Methods and materials for canine breed identification

Patent metadata

Field	Value
Publication number	US-2023279505-A1
Application number	US-202218063532-A
Country	US
Kind code	A1
Filing date	Dec 8, 2022
Priority date	Dec 17, 2003
Publication date	Sep 7, 2023
Grant date	—

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.

First claim

1 - 23 . (canceled)

24 . A method for identifying a breed in a mixed-breed canid and managing healthcare of the mixed-breed canid based on a medical predisposition of the breed, wherein a genome of the mixed-breed canid is from two or more domestic breeds, the method comprising:
(i) contacting the genome of the mixed-breed canid with at least two primers selected from the group consisting of SEQ ID NOs: 1-200 and 244-327; (ii) amplifying sequences of the genome of the mixed-breed canid to obtain amplicons of at least 50 microsatellite markers and at least 50 single nucleotide polymorphism markers, wherein the at least 50 microsatellite markers are selected from REN285G14, C01.673, REN112I02, REN172C02, FH2793, REN143K19, FH2890, C02.466, C02.894, C02.342, FH2895, REN157C08, C03.445, FH2732, FH2776, REN160J02, REN262N08, REN92G21, REN285I23, C05.414, FH2752, REN210I14, REN37H09, REN97M11, REN286L19, FH2860, REN204K13, C08.373, C08.618, C09.173, C09.474, FH2885, C10.781, REN73F08, REN154G10, REN164B05, FH2874, C11.873, REN258L11, REN213F01, REN208M20, REN94K11, REN120P21, REN286P03, C13.758, C14.866, FH3072, FH3802, REN06C11, REN144M10, REN85N14, FH3096, C17.402, REN50B03, REN112G10, REN186N13, FH2795, C18.460, FH2783, REN91I14, REN274F18, FH2887, FH3109, REN293N22, FH2914, FH3069, REN49F22, REN107H05, REN78I16, FH3078, C23.277, REN181K04, REN106I06, FH3083, REN54E19, C25.213, REN87021, C26.733, C27.442, C27.436, REN72K15, FH2759, FH2785, REN239K24, FH3082, REN51C16, FH3053, REN43H24, FH2712, FH2875, FH2790, REN291M20, REN160M18, FH3060, REN314H10, REN01G01, REN112C08, REN106I07, FH2708, and REN86G15; and wherein the at least 50 single nucleotide polymorphism markers are selected from 372-c5t-82, 372-c5t-133, 372-c15t-285, 372-e2s-271, 372-e2s-257, 372-e2s-128, 372-e2s-93, 372-e2s-50, 372-e13t-57, 372-e15t-312, 372-e15t-301, 372-e15t-258, 372-e15t-156, 372-e16s-254, 372-e18t-165, 372-g17t-66, 372-i23s-384, 372-m6t-138, 372-m6t-88, 372-m6t-266, 372-m7s-317, 372-m9t-108, 372-m9t-58, 372-m18t-170, 372-m18t-129, 372-m23t-76, 372-m23t-108, 372-m23t-229, 372-m23t-238, 372-m23t-263, 372-o13s-212, 373-a10s-274, 373-a15t-112, 373-a17t-73, 373-a17t-136, 373-a21s-89, 373-c13s-93, 373-c15t-242, 373-c15t-202, 373-c15t-131, 373-e1t-50, 373-e1t-102, 373-e1t-130, 373-e21t-282, 373-e21t-116, 373-g7t-243, 373-g7t-242, 373-g7t-84, 373-g19t-249, 373-g19t-251, 373-g19t-246, 373-g19t-224, 373-g19t-378, 373-i8s-199, 373-i8s-224, 373416s-312, 373416s-254, 373416s-250, 373416s-249, 373-k8s-181, 373-k8s-224, 373-k10t-261, 373-k10t-264, 372-c5s-112, 372-c5s-168, 372-c15s-121, 372-c15s-196, 372-e15s-67, 372-e15s-71, 372-e15s-165, 372-e15s-221, 372-i23t-97, 372-i23t-224, 372-m6s-67, 372-m6s-73, 372-m6s-100, 372-m6s-108, 372-m6s-127, 372-m6s-147, 372-m6s-186, 372-m7t-100, 372-m7t-273, 372-m18s-131, 373-a14t-290, 373-a14t-197, 373-a14t-160, 373-a14t-55, 373-a21t-93, 373-e21s-136, 373-e21s-175, 373-e21s-191, 373-g7s-263, 373-g7s-266, 373416t-47, 373416t-133, 373416t-173, 373416t-210, 373416t-302, 373416t-319, and 373-k16t-54; (iii) sequencing the amplicons of the at least 50 microsatellite markers and the at least 50 single nucleotide polymorphism markers to produce a plurality of sequences; and (iv) executing, with a processor, computer-readable instructions stored on a computer-readable medium to cause the processor to determine, with a plurality of computational steps, the breed of the mixed-breed canid based on the plurality of sequences, wherein the plurality of computational steps comprises:
(a) inputting the sequences of the amplicons of the at least 50 microsatellite markers and the at least 50 single nucleotide polymorphism markers into a data structure stored in the computer readable medium, wherein the data structure comprises a marker field corresponding to the at least 50 microsatellite markers and the at least 50 single nucleotide polymorphism markers and a genotyping information field comprising the allele identities of the at least 50 microsatellite markers and the at least 50 single nucleotide polymorphism markers;
(b) comparing the marker field and the genotyping information field of the data structure to a database, wherein the database comprises allele identity and allele frequency information of the at least 50 microsatellite markers and the at least 50 single nucleotide polymorphism markers of a plurality of domestic dog breeds, wherein the plurality of domestic dog breeds comprises at least five domestic dog breeds;
(c) identifying the two or more domestic dog breeds of the mixed-breed canid from the allele-identities provided in the data structure; and
(d) calculating a fraction of the genome of the mixed-breed canid that is from each of the plurality of domestic dog breeds, at parent, grandparent, and great-grandparent levels, and wherein the fraction of the genome of the mixed-breed canid from each of the two or more domestic dog breeds is at least 5%;
(v) identifying the medical predisposition based on the breed; and (vi) testing the mixed-breed canid for a disease or a condition based on the medical predisposition.

25 . The method of claim 24 , wherein the plurality of domestic dog breeds comprises Mastiff, Dachshund, Bull Mastiff, Beagle, and Golden Retriever.

26 . The method of claim 24 , wherein the plurality of domestic dog breeds comprises:
(i) Belgian Sheep Dog and Belgian Tervuren, (ii) Collie and Shetland Sheep Dog, (iii) Whippet and Greyhound, (iv) Siberian Husky and Alaskan Malamute, (v) Greater Swiss Mountain Dog and Bernese Mountain Dog, (vi) West Highland White Terrier and Cairn Terrier, and/or (vii) Lhasa Apso, Shih Tzu, and Pekinese.

27 . The method of claim 24 , wherein the plurality of domestic dog breeds comprises between 5 and 500 domestic dog breeds.

28 . The method of claim 24 , wherein (iv)(c) identifying further comprises:
(1) obtaining a health recommendation based on the identified breed, wherein the health recommendation comprises treatments, special diets, or special products; and (2) generating a document comprising the health recommendation, wherein the document comprises information of diseases and predispositions of the mixed breed canid.

29 . The method of claim 24 , wherein (d)(iii) identifying further comprises:
(i) discriminating between the fraction of the genome of the mixed-breed canid that is selected from the group consisting of:
(a) Belgian Sheep Dog and Belgian Tervuren,
(b) Collie and Shetland Sheep Dog,
(c) Whippet and Greyhound,
(d) Siberian Husky and Alaskan Malamute,
(e) Greater Swiss Mountain Dog and Bernese Mountain Dog,
(f) West Highland White Terrier and Cairn Terrier, and/or
(g) Lhasa Apso, Shih Tzu, and Pekinese.

30 . A kit for performing the method of claim 24 .

31 . A kit for identifying a breed in a mixed-breed canid and managing healthcare of the mixed-breed canid based on a medical predisposition of the breed, wherein a genome of the mixed-breed canid is from two or more domestic breeds, the kit comprising:
at least two primers selected from the group consisting of SEQ ID NOs: 1-200 and 244-327, wherein the at least two primers are to contact a genome of a mixed-breed canid and amplify sequences of the genome of the mixed-breed canid to obtain amplicons of at least 50 microsatellite markers and at least 50 single nucleotide polymorphism markers; wherein the at least 50 microsatellite markers are selected from REN285G14, C01.673, REN112102, REN172C02, FH2793, REN143K19, FH2890, C02.466, C02.894, C02.342, FH2895, REN157C08, C03.445, FH2732, FH2776, REN160J02, REN262N08, REN92G21, REN285I23, C05.414, FH2752, REN210I14, REN37H09, REN97M11, REN286L19, FH2860, REN204K13, C08.373, C08.618, C09.173, C09.474, FH2885, C10.781, REN73F08, REN154G10, REN164B05, FH28

Assignees

• Fred Hutchinson Cancer Center

Inventors

• Ostrander Elaine
• Kruglyak Leonid
• Parker Heidi G
• Kim Lisa V
• Stephens Matthew
• Malek Tiffany B
• Sutter Nathan B
• Carlson Scott

Classifications

• C12Q1/6883

  for diseases caused by alterations of genetic material · CPC title

• C12Q1/6888 Primary

  for detection or identification of organisms · CPC title

• G16B20/40

  Population genetics; Linkage disequilibrium · CPC title

• G16B20/20

  Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection · CPC title

• C12Q2600/156

  Polymorphic or mutational markers · CPC title