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A single exon copy number variation prediction method based on target region sequencing

A copy number variation and target region technology, applied in the field of single exon copy number variation prediction, can solve problems such as complex analysis process, achieve low cost and reduce analysis complexity

Active Publication Date: 2022-02-08
杭州迈迪科生物科技有限公司
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  • Description
  • Claims
  • Application Information

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Problems solved by technology

These tools have a complex analysis process, requiring a total of more than 30 control samples or paired control samples

Method used

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  • A single exon copy number variation prediction method based on target region sequencing
  • A single exon copy number variation prediction method based on target region sequencing
  • A single exon copy number variation prediction method based on target region sequencing

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Experimental program
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Effect test

specific Embodiment 1

[0100] Three positive samples known to have exon-level copy number variation were analyzed, and the exon copy number variation information of the three positive samples was as follows.

[0101]

[0102]

[0103] Three positive samples and five negative control samples were subjected to exome sequencing to obtain sequencing data. Perform quality control on the sequencing data, compare it to the hg19 reference genome, and use picard to deduplicate and sort the aligned reads. The software used is trommomatic, bwa, picard. The statistical information of each sample is as follows:

[0104] sample Raw Bases Duplication Q20 Q30 NA05123 18389070300 27.87％ 97.58％ 93.50％ NA09981 17933438100 27.00％ 97.52％ 93.42％ NA23159 18144067200 26.40％ 97.47％ 93.30％ NA05169 23433262500 33.61％ 98.22％ 95.06％ Control1 18983356500 19.88％ 98.7％ 97.8％ Control2 10140261600 19.15％ 95.87％ 93.52％ Control3 23808953400 24.85％ 98.53...

specific Embodiment 2

[0114] For the prediction of deletion variants, we also achieved good results, because the sequencing coverage of the exons in the samples with deletions was almost zero. Taking the NA05169 sample as an example, 40 exons in this sample have copy number deletion mutations, and the predicted results are as follows:

[0115]

[0116]

[0117] This method detected all 40 deletion variants in the NA05169 sample.

[0118] In summary, this method does not use GC content to correct the prediction of copy number duplication and deletion variation, nor does it perform complex modeling like other software for prediction. Only 5 control samples are used, that is, the duplication and deletion Missing mutations were predicted, showing the good application performance of the algorithm. The source of the data is the data obtained from the sequencing of the existing target region, and no additional experimental cost is required.

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Abstract

The present invention relates to a single exon copy number variation prediction method based on target region sequencing, including two steps of sequencing data processing and copy number variation prediction, wherein the copy number variation prediction step includes counting the total number of sequencing sequences covering the target region The target and total number of bases, determine the control exon region, normalize the coverage of the exon region to be analyzed for each control sample and experimental sample, and calculate the average of the coverage of the exon region to be analyzed in the control sample after normalization , standard deviation and coefficient of variation to predict the copy number change steps of the exon region to be analyzed. The present invention does not rely on whole-genome sequencing, but directly uses exon-level coverage information to analyze exon-level copy number variation, and the analysis method is simple without complicated GC correction and modeling.

Description

technical field [0001] The invention relates to the field of biomedicine, in particular to a single exon copy number variation prediction method based on target region sequencing. Background technique [0002] Since the end of the Human Genome Project in 2003, genome sequencing technology has advanced by leaps and bounds, and single nucleotide polymorphism (SNP) detection technology based on high-throughput sequencing technology has become mature and popular. High-throughput sequencing technology can realize tens of thousands of DNA molecules to be synthesized and sequenced at the same time, which greatly improves the sequencing throughput. The cost of sequencing genetic tests is falling even faster than Moore's Law in computing. Based on the application of sequencing technology, biological research has entered the era of omics research from traditional single-gene and single-site research, resulting in a series of research results and clinical applications with social valu...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B30/10G16B20/20
Inventor 朱忠旭周文莉杨克勤吕远栋
Owner 杭州迈迪科生物科技有限公司
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