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A system for the detection of polyploidy and homozygous regions of the genome for Roh based on cnv-seq sequencing data

A detection system and sequencing data technology, applied in the field of prenatal diagnosis cytogenetics detection, can solve the problems of inability to judge SNP sites, inability to judge polyploidy, etc., and achieve the effect of reducing costs

Active Publication Date: 2021-12-14
CAPITALBIO GENOMICS
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Problems solved by technology

Because in the genome-wide high-throughput sequencing data at very low sequencing depth (such as CNV-seq data), the depth of most SNP sites is 1X, and the sequencing depth of a few SNP sites is 2X or 3X (such as figure 1 shown), in this case, it is impossible to make a judgment on the true genotype of each SNP site
Therefore, the CNV-seq method has been limited to the detection of copy number abnormalities. The industry believes that the accuracy and resolution of the CNV-seq method in detecting copy number abnormalities is superior to that of chromosome microarray CMA technology, but it cannot judge polyploidy and ROH

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  • A system for the detection of polyploidy and homozygous regions of the genome for Roh based on cnv-seq sequencing data
  • A system for the detection of polyploidy and homozygous regions of the genome for Roh based on cnv-seq sequencing data
  • A system for the detection of polyploidy and homozygous regions of the genome for Roh based on cnv-seq sequencing data

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[0084] For the convenience of understanding, the allele corresponding to the MAF value is called "A" allele, and the crowd frequency of "A" allele is p; the other allele is called "B" allele, and the crowd frequency of "B" allele is q, q = 1-p. If the comparison results show that both "A" allele and "B" allele exist at a certain SNP site, it is judged as a heterozygous site, otherwise it becomes a homozygous site. It should be noted that the heterozygous site judged at the extremely low sequencing depth in this paper refers to a judgment of whether the site is heterozygous at the current sequencing depth, rather than the genotype in the real situation, because extremely The AB heterozygous type in the real state at low sequencing depth has a high probability of being detected as a homozygous state. In this paper, (1,1) is used to represent the situation where both alleles are detected.

[0085] Theoretical basis of the present invention:

[0086] In the genome-wide high-thro...

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Abstract

The invention discloses a system for detecting ROH in polyploid and homozygous regions of the genome based on CNV-seq sequencing data. The inventors found that the types and proportions of genotypes corresponding to different types of samples or genomic regions are different. Under the extremely low average sequencing depth, although the genotype of each SNP site is unknown, the same sequencing depth The probability of heterozygosity signal P(1,1) observed under different types of samples / genomic regions is different. By merging and calculating N SNP heterozygosity information and calculating the SNP mixed heterozygosity index to determine the ploidy information of the sample and whether there is a homozygous region ROH in the genome. It breaks the limitation that the existing low average sequencing depth data cannot be used to judge ROH and polyploidy, and greatly reduces the cost of ROH and polyploid detection.

Description

technical field [0001] The present invention relates to prenatal diagnosis cytogenetic detection technology, especially the detection system and modeling method of fetal polyploidy and genome homozygous region (ROH, region of homozygosity) based on low sequencing depth whole genome sequencing data. Background technique [0002] Chromosomal abnormalities are important clinical factors leading to spontaneous abortion, multiple fetal malformations and birth defects. Common types of chromosomal abnormality detection include: balanced chromosome translocation (chromosomal copy number unchanged but inversion, translocation, ring formation, etc.), chromosome copy number variation (CNV for short), aneuploidy (triploid , tetraploid, etc.), genome homozygous region (absence of heterozygosity; ROH for short), etc. Approximately 20% of detectable pregnancies end in miscarriage, with chromosomal abnormalities being the most common cause of first-trimester miscarriage. Chromosomal abnor...

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/20G16B20/30G16B30/10
CPCG16B20/20G16B20/30G16B30/10
Inventor 黄铨飞彭春方饶兴蔷陈样宜
Owner CAPITALBIO GENOMICS