Method for judging sample degradation based on CNV result

Abstract

The invention discloses a method for judging sample degradation based on a CNV result. The method comprises the following steps: generating a target coverage CNN file of a test sample; constructing a reference CNN contrast set; detecting copy number variation from the target coverage CNN file of the test sample, generating a specific chromosome interval containing the copy number variation and an intermediate file of variation type information, and obtaining candidate parameter indexes; using the target coverage CNN file of a historical CNV-seq sample as experimental data, constructing a classification model and carrying out evaluation, and using classification features capable of completely distinguishing degraded samples and normal samples and corresponding threshold values as final parameter indexes for judging whether the sample is degraded or not; and judging whether the test sample is degraded or not by comparing the CNV result of the test sample with the final parameter index. According to the method, the parameter indexes capable of accurately discriminating the degraded sample comprise the corresponding threshold range, and degraded samples and normal samples can be automatically, efficiently and accurately distinguished.

Description

technical field [0001] The invention relates to the technical fields of high-throughput sequencing and variation detection in biology and precision medicine, and in particular to a method for determining sample degradation based on CNV results. Background technique [0002] In recent years, with the continuous development of high-throughput sequencing technology (Next-Generation Sequencing, NGS), whole genome sequencing (Whole Genome Sequencing, WGS), whole exome sequencing (Whole ExomeSequencing, WES) and copy number variation sequencing (Copy Number Variation Sequencing, CNVseq) and other detection technologies have been known to more and more people. [0003] To successfully implement these sequencing technologies, the first step is sample DNA extraction. It can be said that DNA extraction is a key step in laying a solid foundation. However, due to the interference of external factors such as temperature, humidity, pH value, oxidation reaction, and microbial infection, D...

AI Technical Summary

Problems solved by technology

[0005] a. Using the glue running method requires design and operation experiments, especially the operation experiment process, which is time-consuming and labor-intensive;

[0006] b. In the process of operating the experiment, it is inevitable that there will be human errors, which will make the result of the judgment inaccurate;

[0007] c. The operation experiment needs to be carried out by people with relevant professional and technical background, and the requirements for judges are relatively high

[0008] In addition, since the above judgment method is completed before sequencing, it is impossible to judge whether the sample is degraded or contaminated during the period from the judgment to the sequencing process.

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