Computer device and computer readable storage medium for screening susceptible population for acute mountain sickness

Abstract

The present invention discloses a computer device and a computer-readable storage medium for screening a population susceptible to acute mountain sickness. The present invention provides a computer device, comprising a memory, a processor, and a computer program stored on the memory, characterized in that: the processor executes the computer program to implement the following steps: s1, data reception: receiving information on whether the subject's SNP rs10801528 site carries allele G, and obtaining sample data; s2, result output: outputting result information from the computer based on the sample data, the result information being whether the subject is an individual susceptible to acute mountain sickness. The computer device and computer-readable storage medium provided by the present invention can be used to avoid or reduce the occurrence of acute mountain sickness.

Description

Technical Field

[0001] The invention belongs to the field of medical care informatics and is a computer device and a computer-readable storage medium for screening a population susceptible to acute mountain sickness. Background Art

[0002] Acute mountain sickness (AMS) refers to a series of non-specific clinical manifestations that occur when people from the plains move rapidly to the plateau (generally above 3000m above sea level) or from the plateau to higher altitude areas, including headache, dizziness, palpitations, vomiting, diarrhea, lack of appetite, insomnia, etc. AMS usually occurs 4-12 hours after arriving at the destination and can last for about a week, which damages human health and seriously affects the implementation of emergency work. Further deterioration of AMS can develop into high-altitude cerebral edema, increasing the risk of death.

[0003] The pathological process of AMS is complex, and the pathogenesis is still unclear. Risk factors include blood pressure, lung function, endothelial function, psychological stress factors, etc. In recent years, more and more research results have shown that there is an individual genetic susceptibility to AMS. Genomic studies have found that multiple single nucleotide polymorphism sites are associated with the risk of AMS, suggesting that susceptibility gene polymorphism sites can be used as an important molecular marker for AMS, thereby providing more medical testing basis for disease prevention, diagnosis, disease severity assessment and treatment strategies. Summary of the invention

[0004] The technical problem to be solved by the present invention is how to screen individuals susceptible to acute mountain sickness or how to predict the susceptibility of subjects to acute mountain sickness.

[0005] The object of the present invention is to provide a computer device and a computer-readable storage medium for screening a population susceptible to acute mountain sickness.

[0006] The present invention provides a computer device, comprising a memory, a processor and a computer program stored in the memory, wherein the processor executes the computer program to implement the following steps:

[0007] s1. Data reception: receiving information on whether the subject's SNP rs10801528 site carries allele G, and obtaining sample data;

[0008] s2. Result output: Outputting result information from the computer based on the sample data, wherein the result information indicates whether the subject is susceptible to acute mountain sickness.

[0009] The logical judgment rule based on the sample data output from the computer is: if the subject carries allele G at the SNPrs10801528 site, the subject is an individual susceptible to acute mountain sickness; if the subject does not carry allele G at the SNPrs10801528 site, the subject is not susceptible to acute mountain sickness.

[0010] The present invention also provides a computer program product, including a computer program, characterized in that: when the computer program is executed by a processor, the above-mentioned steps s1 and s2 are implemented.

[0011] The present invention further provides a computer-readable storage medium on which a computer program is stored, wherein the computer program implements the above-mentioned steps s1 and s2 when executed by a processor.

[0012] The present invention also provides a device for screening individuals susceptible to acute mountain sickness, characterized in that the device comprises the following modules:

[0013] M1, data receiving module: used to receive information about whether the subject's SNP rs10801528 site carries allele G, and obtain sample data;

[0014] M2. Result output module: used to output result information from a computer based on the sample data, wherein the result information is whether the subject is susceptible to acute mountain sickness.

[0015] The logical judgment rule based on the sample data output from the computer is: if the subject carries allele G at the SNPrs10801528 site, the subject is an individual susceptible to acute mountain sickness; if the subject does not carry allele G at the SNPrs10801528 site, the subject is not susceptible to acute mountain sickness.

[0016] The present invention also provides a method for screening individuals susceptible to acute mountain sickness, characterized in that:

[0017] The method comprises the following steps:

[0018] Receive information about whether the subject's SNP rs10801528 site carries allele G, and obtain sample data;

[0019] Result information is output from the computer based on the sample data, wherein the result information indicates whether the subject is an individual susceptible to acute mountain sickness.

[0020] The logical judgment rule based on the sample data output from the computer is: if the subject carries allele G at the SNPrs10801528 site, the subject is an individual susceptible to acute mountain sickness; if the subject does not carry allele G at the SNPrs10801528 site, the subject is not susceptible to acute mountain sickness.

[0021] The present invention also provides a device, which is a device for comparing the susceptibility of subjects to acute mountain sickness, characterized in that the device comprises the following modules:

[0022] M3, data receiving module: used to receive information about whether the subject's SNP rs10801528 site carries allele G, and obtain sample data;

[0023] M4. Result output module: used to output result information from a computer based on the sample data, wherein the result information is that the susceptibility to acute mountain sickness of subjects carrying allele G at the SNP rs10801528 site is higher than the susceptibility to acute mountain sickness of subjects not carrying allele G at the SNP rs10801528 site.

[0024] The present invention also provides a method for comparing the susceptibility of subjects to acute mountain sickness, characterized in that:

[0025] The method comprises the following steps:

[0026] Receive information about whether the subject's SNP rs10801528 site carries allele G, and obtain sample data;

[0027] Result information is output from a computer based on the sample data, wherein the result information indicates that the susceptibility to acute mountain sickness of subjects carrying the G allele at the SNP rs10801528 site is higher than the susceptibility to acute mountain sickness of subjects not carrying the G allele at the SNP rs10801528 site.

[0028] Specifically, the subjects are two or more persons.

[0029] The present invention also provides the use of a primer set or a primer pair in the preparation of a product. The present invention also provides a product, which includes a primer set or a primer pair. The function of the product is to screen individuals susceptible to acute mountain sickness or to compare the susceptibility of subjects to acute mountain sickness. The primer set consists of three primers, which are the single-stranded DNA molecule shown in SEQ ID NO: 1, the single-stranded DNA molecule shown in SEQ ID NO: 2, and the single-stranded DNA molecule shown in SEQ ID NO: 3. The primer pair consists of two primers, which are the single-stranded DNA molecule shown in SEQ ID NO: 4 and the single-stranded DNA molecule shown in SEQ ID NO: 5. If the subject's SNP rs10801528 site carries allele G, the subject is an individual susceptible to acute mountain sickness; if the subject's SNP rs10801528 site does not carry allele G, the subject is not an individual susceptible to acute mountain sickness. The susceptibility to acute mountain sickness of the subject carrying the G allele at the SNP rs10801528 site is higher than the susceptibility to acute mountain sickness of the subject whose result information is that the SNP rs10801528 site does not carry the G allele.

[0030] Specifically, based on SNP rs10801528, the subject's genotype is GG or GA or AA.

[0031] SNP rs10801528 is located in human genomic DNA, and its position corresponds to the 301st nucleotide in SEQ ID NO: 6, and is represented by R. R represents G or A.

[0032] Any of the above subjects may be Chinese.

[0033] Any of the above-mentioned subjects may be Chinese Han people.

[0034] Any of the above-mentioned subjects may be Chinese Han males.

[0035] Any of the above subjects may be Chinese living in plain areas.

[0036] Any of the above-mentioned subjects may be Chinese Han people living in plain areas.

[0037] Any of the above-mentioned subjects may be Chinese Han males living in plain areas.

[0038] Any of the above subjects may be Chinese who have arrived in plateau areas from plain areas.

[0039] Any of the above-mentioned subjects may be Chinese Han people who move from plain areas to plateau areas.

[0040] Any of the above-mentioned subjects may be Chinese Han males who move from plain areas to plateau areas.

[0041] Any of the above subjects may be Chinese who plan to go to high-altitude areas from plain areas.

[0042] Any of the above-mentioned subjects may be Chinese Han people who are expected to move from a plain area to a plateau area.

[0043] Any of the above-mentioned subjects may be Chinese Han males who are expected to move from plain areas to plateau areas.

[0044] Any of the above-mentioned plateau areas may be the Qinghai-Tibet Plateau.

[0045] Any of the plateau areas mentioned above may be the Lhasa area of ​​the Qinghai-Tibet Plateau.

[0046] Any of the above-mentioned plateau areas may be the Ali region, Luhuo region, Ganzi region, Kangding region or Xinduqiao region of the Qinghai-Tibet Plateau.

[0047] The inventors of the present invention found that based on SNP rs10801528, subjects carrying allele G are susceptible to acute mountain sickness, and the risk of AMS in subjects carrying allele G is higher than that in subjects not carrying allele G. In Example 3 and Example 4, the present invention uses samples of different populations as examples to exemplarily show the genotype distribution frequency data in the acute mountain sickness patient group and the normal population. Based on the above findings, the inventors of the present invention developed the above-mentioned computer device and computer-readable storage medium.

[0048] The computer device and computer-readable storage medium provided by the present invention can be used to avoid or reduce the occurrence of acute mountain sickness. BRIEF DESCRIPTION OF THE DRAWINGS

[0049] Figure 1 A computer flow chart. DETAILED DESCRIPTION

[0050] The present invention is further described in detail below in conjunction with specific embodiments, and the examples provided are only for illustrating the present invention, rather than for limiting the scope of the present invention. The examples provided below can be used as a guide for further improvements by those of ordinary skill in the art, and do not constitute a limitation of the present invention in any way.

[0051] The experimental methods in the following examples, unless otherwise specified, are all conventional methods, and are performed according to the techniques or conditions described in the literature in the field or according to the product instructions. The materials, reagents, etc. used in the following examples, unless otherwise specified, can all be obtained from commercial channels.

[0052] p-value:Person test. lnBeta=OR, OR: odds ratio.

[0053] Ethics statement: Each subject signed an informed consent form, and this study was approved by the Medical Ethics Committee of the PLA General Hospital. The 2018 version of the Louis Lake Score was used to assess acute mountain sickness (AMS), and all patients with AMS had a score of ≥3.

[0054] Example 1: Screening for SNPs associated with the risk of acute mountain sickness

[0055] The matched groups consisted of patients with acute mountain sickness and corresponding normal people.

[0056] Multiple paired groups were established, and a large number of whole genome sequencing and sequence comparison analysis were performed to obtain a large number of differential SNPs. The allele frequency and genotype frequency of each differential SNP in the acute mountain sickness patient group and the corresponding normal population were verified in turn for association analysis.

[0057] SNP rs10801528, i.e., the SNP numbered rs10801528 in NCBI, is specifically located at position 196217620 of human chromosome 1 (GRCh38.p14), and the polymorphic form is G / A. In human genomic DNA, SNP rs10801528 and its surrounding nucleotides are shown in sequence 6 of the sequence listing (SNP rs10801528 is the 301st nucleotide in sequence 6 of the sequence listing, represented by R).

[0058] No clinical diagnostic use of SNP rs10801528 has been found in the prior art.

[0059] The inventors found through the aforementioned extensive work that SNP rs10801528 is correlated with the risk of acute mountain sickness, and subjects carrying the G allele have a higher risk of acute mountain sickness.

[0060] Example 2: Establishment of a method for detecting the genotype of a subject based on SNP rs10801528

[0061] 1. Take peripheral blood from the subjects and extract genomic DNA.

[0062] 2. Using the genomic DNA extracted in step 1 as a template, perform PCR amplification using specific primer pairs.

[0063] The specific primer pair consists of primer F1 and primer R1.

[0064] Primer F1 (SEQ ID NO: 1): 5'-ACGTTTGGATGGGTGGCTTTCATTCTGTGGT-3';

[0065] Primer R1 (SEQ ID NO: 2): 5'-ACGTTGGATGTGAGATTGCTACTGAAGTCGATG-3'.

[0066] PCR amplification was performed in a 384-well plate, with one reaction system in each well.

[0067] The composition of the PCR amplification reaction system (5 μL): 0.5 μL 10× PCR buffer (Agena Bioscience, catalog number 11327), 0.4 μL 25 mM MgCl2 solution, 0.1 μL 25 mM dNTP mix, genomic DNA, HotStart Taq DNA polymerase, primer F1, primer R1, and the volume is made up with ultrapure water. In the 5 μL system, the content of genomic DNA is 20-50 ng, the content of HotStart Taq DNA polymerase is 0.5 U, the content of primer F1 is 0.5 pmol, and the content of primer R1 is 0.5 pmol.

[0068] The reaction program of PCR amplification was as follows: 94°C for 4 minutes; 94°C for 20 seconds, 56°C for 30 seconds, 72°C for 1 minute, 45 cycles; 72°C for 3 minutes; and 4°C hold.

[0069] 3. Perform alkaline phosphatase treatment (to remove free dNTPs in the system).

[0070] Take the 384-well plate that has completed step 2, prepare the reaction system and then carry out the reaction.

[0071] The composition of the reaction system (7 μL): 5 μL of the product solution obtained in step 2, 0.3 μL of SAP, 0.17 μL of SAPbuffer, and 1.53 μL of ultrapure water. The SAP content in the reaction system was 0.073 U / μL.

[0072] SAP (shrimp alkaline phosphatase), SAP buffer, iPlex Enzyme (single base extension reaction enzyme), and iPlex Buffer Plus (single base extension reaction buffer) are all components of the kit. Commercial information of the kit: Agena Bioscience, catalog number 10165.

[0073] Reaction conditions: 37°C for 40 minutes; 85°C for 5 minutes; maintain at 4°C.

[0074] 4. Perform single base extension.

[0075] Take the 384-well plate that has completed step 3, prepare the reaction system, and then perform a single base extension reaction.

[0076] The composition of the single base extension reaction system (10 μL): 7 μL of the product solution obtained in step 3, 0.3 μL of the single base extension reaction enzyme, 0.17 μL of the single base extension reaction buffer, 1 μL of the single base extension primer, and 1.53 μL of ultrapure water. In the single base extension reaction system, the content of the single base extension primer is 5 μmol, and the content of the single base extension reaction enzyme is 0.142 U / μL.

[0077] Single base extension primer (SEQ ID NO: 3): 5'-GTGGTCTATTACCTTTTTTAAC-3'.

[0078] The reaction procedure for single base extension is as follows:

[0079] ①94℃ 30 seconds;

[0080] ②94℃ 5 seconds;

[0081] ③52℃ 5 seconds, 80℃ 5 seconds, 5 cycles;

[0082] ④94℃ 5 seconds, 52℃ 5 seconds, 80℃ 5 seconds, 40 cycles;

[0083] ⑤72℃ 3 minutes;

[0084] ⑥Maintain at 4℃.

[0085] 5. Perform resin purification.

[0086] Take the 384-well plate that has completed step 4, add 16 μl of water to each well, then add Clean Resin resin (Sequenom, USA) to each well, seal the film, rotate vertically at low speed for 30 minutes to allow the resin to fully contact with the reactants, then centrifuge to allow the resin to sink to the bottom of the well. The supernatant is the extension product after resin purification.

[0087] 6. Chip spotting.

[0088] The MassARRAY Nanodispenser RS1000 sample dispensing device (SEQUENOM) was started to transfer the extension product after resin purification to a 384-well SpectroCHIP (Sequenom) chip (SEQUENOM).

[0089] 7. Mass spectrometry detection.

[0090] The spotted SpectroCHIP chip was analyzed using MALDI-TOF, and the detection results were typed and output using TYPER 4.0 software (sequenom).

[0091] Example 3: Analysis of SNP rs10801528 and Susceptibility to Acute Mountain Sickness

[0092] Peripheral blood samples were obtained from Lhasa, Ali, Luhuo, Ganzi, Kangding and Xinduqiao from September 2020 to September 2023. 50 peripheral blood samples were obtained from 50 patients with acute mountain sickness, and another 231 peripheral blood samples were obtained from 231 normal people (non-acute mountain sickness patients). The 50 patients with acute mountain sickness and the 231 normal people were all unrelated Chinese Han males who had lived in the plains for a long time (long-term means more than 1 year) and had peripheral blood drawn after arriving in Lhasa, Ali, Luhuo, Ganzi, Kangding or Xinduqiao (above 2500m above sea level). All of them had no history of smoking and drinking, and no autoimmune-related diseases (such as vitiligo, psoriasis, type 1 diabetes, etc.), and no history of high altitude travel before.

[0093] The operation was performed according to the method of Example 2. The genotype of the subject based on SNP rs10801528 was detected.

[0094] Among the 50 patients with acute mountain sickness, 2 had the GG genotype, 6 had the GA genotype, and 42 had the AA genotype, that is, 8 carried the G allele (frequency was 16%), and 42 did not carry the G allele (frequency was 84%). Among the 231 normal people, 0 had the GG genotype, 27 had the GA genotype, and 204 had the AA genotype, that is, 27 carried the G allele (frequency was 11.69%), and 204 did not carry the G allele (frequency was 88.31%).

[0095] The experimental data were processed and analyzed using R 4.0.5 statistical software. After correction by generalized linear mixed model test, the significant P value of SNP rs10801528 and the population was 0.035, and Beta was 0.696. The results showed that SNP rs10801528 was a SNP associated with acute mountain sickness, and the risk of AMS in subjects carrying allele G was higher than that in subjects not carrying allele G.

[0096] Example 4: Analysis of SNP rs10801528 and Susceptibility to Acute Mountain Sickness

[0097] Peripheral blood samples were obtained from Lhasa, Ali, Luhuo, Ganzi, Kangding and Xinduqiao from September 2020 to September 2023. 43 peripheral blood samples were obtained from 43 patients with acute mountain sickness, and another 284 peripheral blood samples were obtained from 284 normal people (non-acute mountain sickness patients). The 43 patients with acute mountain sickness and the 284 normal people were all unrelated Chinese Han males who had lived in the plains for a long time (long-term means more than 1 year) and had peripheral blood drawn after arriving in Lhasa, Ali, Luhuo, Ganzi, Kangding or Xinduqiao (above 2500m above sea level). All of them had no history of smoking and drinking, and no autoimmune-related diseases (such as vitiligo, psoriasis, type 1 diabetes, etc.), and no history of plateau travel before.

[0098] 1. Take peripheral blood from the subjects and extract genomic DNA.

[0099] 2. Using the genomic DNA extracted in step 1 as a template, perform PCR amplification using specific primer pairs.

[0100] The specific primer pair consists of primer F2 and primer R2.

[0101] Primer F2 (SEQ ID NO: 4): 5′-GAGGGTCTCTCTCTTCCCTCA-3′;

[0102] Primer R2 (SEQ ID NO: 5): 5'-TTGACTTCCACTCTCTGATCTGT-3'.

[0103] 3. After completing step 2, the PCR amplification products were recovered and sequenced, and the genotype of the subject based on SNPrs10801528 was obtained according to the sequencing results.

[0104] Among the 43 patients with acute mountain sickness, there was 1 individual with genotype GG, 6 individuals with genotype GA, and 36 individuals with genotype AA, that is, 7 individuals carried the G allele (frequency was 16.28%), and 36 individuals did not carry the G allele (frequency was 83.72%). Among the 284 normal people, there were 2 individuals with genotype GG, 30 individuals with genotype GA, and 252 individuals with genotype AA, that is, 32 individuals carried the G allele (frequency was 11.27%), and 252 individuals did not carry the G allele (frequency was 88.73%).

[0105] The experimental data were processed and analyzed using R 4.0.5 statistical software. After correction by generalized linear mixed model test, the significant P value of SNP rs10801528 and the population was <0.05 (p=0.000081), and Beta was 1.043. Consistent with the results of Example 3, the risk of AMS in subjects carrying allele G was higher than that in subjects not carrying allele G.

[0106] The results of this example further illustrate that SNP rs10801528 is a risk site associated with acute mountain sickness, and can be used to screen individuals susceptible to acute mountain sickness, predict human susceptibility to acute mountain sickness, screen individuals carrying human acute mountain sickness susceptibility genes, and evaluate the risk of acute mountain sickness.

[0107] The present invention has been described in detail above. It will be apparent to those skilled in the art that the present invention may be implemented in a wide range under equivalent parameters, concentrations and conditions without departing from the spirit and scope of the present invention and without the need for unnecessary experimentation. Although the present invention provides specific embodiments, it should be understood that further improvements may be made to the present invention. In short, according to the principles of the present invention, this application intends to include any changes, uses or improvements to the present invention, including changes made by conventional techniques known in the art that depart from the scope disclosed in this application. Applications of some of the basic features may be made within the scope of the following appended claims.

Claims

1. A device for comparing the susceptibility of subjects to acute mountain sickness, characterized in that: The device comprises the following modules: M3, data receiving module: used to receive information about whether the subject's SNP rs10801528 site carries allele G, and obtain sample data; the subject is more than two people; M4. Result output module: used to output result information from a computer based on the sample data, wherein the result information is that the susceptibility to acute mountain sickness of subjects carrying allele G at the SNP rs10801528 site is higher than the susceptibility to acute mountain sickness of subjects not carrying allele G at the SNP rs10801528 site.

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