# US 10,770,183 B2 · Methods of assessing a risk of developing necrotizing meningoencephalitis

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- Number: US 10,770,183 B2
- Document ID: US10770183B2
- Status: Granted
- Kind: B2
- Application number: 16/167,463
- Filed: 2018-10-22
- Published: 2019-02-14
- Granted: 2020-09-08
- Earliest claimed: 2010-05-19
- Assignees: The Translational Genomics Research Institute; University of Georgia Research Foundation, Inc.
- Applicants: The Translational Genomics Research Institute; University of Georgia Research Foundation, Inc.
- Inventors: Matthew Huentelman; Scott Schatzberg; Renee Barber
- Web page: https://patentgrep.com/patent/US10770183B2

## CPC

- G16H 50/30: for calculating health indices; for individual health risk assessment
- C12Q 1/6883: for diseases caused by alterations of genetic material
- A01K 67/02: Breeding vertebrates
- C12Q 2600/106: Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
- C12Q 2600/118: Prognosis of disease development
- C12Q 2600/124: Animal traits, i.e. production traits, including athletic performance or the like
- C12Q 2600/156: Polymorphic or mutational markers
- C12Q 2600/172: Haplotypes
- Y02A 90/10: Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation
- G16H: HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- A01K: ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
- Y02A: TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE

## Abstract

The present invention provides method of classifying a subject into a necrotizing meningoencephalitis (NME) disease risk group. The method may include assessing the presence of one or more marker (e.g., SNPs or risk loci) in a sample from the subject. For example, detection of the presence of one or more markers that are associated with an increased risk of NME can indicate that the subject should be classified into a risk group.

## Claims

### Claim 1

A method for treating a canine subject for necrotizing meningoencephalitis (NME), the method comprising:
extracting genomic DNA from a sample from the canine subject;
assaying the genomic DNA for one or more single nucleotide polymorphisms (SNPs), wherein the SNPs comprise BICF2G630168244 corresponding to position 74522353 on canine chromosome 4 and rs8954494 corresponding to position 53338796 on canine chromosome 15;
detecting an A allele at BICF2G630168244 and a G allele at rs8954494 in the genomic DNA from the sample; and
administering an effective amount of an immunosuppressive treatment to the canine subject having the A allele at BICF2G630168244 and a G allele at rs8954494 in the genomic DNA from the sample.

### Claim 2 (depends on 1)

The method according to claim 1, wherein the canine subject is selected from the group consisting of Pug, Chihuahua, and Maltese.

### Claim 3 (depends on 1)

The method according to claim 1, further comprising assaying the genomic DNA for one or more SNPs selected from the group consisting of: BICF2P608380 corresponding to position 1575622 on SEQ ID NO: 1 and BICF2P178662 corresponding to position 453486 on SEQ ID NO: 1.

### Claim 4 (depends on 1)

The method according to claim 1, further comprising assaying the genomic DNA for one or more SNPs selected from the group consisting of: BICF2S23225431 corresponding to position 503997 on SEQ ID NO: 1, BICF2P22942 corresponding to position 514107 on SEQ ID NO: 1, BICF2P194998 corresponding to position 561837 on SEQ ID NO: 1, rs8856588 corresponding to position 909317 on SEQ ID NO: 1, BICF2P574765 corresponding to position 997440 on SEQ ID NO: 1, BICF2P1186632 corresponding to position 1020913 on SEQ ID NO: 1, BICF2P1185629 corresponding to position 1078280 on SEQ ID NO: 1, BICF2P540937 corresponding to position 1116275 on SEQ ID NO: 1, rs9189886 corresponding to position 1130200 on SEQ ID NO: 1, rs9006653 corresponding to position 1202968 on SEQ ID NO: 1, BICF2P1200278 corresponding to position 1217609 on SEQ ID NO: 1, rs9125534 corresponding to position 1222157 on SEQ ID NO: 1, BICF2S23322760 corresponding to position 1279134 on SEQ ID NO: 1, rs8760645 corresponding to position 1311449 on SEQ ID NO: 1 rs9245050 corresponding to position 1315293 on SEQ ID NO: 1, BICF2P863589 corresponding to position 1346458 on SEQ ID NO: 1, BICF2P1115728 corresponding to position 1350853 on SEQ ID NO: 1, BICF2P1254053 corresponding to position 1435821 on SEQ ID NO: 1, BICF2P402427 corresponding to position 447223 on SEQ ID NO: 1, rs8694179 corresponding to position 1450810 on SEQ ID NO: 1, BICF2P459960 corresponding to position 1470715 on SEQ ID NO: 1, BICF2S22951431 corresponding to position 1483921 on SEQ ID NO: 1, BICF2P1261424 corresponding to position 1486888 on SEQ ID NO: 1, rs9120943 corresponding to position 1505458 on SEQ ID NO: 1, rs9077055 corresponding to position 1525153 on SEQ ID NO: 1, rs8677516 corresponding to position 1543627 on SEQ ID NO: 1, rs9132539 corresponding to position 1586067 on SEQ ID NO: 1, BICF2P1340012 corresponding to position 1597885 on SEQ ID NO: 1, BICF2P1211546 corresponding to position 1607518 on SEQ ID NO: 1, BICF2P738783 corresponding to position 1628812 on SEQ ID NO: 1, BICF2P1313789 corresponding to position 1940424 on SEQ ID NO: 1, BICF2P639740 corresponding to position 1972696 on SEQ ID NO: 1, BICF2P535495 corresponding to position 2080001 on SEQ ID NO: 1, BICF2P1380652 corresponding to position 2095669 on SEQ ID NO: 1, BICF2P1462329 corresponding to position 2118860 on SEQ ID NO: 1, rs8957837 corresponding to position 4109204 on SEQ ID NO: 1, BICF2S23516667 corresponding to position 235408 on SEQ ID NO: 2, BICF2P608380 corresponding to position 1575622 on SEQ ID NO: 1 and BICF2P178662 corresponding to position 453486 on SEQ ID NO: 1.

### Claim 5 (depends on 1)

The method according to claim 1, wherein the assaying the genomic DNA comprises a method selected from the group consisting of Sanger sequencing, next generation sequencing, pyrosequencing, sequencing by ligation, sequencing by synthesis, single molecule sequencing, pooled and barcoded DNA sequencing, PCR, real-time PCR, quantitative PCR, microarray analysis of genomic DNA, restriction fragment length polymorphism analysis, allele specific ligation, and comparative genome hybridization.

### Claim 6

A method for breeding a canine subject to reduce propensity to necrotizing meningoencephalitis (NME) in progeny resulting from the breeding, the method comprising:
extracting genomic DNA from a sample from the canine subject;
assaying the genomic DNA for one or more single nucleotide polymorphisms (SNPs), wherein the SNPs comprise BICF2G630168244 corresponding to position 74522353 on canine chromosome 4 and rs8954494 corresponding to position 53338796 on canine chromosome 15;
detecting a T allele at BICF2G630168244 and an A allele at rs8954494 in the genomic DNA from the sample; and
breeding the canine subject with the T allele at BICF2G630168244 and the A allele at rs8954494 in the genomic DNA from the sample.

### Claim 7 (depends on 6)

The method according to claim 6, wherein the canine subject is selected from the group consisting of Pug, Chihuahua, and Maltese.

### Claim 8 (depends on 6)

The method according to claim 6, wherein the assaying the genomic DNA comprises a method selected from the group consisting of Sanger sequencing, next generation sequencing, pyrosequencing, sequencing by ligation, sequencing by synthesis, single molecule sequencing, pooled and barcoded DNA sequencing, PCR, real-time PCR, quantitative PCR, microarray analysis of genomic DNA, restriction fragment length polymorphism analysis, allele specific ligation, and comparative genome hybridization.