Method for detecting variation of copy numbers of genomes

A technology of copy number variation and genome, applied in the field of detection of genome copy number variation, can solve the problems of unstable probe hybridization efficiency, PCR pollution, low resolution, etc. sexual effect

Active Publication Date: 2016-05-11
YIKON GENOMICS SHANGHAI CO LTD
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Problems solved by technology

Among them, comparative genomic hybridization has relatively low resolution, Mb level, low throughput, and high cost; fluorescent quantitative PCR also has low throughput, high cost, and can only measure one copy number variation at a time; fluorescent in situ hybridization, only for specific positions, Low resolution,...

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  • Method for detecting variation of copy numbers of genomes
  • Method for detecting variation of copy numbers of genomes
  • Method for detecting variation of copy numbers of genomes

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Embodiment 1

[0038] In this embodiment, the copy number variation detection is performed on the cell samples of two generations, and the detection results are compared with the paternal karyotype results.

[0039] 1. Sequencing

[0040] In this embodiment, for the detection of a sample containing a trace amount of nucleic acid, firstly, single-cell whole-genome amplification is performed. Single cell expansion using MALBAC of Yikang Gene Technology Co., Ltd. SingleCellWholeGenomeAmplificationKit, the single cell is a sample containing a small amount of nucleic acid, such as free single cells in blood, urine, and saliva.

[0041] The amplified samples were purified, the library was constructed, and sequenced on the machine. The on-machine sequencing used the HiSeq2500 high-throughput sequencing platform of Illumina, and operated according to the instructions provided by Illumina. The sequencing type is single-end (SingleEnd) sequencing, the sequencing length is 50bp, and the sequencing ...

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Abstract

The invention relates to a method for detecting the variation of copy numbers of genomes. The method specifically comprises the following steps: sequencing sample genomes to obtain genome sequences; aligning the sequences to a reference genome to obtain the positions of the sequences on the genome; dividing the reference genome into windows with a certain length and carrying out statistics on the sequences and basic groups falling on the windows; correcting the windows according to the sequences and GC contents of the basic groups; determining threshold values with normal copy numbers, scanning the windows and determining whether the copy numbers of the windows varies; and precisely scanning the abnormal windows to determine the precise breakpoints and then determine the specific variation position of the copy numbers. According to the method, the sensitivity of the detection for the variation of the copy numbers of the genomes can be improved through utilizing three mean values, carrying out window correction, determining the threshold values with normal copy numbers, precisely scanning the abnormal windows and determining the precise breakpoints and the specific variation positions of the copy numbers; and the method is easy, simple and feasible to operate, high in efficiency, low in cost and beneficial for popularization and application.

Description

technical field [0001] The invention relates to the fields of genome sequence analysis and bioinformatics, in particular to a method for detecting genome copy number variation. Background technique [0002] Copy Number Variations (CopyNumberVariations, CNV) refers to the abnormal copy number of chromosomes or chromosome segments in the sample genome compared with the genome reference sequence, including but not limited to chromosome aneuploidy, deletion, duplication, microdeletion, microdeletion greater than 1000 bp repeat. In the field of biomedical scientific research and clinical application, diseases caused by genome copy number variation are often encountered, such as chromosomal aneuploidy, microdeletion, miscarriage caused by microduplication, embryo implantation failure, various genetic diseases and cancer and more. The detection of genomic copy number variation can be applied to tissue detection such as tumor tissue, amniotic fluid, and flow product tissue, liquid...

Claims

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Application Information

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IPC IPC(8): G06F19/18C12Q1/68
Inventor 陆思嘉薄世平马淑杰
Owner YIKON GENOMICS SHANGHAI CO LTD
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