Biomarker capable of detecting diseases and application of biomarker

A biomarker and disease technology, applied in the field of biomedicine, can solve the problems of time-consuming, undocumented, resource occupation of medical personnel and testing equipment, etc., and achieve the effect of decreasing dependence and improving accuracy.

Active Publication Date: 2016-03-02
AGRO BIOLOGICAL GENE RES CENT GUANGDONG ACADEMY OF AGRI SCI +2
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

There are many studies on these aspects, but none of them can explain the occurrence and pathogenic mechanism of inflammatory bowel disease very well
At present, the research on inflammatory bowel disease is still in progress. In the actual diagnosis, medical personnel often need to use a variety of detection methods, data, and professional experience to better determine the cause of the disease, which takes a long time and requires medical staff and testing. Device resources are occupied more
Although some medical staff or scholars have put forward some i...

Method used

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  • Biomarker capable of detecting diseases and application of biomarker
  • Biomarker capable of detecting diseases and application of biomarker
  • Biomarker capable of detecting diseases and application of biomarker

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0067] sample collection

[0068] All 411 stool samples were collected from 411 volunteers, and the stool samples were collected by Luohu Hospital, Shenzhen, China. Diagnosis of inflammatory bowel disease was carried out according to the standards issued by WHO. Patients with diagnosed inflammatory bowel disease were used as the case group, and other individuals with non-inflammatory bowel disease were used as the control group (see Table 1). Patients with inflammatory bowel disease and normal individuals need to provide frozen stool samples. Volunteers should pay attention to their diet 3 days before sampling. They should eat a light diet and not eat high-fat foods; and do not eat yogurt and other lactic acid products and prebiotics 5 days before sampling. When collecting feces samples, be careful not to mix them with urine samples. And pay attention to the isolation of human pollution and air as far as possible when sampling.

Embodiment 2

[0069] Example 2: DNA extraction and sequencing

[0070] 2.1 Storage of stool samples

[0071] Put the collected stool sample into the sterilized stool collection tube, and store it in the freezer immediately to freeze the stool sample. Frozen samples were sent to the storage point and stored at -80°C until use.

[0072] 2.2 DNA extraction

[0073] 200 mg of frozen feces samples were taken from each part and suspended in a solution containing 250 μL of guanidine thiocyanate, 0.1 M Tris (pH 7.5) and 40 μL of 10% lauroyl sarcosine. The DNA extraction method was the same as described above (Manichanh, C.etal.ReduceddiversityoffecalmicrobiotainCrohn'sdiseaserevealedbyametagenomicapproach.Gut55, 205-211, doi:gut.2005.073817[pii]10.1136 / gut.2005.073817(2006), which is incorporated herein by reference). DNA concentration and molecular weight were determined by Nanodrop instrument (ThermoScientific) and agarose gel electrophoresis, respectively.

[0074] 2.3 DNA library constructi...

Embodiment 3

[0077] Example 3: Identification of biomarkers

[0078] 3.1 Basic processing of sequencing data

[0079] After obtaining the sequencing data of the first phase of 145 samples, it was filtered to remove low-quality sequences containing 'N', adapter pollution sequences and host genome pollution sequences, and finally obtained 378.4Gb high-quality data. On average, high-quality data accounted for 98.1% of all data. In addition, the actual insert length of the PE library is between 313bp and 381bp.

[0080] 3.2 Updating the gene set

[0081] Using the same parameters as the MetaHIT gene set (JunjieQin, RuiqiangLi, JeroenRaes, et al. (2010) Ahumangutmicrobialgenecatalogueestablishedbymetagenomicsequencing.Nature, 464:59-65, which is incorporated herein by reference), SOAPdenovov1.0642 and GeneMarkv2 were used in the first phase, respectively. .743 Perform de novo assembly and gene prediction on the sequencing sequence; then use BLAT software to compare all predicted genes, if th...

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Abstract

The invention discloses a biomarker capable of detecting diseases. The biomarker at least comprises one of the following microbes or the combination of the following microbes: Akkermansia muciniphila, Bacteroides fragilis, Clostridium bolteae, Clostridium hathewayi, Clostridium sp.HGF2, Clostridium symbiosum, Eubacterium limosum, Lactobacillus fermentum, Lactobacillus salivarius, Ruminococcus torques, Streptococcus anginosus, Streptococcus infantis, Bacteroides stercoris, Bacteroides uniformis, Bilophila wadsworthia and Clostridiales sp.SS3/4. The invention further discloses an application of the biomarker for determining inflammatory bowel diseases. The invention also discloses a method, a system and a kit for detecting the biomarker in a tested object. According to the invention, through the research on intestinal flora, and through the high-throughput genome sequencing, the biomarker with high relativity with the inflammatory bowel diseases is screened out, and then the biomarker is utilized for accurately and efficiently detecting and diagnosing the inflammatory bowel diseases, and further used for monitoring the treatment effect for the disease.

Description

technical field [0001] The invention relates to the field of biomedicine, in particular to a biomarker capable of detecting inflammatory bowel disease and its use. Background technique [0002] Inflammatory bowel disease (IBD) is an idiopathic intestinal inflammatory disease involving the ileum, rectum, and colon. Clinical manifestations include diarrhea, abdominal pain, and even bloody stools. The disease includes ulcerative colitis (UC) and Crohn's disease (CD). Ulcerative colitis is a continuous inflammation of the colonic mucosa and submucosa. The disease usually involves the rectum first and gradually spreads to the entire colon. Crohn's disease can involve the entire digestive tract and is a non-continuous full-thickness inflammation. The most commonly involved part is Terminal ileum, colon and perianal area. [0003] The etiology and pathogenesis have not yet been fully clarified. It is known that the inflammatory response caused by the abnormal response of the int...

Claims

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Application Information

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IPC IPC(8): C12Q1/68C12Q1/04C12M1/34
CPCC12Q1/6883C12Q2600/106C12Q2600/136
Inventor 苏海桥
Owner AGRO BIOLOGICAL GENE RES CENT GUANGDONG ACADEMY OF AGRI SCI
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