Method for detection of insertion deletion mutation based on second generation sequencing, device and storage medium

Abstract

The present application discloses a method for detection of insertion deletion mutation based on second generation sequencing, a device and a storage medium. The method comprises the following steps:comparing a sample to be tested with a file of a reference genome to extract a set of candidate mutation sites with mutation allele frequency being greater than or equal to a threshold; filtering to remove sites in a short tandem repeat region; making detail statistics of comparison information of the mutation sites and comparison information surrounding the mutation sites, wherein the comparisoninformation includes InDel site and reference base support number, comparison quality, coverage depth, surrounding non-reference base and other insertion deletion mutations, surrounding read quality;and filtering to remove sites that do not reach the set threshold according to statistical information to obtain mutation results. The method does not require partial assembly, and filters second-generation sequencing data in advance to quickly eliminate most of false positive results caused by the comparison, reduces detection running time and computing resources, improves detection efficiency, has strong sensitivity and specificity, and can quickly and accurately detect InDel mutations.

Description

technical field [0001] The present application relates to the field of gene mutation detection, in particular to a next-generation sequencing-based insertion-deletion mutation detection method, device and storage medium. Background technique [0002] Cancer is one of the most important non-communicable diseases in the world, and it is also a disease with a high mortality rate. In my country, nearly 4.3 million people are diagnosed with cancer every year, and more than 2.8 million people die of cancer. [0003] Anti-tumor targeted drugs are currently more effective means of treating cancer. Some targeted drugs target insertion-deletion mutations in key genes, hereinafter referred to as InDel mutations, to play a role. It is generally recommended clinically that these drugs be tested for the corresponding target genes before being used for tumor treatment to determine whether the targeted drug is suitable or which drug to use. [0004] At present, common methods for detecting...

AI Technical Summary

Problems solved by technology

The PCR method has the characteristics of high sensitivity, and the technology is mature, but each pair of primers can only detect one mutation, and cannot detect too many samples and sites at the same time, and the throughput is low, so it is not suitable for multiple targets in a large number of clinical samples screening or testing

The cost of Sanger sequencing is low, but the amount of sample required is large, and the detection sensitivity for low-frequency mutations is low

Next-generation sequencing has the characteristics of high throughput, and the cost of sequencing is also decreasing year by year, but the current methods and tools commonly used to detect InDel, for example, Varscan detection specificity is not high, Strelka has low sensitivity to low-frequency detection, and Mutect2 uses The local assembly step leads to too long running time, and the above common methods and tools cannot well meet the needs of tumor clinical detection

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