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A method and device for detecting abnormal chromosome structure

A technology for chromosomes and chromosome fragments, applied in the fields of genomics and bioinformatics, can solve problems such as probe design limitations, and achieve the effect of improving effectiveness and reliability

Active Publication Date: 2016-09-14
BGI CLINICAL LAB (SHENZHEN) CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] Fluorescence in situ hybridization (FISH, fluorescence in situ hybridization) method: it can detect deletions, duplications and balanced translocations of smaller fragments, but it needs to pre-determine the detected chromosome fragments to prepare corresponding probes, so it is subject to probe design limits

Method used

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  • A method and device for detecting abnormal chromosome structure
  • A method and device for detecting abnormal chromosome structure
  • A method and device for detecting abnormal chromosome structure

Examples

Experimental program
Comparison scheme
Effect test

Embodiment approach

[0019] According to one embodiment of the present invention, a method for detecting abnormal chromosome structure is provided, comprising the following steps:

[0020] Step1. Obtain the whole genome sequencing results of the target individual.

[0021] The sequencing results include paired read length pairs (also called "reads") Reads, each pair of Reads consists of two read length sequences, which are located at both ends of the measured chromosome segment, and each pair of Reads comes from the positive strand of the corresponding chromosome segment and negative strands, or, each pair of Reads comes from both the positive and negative strands of the corresponding chromosome segment.

[0022] The measured chromosome fragments are usually obtained by fragmenting the chromosome samples from the target individual, and the corresponding library (library) is prepared according to the selected sequencing method. The optional sequencing method includes but is not li...

experiment example 1

[0084] This case is a family study of cat-calling syndrome. The two target individuals in this example belong to a family, where "FA" means father and "SON" means son.

[0085] 1. Perform genome-wide low-multiplier sequencing on the two target individuals, in which the sequencing depth of "FA" is 2.2, and the sequencing depth of "SON" is 3.1.

[0086] 2. Then use the SOAP comparison software to compare the sequencing results of the two target individuals with the reference sequence HG19, and obtain two files FA.sin and SON.sin.

[0087] 3. Perform clustering, filtering and analysis processing on the two files FA.sin and SON.sin, and obtain the result clusters and related parameters output as follows:

[0088] "FA":

[0089] The numbers of the two chromosomes where the paired result cluster is located: chr12, chr5

[0090] The position range of the two ends of the paired result cluster: 14779615-14780233, 23314785-23314205

[0091] Spans at both ends of the paired result cl...

experiment example 2

[0108] This example is a congenital heart disease study. The target individual in this example is a patient with congenital heart disease, denoted by "XX".

[0109] 1. Sequence the entire genome with a low multiplier for the target individual, and the sequencing depth is 2.7.

[0110] 2. Then use the SOAP alignment software to compare the sequencing results with the reference sequence HG19 to obtain XX.sin.

[0111] 3. Perform clustering, filtering and analysis processing on XX.sin to obtain the result clusters and related parameters output as follows:

[0112] "XX":

[0113] The numbers of the two chromosomes where the paired result cluster is located: chr14, chr14

[0114] The position ranges of the two ends of the paired result cluster are 73557040-73557288, 73670432-73670682

[0115] Estimated repeat length: 113392

[0116] Spans at both ends of the paired result cluster: 248, 250

[0117] Number of Reads supporting the pair of result clusters: 4

[0118] Compactnes...

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Abstract

A method and device for detecting abnormal chromosome structure, wherein the method includes: obtaining the whole genome sequencing result of a target individual, that is, multiple pairs of read length pairs located at both ends of the measured chromosome segment; comparing the sequencing result with a reference sequence to obtain An abnormal match set, which includes two read length sequences that match the read length pairs of different chromosomes of the reference sequence; cluster the read length sequences in the abnormal match set into clusters according to the matched positions; use, for example, correlation with compactness The preset requirements of the clustering method are to filter the clusters obtained by clustering to obtain the filtered result clusters, which are used to judge the occurrence of structural abnormalities of chromosome translocations.

Description

technical field [0001] The invention relates to the technical fields of genomics and bioinformatics, in particular to a method and device for detecting abnormal chromosome structure. Background technique [0002] The most common methods of chromosome testing are: [0003] Karyotype analysis: For example, G-band karyotype analysis, because the distribution of 400 to 600 BANDs is used to judge the abnormality of chromosome structure, so usually only abnormalities at the chromosome level can be detected, and in the best case, deletions and duplications of more than 5Mbp can be detected , it is powerless for the detection of smaller fragments (<5M). Moreover, this method requires the cultivation of living cells, and the cells must remain active. [0004] Fluorescence in situ hybridization (FISH, fluorescence in situ hybridization) method: it can detect deletions, duplications and balanced translocations of smaller fragments, but it needs to pre-determine the detected chromo...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/68G06F19/24G16B30/10G16B40/00
CPCG16B30/00C12Q1/6869G16B40/00G16B30/10C12Q2537/165
Inventor 杨传春
Owner BGI CLINICAL LAB (SHENZHEN) CO LTD
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