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Genome structure variation annotation method

A technology of structural variation and genomics, applied in the field of bioinformatics, can solve problems such as methods and systems for structural variation of human genomes that lack structural variation

Pending Publication Date: 2021-09-07
GUANGZHOU BURNING ROCK DX CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0005] In summary, there is currently a lack of methods and systems in the field that can effectively annotate and interpret structural variation, especially human genome structural variation

Method used

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  • Genome structure variation annotation method
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Experimental program
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Embodiment 1

[0081] Example 1. Exemplary Structural Variation (SV) Detection Methods

[0082] Hereinafter, the markSV method is taken as an example to illustrate the method for obtaining information related to structural variation (SV) in a genomic region.

[0083] 1. Sequence comparison file generation: After the samples to be tested undergo library preparation, they are sequenced on the Illumina sequencing platform to generate FASTQ files. After performing quality control on the FASTQ files, use the comparison software BWA-MEM to compare the FASTQ files with the human reference genome (hg19 / b37) and generate a SAM file. After converting the SAM file into a BAM file with samtools software, the BAM file was used as the input file for subsequent detection.

[0084] 2. Insert length outlier calculation: Read the read length in the BAM file to estimate the parameters of the insert length distribution and the threshold of outliers. If the BAM file contains more than 1 million read lengths, ...

Embodiment 2

[0107] Example 2. Structural variation (SV) annotation process

[0108] 1. Read the structural variation result file

[0109] Read and analyze the analysis results of upstream structural variation detection software (such as markSV software) and extract the information needed for annotation, such as: SV type, orientation, breakpoint coordinates (including chromosome number and genome coordinates) and other information. Supported formats include custom format tsv files and VCF format files.

[0110] 2. Gene and structural information annotation

[0111] Structural variation usually includes two breakpoints, and gene and structural information need to be annotated for each breakpoint. The annotation of gene and structural information is divided into three steps: gene annotation, transcript annotation, and gene structure annotation.

[0112] 2.1 Gene annotation

[0113] According to the chromosome number and genome coordinates of the breakpoint, the gene and related infor...

Embodiment 3

[0176] Example 3. Structural variation annotation

[0177] After the samples go through a series of steps of library preparation, they are sequenced on the Illumina sequencing platform to generate FASTQ files. After performing quality control on the FASTQ files, use the comparison software BWA-MEM to compare the FASTQ files with the human reference genome (hg19 / b37) and generate a SAM file. After converting the SAM file into a BAM file with samtools software, the BAM file was used as the input file, and the structural variation results were analyzed with the structural variation detection software. Take the structure variation result as the input file, use this method to analyze and get the analysis result.

[0178] The analysis procedure was as described in Example 2. The analysis results take a lung cancer FFPE sample as an example. After the sample was analyzed by structural variation detection software, there was a case of interchromosomal translocation (CTX) in the d...

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Abstract

The present disclosure relates to methods of annotating genomic structural variations and predicting fusion protein formation. The disclosure also provides a system and device for annotating genomic structural variations and predicting fusion protein formation, and a computer-readable media .

Description

technical field [0001] The present invention belongs to the field of bioinformatics, and in particular relates to methods and systems for annotating structural variations (SVs) in genomes. [0002] technical background [0003] Structural variation (Structural Variants, SV) is the most important form of variation in the human genome. Structural variation includes deletion (Deletion), amplification (Duplication), insertion (Insertion), inversion (Transversion), translocation (Translocation) and more complex forms of variation. Among germline mutations, structural variant polymorphisms are associated with some common diseases. Among systemic mutations, structural variations, often in more complex forms, have been associated with cancer development. [0004] Structural variation is a complex form of variation. In addition to the above-mentioned various types of variation such as deletion, amplification, insertion, inversion, and translocation, it may occur within a gene or bet...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/20
CPCG16B20/20
Inventor 安玥刘成林魏从翀张周张之宏揣少坤汉雨生
Owner GUANGZHOU BURNING ROCK DX CO LTD
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