Urinary sediment genome DNA classification method and device and application

A classification method and classification label technology, applied in the fields of genomics and bioinformatics, which can solve the problems of sequencing errors and strong tumor heterogeneity.

Pending Publication Date: 2020-10-27
BEIJING INST OF GENOMICS CHINESE ACAD OF SCI CHINA NAT CENT FOR BIOINFORMATION +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, tumor heterogeneity is very strong, and the corresponding exfoliated cells may not be able to detect driver gene mutations, and the identification of mutations in a small amount of tumor cfDNA relies on targeted deep sequencing (>5000*), accompanied by sequencing errors

Method used

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  • Urinary sediment genome DNA classification method and device and application
  • Urinary sediment genome DNA classification method and device and application
  • Urinary sediment genome DNA classification method and device and application

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0171] Embodiment 1: the preparation of DNA sample

[0172] 1. Target group

[0173] Urine samples were collected from a total of 313 subjects, such as figure 1 shown. The 313 subjects included 88 healthy people, 65 clear renal cell carcinoma (KIRC) patients, 100 urothelial carcinoma (UC, including bladder cancer UCB, upper tract urothelial carcinoma UTUC) and 60 prostate cancer patients (PRAD) patients.

[0174] 2. Experimental method

[0175] (1) Collect fresh urine (morning urine) from preoperative tumor patients and healthy people (morning urine). The urine is collected in a 50ml centrifuge tube, and the volume of each urine sample is about 45-50ml.

[0176] (2) The collected morning urine samples were centrifuged at 3500 rpm and 4° C. for 10 min, respectively, and the supernatant was removed to obtain urine sediment.

[0177] (3) Wash the urine sediment twice with PBS buffer (add 500ml of PBS buffer each time, centrifuge at 13000g for 1min to remove the supernatant...

Embodiment 2

[0180] Example 2: Whole Genome Bisulfite Sequencing (Whole Genome Bisulfite Sequencing, for short BS-seq or WGBS) library construction

[0181] Take 50-200ng of the DNA samples obtained in Example 1 as the starting DNA for library construction, and add lambda DNA (all CpG sites are unmethylated C) and 5mC DNA (all CpG sites) at a ratio of 3:1000 CpG sites are all methylated C). Then, the DNA was fragmented with a Covaris ultrasonic breaker, so that the main peak of the fragment length was in the range of 400bp. Then use NEBNext Ultra II End Repair / dA-Tailing Module 96rxns (Catalog No. E7546) to repair the end of the fragmented DNA and add polyadenylic acid (polyA), and then use NEBNext Ultra IILigation Module, 96rxns unit (Catalog No. E7595L ) plus a methylated PE linker.

[0182] The obtained water-soluble DNA (library) connected with adapters was treated with bisulfite using the EZ DNA methylhlation Gold kit (Zymo Research), and the specific steps were guided by the ...

Embodiment 3

[0184] Example 3: HiSeq X10 system sequencing

[0185] 1. Sample to be tested:

[0186] The BS-seq library of 313 cases of urinary sediment gDNA prepared in the previous Example 2.

[0187] 2. Experimental method

[0188] Novogene Sequencing Company was commissioned to perform whole-genome sequencing on the BS-seq library of gDNA from 313 cases of urinary sediment.

[0189] 3. Experimental results

[0190]The 150bp pair-end reads (pair-end reads) data of the BS-seq library of 313 cases of urinary sediment gDNA (ie fastq original file) were obtained. Used for subsequent data preprocessing and tumor marker analysis.

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Abstract

The invention belongs to the field of genomics and bioinformatics, and relates to a urinary sediment genome DNA classification method and device and application. Specifically, the DNA classification method comprises the following steps: calculating an MHL value of a DNA methylation haplotype region of a target sample and/or copy number variation data of DNA; calculating the similarity between theMHL value of the DNA methylation haplotype region of the target sample DNA and the MHL value of the DNA methylation haplotype region of each classification label, and/or the similarity between the copy number variation data of the target sample DNA and the DNA copy number variation data of each classification label; and according to the similarity, determining the classification to which the target sample DNA belongs by using a classifier model. The invention provides a novel detection means for urogenital system tumors, and the detection means has good specificity and sensitivity.

Description

technical field [0001] The invention belongs to the field of genomics and bioinformatics, and relates to a classification method, device and application of urinary sediment genome DNA. Background technique [0002] Urogenital tumors refer to tumors that occur in the urinary system. Common tumors of the genitourinary system include renal cancer (RC), bladder cancer (BT), prostate cancer (PCA) and so on. According to the 2018 cancer statistics report, genitourinary system tumors accounted for 3 of the top 20 common tumors in terms of new cases and deaths, and PCA ranked among the top three. [0003] The vast majority of patients with early tumors can be cured by surgery, but once metastasis occurs, the prognosis and survival of patients will be significantly reduced. The current diagnosis of genitourinary system tumors mainly relies on tissue biopsy, while non-invasive diagnosis is immature, and the sensitivity and specificity of corresponding tumor detection are not high. ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/00C12Q1/6886
CPCG16B30/00C12Q1/6886C12Q2600/158C12Q2600/154C12Q2600/172C12Q2600/156G16B40/20G16B20/00
Inventor 慈维敏许争争周利群
Owner BEIJING INST OF GENOMICS CHINESE ACAD OF SCI CHINA NAT CENT FOR BIOINFORMATION
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