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Single exon copy number variation predicting method based on target area sequencing

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

Active Publication Date: 2018-11-30
杭州迈迪科生物科技有限公司
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  • 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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  • Single exon copy number variation predicting method based on target area sequencing
  • Single exon copy number variation predicting method based on target area sequencing
  • Single exon copy number variation predicting method based on target area sequencing

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Experimental program
Comparison scheme
Effect test

specific Embodiment 1

[0099] 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.

[0100]

[0101]

[0102] 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:

[0103] sample

[0104] Use the software bedtools to count the coverage of each exon, and then normalize the coverage of the exons to be analyzed for each sample. The coverage information of the five control samples was formed into a control sample group, and the positive samples were analyzed one by one. The test results are as follows:

[0105] sample

[0106] The overall ...

specific Embodiment 2

[0112] 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:

[0113]

[0114]

[0115] This method detected all 40 deletion variants in the NA05169 sample.

[0116] 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 invention relates to a single exon copy number variation predicting method based on target area sequencing. The method includes: processing sequencing data; predicting copy number variation, to bemore specific, statistically counting the total number of sequencing sequences and basic groups covering a target area, determining control exon areas, standardizing the coverage of the to-be-analyzed exon areas of each control sample and each experiment sample, calculating the average value, standard deviation and variation coefficient of the standardized coverage of the to-be-analyzed exon areas in the control samples, and predicting the copy number variation of to-be-analyzed exon areas. The method has the advantages that whole genome sequencing is not needed, the copy number variation ofexon level is analyzed by directly using the coverage information of the exon level, and the method is simple in analysis and does not need complex 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 Applications(China)
IPC IPC(8): G06F19/20G06F19/24G06F19/28
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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