Detection method for genomic copy number variation and device comprising same

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.

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...

AI Technical Summary

Problems solved by technology

CN106845154A relates to a copy number variation detection device for FFPE samples, including sequencing data acquisition module, sequence comparison module, early data processing module, normalization module, background library screening module, data fluctuation elimination module, GC correction module and output module; CN105574361A It relates to a method for detecting genome copy number variation, which specifically includes the following steps: sequencing a sample genome to obtain a genome sequence; comparing the sequence to a reference genome to obtain the position of the sequence on the genome; dividing the reference genome into sections of a certain length Window, count the sequences and bases falling in each window; correct each window according to the sequence and base GC content of each window; determine the normal threshold of copy number, scan each window, and determine whether the window copy number is Variation: Precisely scan the abnormal window to determine the exact breakpoint to determine the specific location of the copy number variation; however, the detection results of the above-mentioned current technology are high in false positives and low in accuracy, the detection process is cumbersome, and the steps are redundant, which needs to be further improved and optimization

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