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  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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  • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• • A—HUMAN NECESSITIES
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  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P19/00—Drugs for skeletal disorders
  • A61P19/08—Drugs for skeletal disorders for bone diseases, e.g. rachitism, Paget's disease
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P19/00—Drugs for skeletal disorders
  • A61P19/08—Drugs for skeletal disorders for bone diseases, e.g. rachitism, Paget's disease
  • A61P19/10—Drugs for skeletal disorders for bone diseases, e.g. rachitism, Paget's disease for osteoporosis
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • G—PHYSICS
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  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
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  • C12Q2600/00—Oligonucleotides characterized by their use
  • C12Q2600/118—Prognosis of disease development
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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  • C12Q2600/00—Oligonucleotides characterized by their use
  • C12Q2600/156—Polymorphic or mutational markers
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2800/00—Detection or diagnosis of diseases
  • G01N2800/06—Gastro-intestinal diseases
  • G01N2800/065—Bowel diseases, e.g. Crohn, ulcerative colitis, IBS

Definitions

• the invention relates to the field of genetics and medicine. More specifically, the invention relates to methods of diagnosing and treating inflammatory bowel disease including ulcerative colitis and Crohn's disease.
• CD Crohn's disease
• UC ulcerative colitis
• IBD idiopathic inflammatory bowel disease
• CD and UC are thought to be related disorders that share some genetic susceptibility loci but differ at others,
• Various embodiments include a method of diagnosing susceptibility to granuloma in an individual with Crohn's diseaes, comprising obtaining a sample from the individual, assaying the sample to determine the presence or absence of at least one risk genetic variant, assaying the sample to determine the presence or absence of at least one risk serological marker, and diagnosing susceptibility to granuloma in the individual if the at least one risk genetic variant is present, or if the at least one risk serological marker is present, or if the at least one risk genetic variant is present and the at least one risk serological marker is present.
• the at least one risk genetic variant is at the genetic locus of TGFb3, FTO, NPAS2, MUC1, ILK), LRAP, LRRK2, T FSF15, or cytochrome P-450 cluster, or a combination thereof.
• the at least one risk serological marker is selected from the group consisting of anti-Cbirl , A CA, ASCA, anti-OmpC, and anti-12.
• the ASCA is present in high titre.
• the at least one risk genetic variant includes SEQ. ID. NO.: 1, SEQ. ID. NO.: 2, SEQ. ID. NO.: 3, SEQ. ID. NO.: 4, SEQ. ID. NO. : 5, and/or SEQ. ID. NO.: 6.
• the at least one risk genetic variant includes SEQ. ID. NO.: 7, SEQ. ID. NO.: 8, SEQ. ID. NO.: 9, SEQ. ID. NO.: 10, SEQ. ID. NO. : 1 1 , SEQ. ID. NO.: 12, and/or SEQ. ID. NO.: 13.
• the Crohn's disease is associated with a small bowel disease phenotype, an aggressive complicating phenotype, an internal penetrating disease phenotype, a stricturing disease phenotype, or a fibrostenosing disease phenotype, or a combination thereof.
• the first and/or second sample comprises a nucleic acid from the individual.
• Other embodiments include a method of diagnosing granuloma in an individual with Crohn's disease, comprising obtaining a sample from the individual, and assaying the sample to determine the presence or absence of at least one risk genetic variant, assaying the sample to determine the presence or absence of at least one risk serological marker, and diagnosing granuloma in the individual if the at least one risk genetic variant is present, or if the at least one risk serological marker is present, or if the at least one risk genetic variant is present and the at least one risk serological marker is present.
• the at least one risk genetic variant is at the genetic locus of TGFb3, FTO, NPAS2, MUC1 , IL10, LRAP, LRRK2, TNFSF15, or cytochrome P-450 cluster, or a combination thereof.
• the at least one risk serological marker is selected from the group consisting of anti-Cbirl, ANCA, ASCA, anti-OmpC, and anti-12.
• the ASCA is present in high titre.
• the at least one risk genetic variant includes SEQ. ID. NO.: 1 , SEQ. ID. NO.: 2, SEQ. ID. NO.: 3, SEQ. ID. NO.: 4, SEQ. ID. NO. : 5, and/or SEQ. ID.
• the at least one risk genetic variant includes SEQ. ID. NO.: 7, SEQ. ID. NO.: 8, SEQ. ID. NO.: 9, SEQ. ID. NO.: 10, SEQ. ID. NO. : 1 1, SEQ. ID. NO.: 12, and/or SEQ. ID. NO.: 13.
• the Crohn's disease is associated with a small bowel disease phenotype, an aggressive complicating phenotype, an internal penetrating disease phenotype, a stricturing disease phenotype, or a fibrostenosing disease phenotype, or a combination thereof.
• Various embodiments include a method of diagnosing susceptibility to low bone density (LBD) in an individual with an inflammatory bowel disease (IBD), comprising obtaining a sample from the individual, assaying the sample to determine the presence or absence of at least one risk genetic variant, assaying the sample to determine the presence or absence of at least one risk serological marker, and diagnosing susceptibility to LBD in the indi vidual if the at least one risk genetic variant is present, or if the at lea st one risk serological marker is present, or if the at least one risk genetic variant is present and the at least one risk serological marker is present.
• the LBD is osteoporosis or osteopenia.
• the at least one risk genetic variant is at the genetic locus of HLA, laminin, piexin, or NLR family, or a. combination thereof.
• the at least one risk genetic variant is SEQ. ID. NO.: 14 and/or SEQ. ID. NO.: 15.
• the at least one risk serological marker is selected from the group consisting of anti-Cbirl , ASCA, and anti-12.
• the IBD is a perianal disease.
• LBD low bone density
• IBD inflammatory bowel disease
• obtaining a sample from the individual assaying the sample to determine the presence or absence of at least one risk genetic variant, assaying the sample to determine the presence or absence of at least one risk serological marker, and treating LBD in the individual if the at least one risk genetic variant is present, or if the at least one risk serological marker is present, or if the at least one risk genetic variant is present and the at least one risk serological marker is present.
• the at least one risk genetic variant is SEQ. ID. NO.: 14 and/or SEQ. ID. NO.: 15.
• the at least one risk serological marker is selected from the group consisting of anti-Cbirl, ASCA, and anti-12.
• Figure 1 depicts top hits of various listed SNPs and corresponding alleles as associated with granuloma from performed GW AS.
• Figure 2 depicts top hits of various listed SNPs and corresponding alleles as associated with granuloma from performed GWAS.
• IBD as used herein is an abbreviation of inflammatory bowel disease.
• CD Crohn's Disease
• SNP as used herein is an abbreviation of single nucleotide polymorphism.
• any number of sequences may also be used to obtain the various SNPs or genetic var ants referenced herein, and the variants are not limited to the specific sequences or accession numbers provided herein.
• SNPs rsl3148469, rs2050719, rs7760387, rs9399527, rs9784771, rs282792 are provided herein as SEQ. ID. NO,: 1 , SEQ. ID. NO,: 2, SEQ. ID. NO.: 3, SEQ. ID. NO.: 4, SEQ. ID. NO. : 5, and SEQ. ID. NO.: 6, respectively.
• SNPs rs 10440086, rsl 352851 , rsl3148469, rs282792, rs443394, rs8091293, and rsl 0514090 are provided herein as SEQ. ID. NO.: 7, SEQ. ID. NO.: 8, SEQ. ID. NO.: 9, SEQ. ID. NO.: 10, SEQ. ID. NO. : 1 1, SEQ. ID. NO,: 12, and SEQ. ID. NO.: 13, respectively.
• SNPs rsl 1576349 and rs4954555 are provided herein as SEQ. ID. NO.: 14 and SEQ. ID. NO.: 15, respectively.
• biological sample means any biological material from which nucleic acid molecules can be prepared.
• material encompasses whole blood, plasma, saliva, cheek swab, or other bodily fluid or tissue that contains nucleic acid.
• CD Crohn's disease
• CX3CL1 a chemokine involved in CD pathogenesis
• TBD-associated loci 7 were associated with granuloma formation (p ⁇ ().()5), including: MUC1 (KL-6), also associated with granuloma- forming hypersensitivity pneumonitis; ILK), with known irnnxunoregulatory function in the gut; and LRAP, associated with antigen presentation and LRRK2 a leucine- rich rpeat kinase gene.
• MUC1 KL-6
• ILK granuloma- forming hypersensitivity pneumonitis
• ILK known irnnxunoregulatory function in the gut
• LRAP associated with antigen presentation and LRRK2 a leucine- rich rpeat kinase gene.
• P 0.066
• the inventors identified association with granulomatous CD and SNPs across the cytochrome P-450 cluster. Thus, the inventors have demonstrated putative genetic and demographic associations with the presence of granulomas in CD including a number of genes associated with Leprosy suggesting unique pathways in the pathogenesis of this subset of CD.
• the present invention provides a method of diagnosing susceptibility to a subgroup of Crohn's disease in an individual, by obtaining a sample from the individual, and assaying the sample to determine the presence or absence of one or more genetic risk variants and/or risk serological markers, wherein the presence of one or more genetic risk variants and/or risk serological markers is indicative of susceptibility to the subgroup of Crohn's disease.
• the subgroup of Crohn's disease is characterized by granuloma manifestations.
• the one or more genetic risk variants are at the genetic loci of TGFb3, FTO, NPAS2, MUC1, IL10, LRAP, LRRK2, TNFSF I5, and/or cytochrome p450 cluster, in another embodiment, the one or more risk serological markers include a high expression level of ASCA relative to a healthy subject.
• the present invention provides a method of treating Crohn's disease in an individual by determining the presence of one or more genetic risk variants associated with granulomas, and treating the individual.
• IBD IBD related serology
• LBD low bone density
• NBD low bone density
• SNPs (rs 1 1576349 and rs4954555) fell out of the model. These two SNPs were independently associated with LBD (2.41 xl0 's and 1.07 x 10 "5 ) and together this 2. SNP model was highly associated with LBD (p- value linear regression 1.8 x I0 "9 ) and explained 12.6 of the variance. Perianal disease is associated with osteoporosis; further, small bowel disease requiring surgery increases the risk for LBD. Anti-12, anti-CBirl, and ASCA are associated with increased risk for LBD and/or osteoporosis. Genes including HLA, lammin and plexin are associated with LBD. Thus, patients with these risk factors may benefit from more aggressive screening and treatment for osteoporosis.
• the present invention provides a method of diagnosing susceptibility to a condition characterized by low bone density in an individual by obtaining a sample from the individual, assaying the sample to determine the presence or absence of one or more risk factors and/or risk serological markers, where the presence of one or more genetic risk factors and/or risk serological markers is indicative of susceptibility to a condition characterized by low bone density in the individiEal.
• the individual is diagnosed with inflammatory bowel disease (LBD).
• the one or more risk factors include genetic risk variants at the genetic loci of HLA, lammin, and/or plexin.
• the presence of perianal disease is associated with an increased risk of osteoporosis.
• the presence of small bowel disease requiring surgery is associated with an increased risk of susceptibility to LBD, osteopenia, and/or osteoporosis.
• the one or more risk serological markers include 12, Cbirl, and/or ASCA.
• the present invention pro vides a method of treating a condition characterized by low bone density in an individual , by determining the presence of one or more risk factors andVor serological markers, and treating the individual.
• a variety of methods can be used to determine the presence or absence of a variant allele or haplotype.
• enzymatic amplification of nucleic acid from an individual may be used to obtain nucleic acid for subsequent analysis.
• the presence or absence of a variant allele or haplotype may also be determined directly from the individual's nucleic acid without enzymatic amplification.
• Analysis of the nucleic acid from an individual, whether amplified or not, may be performed using any of various techniques. Useful techniques include, without limitation, polymerase chain reaction based analysis, sequence analysis and electrophoretic analysis.
• nucleic acid means a polynucleotide such as a single or double- stranded DNA or RNA molecule including, for example, genomic DNA, cDNA and mRNA.
• nucleic acid encompasses nucleic acid molecules of both natural and synthetic origin as well as molecules of linear, circular or branched configuration representing either the sense or antisense strand, or both, of a native nucleic acid molecule.
• the presence or absence of a variant allele or haplotype may involve amplification of an individual's nucleic acid by the polymerase chain reaction.
• Use of the polymerase chain reaction for the amplification of nucleic acids is well known in the art (see, for example, Mullis et ai. (Eds.), The Polymerase Chain Reaction, Birkhauser, Boston, (1994)).
• a TaqmanB allelic discrimination assay available from Applied Biosystems may be useful for determining the presence or absence of a variant allele.
• a TaqmanB allelic discrimination assay a specific, fluorescent, dye-labeled probe for each allele is constructed.
• the probes contain different fluorescent reporter dyes such as FAM and VICTM to differentiate the amplification of each allele, m addition, each probe has a quencher dye at one end which quenches fluorescence by fluorescence resonant energy transfer (FRET).
• FRET fluorescence resonant energy transfer
• each probe anneals specifically to complementary sequences in the nucleic acid from the individual.
• the 5' nuclease activity of Taq polymerase is used to cleave only probe that hybridize to the allele. Cleavage separates the reporter dye from the quencher dye, resulting in increased fluorescence by the reporter dye.
• the fluorescence signal generated by PCR amplification indicates which alleles are present in
• Minor grove binder include, but are not limited to, compounds such as dihydrocyclopyrroloindole tripeptide (DPI,).
• Sequence analysis also may also be useful for determining the presence or absence of a variant allele or haplotype.
• Restriction fragment length polymorphism (RFLP) analysis may also be useful for determining the presence or absence of a particular allele ( Jarcho et al. in Dracopoli et ai., Current Protocols in Human Genetics pages 2.7.1-2.7.5, John Wiley & Sons, New York; Innis et aL(Ed.), PGR Protocols, San Diego: Academic Press, Inc. ( 1990)).
• restriction fragment length polymorphism analysis is any method for distinguishing genetic polymorphisms using a restriction enzyme, which is an endonuclease that catalyzes the degradation of nucleic acid and recognizes a specific base sequence, generally a palindrome or inverted repeat.
• a restriction enzyme which is an endonuclease that catalyzes the degradation of nucleic acid and recognizes a specific base sequence, generally a palindrome or inverted repeat.
• Allele-specific oligonucleotide hybridization may also be used to detect a disease- predisposing allele. Allele-specific oligonucleotide hybridization is based on the use of a labeled oligonucleotide probe having a sequence perfectly complem.ent.ary, for example, to the sequence encompassing a disease-predisposing allele.
• the allele-specific probe hybridizes to a nucleic acid containing the disease-predisposing allele but does not hybridize to the one or more other alleles, which have one or more nucleotide mismatches as compared to the probe, if desired, a second allele-specific oligonucleotide probe that matches an alternate allele also can be used.
• the technique of allele- specific oligonucleotide amplification can be used to selectively amplify , for example, a disease-predisposing allele by using an allele-specific oligonucleotide primer that is perfectly complementary to the nucleotide sequence of the disease-predisposing allele but.
• an allele-specific oligonucleotide primer to be used in PGR amplification preferably contains the one or more nucleotide mismatches that distinguish between the disease-associated and other alleles at the 3' end of the primer.
• a heteroduplex mobility assay is another well known assay that may be used to detect a SNP or a haplorype.
• HMA is useful for detecting the presence of a polymorphic sequence since a DMA duplex carrying a mismatch has reduced mobility in a polyacrylamide gel compared to the mobility of a perfectly base-paired duplex (Delwart et al., Science 262: 1257-1261 ( 1993); White et al., Genomics 12:301-306 ( 1992)).
• SSCP single strand conformational, polymorphism
• This technique can be used to detect mutations based on differences in the secondary structure of single-strand DNA that produce an altered electrophoretic mobility upon non- denaturing gel electrophoresis. Polymorphic fragments are detected by comparison of the electrophoretic pattern of the test fragment to corresponding standard fragments containing known alleles.
• Denaturing gradient gel electrophoresis also may be used to detect a SNP and/or a haplotype.
• DGGE Denaturing gradient gel electrophoresis
• double-stranded DNA is electrophoresed in a gel containing an increasing concentration of denaturant; double-stranded fragments made up of mismatched alleles have segments that melt more rapidly, causing such fragments to migrate differently as compared to perfectly complementary sequences (Sheffield et al., "Identifying DNA
• multiplex assay For diagnosing or predicting susceptibility to or protection against CD in an individual may be practiced using one or any combmation of the well known assay s described above or another art-recognized genetic assay.
• the inventors identified clinical, serologic and genetic factors associated with granuloma formation in Crohn's disease (CD), 371 patients with CD who underwent disease- related surgical resection by a single surgeon were included in the study. Surgical samples were examined specifically for the presence or not of granulomas. Patients' demographic and clinical characteristics were collected by chart review, and samples drawn for IBD related serology (ASCA, anti-12, anti-OmpC, CBirl and ANCA) and genetic analyses. Genome-wide analyses were performed using Illumina technology. Standard statistical tests for association were used and genetic association was assessed both at the genome-wide level and against known IBD and Leprosy susceptibility loci.
• IBD related serology ASCA, anti-12, anti-OmpC, CBirl and ANCA
• NPAS2 p -1x10-6
• CX3CL1 a chemokine involved in CD pathogenesis
• IBD-associated loci 7 were associated with granuloma formation (p ⁇ 0.05), including: MUC1 (KL-6), also associated with granuloma-forming hypersensitivity pneumonitis; IL10, with known immunoregulatory function in the gut; and LRAP, associated with antigen presentation and LRRK2 a leucine-rich repeat kinase gene.
• MUC1 KL-6
• IL10 with known immunoregulatory function in the gut
• LRAP associated with antigen presentation and LRRK2 a leucine-rich repeat kinase gene.
• Stepwise linear regression was performed and all but 2 SNPs (rsl 1576349 and rs4954555) fell out of the model. These two SNPs were independently associated with LBD (2.41 xIO "5 and 1.07 x 10 " ”) and together this 2. SNP model was highly associated with LBD (p- value linear regression 1.8 x HT 9 ) and explained 12.6 of the variance.
• Perianal disease is associated with osteoporosis; further, small bowel disease requiring surgery increases the risk for LBD.
• Anti-I2, a.nti-CBir- 1, and ASCA are associated with increased risk for LBD and/or osteoporosis. Genes including HLA, laminin and plexin are associated with LBD. Thus, patients with these risk factors may benefit from more aggressive screening and treatment for osteoporosis.
• the numbers expressing quantities of ingredients, properties such as concentration, reaction conditions, and so forth, used to describe and claim certain embodiments of the invention are to be understood as being modified in some instances by the term "about.” Accordingly, in some embodiments, the numerical parameters set forth in the written description and attached claims are approximations that can vary depending upon the desired properties sought to be obtained by a particular embodiment. In some embodiments, the numerical parameters should be construed in light of the number of reported significant digits and by applying ordinary rounding techniques. Notwithstanding that the numerical ranges and parameters setting forth the broad scope of some embodiments of the invention are approximations, the numerical values set forth in the specific examples are reported as precisely as practicable. The numerical values presented in some
• embodiments of the invention may contain certain errors necessarily resulting from the standard deviation found in their respective testing measurements.

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