A method for estimating the wide-area length distribution of genomic microsatellites considering the factor of tumor purity

Abstract

The invention discloses a genome microsatellite wide-area length distribution estimation method considering tumor purity factors, completes data feature extraction; finds microsatellite candidate regions; uses clustering algorithm to screen neglected microsatellite candidate regions; traverses the read segments of the region and segmentation; estimate the tumor purity of a given sequencing sample; estimate the length distribution parameters of tumor tissue microsatellites; use the average length distribution of long microsatellites to reflect its overall length distribution; The average length of satellites, and then use the updated average length of microsatellites to iteratively estimate the coverage of the specified window, and complete the detection of long microsatellites in pure tumor samples; determine the status of long tumor microsatellites to complete the estimation of wide-area length distribution. The invention solves the calculation deviation caused by the purity of the tumor sample in the input data, breaks through the limitation of the length of the sequencing read segment on the length of the detectable genome microsatellite, and realizes the wide-area length detection.

Description

technical field [0001] The invention belongs to the technical field of data science with the application background of precision medicine, and specifically relates to a method for estimating the wide-area length distribution of genome microsatellites considering the factor of tumor purity. Background technique [0002] Genomic microsatellite (English name: micro-satellite, English abbreviation: MS) is a DNA sequence composed of specific oligonucleotide units (usually 1-6 nucleotide fragments) repeated, with diversity in length, Often referred to as the length distribution. Microsatellite instability (English name: micro-satellite instability, English abbreviation: MSI) refers to a hypermutation pattern caused by a defect in the DNA mismatch repair system (English name: defective DNA mismatch repair, English abbreviation: dMMR). It is characterized by extensive length diversity of microsatellite repeats and increased frequency of single nucleotide variants (English name: sin...

AI Technical Summary

Problems solved by technology

[0005] The technical problem to be solved by the present invention is to provide a method for estimating the genome microsatellite wide-area length distribution considering the tumor purity factor to solve the calculation deviation caused by the purity of the tumor sample in the input data. Sequencing read length limits the length of detectable genomic microsatellites, enabling wide-area length detection

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