Genomic microsatellite wide-area length distribution estimation method considering tumor purity factors

Abstract

The invention discloses a genomic microsatellite wide-area length distribution estimation method considering tumor purity factors. The method includes the steps of completing data feature extraction;finding out microsatellite candidate regions; using a clustering algorithm to filter ignored microsatellite candidate regions; traversing read segments of the regions and performing segmentation; estimating the tumor purity of a given sequencing sample; estimating the length distribution parameter of the tumor tissue microsatellite; using the average length distribution of the long microsatelliteto reflect its overall length distribution; estimating the average length of the microsatellite based on the coverage containing the microsatellite specified window, then iteratively estimating the coverage of the specified window using the updated microsatellite mean length, and completing the detection of the pure tumor sample long microsatellite; and determining the long tumor microsatellite state to complete the wide-area length distribution estimation. The invention solves the calculation deviation caused by the purity problem of the tumor sample of the input data, breaks the limitation of the sequencing read segment length on the length of the detectable genomic 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...

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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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