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Structural variation detection method

A technology for structural variation and detection methods, which can be used in the analysis of two-dimensional or three-dimensional molecular structures, genomics, instruments, etc., and can solve the problems of lack of annotations in calculation results, abnormal length of inserted fragments, and no annotation modules.

Active Publication Date: 2020-06-23
BERRY ONCOLOGY CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

If it is paired-end sequencing, the same template will generate two reads after sequencing, and abnormal read pairs that support structural variation can be collected according to whether the comparison of the two paired reads is abnormal. Normally, two reads One segment should be aligned to the positive strand of the genome, and the other should be aligned to the negative strand of the genome, and they are consistent from the perspective of nucleic acid transcription direction, and the length of the inserted segment is within a reasonable distribution range. If the two reads are from the structure For the two parts of the mutated gene, the direction will be abnormal, or the length of the implied interspersed fragments will be abnormal. However, many methods currently released have shortcomings such as long calculation time, low sensitivity, high false positives, and no annotation module.
[0005] The detection of the RNA level often requires the comparison of the two major reference sequences of the genome and the transcriptome. Through the comparison of the transcriptome, the coordinates are mapped to the genome, and then the comparison characteristics of the reads are used to refer to the judgment method of DNA calculation. The mechanism of structural variation events, calculating the type and gene of structural variation, this technical solution not only consumes too much resources, but also often leads to inaccurate calculations due to intron interference, and there are many false positives and false negatives. There is often a lack of comments, which is extremely inconvenient to use

Method used

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Examples

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Effect test

Embodiment 1

[0097] Collected 15,000 samples from patients with solid tumors and hematological tumors, extracted DNA for paired-end second-generation capture library construction and sequencing, and extracted RNA from some samples for capture sequencing. For each sample library obtained by sequencing, for the DNA library, use the BWA alignment software to align with the human reference genome HG19; for the RNA library, use the BWA alignment software to align with the personalized transcriptome. The transcriptome is constructed as follows:

[0098] Select one transcript for each gene as the main transcript. The main transcript should be included in the COSMIC and ONCOKIB databases first. If it is not included, it must be the one recorded in the main transcript database in UCSC. If there is no one in the three databases To determine the main transcript, use the longest one as the main transcript.

[0099] The results obtained by comparison remove PCR duplication and error correction, and ge...

Embodiment 2

[0101] Traverse the alignment result file, take 1 million normal alignment reads (the extraction standard is that no break alignment occurs, and the read pair matches the normal reads, and does not support any structural variation) to count the length of the insert, and calculate the length of the insert The main parameters of the distribution, maximum, minimum, mean.

[0102] Traversing the alignment result file again, accessing all the reads, finding out all the reads with broken alignments and abnormally aligned reads, and respectively classifying the reads with broken alignments and the abnormally aligned reads according to the following characteristics Classification of read pairs: The read segments of the broken alignment are mainly classified according to the comparison of the two parts where the broken alignment occurs. The classification criteria include whether they are aligned to the same chromosome, whether they are aligned to different directions of the The cuttin...

Embodiment 3

[0122] The structural variation detection method of the present invention can simultaneously support the identification of RNA and DNA structural variation, but few methods in the prior art can support both identifications at the same time. For example, both DELLY and GeneFuse only support the identification of DNA structural variation, and TophatFusion only supports Supports RNA structural variation identification. In order to test the performance of the method of the present invention, it was compared with FusionMap, a commercial software capable of supporting both DNA and RNA structural variation identification.

[0123] 269 ​​positive samples were extracted from the sequencing data in Example 1, and each sample had 1-2 fusions that had been verified by experiments. The method of DNA library sequencing analysis and FusionMap software were used to detect structural variation respectively. The results showed that the method in Example 2 can reach a detection rate of 100% (see...

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Abstract

The invention discloses a method for detecting structural variation. The method supports structural variation recognition of RNA and DNA at the same time, and is high in sensitivity, specificity and speed and small in resource consumption. The invention further provides a complete system or device established based on the method, a computer readable storage medium and equipment.

Description

technical field [0001] The invention belongs to the technical field of gene detection, and in particular relates to a method for detecting structural variation and related systems, devices, computer-readable storage media, and equipment. Background technique [0002] Structural variation originating within the genome, including deletions, inversions, duplications within the same chromosome, and abnormal connections between different chromosomes. Regardless of the event, the result often shows that different parts of the two genes are physically linked together. After transcription, a new transcript consisting of parts of the transcripts of two different genes can be obtained at the transcriptional level. Book. These structurally mutated genes have important scientific significance in the occurrence and development of cancer, and have extremely important medical value for the study of the mechanism of tumor occurrence and development, as well as the treatment and monitoring ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/20G16B15/00
CPCG16B20/20G16B15/00
Inventor 伍林军白健茹兰兰郑璐
Owner BERRY ONCOLOGY CO LTD
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