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CfDNA classification method and device and application

A classification method and a classification label technology, applied in the field of genomics and bioinformatics, can solve problems such as false positives

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

At present, the recognized methods for prostate cancer are digital rectal examination and prostate-specific antigen (PSA) examination, but the level of PSA will also be affected by factors such as prostatitis, urinary retention, catheterization and drugs, resulting in a lot of false positive rates

Method used

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  • CfDNA classification method and device and application
  • CfDNA classification method and device and application
  • CfDNA classification method and device and application

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0175] Example 1: Preparation of cfDNA samples

[0176] 1. Target group

[0177] 95 cases of healthy people;

[0178] 172 patients, including: 58 patients with clear renal cell carcinoma (ccRCC), 69 patients with urothelial carcinoma and 45 patients with prostate cancer. Both were confirmed by biopsy of surgical samples.

[0179] A total of 267 cases of healthy people and patients.

[0180] 2. Experimental method

[0181](1) Collect the morning urine of the above-mentioned healthy people and the morning urine of tumor patients before operation. Each case of urine is collected in a 50ml centrifuge tube with a volume of about 20-50ml. Perform extraction to avoid cfDNA degradation.

[0182] (2) The collected morning urine samples were centrifuged at 3500 rpm for 15 minutes, and then the supernatants were taken respectively.

[0183] (3) Using zymo Quick-DNA TM The Urine Kit kit was used for the extraction of cfDNA. After extraction, the concentration was measured with ...

Embodiment 2

[0185] Example 2: Construction of whole genome library

[0186] 1. Experimental samples, reagents and instruments

[0187] 267 cases of cfDNA samples obtained in Example 1 above.

[0188] Urine cell-free DNA extraction kit: ZYMO Quick-DNA Urine Kit (ZYMO, Cat#: D3061).

[0189] Magnetic beads: AMPure XP beads (Beckman Coulter, Cat #: A63880).

[0190] Ordinary centrifuge.

[0191] 2. Experimental method

[0192] (1) Screen cfDNA of 100bp-300bp by magnetic beads (by controlling the ratio of the volume of magnetic beads to the volume of cfDNA samples, the range of the size of DNA fragments adsorbed by magnetic beads can be controlled). The specific operation is as follows:

[0193] Add 0.6 times the volume of magnetic beads to the extracted urine cfDNA, discard the magnetic beads after 5 minutes of adsorption, keep the supernatant, then add 0.3 times the volume of magnetic beads to the supernatant, discard the supernatant after 5 minutes of adsorption, and keep Magnetic ...

Embodiment 3

[0199] Example 3: HiSeq X10 system sequencing

[0200] 1. Reagents and Instruments

[0201] Samples to be tested: 267 libraries prepared in Example 2 above.

[0202] 2. Experimental method

[0203] Perform whole genome sequencing. Sequencing was commissioned by Novogene Sequencing Company.

[0204] 3. Experimental results

[0205] 150bp paired-end sequencing reads (pair-end reads) for each of the 267 libraries were obtained. The output sequencing depth of each sample is about 1X-5X. For subsequent tumor marker analysis.

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Abstract

The invention belongs to the field of genomics and bioinformatics, and relates to a cfDNA classification method and device and application. The cfDNA classification method comprises the following steps: calculating copy number variation data of cfDNA in a target sample; calculating the similarity between the target cfDNA copy number variation data and the cfDNA copy number variation data of each classification label; and determining the classification to which the target cfDNA belongs by using a classifier model according to the similarity. Diagnosis of up to three urogenital system tumors canbe completed at a time, so that the method and device have high sensitivity and specificity. Particularly, the sensitivity and the specificity in the aspects of diagnosis and dynamic monitoring of the urothelial cancer are higher than those of a detection method used clinically at present.

Description

technical field [0001] The invention belongs to the field of genomics and bioinformatics, and relates to a cfDNA classification method, device and application. Background technique [0002] Urogenital tumors (prostate cancer, urothelial cancer, and renal cancer) are serious diseases that endanger human health. However, diagnostic and monitoring methods for genitourinary system tumors are usually invasive, or lack sensitivity and specificity. [0003] Renal cancer accounts for about 3% of adult malignant tumors, accounting for 90%-95% of renal tumors, of which about 75% are renal clear cell carcinomas. Currently, surgical treatment is still the most effective treatment for localized RCC, but about 20%-40% of patients will relapse after surgery. Renal cell carcinoma has low sensitivity to radiotherapy and chemotherapy. The mortality rate of renal cancer patients is as high as 40%. The high mortality rate caused by renal cancer is mainly due to the lack of obvious clinical s...

Claims

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Application Information

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IPC IPC(8): G16B20/00G16B30/00G16B40/00G16H10/60G16H50/20G06K9/62
CPCG16B20/00G16B30/00G16B40/00G16H50/20G16H10/60G06F18/24323G16B20/10G16B40/20C12Q1/6886C12Q2600/158G16H70/60G16H50/70C12Q1/6869
Inventor 慈维敏葛广哲周媛媛李学松
Owner BEIJING INST OF GENOMICS CHINESE ACAD OF SCI CHINA NAT CENT FOR BIOINFORMATION
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