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.
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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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