Single-sample whole-genome allele specific copy number variation prediction method

Abstract

A single-sample whole-genome allele specific copy number variation prediction method comprises the following steps: analyzing and comparing sequencing data of a to-be-detected sample to a reference genome, and extracting tumor purity information, whole-genome replication information and total copy number variation information; performing classification processing according to the total copy number variation information of each segment of the chromosome, converting the total copy number variation information into allele specific copy number variation information, if the total copy number variation information of the chromosome segment is an odd number interval or a zero interval, directly calculating the allele specific copy number variation information, and if the total copy number variation information of the chromosome segment is an odd number interval or a zero interval, directly calculating the allele specific copy number variation information; and if the total copy number variation information of the chromosome segment is a non-zero even interval, obtaining allele specific copy number variation information of the interval through model prediction. According to the method, only a single sample is needed, a normal sample does not need to be paired, the sequencing depth of the needed to-be-detected sample is low, the detection accuracy is high, and the homologous recombination defect of the low-tumor-purity sample can be detected.

Description

technical field [0001] The invention relates to the field of bioinformatics, in particular to a method for predicting allele-specific copy number variation in a single-sample whole genome. Background technique [0002] In recent years, with the emergence and application of Poly ADP-ribose Polymerase inhibitors (Poly ADP-ribose Polymerase inhibitors, PARPi), major breakthroughs have been made in the maintenance treatment of patients with ovarian cancer and other cancers, BRCA mutations and homologous recombination defects (Homologous Recombination The guiding role of Deficiency (HRD) status as a marker is increasingly prominent in clinical practice. Clinically, the beneficiary population of PARP inhibitors has expanded from BRCA mutation patients to HRD positive populations, which means that more cancer patients have the opportunity to benefit from the treatment of PARP inhibitors. At the same time, the applicable cancer types of the drug have also expanded from ovarian canc...

AI Technical Summary

Problems solved by technology

However, the disadvantage is that high-depth sequencing is required, resulting in high sequencing costs; low-depth sequencing strategies can only accurately analyze LST (Large-scale state Transition, large fragment migration) indicators, and high false negatives; for samples with low tumor purity, higher The depth of sequencing, further increasing the cost

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