Method, device and storage medium for point mutation detection and filtering based on next-generation sequencing

Abstract

The invention discloses a next generation sequencing-based point mutation detection filtering method and apparatus, and a storage medium. The method comprises the steps of performing comparison with files of a reference genome by utilizing a to-be-detected sample, and extracting candidate point mutation site sets with variant allele frequencies exceeding a set threshold; preliminarily calculatingsupport numbers of mutant bases and reference bases of candidate point mutation sites, and filtering results with the mutant support numbers lower than the set threshold and / or the variant allele frequencies lower than the set threshold; performing detailed statistics on the candidate point mutation sites and surrounding comparison information, wherein the information comprises at least one of thefollowing information: the support numbers of the mutant bases and the reference bases of the candidate point mutation sites, base and comparison quality, coverage depth, surrounding non reference base and insertion / deletion statuses, and surrounding read quality; and according to the statistical information, filtering the results which do not meet set requirements to obtain a point mutation detection result. While the resource demands and the detection speed are optimized, the sensitivity and specificity of point mutation detection are improved.

Description

technical field [0001] The invention relates to the technical field of mutation detection, in particular to a point mutation detection and filtering method, device and storage medium based on next-generation sequencing. Background technique [0002] At present, common methods for detecting gene point mutations include PCR method, Sanger sequencing method (first-generation sequencing) and next-generation sequencing. The PCR method has the characteristics of high sensitivity, and the technology is mature, but each pair of primers can only detect one mutation, cannot detect too many samples and sites at the same time, and the throughput is low. 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 p...

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, cannot detect too many samples and sites at the same time, and the throughput is low

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. However, the current methods and tools commonly used to detect point mutations are not high in detection specificity (such as Varscan), and the sensitivity to low-frequency detection is also low (such as Mutect). Or the use of local assembly steps leads to too long running time (such as Mutect2), which cannot well meet the needs of point mutation detection

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