Method, computing device and storage medium for predicting the copy number of a gene to be tested

Abstract

The invention relates to a method for predicting the copy number of a gene to be tested, a computing device and a storage medium. The method includes: obtaining sequencing sequence data of the sample to be tested, the sequencing sequence data is a third-generation sequencing sequence of the gene to be tested obtained through the third-generation sequencing technology; based on the obtained sequencing sequence data, determining a single sequence of the gene to be tested The number of haplotypes and the sequencing depth; and based on the determined number of haplotypes and the sequencing depth, determining a prediction result about the copy number of the gene to be tested in the sample to be tested. The invention can accurately determine the gene copy number for repeated regions or highly homologous genes at low cost.

Description

technical field [0001] The present invention generally relates to biological information processing, and in particular, to a method, computing device and computer storage medium for predicting the copy number of a gene to be tested. Background technique [0002] In the field of genetics, the determination of gene copy number is very important, especially for some dose-sensitive genes, such as HBA gene, which has 4 copies in healthy people, when the copy number is 3, it will cause quiescent α-thalassemia; when the copy number is 3 When the copy number is 2, it will cause α-thalassemia minor; when the copy number is 1, it will cause hemoglobin H disease (hemoglobin H disease, HbH disease), and the patient needs regular blood transfusion treatment; when the copy number is 0, it will cause Hb Bart's edema fetus Syndrome and death in fetus. In addition, the severity of the HBA phenotype is also affected by the number of copies of the HBB gene. For another example, for the SMN1 ...

AI Technical Summary

Problems solved by technology

Regarding multiple ligation probe amplification technology, one reaction can detect changes in the copy number of dozens of nucleotide sequences, so it has the characteristics of high efficiency and specificity, but the throughput of this technology is low, and specific base information cannot be obtained

Regarding the low-depth / high-depth genome-wide NGS sequencing technology, it has the characteristics of high throughput, but the accuracy and resolution are low, and the cost is high, especially for repetitive regions or highly homologous genes, it is difficult to accurately determine the gene copy number

[0004] In summary, the disadvantages of the traditional methods for predicting the copy number of the gene to be tested are: it is difficult to accurately determine the gene copy number for repetitive regions or highly homologous genes at low cost

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