CN114317726A - Gene marker for detecting amyotrophic lateral sclerosis, detection method and application - Google Patents
Gene marker for detecting amyotrophic lateral sclerosis, detection method and application Download PDFInfo
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Abstract
The invention discloses a gene marker for detecting amyotrophic lateral sclerosis, a detection method and application, and belongs to the technical field of high-throughput sequencing. The detection method comprises the following steps: extracting the genome DNA of a detection object, and sequentially carrying out fragmentation, purification and Pre-PCR amplification reaction on the genome DNA to obtain a target region DNA library; capturing and enriching a target gene coding region of a target region DNA library and DNA adjacent to a shearing region through a chip to obtain a target region library; and performing gene detection on the target region library by using a high-throughput sequencing platform, comparing the obtained sequencing data with a reference sequence of the genomic DNA, finding out existing gene mutation, and performing data analysis to obtain gene mutation information related to the pathogenic effect of the amyotrophic lateral sclerosis. The invention has the advantages of high sensitivity, strong pertinence, comprehensive coverage, large flux, high accuracy and the like, and has huge application space in the aspects of clinical diagnosis and drug development.
Description
Technical Field
The invention belongs to the technical field of high-throughput sequencing, and particularly relates to a gene marker for detecting amyotrophic lateral sclerosis, a detection method and application.
Background
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease, mainly involving pyramidal tract, brain stem and spinal cord anterior horn cells, clinically manifested by progressive aggravation of muscular atrophy, weakness and spasm, cognitive impairment and the like, partially overlaps with clinical manifestations of frontotemporal dementia, and is the most common type of motor neuron disease.
ALS occurs between the ages of 50-60 years with an incidence of 2/100000 and is characterized by selective upper and lower motor neuron death, resulting in progressive muscle atrophy, weakness and stiffness. The median survival of ALS from morbidity to mortality is 39 months, with most patients dying due to respiratory failure typically occurring in 3-5 years. About 5-10% of familial ALS is usually autosomal dominant; 90-95% of ALS cases belong to sporadic ALS (Nat Rev Neurosci 2001; 2: 806-819; Annu Rev Neurosci 2004; 27: 723-749). About 20% of the familial ALS is caused by mutations in the Cu/Zn superoxide dismutase (SOD1) gene. Because sporadic and familial ALS appear similar clinically, elucidation of the underlying mechanisms of familial ALS has facilitated the study of both forms of ALS.
In addition, studies have found that the RNA metabolism protein TDP-43 gene mutation exists in the autosome of familial ALS, and the TDP-43 protein pathological change also exists in most sporadic ALS patients, which suggests that TDP-43 may have great significance in understanding sporadic and familial ALS (Proc Natl Acad Sci U S A2007; 104: 12524-. The pathogenesis of ALS is complex, with current biological hypotheses including oxidative damage, intracellular aggregate accumulation, mitochondrial dysfunction, loss of axonal transport, growth factor deficiency, glial cell pathology, and glutamate excitotoxicity (Ann neurol.2009jan65suppl 1: S3-9).
Because the etiology and pathogenesis of ALS are not clear, an effective radical treatment means is lacked in the current clinical treatment, a special method/medicine is not available for reversing and stopping the progress of the disease, the early symptomatic treatment is mainly carried out, and the existing treatment only can improve symptoms and cannot organize or reverse the progress of the disease. Therefore, the search for gene markers related to amyotrophic lateral sclerosis, especially early warning monitoring and early diagnosis markers, improves the diagnosis rate of early amyotrophic lateral sclerosis, realizes early diagnosis and intervention, and obviously reduces the harm of ALS, thereby relieving the burden of society and families.
Disclosure of Invention
Aiming at the problems in the detection and diagnosis of amyotrophic lateral sclerosis in the prior art, the invention provides a gene marker for detecting amyotrophic lateral sclerosis, a detection method and application thereof, which are used for simultaneously detecting multiple mutations of the causative genes of the amyotrophic lateral sclerosis in one sample through high-throughput sequencing detection and have the advantages of high sensitivity, strong pertinence, comprehensive coverage, large flux, high accuracy and the like.
In order to achieve the purpose, the invention adopts the technical scheme that:
the invention provides a gene marker for detecting amyotrophic lateral sclerosis, which comprises one or more than two of the following genes: SOD1, ALS2, SQSTM1, SETX, FUS, SPG11, VAPB, ANG, TARDBP, FIG4, OPTN, VCP, UBQLN2, SIGMAR1, CHMP2B, PFN1, ERBB4, HNRNPA1, DCTN1, PRPH, NEFH, SPAST, NIPA1, PNPLA6, SMN1, CHRNA4, DAO, HFE, APOE, DIAPH3, DPP6, MAPT, PARK7, BCL6, EWSR1, TAF15, OGG1, CRYM, GRN, ITPR2, VEGFA, PON1, ALAD, PNPLA6, TFA 3, TRPHASP 3652A 2, SOX 36CAP 2, SRRNPA 362B 36XA, HNPR 2, SHYP 2, SHFORCN 2, SHFO 2, PHB 2, PHTHPAP 2, PHTHCP 2, TFAS 2, TFSC 2, TFAS 2, TFSC 2, TFAS 2, TFAS 2, TFSC 2, TFAS 2, TFS 2, TFSC 2, TFAS 2, 363636363636363636363672, 2, 363672, 36363636363672, 36363672, 2, 363636363636363672, 36363636363636363672, 3636363672, 363636363672, 36363672, 2, 363636363636363636363636363636363672, 36363672, 2, 363636363636363672, 2, 363672, 2, 363636363672, 2, 3636363672, 2, 363636363672, 2, 363672, 2, 3636363672, 2, 3636363672, 2, 36363672, 2, 3636363636363672, 2, 363672, 2, 3636363672, 2, 36363636363636363672, 36363636363636363636363672, 363636363636363636363636363672, 2, 3636363672, 2, 363672, 363636363672, 36363636363672, 2, 36363672, 2, 36363636363636363636363672, 2, 363672, 2, 3636363636363636363672, 363636363672, 36363672, 2, 36363672, 2, 36.
Preferably, the genetic marker comprises CDH 13.
The invention also provides application of the gene marker for detecting amyotrophic lateral sclerosis in preparation of a medicine or a detection reagent for diagnosing amyotrophic lateral sclerosis.
Preferably, the detection reagent is in the form of a kit.
The invention also provides a method for detecting the gene mutation related to the pathogenesis of amyotrophic lateral sclerosis, which comprises the following steps:
s1, extracting the genome DNA of the detection object;
s2, sequentially fragmenting, purifying and performing Pre-PCR amplification reaction on the genome DNA to obtain a target region DNA library;
s3, capturing and enriching the target gene coding region of the target region DNA library and the DNA adjacent to the shearing region through the chip to obtain a target region library;
s4, carrying out gene detection on the target region library by using a high-throughput sequencing platform to obtain sequencing data;
s5, comparing the obtained sequencing data with the reference sequence of the genome DNA, finding out existing gene mutation, and carrying out data analysis to obtain gene mutation information related to the pathogenic effect of amyotrophic lateral sclerosis;
the genomic DNA is selected from the group consisting of: SOD1, ALS2, SQSTM1, SETX, FUS, SPG11, VAPB, ANG, TARDBP, FIG4, OPTN, VCP, UBQLN2, SIGMAR1, CHMP2B, PFN1, ERBB4, HNRNPA1, DCTN1, PRPH, NEFH, SPAST, NIPA1, PNPLA6, SMN1, CHRNA4, DAO, HFE, APOE, DIAPH3, DPP6, MAPT, PARK7, BCL6, EWSR1, TAF15, OGG1, CRYM, GRN, ITPR2, VEGFA, PON1, ALAD, PNPLA6, TFA 3, TRPHASP 3652A 2, SOX 36CAP 2, SRRNPA 362B 36XA, HNPR 2, SHYP 2, SHFORCN 2, SHFO 2, PHB 2, PHTHPAP 2, PHTHCP 2, TFAS 2, TFSC 2, TFAS 2, TFSC 2, TFAS 2, TFAS 2, TFSC 2, TFAS 2, TFS 2, TFSC 2, TFAS 2, 363636363636363636363672, 2, 363672, 36363636363672, 36363672, 2, 363636363636363672, 36363636363636363672, 3636363672, 363636363672, 36363672, 2, 363636363636363636363636363636363672, 36363672, 2, 363636363636363672, 2, 363672, 2, 363636363672, 2, 3636363672, 2, 363636363672, 2, 363672, 2, 3636363672, 2, 3636363672, 2, 36363672, 2, 3636363636363672, 2, 363672, 2, 3636363672, 2, 36363636363636363672, 36363636363636363636363672, 363636363636363636363636363672, 2, 3636363672, 2, 363672, 363636363672, 36363636363672, 2, 36363672, 2, 36363636363636363636363672, 2, 363672, 2, 3636363636363636363672, 363636363672, 36363672, 2, 36363672, 2, 36.
Preferably, the genomic DNA is derived from human blood, saliva or isolated tissue.
Preferably, the gene mutation is a point mutation or a deletion insertion mutation within 20 bp.
Preferably, the genetic mutation is located in CDH 13.
Preferably, the detection of the gene mutation related to the pathogenesis of amyotrophic lateral sclerosis is performed in the form of a kit.
Compared with the prior art, the invention has the following beneficial effects: the invention takes the genome DNA of blood, saliva or other isolated tissue sources of a detected person as a detection material, firstly breaks the genome DNA and prepares a library, then captures and enriches the DNA of a target gene coding region and a near shearing region through a chip, carries out gene exon coding region sequencing by using a high-throughput sequencing platform, and finally compares the sequencing with a reference sequence to discover possible gene mutation.
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FIG. 1 is a comparison of the reference sequence (A) and the sequencing result (B) of the CDH13 gene in example 1.
Detailed Description
The technical scheme of the present invention will be further described by the following specific examples. It should be understood that the following specific examples are illustrative only and are not limiting upon the present invention. The described embodiments are only a part of the embodiments of the present invention, and not all embodiments, and all other embodiments obtained without any inventive work by those skilled in the art are within the scope of the present invention.
The following examples of genetic markers for detecting amyotrophic lateral sclerosis include combinations of one or more of the following genes: SOD1, ALS2, SQSTM1, SETX, FUS, SPG11, VAPB, ANG, TARDBP, FIG4, OPTN, VCP, UBQLN2, SIGMAR1, CHMP2B, PFN1, ERBB4, HNRNPA1, DCTN1, PRPH, NEFH, SPAST, NIPA1, PNPLA6, SMN1, CHRNA4, DAO, HFE, APOE, DIAPH3, DPP6, MAPT, PARK7, BCL6, EWSR1, TAF15, OGG1, CRYM, GRN, ITPR2, VEGFA, PON1, ALAD, PNPLA6, TFA 3, TRPHASP 3652A 2, SOX 36CAP 2, SRRNPA 362B 36XA, HNPR 2, SHYP 2, SHFORCN 2, SHFO 2, PHB 2, PHTHPAP 2, PHTHCP 2, TFAS 2, TFSC 2, TFAS 2, TFSC 2, TFAS 2, TFAS 2, TFSC 2, TFAS 2, TFS 2, TFSC 2, TFAS 2, 363636363636363636363672, 2, 363672, 36363636363672, 36363672, 2, 363636363636363672, 36363636363636363672, 3636363672, 363636363672, 36363672, 2, 363636363636363636363636363636363672, 36363672, 2, 363636363636363672, 2, 363672, 2, 363636363672, 2, 3636363672, 2, 363636363672, 2, 363672, 2, 3636363672, 2, 3636363672, 2, 36363672, 2, 3636363636363672, 2, 363672, 2, 3636363672, 2, 36363636363636363672, 36363636363636363636363672, 363636363636363636363636363672, 2, 3636363672, 2, 363672, 363636363672, 36363636363672, 2, 36363672, 2, 36363636363636363636363672, 2, 363672, 2, 3636363636363636363672, 363636363672, 36363672, 2, 36363672, 2, 36.
In some embodiments, the genetic marker comprises CDH13, the gene encoding a member of the cadherin superfamily, the encoded protein located on the surface of the cell membrane and anchored by the GPI moiety, but not by the transmembrane domain, the protein acting as a negative regulator of axon growth during neural differentiation, and the diseases associated with CDH13 including acantho-sustained wave epilepsy in slow wave sleep and Landau-Kleffner syndrome.
The gene markers for detecting amyotrophic lateral sclerosis in the following examples can be used for preparing a medicament or a detection reagent for diagnosing amyotrophic lateral sclerosis, and for example, the detection reagent can be in the form of a kit.
In the following examples, a method (e.g., in the form of a kit) for detecting mutations in genes associated with the pathogenesis of amyotrophic lateral sclerosis is used, and the main technical procedures include genomic DNA extraction, library preparation, library quality inspection and quantification, on-machine sequencing, and data comparison and analysis, and include the following steps:
s1, extracting the genome DNA of the detection object, wherein the genome DNA comprises the following genes: SOD1, ALS2, SQSTM1, SETX, FUS, SPG11, VAPB, ANG, TARDBP, FIG4, OPTN, VCP, UBQLN2, SIGMAR1, CHMP2B, PFN1, ERBB4, HNRNPA1, DCTN1, PRPH, NEFH, SPAST, NIPA1, PNPLA6, SMN1, CHRNA4, DAO, HFE, APOE, DIAPH3, DPP6, MAPT, PARK7, BCL6, EWSR1, TAF15, OGG1, CRYM, GRN, ITPR2, VEGFA, PON1, ALAD, PNPLA6, 3652A 3, 3652A 2, SOX 36CAP, 362B 2, HNRNPA 36XA, HNPR 2, EPGFASP 2, HSP 2, TFSACK 2, TFS 2, TFAS 2, TFSC 2, TFS 2, TFSC 2, TFS 2, TFSC 2, TFS 2, TFSC 2, TFS 2, TFS 2, TFS 2, TFS 2, TFS 2, TFS 2, TFP 2, TFP 2, TFS 2, TFP 2, TFS 2, TFS 2, TFAS 2, TFP 2, TFS 2, TFP 2, TFS 2, TFP 2, TFS 2, TFP 2, TFS 2, 36363672, 2, 363672, 2, 36363672, 2, TFP 2;
s2, sequentially fragmenting, purifying and performing Pre-PCR amplification reaction on the genome DNA to obtain a target region DNA library;
s3, capturing and enriching the target gene coding region of the target region DNA library and the DNA adjacent to the shearing region through the chip to obtain a target region library;
s4, carrying out gene detection on the target region library by using a high-throughput sequencing platform to obtain sequencing data;
and S5, comparing the obtained sequencing data with a reference sequence of the genome DNA, finding out existing gene mutation, and analyzing the data to obtain the gene mutation information related to the pathogenic effect of the amyotrophic lateral sclerosis.
In some embodiments, the genomic DNA may be derived from human blood, saliva, or ex vivo tissue.
In some embodiments, the gene mutation is a point mutation or a deletion insertion mutation within 20 bp.
In some embodiments, the genetic mutation is in CDH 13.
In some embodiments, the detection of mutations in genes associated with the pathogenesis of amyotrophic lateral sclerosis may be performed using a kit.
The technical solution of the present invention is explained below by specific examples.
Example 1
Proband plum, male, age 63, submitting to hospital: shanghai university of traffic medical school affiliated Ruikin Hospital.
Sample type: whole blood.
The clinical manifestations are as follows: the limbs are weak and the movement is inconvenient for many years.
Detecting items: mutations in genes involved in the pathogenesis of amyotrophic lateral sclerosis.
Detection numbering: ALS-2021091802.
Detection area: exon regions of about 106 genes in human genomic DNA.
And (3) detection strategy: and analyzing the specific pathogenic relation genes recorded in the OMIM database.
The detection method comprises the following steps: NGS chips capture high throughput sequencing.
And (3) detection results: 1 single gene mutation or variation significantly associated with the clinical phenotype was detected in the proband described above, as shown in table 1 and fig. 1.
TABLE 1
FIG. 1 is a comparison of the reference sequence (FIG. 1A) and the sequencing results (FIG. 1B) of the CDH13 gene in example 1. The detection method of NGS sequencing is used for sequencing all exons of a sample of a detected person, and bioinformatics analysis is carried out by combining clinical phenotypes of the detected person, so that the c.C502G base heterozygous change exists on the No. 5 exon of the CDH13 gene in the sample of the detected person, and the 168 codon coded by the gene is changed from tyrosine to cysteine. Bioinformatics Software (SIFT) predicted its pathogenicity (PP3), and this gene was found to be associated with alterations in the amyotrophic lateral sclerosis frontal cortical cadherin binding protein, a site for which no pathogenicity was reported. The CDH13 gene (MIM:601364) is associated with amyotrophic lateral sclerosis, high adiponectin levels, epilepsy with continuous spiny slow waves in slow wave sleep, and Landau-Kleffner syndrome, and it can be seen from the combination of FIG. 1 that CDH13 is associated with ALS pathogenesis.
In summary, the invention uses genomic DNA from blood, saliva or other tissues of a subject as a detection material, firstly breaks the DNA and prepares a library, then captures and enriches the DNA of a target gene coding region and a near-cutting region through a chip, and finally performs mutation detection by using a high-throughput sequencing platform to find out possible gene mutation.
It should be noted that the present invention is suitable for point mutation and deletion insertion mutation (minor mutation) within 20bp, and is not suitable for detecting special types of mutations such as heterozygous gene large-fragment copy number variation, dynamic mutation, complex recombination, etc., and is also not suitable for detecting genomic structure variation (such as large-fragment deletion, replication and inversion rearrangement), large-fragment heterozygous insertion mutation (such as Alu-mediated insertion), and mutations located in gene regulatory regions and deep intronic regions. In addition, due to the fact that part of genes have high-repetition low-complexity regions or pseudogenes, detection cannot completely cover all exon regions of the genes, but the overall coverage can reach more than 95%, the method has the advantages of being high in sensitivity, strong in pertinence, complete in coverage, large in flux, high in accuracy and the like, is beneficial to finding and verifying target genes and key sites related to amyotrophic lateral sclerosis, is used for delaying or even preventing ALS, and has a huge application space in the aspects of clinical diagnosis and drug development.
The above description is only for the purpose of illustrating the preferred embodiments of the present invention and is not to be construed as limiting the invention, and any modifications, equivalents, improvements and the like that fall within the spirit and principle of the present invention are intended to be included therein.
Claims (9)
1. A genetic marker for detecting amyotrophic lateral sclerosis, comprising a combination of one or more of the following genes: SOD1, ALS2, SQSTM1, SETX, FUS, SPG11, VAPB, ANG, TARDBP, FIG4, OPTN, VCP, UBQLN2, SIGMAR1, CHMP2B, PFN1, ERBB4, HNRNPA1, DCTN1, PRPH, NEFH, SPAST, NIPA1, PNPLA6, SMN1, CHRNA4, DAO, HFE, APOE, DIAPH3, DPP6, MAPT, PARK7, BCL6, EWSR1, TAF15, OGG1, CRYM, GRN, ITPR2, VEGFA, PON1, ALAD, PNPLA6, TFA 3, TRPHASP 3652A 2, SOX 36CAP 2, SRRNPA 362B 36XA, HNPR 2, SHYP 2, SHFORCN 2, SHFO 2, PHB 2, PHTHPAP 2, PHTHCP 2, TFAS 2, TFSC 2, TFAS 2, TFSC 2, TFAS 2, TFAS 2, TFSC 2, TFAS 2, TFS 2, TFSC 2, TFAS 2, 363636363636363636363672, 2, 363672, 36363636363672, 36363672, 2, 363636363636363672, 36363636363636363672, 3636363672, 363636363672, 36363672, 2, 363636363636363636363636363636363672, 36363672, 2, 363636363636363672, 2, 363672, 2, 363636363672, 2, 3636363672, 2, 363636363672, 2, 363672, 2, 3636363672, 2, 3636363672, 2, 36363672, 2, 3636363636363672, 2, 363672, 2, 3636363672, 2, 36363636363636363672, 36363636363636363636363672, 363636363636363636363636363672, 2, 3636363672, 2, 363672, 363636363672, 36363636363672, 2, 36363672, 2, 36363636363636363636363672, 2, 363672, 2, 3636363636363636363672, 363636363672, 36363672, 2, 36363672, 2, 36.
2. A genetic marker for detecting amyotrophic lateral sclerosis according to claim 1, wherein said genetic marker comprises CDH 13.
3. Use of the gene marker for detecting amyotrophic lateral sclerosis according to claim 1 or 2 in the preparation of a medicament or a detection reagent for diagnosing amyotrophic lateral sclerosis.
4. The use of claim 3, wherein the detection reagent is in the form of a kit.
5. A method for detecting a gene mutation associated with the pathogenesis of amyotrophic lateral sclerosis, comprising the steps of:
s1, extracting the genome DNA of the detection object;
s2, sequentially fragmenting, purifying and performing Pre-PCR amplification reaction on the genome DNA to obtain a target region DNA library;
s3, capturing and enriching the target gene coding region of the target region DNA library and the DNA adjacent to the shearing region through the chip to obtain a target region library;
s4, carrying out gene detection on the target region library by using a high-throughput sequencing platform to obtain sequencing data;
s5, comparing the obtained sequencing data with the reference sequence of the genome DNA, finding out existing gene mutation, and carrying out data analysis to obtain gene mutation information related to the pathogenic effect of amyotrophic lateral sclerosis;
the genomic DNA is selected from the group consisting of: SOD1, ALS2, SQSTM1, SETX, FUS, SPG11, VAPB, ANG, TARDBP, FIG4, OPTN, VCP, UBQLN2, SIGMAR1, CHMP2B, PFN1, ERBB4, HNRNPA1, DCTN1, PRPH, NEFH, SPAST, NIPA1, PNPLA6, SMN1, CHRNA4, DAO, HFE, APOE, DIAPH3, DPP6, MAPT, PARK7, BCL6, EWSR1, TAF15, OGG1, CRYM, GRN, ITPR2, VEGFA, PON1, ALAD, PNPLA6, TFA 3, TRPHASP 3652A 2, SOX 36CAP 2, SRRNPA 362B 36XA, HNPR 2, SHYP 2, SHFORCN 2, SHFO 2, PHB 2, PHTHPAP 2, PHTHCP 2, TFAS 2, TFSC 2, TFAS 2, TFSC 2, TFAS 2, TFAS 2, TFSC 2, TFAS 2, TFS 2, TFSC 2, TFAS 2, 363636363636363636363672, 2, 363672, 36363636363672, 36363672, 2, 363636363636363672, 36363636363636363672, 3636363672, 363636363672, 36363672, 2, 363636363636363636363636363636363672, 36363672, 2, 363636363636363672, 2, 363672, 2, 363636363672, 2, 3636363672, 2, 363636363672, 2, 363672, 2, 3636363672, 2, 3636363672, 2, 36363672, 2, 3636363636363672, 2, 363672, 2, 3636363672, 2, 36363636363636363672, 36363636363636363636363672, 363636363636363636363636363672, 2, 3636363672, 2, 363672, 363636363672, 36363636363672, 2, 36363672, 2, 36363636363636363636363672, 2, 363672, 2, 3636363636363636363672, 363636363672, 36363672, 2, 36363672, 2, 36.
6. The method of claim 5, wherein the genomic DNA is derived from human blood, saliva or isolated tissue.
7. The method of claim 5, wherein the genetic mutation is a point mutation or a deletion insertion mutation within 20 bp.
8. The method of claim 7, wherein the genetic mutation is located in CDH 13.
9. The method for detecting the gene mutation related to the pathogenesis of amyotrophic lateral sclerosis according to claim 5, wherein the detection of the gene mutation related to the pathogenesis of amyotrophic lateral sclerosis is performed in the form of a kit.
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| CN114703278A (en) * | 2022-04-29 | 2022-07-05 | 中南大学湘雅医院 | Amyotrophic lateral sclerosis pathogenic gene, detection kit and primer group |
| CN117603982A (en) * | 2024-01-22 | 2024-02-27 | 中国医学科学院北京协和医院 | P.P374TfsTer18 mutant pathogenic gene of SQSTM1 for amyotrophic lateral sclerosis and application thereof |
| CN117603982B (en) * | 2024-01-22 | 2024-04-19 | 中国医学科学院北京协和医院 | P.P374TfsTer18 mutant pathogenic gene of SQSTM1 for amyotrophic lateral sclerosis and application thereof |
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