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Haplodiploid detection method based on NGS-trio and application
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A detection method, a technique for diploidy, applied in the field of bioinformatics analysis
Pending Publication Date: 2020-10-30
GUANGZHOU KINGMED DIAGNOSTICS CENT +1
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But based on the sequencing data of a single sample, as disclosed in CN110211630A, UPD can only be inferred indirectly through LOH
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Embodiment 1
[0124] A method for detecting uniparental diploids based on NGS-trio, the process of which is as follows figure 1 shown, including the following steps:
[0126] Obtain NGS sequencing data of the same group of trio samples. It can be understood that the NGS sequencing data may be whole exome sequencing data or whole genome sequencing data.
[0127] As for the sample, the proband sample, the paternal sample and the maternal sample are required to be complete.
[0129] For a group of trio samples, the mutation sites that meet the predetermined conditions in each sample are selected respectively, and defined as the qualified mutation sites of the sample, and the mutation sites that are screened and removed are positioned as the unqualified mutation sites of the sample, according to Filter by:
[0130] 1. Screen high-quality mutation sites in whole exome sequencing (GATK-VQSR quality control PASS, total coverag...
Embodiment 2
[0161] A screening device for uniparental diploid based on NGS-trio, such as Figure 4 As shown, it includes: a data acquisition module, a data analysis module and a UPD judgment module.
[0162] The data acquisition module is used to acquire the NGS sequencing data of the same group of trio samples.
[0163] The data analysis module is used to analyze the above-mentioned sequencing data, and divides the mutation sites into: sites that conform to parental inheritance, sites that only conform to uniparental inheritance, and sites that do not conform to genetic laws; the data analysis module is implemented according to Steps 2 to 4 in Example 1 were analyzed.
[0164] The UPD judgment module is used to perform UPD judgment on the above-mentioned mutation site according to preset rules, and obtain a judgment result; the UPD judgment module performs judgment according to step 5 to step 8 in Embodiment 1.
Embodiment 3
[0166] A kind of uniparental diploid screening based on NGS-trio is carried out with a certain group (NP19E1936-NP19E1937-NP19F0086) of clinical samples, using the screening device in Example 2.
[0167] The result is as image 3 As shown, there are almost only Norm (normal) loci in this sample, and other types of loci are scattered, which may be sequencing errors or new mutations in the genetic process, and the results are shown as normal samples.
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Abstract
The invention relates to a haplodiploid detection method based on NGS-trio and application, and belongs to the technical field of bioinformatics analysis. According to the method, by obtaining NGS-trio sequencing data and through analysis and judgment, the chromosome genetic source of a proprietor can be directly inferred, so that whether UPD is indirectly inferred through LOH or not is directly judged, and the diagnosis positive rate is increased on the premise of not increasing any cost. Moreover, the method can also be used for assisting in judging the heterozygous deletion of large fragments, the density resolution can reach 1Mbp according to mutation sites, and the method has excellent detection performance.
Description
technical field [0001] The invention relates to the technical field of bioinformatics analysis, in particular to an NGS-trio-based uniparental diploid detection method and application. Background technique [0002] Genomic imprinting, also known as genetic imprinting, is a genetic process that marks a gene or genome domain on its parental source information through biochemical pathways. Such genes are called imprinted genes, and whether they are expressed or not depends on the source of their chromosomes (paternal or maternal), and whether the gene is silenced on the chromosome of its origin (the silencing mechanism is mainly methylation). Some imprinted genes are expressed only from the maternal chromosome, while others are expressed only from the paternal chromosome. [0003] In normal diploid, a pair of homologous chromosomes comes from the father and mother, respectively, and uniparental disomy (UniParental Disomy, referred to as UPD) refers to a pair of homologous chro...
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