Methods and devices for inferring tumor purity and ploidy

Abstract

The present invention provides a method and device for inferring the purity and ploidy of tumors. The method preprocesses the genome sequencing data of tumor samples and paired samples, and performs chromosome window statistics on the preprocessed results to obtain each chromosome of the tumor sample. GC content and first coverage for binned and second coverage for each chromosome bin for paired samples; first coverage corrected based on previous results; heterozygous germline variants identified from preprocessed tumor sample genome sequencing data The allele frequency with the highest mutation frequency corresponding to the site; re-segment the autosomes of the cancer genome of the tumor sample according to the corrected first coverage, and determine the number of segments, the length corresponding to each segment, and the length of each segment. The observed copy number corresponding to each segment; the purity of the tumor sample and the ploidy of the tumor cells were determined according to the above results. The invention provides a robust detection method for tumor concentration and ploidy, and the detection accuracy is higher.

Description

technical field [0001] The invention relates to the technical field of tumor detection, in particular to a method and device for inferring tumor purity and ploidy. Background technique [0002] Cancer is a heterogeneous group of diseases, each with its own biological characteristics. Discovery of these biological signatures may provide highly informative markers and targets for cancer therapy. More recently, next-generation sequencing has enabled researchers to search for these cancer signatures on a genome-wide scale. However, due to the contamination of normal cells in tumor tissue, high-throughput data obtained from tumor samples are mixed signals of cancer cells and normal cells. Tumor purity and ploidy of tumor cells have a major impact on next-generation sequencing data analysis of tumor samples, and may alter the biological and clinical interpretation of the results. Therefore, tumor purity and tumor ploidy effects must be considered in the analysis of sample chrom...

AI Technical Summary

Problems solved by technology

[0005] The present invention provides a method and device for inferring the purity and ploidy of tumors, which are used to solve the defects of harsh or inaccurate conditions in the algorithm for calculating the purity and ploidy of tumor samples in the prior art, and realize the calculation of Algorithms for Purity and Ploidy of Tumor Samples

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