Method and device for identifying tumor purity and absolute copy number based on sequencing data

Abstract

The invention discloses a method and a device for identifying tumor purity and absolute copy number based on sequencing data. The method comprises the following steps: comparing offline data after quality control to a reference genome, and carrying out variation detection and population database annotation; testing the preprocessed data of the tumor and the normal sample by using purity predictionsoftware to obtain a purity and copy number information model; and for the model conforming to normal distribution, further screening out the model with the maximum probe support number in the high tumor cell fraction subcloning region, and defining an optimal model in combination with the matching rate of BAF and alle1 and alle2 copy numbers. According to the method, the model of purity detection software is rapidly and efficiently corrected, and the purity and absolute copy number information of tumors can be obtained more accurately; the accuracy is guaranteed, the tedious process of manual verification is avoided, the labor cost is saved, and a foundation is laid for follow-up tumor genome evolution and tumor heterogeneity research.

Description

technical field [0001] The present application relates to the technical field of tumor research, in particular to a method and device for identifying tumor purity and absolute copy number based on sequencing data. Background technique [0002] Estimating tumor purity and ploidy facilitates studies of tumor genome evolution and intratumoral heterogeneity. The occurrence of tumors is accompanied by a large number of genomic variations, and the definition of chromosome copy number and allele ratio is the basis for understanding the structure and history of tumor genomes. Current genomic identification techniques measure somatic changes in tumor samples in genomic units, ie, DNA quality, and the significance of this measurement depends on the purity and overall ploidy of the tumor. Tumor purity affects the calculation of DNA copy number variation (CNV) to some extent, and ideally, copy number should be measured in copies per tumor cell. Measurement of somatic copy number alter...

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Problems solved by technology

For example, purity estimation software such as ABSOLUTE can predict tumor purity from low-coverage whole-genome sequencing data samples, and is currently one of the most commonly used methods for evaluating tumor purity; its method uses the CNV information of tumor samples to estimate tumor purity. However, due to the complexity of tumor samples, the method also needs to combine SNV information to estimate the tumor purity to achieve higher accuracy. The software will automatically base the predesigned cancer karyotype, somatic mutation frequency and Somatic cell copy number changes are scored and the model with the highest score is selected; however, the model with the highest score is not necessarily the optimal model, which requires manual verification of the results, increasing the complexity of obtaining tumor sample purity information

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