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Method and application for determining donor and acceptor differential SNPs

A donor and acceptor technology, applied in the field of bioinformatics, to achieve the effect of intuitive digital results display

Active Publication Date: 2019-10-22
BGI GUANGZHOU MEDICAL LAB CO LTD +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0006] Existing methods for determining donor cell-free DNA (cfdDNA) content in recipients, as well as means for detecting organ transplant rejection, need to be improved or supplemented

Method used

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  • Method and application for determining donor and acceptor differential SNPs
  • Method and application for determining donor and acceptor differential SNPs
  • Method and application for determining donor and acceptor differential SNPs

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0060] The method and / or device for determining differential SNPs of the present invention are used in the monitoring of immune rejection of organ transplantation, and the idea of ​​the experimental part is as follows figure 1 As shown, it can be divided into two steps:

[0061] (1) Perform target region capture sequencing on donors and recipients of organ transplantation for genotyping, enabling the distinction of donors and recipients at the genetic level;

[0062] (2) Whole-genome sequencing was performed on the plasma cfDNA of each blood collection point, and the percentage of donor cfDNA in the plasma of each blood collection point to the total cfDNA was analyzed and evaluated.

[0063] 1. Genomic target region capture for SNP typing

[0064] The experimental procedure of this part is as follows: figure 2 As shown, the genomic DNA is first broken into a small fragment DNA of 150-250bp in the main band, and the ends of the broken DNA fragments are blunted. After adding ...

Embodiment 2

[0083] In order to prove that the experimental method is feasible, the inventor designed this embodiment. The design idea is as follows: take 2 normal human blood samples (taken from volunteers), one as a donor and the other as a recipient for simulation. The collected blood samples are separated from blood cells and plasma. After the genomic DNA is extracted from the blood cells, the DNA is interrupted and the target region is captured and sequenced for genotyping. After the cfDNA is extracted from the plasma, Agelint 2100 measures its exact concentration. , 0.5%, 1.5%, 3.5%, 5.5%, and 8% were mixed, and then the mixed cfDNA library was sequenced to test the reliability of this experimental method. According to the above experimental steps, the steps of this example are divided into two steps, 1. Genome target region capture and sequencing; 2. Each mixed cfDNA library construction and sequencing. details as follows.

[0084] In the examples, adapters and PCR amplification p...

Embodiment 3

[0272] After obtaining the sequencing data, the flow of the data analysis method is as follows: Figure 6 generally include the following steps:

[0273] 1. Alignment with the reference genome. The effective sequencing data of BGISEQ-100 was aligned to the reference genome using the tmap tool to obtain accurate alignment results. where the tmap tool is derived from: https: / / github.com / iontorrent / TS / tree / master / Analysis / TMAP .

[0274] 2. Compare the results to remove PCR duplicates. The BamDuplicates tool was used to remove PCR duplicates from the results (bam format) compared with the tmap tool. Among them, the BamDuplicates tool comes from Ion TorrentSystems.

[0275] 3. Statistics and quality control. Count the ratio of the data volume of the target area to the total data volume, the average sequencing depth of the target area, the coverage rate of the target area, etc., and generate a series of quality control indicators to judge the quality of the sequencing dat...

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Abstract

The present invention discloses a method for determining the differential SNP between a donor and a receptor. The method comprises: obtaining first sequencing data and second sequencing data; respectively comparing the first sequencing data and the second sequencing data to a reference sequence to obtain a first comparing result and a second comparing result; respectively based on the first comparing result and the second comparing result, carrying out SNP detection to obtain a first typing results and a second typing result; and comparing the first typing result to the second typing results to determine the differential SNP. The invention discloses a method for determining the proportion of the donor-derived cfDNA in a receptor, and a method and an apparatus for monitoring organ transplant rejection. With the method and / or apparatus of the present invention, the differential SNP between the donor and the receptor can be determined, and the proportion of the donor-derived cfDNA in the receptor can be accurately determined. The method and / or the apparatus of the present invention can be adopted as the assisted or supplementing way for the organ transplant rejection monitoring.

Description

technical field [0001] The present invention relates to the field of biological information. Specifically, the present invention relates to a method and application for determining the difference SNP between a donor and a recipient. More specifically, the present invention relates to a method for determining a difference SNP between a donor and a recipient, a method for determining Method for the proportion of donor-derived cfDNA in a recipient, a method and device for monitoring organ transplant rejection. Background technique [0002] Routine clinical detection methods for organ transplant rejection are usually laboratory and immunological examinations, imaging examinations, cytology and histology examinations. The sensitivity and specificity of conventional noninvasive examinations are not strong, and often cannot truly reflect the degree of rejection. Invasive biopsy is the gold standard for detection of organ transplant rejection such as heart transplantation, but it h...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B30/10C12Q1/6858C12M1/34
Inventor 曾柳红张纪斌杨青周天亮文易鑫叶明芝袁盛建
Owner BGI GUANGZHOU MEDICAL LAB CO LTD
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