Method and system for determining HPV integration site in genome from human cervical carcinoma sample

Abstract

The invention discloses a method and a system for determining HPV integration site in genome from a human cervical carcinoma sample. The method provided by the invention comprises the following steps: carrying out first sequencing on genomic DNA from a human cervical carcinoma sample so as to obtain a sequencing result; determining a DNA fragment containing both HPV sequence and human genomic sequence based on the sequencing result; determining an amplification primer pair based on the DNA fragment containing both HPV sequence and human genomic sequence; carrying out PCR amplification on the genomic DNA from the human cervical carcinoma sample by the utilization of the amplification primer pair so as to obtain a PCR product; and carrying out second sequencing on the PCR product so as to determine the HPV integration site in the genome from the human cervical carcinoma sample. The method provided by the invention is simple and easy to operate, requires low cost, and has high efficiency and good repeatability. By the utilization of the method, all HPV types can be detected at a time, and detailed sequence information and the integration site can be determined rapidly and accurately.

Description

technical field [0001] The present invention relates to a method and a system for determining the HPV integration site in the genome of a human cervical cancer sample. Background technique [0002] Human papillomavirus (HPV for short) is a closed circular deoxyribonucleotide virus. 118 subtypes have been found so far. Among them, virus subtypes related to human malignant tumors include 5, 6, 8, 11, 16, 18, 31, 33 and other types. The viral oncogenes (such as E6, E7) carried by them will be integrated into the host genome along with the viral DNA during the early development of cancer, resulting in changes in the expression of these two oncogenes (E6, E7). The proteins p53(E6) and pRB(E7) encoded by these two genes accelerate the degradation of host cells and contribute greatly to the oncogenicity of HR-HPV. These two oncoproteins interfere with the replication and segregation machinery during chromosome mitosis, inducing severe chromosomal instability. Studies have confi...

AI Technical Summary

Problems solved by technology

However, these methods can only detect one HPV type at a time, or have other technical deficiencies, such as the signal detection problem of in situ hybridization and the harsh conditions of PCR analysis, which are not conducive to the detection of complex integration situations

The above traditional methods are not only time-consuming and laborious, but also difficult to discover new integration sites

[0004] Therefore, at this stage, the method for determining the HPV integration site in the genome of human cervical cancer samples still needs to be improved.

Images