Method and device for simultaneously detecting methylation level, genome variation and insert fragment

An insert and methylation technology, applied in the field of bioinformatics, can solve the problems of DNA damage, inability to detect DNA sequencing data, and inability to perform genomic variation and insert analysis.

Active Publication Date: 2020-10-09
深圳吉因加医学检验实验室
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

Since more than 90% of C in BS sequencing data is transformed, and DNA damage will be generated during the transformation process, genomic variation and insert fragment analysis cannot be performed
Therefore, ...

Method used

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  • Method and device for simultaneously detecting methylation level, genome variation and insert fragment
  • Method and device for simultaneously detecting methylation level, genome variation and insert fragment
  • Method and device for simultaneously detecting methylation level, genome variation and insert fragment

Examples

Experimental program
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Embodiment 1

[0085] Embodiment 1: the application example of the inventive method

[0086] S1 step:

[0087] Take 100ng of human blood cfDNA, 0.2ng of methylated pUC19 DNA (methylated ginseng DNA), unmethylated lambda DNA (methylated yin ginseng DNA) and mix them for interruption. Bisulfate sequencing. The construction of the sequencing library refers to Example 4 of the Chinese patent application whose application number is CN201911159400 and the title of the invention is "whole genome methylated non-bisulfite sequencing library and construction" of the applicant of the present invention, and the sequencing platform adopts Gene+Seq platform. After sequencing, get off-machine data L1_R1.fq.gz, L1_R2.fq.gz, L1_R1.clean.fq.gz, L2_R2.clean.fq.gz.

[0088] S2 step:

[0089] Use the command fastp-i R1.fq.gz-I R2.fq.gz-o R1.clean.fq.gz-O R2.clean.fq.gz to remove joints and filter the quality of the off-machine data to obtain the filtered Sequence data, as shown in the table below:

[0090]...

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Abstract

The invention provides a method for simultaneously detecting a methylation level, genome variation and an insert fragment by utilizing a methylation non-bisulfite sequencing technology. The genome variation comprises gene mutation, copy number variation and structural variation. The invention also provides a device and equipment for implementing the method, and a corresponding computer readable medium. According to the invention, for methylated non-bisulfite sequencing data, one-step detection and analysis from offline data to multiple dimensions of methylation level, genome variation and insert fragments are realized, the method is suitable for whole genome and targeted capture data types of methylated non-bisulfite, and analysis of a single cancer sample and paired samples (cancer samples containing control samples) can be carried out.

Description

technical field [0001] The present invention relates to the technical field of bioinformatics, in particular to a method for simultaneously detecting methylation levels, genome variations and inserts, devices and equipment for implementing the method, and corresponding computer-readable media. Background technique [0002] DNA methylation is a kind of chemical modification of DNA, which can change the genetic material without changing the DNA sequence. As early as 1925, DNA methylation modification has been discovered. Numerous studies have shown that DNA methylation has an epigenetic role in gene regulation. Among DNA methylation, the most studied is 5-methylcytosine (5mC), which is generally regarded as a stable repressive regulator of gene expression. The current DNA methylation detection method based on next-generation sequencing technology is to convert unmethylated cytosine (C) into uracil (U) by bisulfite, and then use U tolerance in the PCR process. The polymerase...

Claims

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Application Information

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IPC IPC(8): G16B20/50G16B30/00G16B20/20
CPCG16B20/20G16B20/50G16B30/00
Inventor 杨玲张燕艳管彦芳姬利延马梦亚
Owner 深圳吉因加医学检验实验室
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