Method for carrying out polynucleotide variation identification and annotation on multiple species

A polynucleotide and multi-species technology, applied in the field of polynucleotide variation identification and annotation, can solve problems such as MNV annotation that cannot be larger than double points, and achieve the effect of reducing time and avoiding errors

Active Publication Date: 2022-07-08
HUAZHONG AGRI UNIV
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  • Claims
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Problems solved by technology

At present, the identification of MNVs only involves the identification of double-point MNVs, and traditional genetic variation annotation tools (databases and software) are usually unable to annotate MNVs larger than double points

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  • Method for carrying out polynucleotide variation identification and annotation on multiple species

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Embodiment Construction

[0055] In order to facilitate the understanding and implementation of the present invention by those of ordinary skill in the art, the present invention will be further described in detail below with reference to the embodiments. It should be understood that the embodiments described herein are only used to illustrate and explain the present invention, but not to limit the present invention.

[0056] In this embodiment, a method for identifying and annotating polynucleotide variants for multiple species is to identify and annotate MNVs from species-oriented standard variant call format data (the variant call format, VCF). Specifically, as figure 1 shown, follow the steps below:

[0057] Step 1. Use the directional data in standard variant format of adrenocortical carcinoma (hereinafter referred to as data set VCF). First, use the traditional polynucleotide variant identification tool (identify_mnv, https: / / github.com / macarthur-lab / gnomad_mnv) to obtain all two-point MNVs as t...

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Abstract

The invention discloses a method for performing polynucleotide variation identification and annotation on multiple species, which comprises the following steps of: obtaining all double-point MNVs as a data set TwoPointMNV according to an oriented data set VCF; splitting all identified double-point MNVs in the data set TwoPointMNV into single-point data sets SNVs, and acquiring row information of the single points from the data set VCF according to the data sets SNVs to serve as data sets SNVInfoVCF; identifying the MNV from the 7th site to the 2nd site, obtaining the identified MNV, and carrying out gene-based annotation, non-coding region-based annotation and regulatory region-based annotation. According to the method, identification of MNVs larger than two points is supported, the number of the identified MNVs is increased, the MNVs which are wrongly identified originally are filtered out, and the MNVs are effectively annotated.

Description

technical field [0001] The invention belongs to the field of biotechnology, in particular to a method for identifying and annotating polynucleotide variations for multiple species Background technique [0002] In recent years, many countries have invested a lot of money to launch precision medicine programs, and mankind has gradually entered the era of precision medicine. Therefore, analyzing the genetic differences of different individuals is an important prerequisite for the implementation of precision medicine. With the development of technology, the time and cost of obtaining genetic information have been greatly reduced, and a large number of multi-nucleotide variants (MNVs) have been identified in human disease research. MNV refers to the presence of two or more nucleotide variations on the same haplotype in an individual, which will lead to changes in protein sequence, compared with single nucleotide variations (single-point nuclear variation on the same haplotype) ...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/20G16B50/30G16B50/10
CPCG16B20/20G16B50/30G16B50/10Y02A90/10
Inventor 龚静金炜炜蒋政曹文
Owner HUAZHONG AGRI UNIV
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