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Novel genomic biomarkers for irritable bowel syndrome diagnosis

A technology of irritable bowel syndrome and biomarkers, applied in disease diagnosis, biological testing, genetic engineering, etc., can solve problems such as differential diagnosis of early disease and obstacles to effective treatment, difficulties in rapid and accurate diagnosis, and patient differentiation

Inactive Publication Date: 2013-01-02
NESTEC SA
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

For example, a patient with inflammatory bowel disease (IBD) who exhibits mild signs and symptoms such as gas, diarrhea, constipation, and abdominal pain may be difficult to distinguish from a patient with IBS
Thus, the similarity of symptoms between IBS and IBD makes rapid and accurate diagnosis difficult
Difficulty in differentially diagnosing IBS and IBD hampers early and effective treatment of these disorders
Unfortunately, there is currently no rapid and accurate diagnostic method that can be used to definitively differentiate IBS from other bowel diseases or conditions that present similar symptoms

Method used

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  • Novel genomic biomarkers for irritable bowel syndrome diagnosis
  • Novel genomic biomarkers for irritable bowel syndrome diagnosis
  • Novel genomic biomarkers for irritable bowel syndrome diagnosis

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0242] This example describes blood sample collection and RNA isolation therefrom. Briefly, blood samples were collected from 3 IBS-D patients, 2 IBS-C patients and 3 healthy volunteers. All IBS patients met Rome III criteria, and healthy volunteers had no history of IBS or other active comorbidities. In this case, approximately 2.4 ml of whole blood was collected from each subject. Blood samples were divided into 2 aliquots and one was processed according to the leukocyte protocol described above, while the other was collected in the PAXgene system (PreAnalytX; Hombrechtikon, Switzerland) and processed accordingly.

[0243]Since the main difference between these 2 techniques is the inclusion of RNA from the erythrocyte fraction, it was investigated whether the excessively large amount of hemoglobin mRNA could explain the difference in expression between whole blood and leukopoietic samples. Additional RNA was isolated from whole blood from healthy subjects using the PAXgene...

Embodiment 2

[0245] This example describes hybridization of extracted mRNA samples to oligonucleotide arrays. For the analysis of IBD and control serum RNA samples, the Affymetric human gene 1.0ST array (Affymatrix, Santa Clara, CA) was used. These arrays are oligonucleotide probe-based gene array chips containing ~35,000 transcripts, which provide comprehensive coverage of the whole human genome.

[0246] To prepare RNA samples for hybridization, 8 μg of total RNA was used for cDNA synthesis. Following the manufacturer's protocol (Affymatrix, San Diego, California), the T7 promoter sequence introduced during first-strand synthesis was then used to direct cRNA synthesis, which was labeled with biotinylated deoxynucleotide triphosphates. After fragmentation, the biotinylated cRNA was hybridized to the GeneChip array at 45°C for 16 hours. Chips were washed, stained with phycoerythrin-streptavidin, and scanned with Gene Chip Scanner 3000. After background correction, preliminary data analy...

Embodiment 3

[0248] This example describes data analysis of microarrays performed as described in the previous examples. Analyze the RNA Integrity Number (RIN) of each sample and the performance of each microarray experiment for quality control purposes. The results are given in Table 3.

[0249] Table 3. RNA sample and microarray quality control matrix.

[0250]

[0251] The fluorescence intensity of each probe set was uploaded to Array Assist 6.5 and Gene Spring GX10.0 (Agilent Technologies, Santa Clara) software. Data were normalized by quantitative normalization and then log-transformed for further analysis to identify changes in specific genes in IBS patients. To compare changes in gene expression, the data were further normalized by using the 50 RFU fluorescence value as a threshold, and statistical analyzes showing fold changes (p ≤ 0.05) were determined. Using the 2 log2 fold change as cutoff, the top 72 markers were identified and are shown in Table 4.

[0252] Table 4. Top...

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Abstract

The invention provides novel biomarkers, kits, and methods of diagnosing, prognosing, and subtyping IBS. In one aspect, the invention provides novel genomic biomarkers for diagnosing, classifying, providing a prognosis for, and assigning therapy for IBS in a subject in need thereof. In another aspect, the present invention provides novel algorithms for the diagnosis and prognosis of IBS.

Description

[0001] Cross references to related applications [0002] This application claims priority to US Application No. 61 / 264,634, filed November 25, 2009, the teachings of which are incorporated herein by reference in their entirety for all purposes. Background of the invention [0003] Irritable bowel syndrome (IBS) is the most common of all gastrointestinal disorders, affecting 10-20% of the total population and accounting for more than 50% of all patients with digestive diseases. However, studies show that only about 10%-50% of patients afflicted with IBS actually seek medical help. Patients with IBS present with varying symptoms such as abdominal pain primarily related to bowel movements, diarrhea, constipation, or alternating diarrhea and constipation, bloating, gas, and excess mucus in the stool. More than 40 percent of people with IBS have severe symptoms that force them to take vacations, simplify their social lives, avoid sexual intercourse, cancel appointments, stop trave...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68C12N15/12G01N33/68
CPCC12Q2600/112G01N33/6893C12Q2600/158C12Q1/6883G01N2800/065A61P1/00A61P1/10A61P1/12A61P25/04A61P25/08A61P25/24A61P31/04A61P43/00
Inventor H·宫S·辛格N·霍
Owner NESTEC SA
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