the set of markers in the canid populations.

Claims

1. A method for determining the contributions of canid populations to a canid genome, comprising:

(a) obtaining the identity of one or both alleles in a test canid genome for each of a set of markers; and

(b) determining the contributions of canid populations to the test canid genome by comparing the alleles in the test canid genome to a database comprising canid population profiles, wherein each canid population profile comprises genotype information for the set of markers in the canid population.

2. The method of claim 1, wherein the set of markers comprises at least about five markers.

3. The method of claim 1, wherein the set of markers comprises microsatellite markers.

5. The method of claim 1, wherein the set of markers comprises single nucleotide polymorphisms (SNPs).

6. The method of claim 5, wherein the SNP markers comprise at least 5 of the SNP markers set forth in Table 2.

7. The method of claim 1, wherein the set of markers comprises one or more population-specific markers.

8. The method of claim 7, wherein the one or more population-specific markers comprise one or more SNP markers.

9. The method of claim 8, wherein the one or more SNP markers are selected from the group consisting of 372c5t-82, 372e13t-57, 372 m6t-88, 372 m23t-76, 373a15t-112, 373e1t-50, 373e1t-130, 373g19t-246, 373i8s-224, 373k8s-181, 372c5s-168, 372C15s-196, 372e15s-71, and 373a21t-93.

10. The method of claim 1, wherein the genotype information in a canid population profile comprises identities of one or both alleles of each of the set of markers.

11. The method of claim 1, wherein the genotype information in a canid population profile comprises allele frequencies for at least one allele of each of the set of markers.

12. The method of claim 1, wherein the database of canid population profiles comprises between about five and about 500 canid population profiles.

13. The method of claim 1, wherein the database of canid populations profiles comprise profiles for at least about five American Kennel Club registered breeds.

14. The method of claim 1, wherein the set of markers comprises fewer than about 1500 SNP markers and wherein the method determines the contributions of at least 87 canid populations to the test canid genome.

15. The method of claim 1, wherein the set of markers comprises fewer than about 200 SNP markers and wherein the method determines the contributions of at least 87 canid populations to the test canid genome.

16. The method of claim 1, wherein step (a) comprises amplifying genomic DNA of the test canid using primers specific for each of the set of markers and determining the size of the amplification product.

17. The method of claim 1, wherein step (b) comprises using a genotype clustering program.

18. The method of claim 1, wherein step (b) comprises using an assignment algorithm.

19. The method of claim 1, wherein step (b) comprises determining the probability that a specific canid population contributed to the genome of the test canid by determining the conditional probability that the alleles in the test canid genome would occur in the specific canid population divided by the sum of conditional probabilities that the alleles in the test canid genome would occur in each canid population in the database.

20. The method of claim 1, wherein step (b) comprises discriminating between the contributions of two or more genetically related canid populations to the test canid genome by comparing the alleles in the test canid genome to a database comprising profiles of the two or more genetically related canid populations.

21. The method of claim 20, wherein the two or more genetically related canid populations comprise Belgian Sheep Dog and Belgian Tervuren.

22. The method of claim 20, wherein the two or more genetically related canid populations comprise Collie and Shetland Sheep Dog.

23. The method of claim 20, wherein the two or more genetically related canid populations comprise Whippet and Greyhound.

24. The method of claim 20, wherein the two or more genetically related canid populations comprise Siberian Husky and Alaskan Malamute.

25. The method of claim 20, wherein the two or more genetically related canid populations comprise Mastiff and Bullmastiff.

26. The method of claim 20, wherein the two or more genetically related canid populations comprise Greater Swiss Mountain Dog and Bemese Mountain Dog.

27. The method of claim 20, wherein the two or more genetically related canid populations comprise West Highland White Terrier and Cairn Terrier.

28. The method of claim 20, wherein the two or more genetically related canid populations comprise Lhasa Apso, Shih Tzu, and Pekinese.

29. The method of claim 1 further comprising the step of providing a document displaying the contributions of one or more canid populations to the genome of the test canid genome.

30. The method of claim 29, wherein the document provides information regarding the one or more canid populations that contributed to the genome of the test canid or the test canid.

31. The method of claim 30, wherein the information is health-related information.

32. The method of claim 30, wherein the information is insurance information.

33. The method of claim 29, wherein the document provides a certification of the contributions of one or more canid populations to the genome of the test canid genome.

34. The method of claim 29, wherein the document provides a representation of the one or more canid populations that contributed to the genome of the test canid.

4. The method of claim 4, wherein the microsatellite markers comprise at least 5 of the microsatellite markers set forth in Table 1.

35. A method for defining one or more canid populations, comprising:

(a) for each of a set of canid genomes, obtaining the identity of one or both alleles for each of a set of markers; and

(b) defining one or more canid populations by determining the likelihood that one or more members of the set of canid genomes define distinct canid populations characterized by a set of allele frequencies for each marker using statistical modeling.

36. A computer-readable medium comprising a data structure stored thereon for use in distinguishing canid populations, the data structure comprising:

(a) a marker field, which is capable of storing the name of a marker or of an allele of the marker; and

(b) a genotype information field, which is capable of storing genotype information for the marker in a canid population, wherein a record comprises an instantiation of the marker field and an instantiation of the genotype information field and a set of records represents a canid population profile.

37. A computer readable medium comprising stored thereon:

(a) a data structure stored thereon for use in distinguishing canid populations, the data structure comprising;

(i) a marker field, which is capable of storing the name of a marker or of an allele of the marker; and

(ii) a genotype information field, which is capable of storing genotype information for the marker in a canid population, wherein a record comprises an instantiation of the marker field and an instantiation of the genotype information field and a set of records represents a canid population profile; and

(b) computer-executable instructions for implementing a method for determining the contributions of canid populations to a canid genome, comprising;

(i) obtaining the identity of one or both alleles in a test canid genome for each of a set of markers; and

(ii) determining the contributions of canid populations to the test canid genome by comparing the alleles in the test canid genome to a database comprising canid population profiles, wherein each canid population profile comprises genotype information for the set of markers in the canid population.