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A method and system for analyzing chromosomal aneuploidy

A technology of aneuploidy and analysis methods, applied in biostatistics, genomics, instruments, etc., can solve the problem that the number of heterozygous SNP sites in the sample to be tested is not fixed, abnormal chromosomes cannot be further judged, and the accuracy of sample detection is affected and other issues to achieve the effect of short sequencing cycle, high accuracy and stable sequencing data

Active Publication Date: 2020-09-25
SIMCERE DIAGNOSTICS CO LTD +2
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  • Abstract
  • Description
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AI Technical Summary

Problems solved by technology

[0006] In the prior art, there are few NGS methods for detecting 1p19q LOH, some of which only involve the detection of chromosome deletion based on the distribution difference signal of SNP, and do not use the signal of sequencing depth, and its disadvantages are significant: 1) It can only determine whether the chromosome is euploid 2) The number of heterozygous SNP sites in the sample to be tested is not fixed, and if all are homozygous SNPs or there are too few heterozygous SNP sites, it will directly affect the detection of the sample Accuracy

Method used

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  • A method and system for analyzing chromosomal aneuploidy
  • A method and system for analyzing chromosomal aneuploidy
  • A method and system for analyzing chromosomal aneuploidy

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Experimental program
Comparison scheme
Effect test

Embodiment 1B

[0044] Embodiment 1Backbone region probe design and on-machine sequencing

[0045] 1) Select the area with high contrast accuracy

[0046] The present invention selects the Backbone region according to the sequence information disclosed by the UCSC website, such as figure 1 , figure 1 The abscissa in is the reference sequence position of chr1:q, and the ordinate is the accuracy value mappability. When mappability=1, it means that the 100bp sequence from this region can be uniquely compared back to this region, indicating that the alignment accuracy is the highest, which means This area is black in the figure; when mappability<1, it indicates that the alignment accuracy is low, and this area is gray in the figure.

[0047] 2) Screening of SNP sites

[0048] According to the public population mutation database gnomAD / exAC / 1000 Genomes and other databases, the SNP sites with a population frequency greater than 5% were screened out.

[0049] 3) Probe design

[0050] In the Ma...

Embodiment 2

[0052] Example 2 Quality Control of Sequencing Data Based on NGS Platform

[0053] Use the fastp software to remove the splice from the fastq.gz sequence data obtained from the sequencing machine to obtain the XXXFP.trim.R1.fastq.gz file, and use the XXXFP.trim.R1.fastq.gz file after the splice removal and the human reference genome BWA mem is compared, the comparison parameter is bwa mem-Y-R, and the XXX.align.bam file is obtained by comparison. For XXX.align.bam, use sambamba software to sort the reads according to the alignment position, and obtain the XXX.align.sort.bam file. Use bamdst software to count XXX.align.sort.bam files to obtain QC indicators such as Mapped ratio, raw Q30 rate, target_ratio_base, median_umi_depth, median_insert_size, etc.

[0054] According to the standards in Table 1, determine whether the quality of sample library construction and sequencing is qualified;

[0055] Table 1. Quality control indicators

[0056]

[0057]

Embodiment 3

[0058] Embodiment 3 Analysis based on Zscore

[0059] 1) Construct negative sample sequencing depth reference set

[0060] Select 54 cases of clinically negative FFPE samples, follow the NGS sample on-machine sequencing experiment process for library construction, hybridization capture, and on-machine sequencing to obtain the corresponding sequence data, and refer to Example 2 to perform quality control on the sequencing data, and the sample data that passed the quality control Perform the following data analysis:

[0061] ① Extract the sequencing depth data after removing PCR repetitions:

[0062] Use Bamdst software to analyze the XXX.align.sort.bam file to obtain the depth.tsv.gz file. After opening the depth.tsv.gz file, you can get the data list as in Table 2. The first column is the chromosome number, and the second column is is the base position, the third column is the original sequencing depth, and the fourth column is the sequencing depth after removing PCR repeats...

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Abstract

The invention provides a chromosome aneuploidy analysis method and a chromosome aneuploidy analysis system. According to the method, sample sequencing depth is subjected to statistical analysis basedon a Zscore algorithm, and the condition of chromosome aneuploidy is comprehensively judged in combination with statistical analysis of SNP allele frequency of samples. The method provided by the invention is high in accuracy, is not influenced by the SNP locus number of a sample to be detected, has high specificity and sensitivity (up to 100%), and can also be used for judging whether abnormal chromosomes are deleted or amplified.

Description

technical field [0001] The invention relates to the technical field of genetic engineering, in particular to a data analysis method and system for chromosomal aneuploidy. Background technique [0002] In the process of tumors, especially brain tumors, cells will undergo unbalanced translocation, resulting in the loss / increase of a long and short arm of a chromosome, or even an entire chromosome. Glioma is the most common primary intracranial malignant tumor. In adults, glioma is the most common primary intracranial tumor, accounting for about 30-40% of all brain tumors. Among primary malignant central nervous system tumors, glioblastoma (Glioblastoma) has the highest incidence rate, accounting for 46.1%. Globally, the incidence of glioblastoma or the number of new visits is about 2 to 3 per 100,000 people, the median age of onset is 65 years old, and the median survival period is 14.6 months. The overall treatment effect is not ideal . [0003] Clinically, glioblastoma ha...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/20G16B20/10G16B20/30G16B40/10
CPCG16B20/10G16B20/20G16B20/30G16B40/10
Inventor 吴增丁邓望龙肖念清任用
Owner SIMCERE DIAGNOSTICS CO LTD
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