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Method for predicting element being rich in riboSnitch or with lost riboSnitch in cancer genome and related equipment

A genomics and cancer technology, applied in genomics, proteomics, instrumentation, etc., can solve problems such as unclear role of riboSNitch

Inactive Publication Date: 2019-09-20
FUDAN UNIV
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Problems solved by technology

However, the role of riboSNitch in cancer genomes is still unclear, so we decided to use two cancer genome databases, TCGA and ICGC, to analyze riboSNitch in cancer genomes to clarify whether riboSNitch is in the non-coding regions of cancer genomes (including UTR regions of coding genes and long non-coding genes), whether it is related to tumorigenesis

Method used

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  • Method for predicting element being rich in riboSnitch or with lost riboSnitch in cancer genome and related equipment
  • Method for predicting element being rich in riboSnitch or with lost riboSnitch in cancer genome and related equipment
  • Method for predicting element being rich in riboSnitch or with lost riboSnitch in cancer genome and related equipment

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Embodiment

[0049] 1.1 Materials and methods

[0050] 1.1.1 Data collection

[0051] Most cancer somatic mutation data used in this study came from ICGC and TCGA databases. In addition, we collected somatic mutations in 25 whole-genome sequenced melanomas and 100 whole-genome sequenced gastric cancers 20,21 . The mutation data set of normal people is obtained from the Thousand Genomes database, and the present invention uses the data of Phase 3 22 .

[0052] First, we filtered out all indels and only kept point mutations for further analysis. Then, use the UCSC liftOver toolkit to change all hg38-annotated mutations to hg19 mutations23 . In order to remove low-confidence SNVs, we filter the somatic mutations of the cancer database and the germline mutations of the Thousand Genomes. The filtered interval collection is downloaded from the Broad Institute (https: / / personal.broadinstitute.org / anshul / projects / encode / rawdata / blacklists). This list is a collection of all blacklisted regi...

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Abstract

The invention relates to the technical field for detecting influence of mutation to an RNA secondary structure, and particularly to a method for predicting an element being rich in riboSnitch or with lost riboSnitch in a cancer genome and related equipment. The invention provides software which is named as SNIPER. The software can be used for predicting the riboSNitch and identifying a non-coded element which is rich in riboSNitch or has lost riboSnitch in a tumor. The content of the invention includes introduction to the software SNIPER and firstly analyzes the riboSnitch in somatic cell mutation in a cancer.

Description

technical field [0001] The invention relates to the technical field of detecting the impact of mutations on RNA secondary structures, in particular to a method and related equipment for predicting the enrichment or deletion of riboSnitch elements in cancer genomes. Background technique [0002] RNA secondary structure can affect cellular processes in many ways, including RNA stability, RNA localization, RNA transcription, RNA processing, and even protein translation. Among them, the single nucleotide variation (SNV) that changes the secondary structure of RNA is called riboSNitch. These mutations may affect human health and cause certain human diseases. Especially for mutations in some non-coding regions, their secondary structures are closely related to gene transcription and translation. RiboSNitch in non-coding regions is specifically studied in the present invention, especially the untranslated regions (UTRs) and non-coding RNAs (ncRNAs) of genes. At present, human st...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/20G16B20/50G16B25/00G16B30/00G16B40/00G16B5/00
CPCG16B5/00G16B20/20G16B20/50G16B25/00G16B30/00G16B40/00
Inventor 苏志熙何馥男
Owner FUDAN UNIV
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