Tumor genome copy number variation characteristic pattern recognition method and application thereof

A copy number variation and characteristic pattern technology, applied in the field of tumor genome copy number variation characteristic pattern recognition, can solve the problem of lack of practical tools

Pending Publication Date: 2021-03-16
SHANGHAI TECH UNIV
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Problems solved by technology

Copy number variation is an important driving force for the occurrence and development of various cancers. However, practical tools for studying the characteristic patterns of copy numb

Method used

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  • Tumor genome copy number variation characteristic pattern recognition method and application thereof
  • Tumor genome copy number variation characteristic pattern recognition method and application thereof
  • Tumor genome copy number variation characteristic pattern recognition method and application thereof

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Embodiment 1

[0057] The method for recognizing the pattern of the copy number variation characteristic of the prostate cancer genome comprises the following steps:

[0058] 1) The high-throughput Whole Exome Sequencing (WES) results of the prostate cancer genome were extracted from the dbGap public database, with a total of 937 pairs of tumor and normal control tissues;

[0059] 2) Using Sequenza software, extract the absolute copy number information of each tumor sample from the above WES sequencing results;

[0060] 3) Record the value of the copy number variation feature, the identification process of the copy number variation feature is as follows figure 1 shown. Eight types of copy number variation signatures were calculated for each tumor: the number of breakpoints per 10Mb (named BP10MB); the number of breakpoints per chromosome arm (named BPArm); the absolute copy number of DNA fragments (named CN); Copy number difference between DNA fragments (called CNCP); length of oscillating...

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Abstract

The invention relates to a tumor genome copy number variation characteristic pattern recognition method and application thereof, and belongs to the technical field of gene diagnosis. According to themethod, systematic classification is carried out on tumor genome copy number variation characteristics, 80 numerical values of eight types of tumor genome copy number variation characteristics are specifically extracted, a copy number variation characteristic mode of a tumor sample is extracted by utilizing a non-negative matrix factorization algorithm, and then the tumor is typed according to thecopy number variation characteristic mode. Therefore, accurate prediction of clinical prognosis of tumors can be realized.

Description

technical field [0001] The invention relates to a tumor genome copy number variation characteristic pattern recognition method and an application thereof, belonging to the technical field of gene diagnosis. Background technique [0002] Cancer is primarily caused by mutations in the genomic DNA of somatic cells. According to the size and characteristics of the genomic variation, these cancer-associated DNA variations can be divided into the following four types: single base substitution (SBS), small insertion / deletion (INDEL), structural change (including translocations / inversions) and copy number alterations. Copy number variation of somatic DNA is extremely prevalent in cancer and has been reported to be an important driver of progression in many types of cancer. Characteristic patterns of genomic DNA variation are recurring genomic patterns that are imprints of mutagenic processes accumulated during cancer cell development. Copy number variation signature patterns refl...

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Application Information

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IPC IPC(8): G16B20/10G16B20/20G06K9/62G06Q10/04
CPCG16B20/10G16B20/20G06Q10/04G06F18/23
Inventor 刘雪松王诗翔
Owner SHANGHAI TECH UNIV
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