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Method and system for detecting SMN1 gene mutation by means of high-throughput sequencing

A sequencing and gene technology, applied in the fields of genomics, biochemical equipment and methods, computer-aided medical procedures, etc., can solve the problem of inappropriate SMA molecular diagnosis, and achieve the effect of high detection rate and accuracy

Active Publication Date: 2020-06-16
北京智因东方诊断科技有限公司
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Due to the high homology of SMN1 and SMN2 genes, it is difficult to distinguish the two by conventional data analysis methods of WES, so it is considered not suitable for the molecular diagnosis of SMA

Method used

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  • Method and system for detecting SMN1 gene mutation by means of high-throughput sequencing
  • Method and system for detecting SMN1 gene mutation by means of high-throughput sequencing
  • Method and system for detecting SMN1 gene mutation by means of high-throughput sequencing

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0074] Example 1. Detection of SMN1 Homozygous Deletion in Subjects Clinically Diagnosed as SMA

[0075] This example involves using the detection system of the present invention to detect homozygous deletion of SMN1 in subjects clinically diagnosed as SMA.

[0076] Subject selection

[0077] The subjects in this example were patients who visited the hospital from June 2015 to July 2018, and peripheral whole blood biological samples were obtained from these patients during the visit. The enrolled cases all had the characteristic phenotype of neuromuscular disease, and the physicians who submitted for examination provided a description of the clinical characteristics and various special examination results corresponding to each patient (the private information such as the patient's name has been hidden). For the use of sample test results for clinical research and data publication, written informed consent has been obtained from patients or guardians and family members par...

Embodiment 2

[0090] Example 2. Differential diagnosis for subjects with non-SMN1 homozygous deletion

[0091] Adopt the general method of whole exome to detect genetic disease to analyze whether subjects (especially 118 subjects identified as non-SMN1 homozygous deletion in embodiment 1) have other neuromuscular diseases similar to SMA phenotype, for a differential diagnosis.

[0092] The concrete steps of described general method comprise:

[0093] 1) Raw data yield statistics: Remove adapter contamination, filter out reads with an average quality value lower than 20, and filter out bases with a quality value lower than 20 from the end of the reads.

[0094] 2) Alignment: The comparison statistics between the data and the reference sequence (comparison software BWA), the reference genome adopts the hg19 genome.

[0095] 3) Mutation detection: Use GATK to compare the results for alignment rearrangement and quality correction, and then use GATK's HaplotypeCaller algorithm to call mutati...

Embodiment 3

[0104] Example 3. Detection of SMN1 Homozygous Deletion in Subjects Clinically Suspected of SMA

[0105] As of August 2018, among all the subjects who had the clinical features of neuromuscular disease but were not suspected of SMA in the initial diagnosis, for the subjects whose genetic pathogenic factors could not be ruled out, as in Example 1, the inventors The detection means of the present invention described above detected 56 subjects carrying SMN1 homozygous deletion mutations (see Table 2).

[0106] Table 2

[0107]

[0108] *ns: not significant

[0109] Based on the results obtained in Examples 1 to 3, it can be seen that the method of the present invention can provide the following comprehensive diagnostic information for subjects with different conditions.

[0110] 1) Differential diagnosis was carried out on 240 patients who were preliminarily judged as SMA:

[0111] A. 122 confirmed cases of SMA (122 / 240, 50.8%): Among all 240 patients who were preliminarily...

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Abstract

The invention relates to a device, a method and a system for detecting SMN1 gene mutation by analyzing a high-throughput sequencing result, in particular the homozygous deletion of a seventh exon of an SMN1 gene. The invention also relates to the use of the device, method and system according to the invention to diagnose spinal muscular atrophy (SMA) or differentially diagnose SMA and other diseases that are susceptible to confusion with the SMA phenotype, as well as to a machine-readable medium and a terminal device on which the method according to the invention is stored.

Description

technical field [0001] The invention belongs to the field of gene detection and analysis. Specifically, the present invention relates to a device, method and system for detecting SMN1 gene mutations, especially for detecting homozygous deletion of exon 7 of SMN1 gene, through high-throughput sequencing and special analysis methods. The present invention also relates to the diagnosis of spinal muscular atrophy (SMA) or the differential diagnosis of SMA and other diseases confounded with the SMA phenotype using the device, method and system of the present invention, and a machine on which the method of the present invention is stored Readable Media and Devices. Background technique [0002] Spinal muscular atrophy (SMA; OMIM #253300) is a neuromuscular disorder resulting from the loss of motor neurons in the brainstem and anterior horns of the spinal cord. 1 (SMN1) gene due to homozygous deletion. In the Chinese population, the probability of carrying SMA-related SMN1 heter...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/50G16B20/20G16B20/10G16B30/10G16H50/20C12Q1/6869C12Q1/6883
CPCC12Q1/6869C12Q1/6883C12Q2600/156G16H50/20G16B20/10G16B20/20G16B20/50G16B30/10C12Q2535/122
Inventor 谷为岳
Owner 北京智因东方诊断科技有限公司
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