NGS-based chromosome equilibrium translocation detection and analysis system and application

A balanced translocation and analysis system technology, applied in the field of chromosome balanced translocation detection and analysis system, can solve the problems of high false positive rate, excessive time consumption, complicated process, etc., and achieve wide application range, high analysis accuracy and simple steps Effect

Active Publication Date: 2020-06-12
GUANGZHOU KINGMED TRANSFORMATIVE MEDICINE INST CO LTD
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  • Application Information

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Problems solved by technology

However, in this method, the construction of the Chinese library needs to be customized, and the breakpoint cannot be accurately judged; in addition, a deeper sequencing depth is required, which increases the cost
(3) Screening based on the method of finding junction fragments or soft trimmed, soft clipped, but because there is no follow-up algorithm support, follow-up analysis needs to be done manually and cannot be processed in batches, which greatly increases the time
(4) The method based...

Method used

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  • NGS-based chromosome equilibrium translocation detection and analysis system and application
  • NGS-based chromosome equilibrium translocation detection and analysis system and application
  • NGS-based chromosome equilibrium translocation detection and analysis system and application

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0043] A method for detecting and analyzing chromosome balanced translocation based on NGS is carried out according to the following steps, and its technical route is as follows: figure 1 shown.

[0044] 1. Data acquisition.

[0045] Obtain the reads data obtained by NGS detection. In order to ensure that the fastq sequences used for comparison meet the quality requirements, use the fastq data quality control filtering software and fastp software to filter the fastq files obtained from the sequencing result data.

[0046] 2. Genome comparison.

[0047] figure 2 It is a schematic diagram of a balanced translocation of chromosomes; where: A indicates a paired chromosome, B indicates a translocation between chromosomes, and C indicates that there are three situations of reads obtained by sequencing after the translocation occurs.

[0048] (1) The paired reads can be completely aligned to the chromosome chr M or chr N of the human genome.

[0049] (2) One of the paired reads ...

Embodiment 2

[0282]An NGS-based balanced chromosome translocation detection and analysis system, including: a data acquisition module, a genome comparison module, a sliding cutting module, a short sequence comparison module, a breakpoint analysis module and a result output module.

[0283] The data acquisition module is used to acquire the reads data detected by NGS;

[0284] The genome comparison module is used to compare the above-mentioned reads with the human reference genome respectively, and obtain the first set of reads that cannot match the human reference genome;

[0285] The sliding cutting module is used to perform sliding cutting on the reads in the first reads set to obtain the subsequences of each reads, and use the arithmetic sequence to mark and number to obtain the second reads set composed of the above subsequences;

[0286] The short sequence alignment module is used to compare each subsequence in the above-mentioned second reads set with the human reference genome, and ...

Embodiment 3

[0291] Using the NGS-based balanced chromosome translocation detection and analysis system of Example 2, the sample data of two cases were analyzed, and after the reads data obtained by NGS detection were obtained, genome alignment, sliding cutting, and short sequence alignment were performed to obtain the following The two ends are respectively compared to the third reads set of different chromosomes of the human reference genome.

[0292] Table 1. The third reads set obtained from the analysis of two samples

[0293]

[0294] The above-mentioned reads were analyzed and calculated, and the result of balanced chromosome translocation was obtained as follows.

[0295] Table 2. Balanced Chromosomal Translocations

[0296]

[0297]

[0298] Note: In the above table of matching chromosome position results, the last 1 or -1 indicates the correlation analysis results, all of which are 1 or -1.

[0299] The above-mentioned samples were simultaneously tested for balanced ch...

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Abstract

The invention relates to an NGS-based chromosome equilibrium translocation detection and analysis system and application, and belongs to the technical field of gene detection biological information. The detection and analysis system comprises a data acquisition module, a genome comparison module, a sliding cutting module, a short sequence comparison module, a breakpoint analysis module and a result output module. Firstly, reads which cannot be simultaneously compared to a human reference genome at two ends are screened out and cut into continuous short sub-sequences by sliding; the sub-sequences are compared to the human reference genome again, so that the reads sequence originally comprising balanced translocation points can be compared with the human genome through short fragments aftercutting; and through clustering grouping of comparison positions and a correlation covariance weighting algorithm of corresponding sub-sequence numbers, reads of which the two ends are respectively compared with different chromosomes can be quickly screened out, and a balanced translocation breakpoint is accurately positioned, so that a sequence designed by a primer is provided for subsequent Sanger sequencing verification. The application range comprises NIPT, PGS, PGD, common NGS sequencing results and the like.

Description

technical field [0001] The invention relates to the technical field of gene detection biological information, in particular to an NGS-based balanced chromosome translocation detection and analysis system and its application. Background technique [0002] Chromosomal balanced translocation refers to the occurrence of a break in each of the two chromosomes and the exchange of their acentric segments, forming two new derivative chromosomes called reciprocal translocations. It involves reciprocal translocations between homologous and nonhomologous chromosomes. Although reciprocal translocations cause changes in the position of chromosomal fragments, but still retain the total number of genes, it is called balanced translocations. Balanced translocation carriers were detected approximately 10 times more frequently in recurrent abortion couples than in the general population. The miscarriage rate of pregnancy in patients with balanced chromosome translocation is very high, or th...

Claims

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Application Information

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IPC IPC(8): G16B30/00
CPCG16B30/00
Inventor 蒙裕欢陈美君严慧孟博于世辉
Owner GUANGZHOU KINGMED TRANSFORMATIVE MEDICINE INST CO LTD
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