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Method for predicting transcript degradation caused by nonsense mutation

A technology of transcripts and mutation points, applied in the fields of instrumentation, genomics, proteomics, etc., can solve the problems of complex surrounding sequences, achieve strong real objectivity, accurately evaluate models, and facilitate expansion.

Pending Publication Date: 2022-01-28
哈尔滨因极科技有限公司
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Problems solved by technology

At present, all prediction software for judging whether NMD occurs is based on the above three criteria, but due to the complexity of the surrounding sequences of nonsense mutations, the accuracy rate of prediction based on the above criteria is currently only 70% at most

Method used

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Embodiment Construction

[0025] The following examples are only used to illustrate the technical solutions of the present invention more clearly, and therefore are only examples, rather than limiting the protection scope of the present invention.

[0026] A method for predicting the degradation of transcripts caused by nonsense mutations provided in this example comprises the following steps:

[0027] S1: Select at least 400 groups of real samples for gene sequencing, and screen and annotate all mutation points, and only obtain nonsense mutations;

[0028] S2: Determine whether NMD occurs in a gene carrying a nonsense mutation. The specific determination method is as follows:

[0029] The obtained nonsense mutations were mapped to genes, and the transcriptional expression value RPKM of all sample genes was obtained. According to whether the samples carried nonsense mutations, they were divided into two groups, that is, samples with nonsense mutations and samples without nonsense mutations; The RPKM o...

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Abstract

The invention belongs to the technical field of genome sequencing analysis and relates to a method for predicting transcript degradation caused by nonsense mutation. According to the method for predicting transcript degradation caused by nonsense mutation, a prediction model is constructed based on real data, meanwhile, multiple factors are included when the prediction model is constructed, and thus, the occurrence of NMD can be evaluated systematically, completely and comprehensively. The method has higher real objectivity, and can more accurately and accurately predict the occurrence of the NMD.

Description

technical field [0001] The invention relates to the technical field of genome sequencing analysis, in particular to a method for predicting the degradation of transcripts caused by nonsense mutations. Background technique [0002] Nonsense mutation refers to that the codon representing a certain amino acid is mutated into a stop codon due to a change in a certain base, so that the synthesis of the peptide chain is terminated in advance. The early appearance of stop codons in immature transcripts can degrade transcripts, leading to a decrease in gene transcription levels and even inactivation. This phenomenon is called nonsense-mediated mRNA degradation pathway (nonsense-mediated mRNA decay, NMD) . For important genes, NMD can lead to monogenic diseases or tumors, and even lead to the death of infants and young children. Therefore, when looking for the pathogenic factor of the disease, it is particularly important to judge whether a nonsense mutation causes NMD. [0003] N...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/50G16B40/00
CPCG16B20/50G16B40/00
Inventor 王海宁刘珍姜玥
Owner 哈尔滨因极科技有限公司
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