# US 11,111,539 B2 · Identification of pediatric onset inflammatory bowel disease loci and methods for use thereof for the diagnosis and treatment of the same

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- Number: US 11,111,539 B2
- Document ID: US11111539B2
- Status: Granted
- Kind: B2
- Application number: 15/899,811
- Filed: 2018-02-20
- Published: 2019-07-18
- Granted: 2021-09-07
- Earliest claimed: 2008-02-19
- Assignees: The Children's Hospital of Philadelphia
- Applicants: The Children's Hospital of Philadelphia
- Inventors: Hakon Hakonarson; Jonathan Bradfield; Marcin Imielinski; Struan F. A. Grant
- Web page: https://patentgrep.com/patent/US11111539B2

## CPC

- C12Q 1/6883: for diseases caused by alterations of genetic material
- C12Q 2600/136: Screening for pharmacological compounds
- C12Q 2600/156: Polymorphic or mutational markers
- C12Q 2600/158: Expression markers
- C12Q 2600/172: Haplotypes
- 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

## Abstract

Compositions and methods for the detection and treatment of inflammatory bowel disease are provided.

## Claims

### Claim 1

A method for treating inflammatory bowel disease (IBD) comprising detecting the presence of at least one IBD-associated single nucleotide polymorphism (SNP) in a target polynucleotide comprising:
(a) isolating nucleic acids from a biological sample from a subject;
(b) detecting in the nucleic acids the presence of at least one IBD-associated-SNP selected from a Tat rs2315008 in the TNFRSF6B gene, an A at rs4809330 on chromosome 20 in the TNFRSF6B gene, and an A at rs2836878 on chromosome 21; and diagnosing the subject as having IBD or an increased risk of IBD based on the presence of the detected IBD-associated-SNP; and
(c) administering to the subject a therapeutically effective amount of a therapy useful for treating IBD.

### Claim 2 (depends on 1)

The method of claim 1, further comprising, detecting in the sample the presence of an IBD-associated SNP of an A at rs1968752.

### Claim 3 (depends on 1)

The method of claim 1, wherein the target nucleic acid is amplified prior to detection.

### Claim 4 (depends on 1)

The method of claim 1, wherein the target nucleic acid is DNA.

### Claim 5 (depends on 1)

The method of claim 1, wherein nucleic acids comprising said polymorphism are obtained from an isolated cell of a human subject.

### Claim 6 (depends on 2)

The method of claim 2, wherein the target nucleic acid is amplified prior to detection.

### Claim 7 (depends on 2)

The method of claim 2, wherein detecting the presence of said single nucleotide polymorphism further comprises the step of analyzing a polynucleotide sample to determine the presence of said single nucleotide polymorphism by performing a process selected from the group consisting of detection of specific hybridization, measurement of allele size, restriction fragment length polymorphism analysis, allele-specific hybridization analysis, single base primer extension reaction, and sequencing of an amplified polynucleotide.

### Claim 8 (depends on 2)

The method of claim 2, wherein the target nucleic acid is DNA.

### Claim 9 (depends on 2)

The method of claim 2, wherein nucleic acids comprising said polymorphism are obtained from an isolated cell of a human subject.

### Claim 10 (depends on 1)

The method of claim 1 further comprising, detecting in the sample the presence of at least one IBD-associated SNP selected from a G at rs4625, a T at rs11190140, a T at rs10488959, a C at rs1108458, a G at rs7720838, a T at rs16991082, an A at rs11671391, an A at rs762421, a C at rs17809115, a T at rs2137424, an A at rs2056153, an A at rs2412973, a C at rs3742704, a C at rs1159502, a C at rs11585347, a G at rs17370612, a C at rs511973, a G at rs2548993, a G at rs4811050, a C at rs13219796, a T at rs4529739, an A at rs17170842, a C at rs13232099, a C at rs11585347, an A at rs6722598, an A at rs10759736, an A at rs474816, an A at rs1597317, a T at rs7676830, a G at rs13098182, a C at rs17475446, an A at rs12671457, a T at rs10044354, an A at rs2476601, a T at rs11465804, a T at rs2274910, a G at rs9286879, a G at rs12122721, an A at rs3024505, a G at rs13003464, a C at rs780094, a C at rs6752254, an A at rs2241880, a G at rs7611991, an A at rs3197999, a C at rs4613763, an A at rs7724915, a T at rs2188962, a G at rs7714584, an A at rs10045431, a G at rs2395185, an A at rs660895, a T at rs6908425, an A at rs12529198, an A at rs4959832, an A at rs6938089, a T at rs2301436, a G at rs1456893, a C at rs6478108, a G at rs7130588, a T at rs11174631, a G at rs3764147, a C at rs1667394, a C at rs991804, an A at rs744166, a G at rs1893217, an A at rs7228236, a T at rs16960173, an A at rs3749946, a T at rs2000662, an A at rs2456449, an A at rs4833103, a G at rs9271568, a G at rs1551398, a T at rs2844482, a T at rs2844480, and an A at rs10492494.

### Claim 11 (depends on 1)

The method of claim 1 further comprising, detecting in the sample the presence of at least one IBD-associated SNP selected from rs12261843, rs4077515, rs10758669, rs11713694, rs8049439, rs1052176, rs2872507, rs13294, rs917997, rs12360212, rs4676410, rs4676406, and rs16950687, wherein each SNP has an OR value and wherein an OR greater than 1 indicates that the minor allele is the risk allele.

### Claim 12 (depends on 1)

The method of claim 1, wherein detecting the presence of said single nucleotide polymorphism further comprises the step of analyzing a polynucleotide sample to determine the presence of said single nucleotide polymorphism by performing a process selected from the group consisting of detection of specific hybridization, measurement of allele size, restriction fragment length polymorphism analysis, allele-specific hybridization analysis, single base primer extension reaction, and sequencing of an amplified polynucleotide.