Method and device for detecting human genome virus integration site

Abstract

The invention relates to a method and a device for detecting a human reference genome virus integration site, and belongs to the technical field of gene detection bioinformatics analysis. The method comprises the steps of genome alignment, sliding cutting, short sequence alignment and integration. According to the method, reads which are not compared with a human reference genome and a virus genome at the same time are subjected to sliding cutting, the cut sub-sequences (or short sequences) are compared again, through clustering, correlation and covariance processing of the comparison positions and the sequence of a certain reads segmentation sequence, all highly possible comparison positions can be listed in the analysis process, reads for simultaneously comparing human reference genomesand virus genomes can be accurately found out and accurately positioned, and the error range is within 3bp. The method is low in calculation resource requirement and high in operation speed, and has relatively high practical value.

Description

Technical field [0001] The present invention relates to the technical field of gene detection bioinformatics analysis, in particular to a method and device for detecting integration sites of human genome viruses. Background technique [0002] Many viruses that infect humans can integrate their genomes into the human genome. The interaction between viral genes and the human host genome can lead to diseases such as cancer and AIDS. Studies have shown that 10-15% of cancers are caused by viral infections, such as HPV or HBV. The integration of these viruses into the human genome is likely to be the main cause of cancer. [0003] Accurate detection of virus integration sites can provide useful information for virus-related cancer pathogenesis, tumor evolution and tumor treatment, and next generation sequencing (NGS) can provide technical and data support for the detection of viral genome integration into human genome. [0004] At present, the most common detection method is the blastn m...

AI Technical Summary

Problems solved by technology

[0004] At present, the more common detection method is the blastn method, which uses NGS reads to compare human and virus accounting libraries. It mainly detects which viruses are integrated into the human genome. However, due to the large sample library and relatively sensitive comparison, As a result, the comparison of blastn is complicated and diverse, with many results, complex and cumbersome processing, and many false positives and false negatives; more importantly, its integration site information needs to be reprocessed and calculated

[0005] Another method is to use soft-clipping reads for processing. For example, software such as ViralFusionSeq, Virus-Clip, HGT-ID, and VirTect are all processed based on this method, but due to the soft-clipping reads obtained by the comparison software bwa or bowtie2 It does not consider comparing to both ends, which will make subsequent processing more difficult, and cannot ensure that the two ends of the reads can be compared to the human genome and viral genome respectively

[0006] Others are based on reads that have not been compared to the human genome using de novoassembly and then aligning, which can ensure the length and integrity of the viral sequence, but because reassembly requires a lot of memory and computing resources, There are also many possibilities for the constructed conting, and the accuracy cannot be guaranteed. The software based on this method includes ViralFusionSeq and VirusFinder

[0007] There are also methods based on combining human reference genes with viral genes and reconstructing new mixed reference genomes to determine integration sites, such as VirusFinder and VERSE. The accuracy of the reference genome also has the problem of being unable to quickly and accurately locate the integration site

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