Identification method of group of genomic characteristic mutation fingerprints associated with homologous recombination repair defects

A homologous recombination, genome technology, applied in the determination/inspection of microorganisms, biochemical equipment and methods, etc., can solve problems such as statistical differences

Pending Publication Date: 2019-12-03
THE WEST CHINA SECOND UNIV HOSPITAL OF SICHUAN +1
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  • Abstract
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  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The hHRD mutation spectrum fingerprint accounts for a significant proportion in HBV-related liver cancer, but does not appear in HBV-negative liver cancer, with a significant statistical difference

Method used

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  • Identification method of group of genomic characteristic mutation fingerprints associated with homologous recombination repair defects
  • Identification method of group of genomic characteristic mutation fingerprints associated with homologous recombination repair defects
  • Identification method of group of genomic characteristic mutation fingerprints associated with homologous recombination repair defects

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0059] Example 1 Genomic Tumor Mutation Burden of HBV-related Liver Cancer

[0060] Methods: Surgical sampling of fresh liver cancer and blood tissue, sampling volume> 1cm 3 , the blood sample was 5 ml of anticoagulated blood, and the blood cells were collected by centrifugation. The samples were quickly frozen in liquid nitrogen and placed in individual sealed packages to prevent contamination between samples, and basic clinical information was marked on the packaging containers. The samples were stored at -80°C and shipped to the sequencing company within two weeks on dry ice for sample quality inspection, nucleic acid extraction and sequencing. After genome purification, use Qubit and 1% AGE to detect the degradation of the sample. The concentration is ≥20ng / ul and the total amount is ≥500ng. The sample has no obvious degradation band and can be used for downstream analysis and sequencing.

[0061] The sequencing platform uses the illumina2000 sequencer, and the sequencin...

Embodiment 2

[0068] Example 2 Single nucleotide variation characteristics of hHRD type in HBV-related liver cancer genome

[0069] Method: According to the definition of 30 types of point mutation signatures published by the Sanger Institute in Cambridge, UK in 2013 (Nature.2013 Aug22; 500 (7463): 415-21), the 16 cases of HBV in Example 1 were further correlated Analyze the clustering characteristics of single nucleotide variants in liver cancer samples. The single-nucleotide variation label extraction strategy adopts the 30 types of standard single-nucleotide variation characteristics defined in the COSMIC database in a single sample, and uses the deconstructSigs software to decompose the mutation characteristics and their composition ratios in a single tumor sample (

[0070] Genome Biol. 2016 Feb22;17:31., the full text is incorporated by reference). The deconstructSigs software analysis method can perform single-nucleotide variation tag analysis on a single sample. Compared with the...

example 3

[0095] Example 3 Compositional characteristics of genome-wide small fragment insertion-deletion mutations in HBV-related liver cancer

[0096] Method: The specific analysis method of small fragment indels is as follows: Figure 8 show:

[0097] Small fragment indel detection software uses Strelka. The analysis strategy or method for small fragment insertion-deletion features is

[0098] 1. The small fragment deletion events that define the repeat sequence are 1-50bp small fragment deletions that occur in the short tandem repeat region.

[0099] 2. Define the small fragment deletion event of the micro-homology sequence as the 1-50bp small fragment deletion in the non-short tandem repeat region, accompanied by homology sequences > 3bp on both sides.

[0100] 3. Define other types of deletions as small fragment deletions of 1-50 bp in non-short tandem repeat regions, and not accompanied by homologous sequences > 3 bp on both sides, and the range of homologous sequences is defi...

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Abstract

The present invention discloses a genomic characteristic mutation fingerprint related to hHRD type homologous recombination repair defects and comprises a combination characteristic of a single nucleotide variation (SNV) and insertion deletion (Indel) genomic fingerprint, and an identification method thereof. The fingerprint characteristics can be subjected to high-throughput whole-genome resequencing, bioinformatics software analysis and statistical correlation analysis and are used to identify infectious diseases or tumors with the characteristic mutation fingerprints, especially hepatitis Bvirus infection and related diseases, including liver cirrhosis, liver fibrosis and liver cancer. The mutation fingerprint can also be used to guide methods and uses of treatments of targeted drugs targeting the homologous recombination defects on a variety of the various tumors with the hHRD homologous recombination repair defects, including but not limited to breast cancer, ovarian cancer, endometrial cancer, endometrioid carcinoma, ovarian clear cell carcinoma, prostate cancer, gastric cancer, skin cancer, hepatitis B virus infection or related liver cirrhosis, liver cancer and bile duct cell cancer.

Description

technical field [0001] The invention belongs to the field of gene detection and detection reagents, and in particular relates to a marker for identifying homologous recombination repair-deficient genomic mutations and a bioinformatics identification method, the marker having a characteristic somatic mutation (Fingerprint) ), using the marker to detect virus infection, tumor or intermediate pathological state with this feature. Background technique [0002] Homologous recombination repair-deficient types of diseases are gaining more and more attention in the field of oncology. The mutation or abnormal expression of breast cancer genes BRCA1 and BRCA2 leads to defects in homologous recombination repair, and is also an important cause of breast cancer, ovarian cancer, prostate cancer and gastric cancer. These diseases are collectively referred to as BRCA type tumors (BRCAness). However, the use of BRCA1 and BRACA2 gene mutation detection as the clinical classification and clin...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/70C12Q1/6886C12Q1/6883
CPCC12Q1/706C12Q1/6886C12Q1/6883C12Q2600/156C12Q2600/106
Inventor 唐子执刘聪曾鸣张臣良姜长安母得志
Owner THE WEST CHINA SECOND UNIV HOSPITAL OF SICHUAN
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