A Single-Sample Genome-Wide Method for Predicting Allele-Specific Copy Number Variations

Abstract

A single-sample genome-wide method for predicting allele-specific copy number variations, the method comprising: analyzing the sequencing data of a test sample compared to a reference genome, extracting tumor purity information, genome-wide replication information, and total copy number variations information, and then perform classification processing according to the total copy number variation information of each segment of the chromosome, and convert 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 interval or 0 interval, the allele-specific copy number variation information is directly deduced, and if the total copy number variation information of the chromosome segment is a non-zero even interval, the allele-specific copy number variation of the interval is obtained through model prediction information. The invention only needs a single sample and does not need paired normal samples. The required sample to be tested has a low sequencing depth and high detection accuracy, and can detect homologous recombination defects in samples with low tumor purity.

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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