WO2011088306A1 - Procédés d'utilisation de variants génétiques pour diagnostiquer la maladie de crohn - Google Patents
Procédés d'utilisation de variants génétiques pour diagnostiquer la maladie de crohn Download PDFInfo
- Publication number
- WO2011088306A1 WO2011088306A1 PCT/US2011/021282 US2011021282W WO2011088306A1 WO 2011088306 A1 WO2011088306 A1 WO 2011088306A1 US 2011021282 W US2011021282 W US 2011021282W WO 2011088306 A1 WO2011088306 A1 WO 2011088306A1
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- disease
- nod2
- individual
- crohn
- risk
- Prior art date
Links
- 208000011231 Crohn disease Diseases 0.000 title claims abstract description 51
- 238000000034 method Methods 0.000 title claims description 38
- 230000002068 genetic effect Effects 0.000 title abstract description 13
- 101001125026 Homo sapiens Nucleotide-binding oligomerization domain-containing protein 2 Proteins 0.000 claims abstract description 43
- 102100029441 Nucleotide-binding oligomerization domain-containing protein 2 Human genes 0.000 claims abstract description 41
- 239000002773 nucleotide Substances 0.000 claims description 12
- 125000003729 nucleotide group Chemical group 0.000 claims description 12
- 210000004369 blood Anatomy 0.000 claims description 7
- 239000008280 blood Substances 0.000 claims description 7
- 210000003467 cheek Anatomy 0.000 claims description 7
- 210000002381 plasma Anatomy 0.000 claims description 7
- 102000054765 polymorphisms of proteins Human genes 0.000 claims description 7
- 210000003296 saliva Anatomy 0.000 claims description 7
- 210000002966 serum Anatomy 0.000 claims description 7
- 210000002700 urine Anatomy 0.000 claims description 7
- 238000003205 genotyping method Methods 0.000 claims description 6
- 238000011282 treatment Methods 0.000 abstract description 7
- 238000003745 diagnosis Methods 0.000 abstract description 5
- 238000004393 prognosis Methods 0.000 abstract description 3
- 108700028369 Alleles Proteins 0.000 description 35
- 239000000523 sample Substances 0.000 description 20
- 108020004707 nucleic acids Proteins 0.000 description 16
- 102000039446 nucleic acids Human genes 0.000 description 16
- 150000007523 nucleic acids Chemical class 0.000 description 16
- 208000022559 Inflammatory bowel disease Diseases 0.000 description 15
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 description 13
- 201000010099 disease Diseases 0.000 description 11
- 102000054766 genetic haplotypes Human genes 0.000 description 11
- 108090000623 proteins and genes Proteins 0.000 description 10
- 108020004414 DNA Proteins 0.000 description 8
- 238000004458 analytical method Methods 0.000 description 8
- 238000003556 assay Methods 0.000 description 8
- 206010009900 Colitis ulcerative Diseases 0.000 description 7
- 108091034117 Oligonucleotide Proteins 0.000 description 7
- 201000006704 Ulcerative Colitis Diseases 0.000 description 7
- 230000003321 amplification Effects 0.000 description 6
- 239000000975 dye Substances 0.000 description 6
- 238000003199 nucleic acid amplification method Methods 0.000 description 6
- 102100038366 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-4 Human genes 0.000 description 5
- 101000605565 Homo sapiens 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-4 Proteins 0.000 description 5
- 101000975421 Homo sapiens Inositol 1,4,5-trisphosphate receptor type 2 Proteins 0.000 description 5
- 102100024037 Inositol 1,4,5-trisphosphate receptor type 2 Human genes 0.000 description 5
- 239000012634 fragment Substances 0.000 description 5
- 239000000463 material Substances 0.000 description 5
- 210000000349 chromosome Anatomy 0.000 description 4
- 230000000295 complement effect Effects 0.000 description 4
- 238000009396 hybridization Methods 0.000 description 4
- 238000003752 polymerase chain reaction Methods 0.000 description 4
- 238000007894 restriction fragment length polymorphism technique Methods 0.000 description 4
- 102000053602 DNA Human genes 0.000 description 3
- 208000027138 indeterminate colitis Diseases 0.000 description 3
- SIKJAQJRHWYJAI-UHFFFAOYSA-N Indole Chemical compound C1=CC=C2NC=CC2=C1 SIKJAQJRHWYJAI-UHFFFAOYSA-N 0.000 description 2
- 101150083031 Nod2 gene Proteins 0.000 description 2
- 108020005187 Oligonucleotide Probes Proteins 0.000 description 2
- 238000012408 PCR amplification Methods 0.000 description 2
- 238000012300 Sequence Analysis Methods 0.000 description 2
- 108091008874 T cell receptors Proteins 0.000 description 2
- 102000016266 T-Cell Antigen Receptors Human genes 0.000 description 2
- 108010006785 Taq Polymerase Proteins 0.000 description 2
- 230000004721 adaptive immunity Effects 0.000 description 2
- 239000011230 binding agent Substances 0.000 description 2
- 239000012472 biological sample Substances 0.000 description 2
- 238000006243 chemical reaction Methods 0.000 description 2
- 238000003776 cleavage reaction Methods 0.000 description 2
- 238000003935 denaturing gradient gel electrophoresis Methods 0.000 description 2
- 208000035475 disorder Diseases 0.000 description 2
- 239000003814 drug Substances 0.000 description 2
- 230000002255 enzymatic effect Effects 0.000 description 2
- 239000000499 gel Substances 0.000 description 2
- 208000001234 inflammatory bowel disease 5 Diseases 0.000 description 2
- 208000027866 inflammatory disease Diseases 0.000 description 2
- 230000000968 intestinal effect Effects 0.000 description 2
- 230000007709 intracellular calcium signaling Effects 0.000 description 2
- 208000002551 irritable bowel syndrome Diseases 0.000 description 2
- 239000002751 oligonucleotide probe Substances 0.000 description 2
- 230000007310 pathophysiology Effects 0.000 description 2
- 230000037361 pathway Effects 0.000 description 2
- 230000007017 scission Effects 0.000 description 2
- 230000011664 signaling Effects 0.000 description 2
- 229940124597 therapeutic agent Drugs 0.000 description 2
- 241000894006 Bacteria Species 0.000 description 1
- 108091060290 Chromatid Proteins 0.000 description 1
- 108020003215 DNA Probes Proteins 0.000 description 1
- 239000003298 DNA probe Substances 0.000 description 1
- 108010042407 Endonucleases Proteins 0.000 description 1
- 102000004533 Endonucleases Human genes 0.000 description 1
- 108090000790 Enzymes Proteins 0.000 description 1
- 102000004190 Enzymes Human genes 0.000 description 1
- 208000018522 Gastrointestinal disease Diseases 0.000 description 1
- 208000034826 Genetic Predisposition to Disease Diseases 0.000 description 1
- 206010071602 Genetic polymorphism Diseases 0.000 description 1
- 108091027305 Heteroduplex Proteins 0.000 description 1
- 101710163270 Nuclease Proteins 0.000 description 1
- 108091006764 Organic cation transporters Proteins 0.000 description 1
- 108091006737 SLC22A4 Proteins 0.000 description 1
- 108091006736 SLC22A5 Proteins 0.000 description 1
- 108020004682 Single-Stranded DNA Proteins 0.000 description 1
- 102100036928 Solute carrier family 22 member 4 Human genes 0.000 description 1
- 102100036924 Solute carrier family 22 member 5 Human genes 0.000 description 1
- 230000005856 abnormality Effects 0.000 description 1
- 230000002776 aggregation Effects 0.000 description 1
- 238000004220 aggregation Methods 0.000 description 1
- 125000003275 alpha amino acid group Chemical group 0.000 description 1
- 230000000692 anti-sense effect Effects 0.000 description 1
- 238000013459 approach Methods 0.000 description 1
- 230000008901 benefit Effects 0.000 description 1
- 239000012620 biological material Substances 0.000 description 1
- 210000001124 body fluid Anatomy 0.000 description 1
- 230000036996 cardiovascular health Effects 0.000 description 1
- 230000015556 catabolic process Effects 0.000 description 1
- 210000004027 cell Anatomy 0.000 description 1
- 210000004756 chromatid Anatomy 0.000 description 1
- 230000001684 chronic effect Effects 0.000 description 1
- 238000010367 cloning Methods 0.000 description 1
- 239000002299 complementary DNA Substances 0.000 description 1
- 150000001875 compounds Chemical class 0.000 description 1
- 230000001268 conjugating effect Effects 0.000 description 1
- 238000012937 correction Methods 0.000 description 1
- 238000006731 degradation reaction Methods 0.000 description 1
- 239000003398 denaturant Substances 0.000 description 1
- 238000003936 denaturing gel electrophoresis Methods 0.000 description 1
- 230000000694 effects Effects 0.000 description 1
- 238000001962 electrophoresis Methods 0.000 description 1
- 238000005516 engineering process Methods 0.000 description 1
- 210000001035 gastrointestinal tract Anatomy 0.000 description 1
- 238000012252 genetic analysis Methods 0.000 description 1
- PZOUSPYUWWUPPK-UHFFFAOYSA-N indole Natural products CC1=CC=CC2=C1C=CN2 PZOUSPYUWWUPPK-UHFFFAOYSA-N 0.000 description 1
- RKJUIXBNRJVNHR-UHFFFAOYSA-N indolenine Natural products C1=CC=C2CC=NC2=C1 RKJUIXBNRJVNHR-UHFFFAOYSA-N 0.000 description 1
- 238000007477 logistic regression Methods 0.000 description 1
- 108020004999 messenger RNA Proteins 0.000 description 1
- 230000016379 mucosal immune response Effects 0.000 description 1
- 230000035772 mutation Effects 0.000 description 1
- 230000008506 pathogenesis Effects 0.000 description 1
- 230000007170 pathology Effects 0.000 description 1
- 229920002401 polyacrylamide Polymers 0.000 description 1
- 108091033319 polynucleotide Proteins 0.000 description 1
- 102000040430 polynucleotide Human genes 0.000 description 1
- 239000002157 polynucleotide Substances 0.000 description 1
- 230000000069 prophylactic effect Effects 0.000 description 1
- 239000000376 reactant Substances 0.000 description 1
- 238000011084 recovery Methods 0.000 description 1
- 238000011160 research Methods 0.000 description 1
- 108091008146 restriction endonucleases Proteins 0.000 description 1
- 238000012163 sequencing technique Methods 0.000 description 1
- 208000011580 syndromic disease Diseases 0.000 description 1
- 238000012360 testing method Methods 0.000 description 1
- 230000001225 therapeutic effect Effects 0.000 description 1
- 210000001519 tissue Anatomy 0.000 description 1
- 230000000451 tissue damage Effects 0.000 description 1
- 231100000827 tissue damage Toxicity 0.000 description 1
- 238000012546 transfer Methods 0.000 description 1
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- 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
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- 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
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
Definitions
- the invention relates generally to the field of inflammatory disease, specifically to Crohn's disease.
- IBD idiopathic inflammatory bowel disease
- IBD pathogenesis Genetic factors play an important role in IBD pathogenesis, as evidenced by the increased rates of IBD in Ashkenazi Jews, familial aggregation of IBD, and increased concordance for IBD in monozygotic compared to dizygotic twin pairs (3).
- genetic analyses have linked IBD to specific genetic variants, especially NOD2 (CARD 15) variants on chromosome 16ql2 and the IBD5 haplotype (spanning the organic cation transporters, SLC22A4 and SLC22A5, and other genes) on chromosome 5q31 (3-7).
- CD and UC are thought to be related disorders that share some genetic susceptibility loci but differ at others.
- the invention provides a method of diagnosing susceptibility to Crohn's disease in an individual, comprising: obtaining a sample from the individual, assaying the sample to determine the presence or absence of a NOD2 risk variant, and diagnosing susceptibility to Crohn's disease in the individual based on the presence of the NOD2 risk variant.
- the NOD2 risk variant can be selected from the group consisting of rs2291263, rs2306549, rs8115510, rs7268671 , and rs7866759.
- the NOD2 risk variants can be located at loci including, but not limited to ITPR2 and PLCB4.
- Assaying of the sample comprises genotyping for one or more single nucleotide polymorphisms.
- the sample can be whole blood, plasma, serum, saliva, cheek swab, urine, or stool.
- the invention provides a method of prognosing Crohn's disease in an individual, comprising: obtaining a sample from the individual, assaying the sample for the presence or absence of one or more genetic risk variants, and prognosing an aggressive form of Crohn's disease based on the presence of one or more NOD2 risk variants.
- the NOD2 risk variant can be selected from the group consisting of rs2291263, rs2306549, rs81 15510, rs7268671 , and rs7866759.
- the NOD2 risk variants can be located at loci including, but not limited to ITPR2 and PLCB4.
- Assaying of the sample comprises genotyping for one or more single nucleotide polymorphisms.
- the sample can be whole blood, plasma, serum, saliva, cheek swab, urine, or stool.
- the invention provides method of treating an individual for Crohn's disease, comprising: prognosing an aggressive form of Crohn's disease in the individual based on the presence of one or more NOD2 risk variants, and treating the individual, wherein the one or more NOD2 risk variants are selected from rs2291263, rs2306549, rs8115510, rs7268671 , and rs7866759.
- the NOD2 risk variants can be located at loci including, but not limited to ITPR2 and PLCB4.
- Assaying of the sample comprises genotyping for one or more single nucleotide polymorphisms.
- the sample can be whole blood, plasma, serum, saliva, cheek swab, urine, or stool.
- FIG. 1 Multidimensional Scaling (MDS) cluster plot used to identify Ashkenazi Jewish subjects.
- IBD inflammatory bowel disease
- CD Crohn's disease
- UC ulcerative colitis
- IC indeterminate colitis
- IBS irritable bowel syndrome
- Risk variant refers to genetic variants, the presence of which correlates with an increase or decrease in susceptibility to Crohn's disease.
- Risk variants of Crohn's disease include, but are not limited to NOD2 variants at various genetic locus, such as “haplotypes” and/or a set of single nucleotide polymorphisms (SNPs) on a gene or chromatid that are statistically associated.
- Risk variants can include, but are not limited to rs2291263, rs2306549, rs81 15510, rs7268671 , and rs7866759.
- Genetic locus can include, but are not limited to ITPR2 and PLCB4.
- NOD2 risk variant
- NOD2 means a nucleotide sequence of a NOD2 gene containing one or more changes as compared to the wild-type NOD2 gene or an amino acid sequence of a NOD2 polypeptide containing one or more changes as compared to the wild-type NOD2 polypeptide sequence.
- NOD2 also known as CARD 15, has been localized to the IBDl locus on chromosome 16 and identified by positional-cloning (4) as well as a positional candidate gene strategy (5).
- Treatment or “treating,” as used herein refer to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent, slow down and/or lessen the disease even if the treatment is ultimately unsuccessful.
- Those in need of treatment include those already with Crohn's disease as well as those prone to have Crohn's disease or those in whom Crohn's disease is to be prevented.
- a therapeutic agent may directly decrease the pathology of IBD, or render the cells of the gastroenterological tract more susceptible to treatment by other therapeutic agents.
- diagnosis refers to determining the nature or the identity of a condition or disease.
- a diagnosis may be accompanied by a determination as to the severity of the disease.
- Diagnosis as it relates to the present invention, relates to the diagnosis of Crohn's disease.
- prognostic refers to predicting the probable course and outcome of IBD or the likelihood of recovery from IBD.
- the prognosis can include the presence, the outcome, or the aggressiveness of the disease.
- biological sample means any biological material obtained from an individual from which nucleic acid molecules can be prepared.
- examples of a biological sample include, but are not limited to whole blood, plasma, serum, saliva, cheek swab, urine, stool, or other bodily fluid or tissue that contains nucleic acid.
- novel CD susceptibility loci were identified in a genome-wide association study (GWAS) performed in Ashkenazi subjects selected by genetically derived ethnicity information.
- GWAS genome-wide association study
- the inventors replicated some previously described associations between CD and NOD2 risk variants in the Ashkenazi Jewish population ( Figure 2) and identified several other novel NOD2 risk variants as susceptibility genes in CD.
- These genes act in the intracellular calcium signaling pathway which is important for T cell receptor signaling, and further implicates adaptive immunity in the pathophysiology of CD.
- the newly discovered NOD2 risk variants that are associated with CD include, but are not limited to rs2291263, rs2306549, rs8115510, rs7268671, and rs7866759.
- the present invention provides a method of diagnosing susceptibility to Crohn's disease in an individual by determining the presence or absence of a NOD2 risk variant, where the presence of the NOD2 risk variant is indicative of susceptibility to Crohn's disease in the individual.
- NOD2 risk variants can include, but are not limited to rs2291263, rs2306549, rs81 15510, rs7268671, and rs7866759.
- the individual is Ashkenazi Jewish.
- the present invention provides a method of prognosing Crohn's disease in an individual by determining the presence or absence of a NOD2 risk variant, where the presence of the NOD2 risk variant is indicative of a complicated form of Crohn's disease in the individual.
- NOD2 risk variants can include, but are not limited to rs2291263, rs2306549, rs8115510, rs7268671, and rs7866759.
- the individual is Ashkenazi Jewish.
- the present invention provides a method of treating Crohn's disease in an individual by determining the presence of a NOD2 risk variant and treating the individual.
- NOD2 risk variants can include, but are not limited to rs2291263, rs2306549, rs8115510, rs7268671, and rs7866759.
- the individual is Ashkenazi Jewish.
- a variety of methods can be used to determine the presence or absence of a NOD2 risk variant.
- enzymatic amplification of nucleic acid from an individual may be used to obtain nucleic acid for subsequent analysis.
- the presence or absence of a NOD2 risk variant may also be determined directly from the individual's nucleic acid without enzymatic amplification.
- nucleic acid means a polynucleotide such as a single or double-stranded DNA or R A 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 NOD2 risk variant 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 (8).
- 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.
- 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 the sample.
- Mismatches between a probe and allele reduce the efficiency of both probe hybridization and cleavage by Taq polymerase, resulting in little to no fluorescent signal.
- Improved specificity in allelic discrimination assays can be achieved by conjugating a DNA minor grove binder (MGB) group to a DNA probe as described, previously (9).
- Minor grove binders include, but are not limited to, compounds such as dihydrocyclopyrrolo indole tripeptide (DPI).
- Restriction fragment length polymorphism (RFLP) analysis may also be useful for determining the presence or absence of a particular allele (10-11).
- 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.
- 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 complementary, for example, to the sequence encompassing a disease-predisposing allele. Under appropriate conditions, 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 which has one or more mismatches as compared to other alleles (8).
- an allele-specific oligonucleotide primer that is perfectly complementary to the nucleotide sequence of the disease-predisposing allele but which has one or more mismatches as compared to other alleles (8).
- the one or more nucleotide mismatches that distinguish between the disease-predisposing allele and one or more other alleles are preferably located in the center of an allele-specific oligonucleotide primer to be used in allele-specific oligonucleotide hybridization.
- an allele-specific oligonucleotide primer to be used in PCR 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.
- HMA heteroduplex mobility assay
- 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 (11).
- CD subjects of mixed Caucasian ethnicity and 3970 controls from the Cardiovascular Health Study were geno typed, using Illumina technology (Human 610Quad, Human 317Duo or the HumanCNV370-Duo platform). 234,637 SNPs were available for analyses in all datasets. Multidimensional Scaling was used to detect population substructure. Ten principal components were calculated and principal components 1 and 2 were plotted to generate informative cluster plots for ethnicity. Self-reported ethnicity in CD cases was used to confirm the Ashkenazi Jewish "cluster" and select cases and controls ethnically matched by principal components. Association with case/control status was performed using a logistic regression model.
- the inventors identified 247 Ashkenazi Jewish CD cases and 320 ethnically matched controls by principal components. Genomic inflation was calculated at ⁇ . ⁇ . A Q-Q plot of P values showed a modest increase of significant associations above the expected under the null hypothesis.
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Health & Medical Sciences (AREA)
- Organic Chemistry (AREA)
- Wood Science & Technology (AREA)
- Analytical Chemistry (AREA)
- Zoology (AREA)
- Genetics & Genomics (AREA)
- Engineering & Computer Science (AREA)
- Pathology (AREA)
- Immunology (AREA)
- Microbiology (AREA)
- Molecular Biology (AREA)
- Biotechnology (AREA)
- Biophysics (AREA)
- Physics & Mathematics (AREA)
- Biochemistry (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- General Health & Medical Sciences (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Abstract
La présente invention concerne le pronostic, le diagnostic, et le traitement de la maladie de Crohn. L'invention concerne également un pronostic, un diagnostic, et un traitement qui sont basés sur la présence d'un ou de plusieurs facteurs de risque génétique comprenant des variants NOD2.
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US29537910P | 2010-01-15 | 2010-01-15 | |
US61/295,379 | 2010-01-15 |
Publications (1)
Publication Number | Publication Date |
---|---|
WO2011088306A1 true WO2011088306A1 (fr) | 2011-07-21 |
Family
ID=44304665
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
PCT/US2011/021282 WO2011088306A1 (fr) | 2010-01-15 | 2011-01-14 | Procédés d'utilisation de variants génétiques pour diagnostiquer la maladie de crohn |
Country Status (1)
Country | Link |
---|---|
WO (1) | WO2011088306A1 (fr) |
Cited By (6)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US9580752B2 (en) | 2008-12-24 | 2017-02-28 | Cedars-Sinai Medical Center | Methods of predicting medically refractive ulcerative colitis (MR-UC) requiring colectomy |
WO2017087735A1 (fr) * | 2015-11-18 | 2017-05-26 | Millennium Pharmaceuticals, Inc. | Procédé de traitement de la maladie de crohn |
US10316083B2 (en) | 2013-07-19 | 2019-06-11 | Cedars-Sinai Medical Center | Signature of TL1A (TNFSF15) signaling pathway |
US10633449B2 (en) | 2013-03-27 | 2020-04-28 | Cedars-Sinai Medical Center | Treatment and reversal of fibrosis and inflammation by inhibition of the TL1A-DR3 signaling pathway |
US11186872B2 (en) | 2016-03-17 | 2021-11-30 | Cedars-Sinai Medical Center | Methods of diagnosing inflammatory bowel disease through RNASET2 |
US11236393B2 (en) | 2008-11-26 | 2022-02-01 | Cedars-Sinai Medical Center | Methods of determining responsiveness to anti-TNFα therapy in inflammatory bowel disease |
Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US20040077020A1 (en) * | 2001-11-30 | 2004-04-22 | Mannick Elizabeth E. | Diagnostic microarray for inflammatory bowel disease, crohn's disease and ulcerative colitis |
US20070072180A1 (en) * | 2002-08-30 | 2007-03-29 | Abreu Maria T | Mutations in nod2 are associated with fibrostenosing disease in patients with crohn's disease |
US20080200568A1 (en) * | 2005-08-30 | 2008-08-21 | Stephanie Chissoe | Genes Associated With Type ll Diabetes Mellitus |
-
2011
- 2011-01-14 WO PCT/US2011/021282 patent/WO2011088306A1/fr active Application Filing
Patent Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US20040077020A1 (en) * | 2001-11-30 | 2004-04-22 | Mannick Elizabeth E. | Diagnostic microarray for inflammatory bowel disease, crohn's disease and ulcerative colitis |
US20070072180A1 (en) * | 2002-08-30 | 2007-03-29 | Abreu Maria T | Mutations in nod2 are associated with fibrostenosing disease in patients with crohn's disease |
US20080200568A1 (en) * | 2005-08-30 | 2008-08-21 | Stephanie Chissoe | Genes Associated With Type ll Diabetes Mellitus |
Non-Patent Citations (2)
Title |
---|
DATABASE NCBI [online] 2001, retrieved from http://www.ncbi.nlm.nih.gov/projects/SNP/snp ref.cgi?rs=2291263 Database accession no. rs2291263. * |
VAN ES ET AL.: "ITPR2 as a susceptibility gene in sporadic amyotrophic lateral sclerosis: a genome -wide association study.", LANCET NEUROLOGY, vol. 6, 2007, pages 869 - 877, XP022256808, DOI: doi:10.1016/S1474-4422(07)70222-3 * |
Cited By (9)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US11236393B2 (en) | 2008-11-26 | 2022-02-01 | Cedars-Sinai Medical Center | Methods of determining responsiveness to anti-TNFα therapy in inflammatory bowel disease |
US12084722B2 (en) | 2008-11-26 | 2024-09-10 | Cedars-Sinai Medical Center | Methods of determining responsiveness to anti-TNFα therapy in inflammatory bowel disease |
US9580752B2 (en) | 2008-12-24 | 2017-02-28 | Cedars-Sinai Medical Center | Methods of predicting medically refractive ulcerative colitis (MR-UC) requiring colectomy |
US10633449B2 (en) | 2013-03-27 | 2020-04-28 | Cedars-Sinai Medical Center | Treatment and reversal of fibrosis and inflammation by inhibition of the TL1A-DR3 signaling pathway |
US10316083B2 (en) | 2013-07-19 | 2019-06-11 | Cedars-Sinai Medical Center | Signature of TL1A (TNFSF15) signaling pathway |
US11312768B2 (en) | 2013-07-19 | 2022-04-26 | Cedars-Sinai Medical Center | Signature of TL1A (TNFSF15) signaling pathway |
US12269873B2 (en) | 2013-07-19 | 2025-04-08 | Cedars-Sinai Medical Center | Signature of TL1A (TNFSF15) signaling pathway |
WO2017087735A1 (fr) * | 2015-11-18 | 2017-05-26 | Millennium Pharmaceuticals, Inc. | Procédé de traitement de la maladie de crohn |
US11186872B2 (en) | 2016-03-17 | 2021-11-30 | Cedars-Sinai Medical Center | Methods of diagnosing inflammatory bowel disease through RNASET2 |
Similar Documents
Publication | Publication Date | Title |
---|---|---|
EP2689036B1 (fr) | Méthodes de diagnostic et de traitement des granulomes intestinaux et de la faible densité osseuse dans la maladie intestinale inflammatoire | |
US20100184050A1 (en) | Diagnosis and treatment of inflammatory bowel disease in the puerto rican population | |
US20110177969A1 (en) | The role of il17rd and the il23-1l17 pathway in crohn's disease | |
US20200270692A1 (en) | Predicting age-related macular degeneration with single nucleotide polymorphisms within or near the genes for complement component c2, factor b, plekha1, htra1, prelp, or loc387715 | |
US20100240043A1 (en) | Methods of using genetic variants to diagnose and predict inflammatory bowel disease | |
US20100144903A1 (en) | Methods of diagnosis and treatment of crohn's disease | |
US8153443B2 (en) | Characterization of the CBir1 antigenic response for diagnosis and treatment of Crohn's disease | |
US11542556B2 (en) | Single nucleotide polymorphism in HLA-B*15:02 and use thereof | |
US20100021917A1 (en) | Methods of using genes and genetic variants to predict or diagnose inflammatory bowel disease | |
US20130012602A1 (en) | Methods of using znf365 genetic variants to diagnose crohn's disease | |
WO2011088306A1 (fr) | Procédés d'utilisation de variants génétiques pour diagnostiquer la maladie de crohn | |
US20110117552A1 (en) | Methods of using a nod2/card15 haplotype to diagnose crohn's disease | |
US9305137B1 (en) | Methods of identifying the genetic basis of a disease by a combinatorial genomics approach, biological pathway approach, and sequential approach | |
EP2689034B1 (fr) | Rôle de la méthylation de l'interféron gamma dans la maladie intestinale inflammatoire | |
US20120041082A1 (en) | Methods of using smad3 and jak2 genetic variants to diagnose and predict inflammatory bowel disease | |
US20140017711A1 (en) | Methods of diagnosing ulcerative colitis and crohn's disease | |
WO2009055596A2 (fr) | Procédés d'utilisation de variants génétiques permettant de diagnostiquer et de prédire un syndrome métabolique et des traits associés |
Legal Events
Date | Code | Title | Description |
---|---|---|---|
NENP | Non-entry into the national phase |
Ref country code: DE |
|
122 | Ep: pct application non-entry in european phase |
Ref document number: 11733433 Country of ref document: EP Kind code of ref document: A1 |