Detection method for genomic copy number variation and device comprising same

A copy number variation and detection method technology, applied in the field of detection methods and devices including the method, can solve the problems of low accuracy, redundant steps, high false positive detection results, etc.

CN108573125AActive Publication Date: 2018-09-25YIKON GENOMICS SHANGHAI CO LTD
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Patent Information

Authority / Receiving Office
CN · China
Current Assignee / Owner
Publication Date
2018-09-25

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Abstract

The invention provides a detection method for genomic copy number variation and a device comprising the method. The method comprises the following steps: inputting original data, cleaning quality control, aligning sequences to a reference genome, calculating a unique alignment sequence number by using windows of different sizes, performing GC correction and reference correction, shielding undetectable areas, segmenting CBS, integrating karyotype reports and generating reports, a complete set of the detection methods and devices is established through experimental exploration and optimization,through successive application of the specific sequential steps, the step of the reference correction is creatively adopted, and the windows with different sizes are used for performing alignment andintegration, the steps cooperate mutually, and finally the sensitivity and specificity are improved, so that the detection accuracy and result forms can conform to clinical demands, and the detectionmethod for the genomic copy number variation and the device comprising the method are high in automation degree, easy to expand, high in detection accuracy, capable of lowering the cost of data analysis, and extremely high in application value.
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Description

technical field

[0001] The invention relates to the technical field of bioinformatics, in particular to a detection method for genome copy number variation and a device comprising the method. Background technique

[0002] Copy number variation (CNV) mainly refers to deletions, insertions, duplications, etc., of genomic DNA fragments ranging in size from 1 kb to several Mb, including abnormal numbers and structures. Copy number mosaicism refers to the number of chromosomal copy number variations between integers, for example, 2.5-fold copy number variation is 50% triploid mosaicism. In addition to scientific research, in the field of clinical application, copy number variation detection can be used for detection of single cell copy number variation, detection of copy number variation of apoptotic tissues, detection of genetic diseases and tumors with copy number variation, etc. ; Among them, single-cell copy number variation refers to the analysis of copy number variation of...

Examples

Embodiment 1

[0083] Example 1 Assembly of a device for detecting gene copy number abnormalities

[0084] The following modules were assembled as a means to detect genomic copy number variation:

[0085] (1) Sequencing data acquisition module: used to acquire the raw data of the sample and perform quality control and cleaning;

[0086] (2) Sequence comparison module: used to compare, sort and deduplicate the sequencing data with the reference genome;

[0087] (3) Data processing module: used to divide the reference genome into at least two windows of different sizes, and calculate the number of uniquely aligned sequences falling into the windows;

[0088] (4) GC correction module: used for counting the GC content falling into the window described in the data processing module, and performing GC correction;

[0089] (5) Reference correction module: used to use the reciprocal of the median of the window count results obtained after GC correction as a weight for reference correction, and to ...

Embodiment 2

[0095] In the present invention, the device in Example 1 is used to detect copy number variation, and the complete data flow chart is shown in figure 1 As shown, the specific steps are as follows;

[0096] 1. Amplify the whole genome, build a library, and sequence the sample

[0097] In this example, the test sample is a national reference product for preimplantation chromosomal aneuploidy, which is used for performance evaluation of preimplantation chromosomal aneuploidy detection kits by high-throughput sequencing, and the evaluation is high The detection capability of a throughput sequencing method for CNVs of different chromosomal sizes in blastocyst screening.

[0098] The whole genome amplification method used the MALBAC-LAB early embryo preimplantation chromosomal aneuploid detection library preparation kit, and the amplification and library construction method was operated in accordance with the product instructions provided by Shanghai Yikang Medical Laboratory Co., ...