A method for judging sample degradation based on CNV results

Abstract

The invention discloses a method for determining sample degradation based on CNV results, comprising the following steps: generating a target coverage CNN file of a test sample; constructing a reference CNN comparison set; detecting copy number variation from the target coverage CNN file of the test sample, Generate an intermediate file containing the specific chromosome interval and variation type information of copy number variation to obtain candidate parameter indicators; use the target coverage CNN file of historical CNV-seq samples as experimental data, construct a classification model and evaluate it, which will be able to completely distinguish degraded samples The classification features and corresponding thresholds of normal samples are used as the final parameter index to judge whether the sample is degraded; the CNV results of the test sample are used to compare the final parameter index to judge whether the test sample is degraded. The method provides the parameter indexes that can accurately identify the degraded samples including the corresponding threshold range, and can automatically, efficiently and accurately distinguish the degraded samples from the normal samples.

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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