Method and device for jointly detecting SNV, CNV and FUSEON variations

Abstract

The invention relates to a method and device for jointly detecting SNV, CNV and FUSEON variations. More specifically, the device comprises a sequencing data reading module, an SNV detection module, a CNV detection module, a FUSEON variation detection module and a result output module, wherein the CNV detection module comprises a BAF calculation module, a BAF correction module, a BAF separation and identification module, a sequencing depth calculation module, a logR correction module, a logR background noise calculation module and a CNV judgment module. The method and device, based on BAF+logR information, detect the SNV, CNV and FUSEON variations in a sample with an extremely low ctDNA proportion, especially the CNV variation with low copy number amplification, with high sensitivity and high specificity.

Description

Technical field [0001] The present invention belongs to the field of gene detection, and more particularly to methods, systems and devices, systems, and devices, systems, and devices in combination detection samples, in particular, to detect CNVs in samples, and methods, systems, and fition mutations in combination detection samples. Background technique [0002] The DNA of the cells enters the blood circulation system through a variety of mechanisms such as apoptosis, secretion or phagocytosis, which referred to as cell free DNA (Cell Free DNA, CFDNA) with a size of from 160 to 180 bp. [0003] For patients with tumor, CFDNA in plasma has partially derived from tumor cells, in addition to tumor cells, DNA carrying tumor cell specific information, called circulating tumor DNA (CTDNA). The proportion of CTDNA in cfDNA is generally 0.1% -10%, and with different differences in the condition phase. In CTDNA in tumor patients, common variation types include point mutant, SNVs, inserte...

AI Technical Summary

Problems solved by technology

Fluorescence in situ hybridization technology has high detection specificity, but the sample processing cycle is long, the cost is high (probes are expensive), and high throughput cannot be achieved, and the result interpretation is highly professional and subjective; digital PCR can realize accurate amplification Absolute quantification, but the requirement for the genome of the sample is high, and the correct result cannot be given in the case of genome disorder, and even false positives; Southern blot hybridization technology can also detect CNV, but the operation is complicated and cumbersome, and it is prone to false positives. Clinical promotion It is difficult; some existing second-generation detection technologies cannot perform accurate detection at the cfDNA level, mainly due to insufficient sensitivity and a high false negative rate in blood samples with a low proportion of tumors

[0006] It can be seen from the above that due to the low concentration of cell-free DNA (cfDNA) with gene copy number variation in plasma, the current methods for detecting CNV in cfDNA have low sensitivity, low specificity, low accuracy, and cumbersome operations. shortcoming

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