A data analysis method, system and storage medium for red-green color vision abnormality

Abstract

The present invention provides a data analysis method, system and storable medium for red-green color vision abnormality, and relates to the field of intelligent medical care. The method comprises: obtaining a reference genome, sequencing data of gene OPN1LW (L) and gene OPN1MW (M) of a subject; obtaining a genome of a single copy of gene L and a single copy of gene M based on the reference genome; aligning the sequencing data to the genome of a single copy of gene L and a single copy of gene M, calculating the copy number of exon 5 of gene L and gene M, and obtaining an estimated copy number of gene L and an estimated copy number of gene M; when the estimated copy number of gene L is equal to 0 or the estimated copy number of gene M is equal to 0, it indicates that the subject is a positive patient. The method provided by the present invention can be used as an auxiliary screening method to provide a reliable genetic basis for the early diagnosis and individualized treatment of red-green color vision abnormality, and has important scientific research significance and clinical value.

Description

Technical Field

[0001] The present invention belongs to the field of intelligent medical treatment, and more specifically, relates to a data analysis method, system, device, computer-readable storage medium and application thereof for red-green color vision abnormality. Background Art

[0002] Color vision disorders are divided into color blindness and color weakness according to the degree. The color discrimination ability of color-weak people varies greatly between individuals. Some color-weak people have color discrimination abilities close to those with normal color vision, while some color-weak people are close to color blindness. The most common color blindness is red-green color blindness. The tests commonly used in clinical practice currently have certain limitations. The tests commonly used in clinical practice currently include the following: 1. Pseudoisochromatic diagram, also known as color blindness book. This method is suitable for large-scale screening and can efficiently screen out people with abnormal color vision, but it cannot distinguish between color blindness and color weakness, the degree of color weakness, and abnormal red or green vision; 2. Hue arrangement method; this method can only screen out color blindness or severe color weakness. 3. Color blindness mirror. The color blindness mirror is currently recognized as the most accurate instrument for detecting and classifying abnormal color vision, but it is expensive, inconvenient to carry, and requires professional technicians to operate. It takes an average of about 30 minutes for one examinee, which is not suitable for large-scale clinical examinations.

[0003] Next-generation sequencing (NGS) is a technology that can sequence hundreds of thousands to millions of nucleic acid molecules at a time. NGS technology has the advantages of high sensitivity and low cost, but the highly homologous sequences (true and false genes) in the genome have a high mismatch rate during the sequence alignment stage. This is because the size of NGS fragments is usually 300-500bp. Each molecule obtained by sequencing is read, and then the best alignment is found on the reference genome. If the similarity between two genes is very high, misalignment is prone to occur.

[0004] Human red-green color vision is associated with the OPN1LW and OPN1MW genes, which are highly homologous (up to more than 96%) and are arranged in tandem on the X chromosome. The OPN1LW and OPN1MW genes can be considered a pair of true and false genes, and a pseudogene refers to a non-functional fragment homologous to the DNA of a functional gene. However, both genes encode protein products, and there is no other difference in the protein products except for the difference in spectral sensitivity peaks. The copy number of the OPN1LW and OPN1NW genes is variable in the general population. 90% of men carry one copy of the OPN1LW gene, and some carry more than two copies; most men carry one or two copies of OPN1MW. At present, conventional bioinformatics processing procedures cannot analyze the copy number of OPN1LW and OPN1MW, and cannot further determine whether the subject is a positive patient for red-green color vision disorder and the possible typing and severity level of potential positive patients based on high-throughput sequencing data. Summary of the invention

[0005] In response to the problem that OPN1LW and OPN1MW are highly homologous and conventional bioinformatics analysis methods cannot calculate the copy numbers of OPN1LW and OPN1MW, the present application provides a data analysis method, system, device, computer-readable storage medium and application thereof for red-green color vision abnormalities.

[0006] The present application discloses a data analysis method for red-green color vision abnormalities, the reliability of which is verified by using about 850 cases in the internal database of Spectrum Gene. The method comprises:

[0007] S1: Acquire the sequencing data of the reference genome, the gene OPN1LW and the gene OPN1MW of the subject, wherein the gene OPN1LW is abbreviated as Gene_L, and the gene OPN1MW is abbreviated as Gene_M;

[0008] S2: Based on the reference genome, a genome with a single copy of Gene_L and a single copy of Gene_M is obtained;

[0009] S3: aligning the sequencing data to the genome of the single copy of Gene_L and the single copy of Gene_M, calculating the copy numbers of exon 5 of Gene_L and Gene_M, and obtaining the estimated copy number of Gene_L and the estimated copy number of Gene_M;

[0010] S4: When the estimated copy number of Gene_L is equal to 0 or the estimated copy number of Gene_M is equal to 0, it indicates that the subject is a positive patient.

[0011] Further, the analysis step of S2 includes:

[0012] S2.1: Align Gene_L and Gene_M with the reference genome to obtain aligned_Gene_L and aligned_Gene_M;

[0013] S2.2: Divide aligned_Gene_L into first_Gene_L and redundant_Gene_L according to their order of arrangement on the reference genome; divide aligned_Gene_M into first_Gene_M and redundant_Gene_M according to their order of arrangement on the reference genome;

[0014] The first_Gene_L refers to the aligned_Gene_L that appears for the first time on the reference genome, the first_Gene_M refers to the aligned_Gene_M that appears for the first time on the genome, the redundant_Gene_L refers to the aligned_Gene_L other than the first_Gene_L on the reference genome, and the redundant_Gene_M refers to the aligned_Gene_M other than the first_Gene_M on the reference genome;

[0015] S2.3: Replace the base sequences of redundant_Gene_L and redundant_Gene_M on the reference genome with N to obtain a genome with a single copy of Gene_L and a single copy of Gene_M.

[0016] Furthermore, the method further comprises:

[0017] S5: Obtain the sequencing data of Gene_L and Gene_M of the subject;

[0018] S6: obtaining the base sequences of Gene_L and Gene_M of the subject based on the sequencing data of Gene_L and Gene_M of the subject;

[0019] S7: Based on the base sequences of Gene_L and Gene_M of the subject, determine whether the subject has a hotspot mutation, wherein the hotspot mutation refers to when c.-112A>C occurs in the subject, and the subject is a green-blind or green-weak patient.

[0020] Furthermore, the method further comprises:

[0021] S8: Based on the base sequences of Gene_L and Gene_M of the positive patient, the mutation information of the light-sensitive site is obtained, and the light-sensitive site includes any one or more of the following: p.S116T, p.S180A, p.I230T;

[0022] S9: obtaining a spectral shift based on the mutation information of the light sensitivity site;

[0023] S10: Obtaining a color blindness severity grading result for a positive patient based on the spectral shift.

[0024] Furthermore, the positive patients include red-eye blind patients and green-eye blind patients, and the grading standards for the color blindness severity grading results of red-eye blind patients and green-eye blind patients include:

[0025] For patients with red-eye blindness: when the spectrum shifts 20nm, it is severe red-eye blindness; when the spectrum shifts 17nm, it is moderate red-eye blindness; when the spectrum shifts less than 14nm, it is mild red-eye blindness;

[0026] For patients with green-color blindness: when the spectrum shifts 17.5-20nm, it is severe green-color blindness; when the spectrum shifts 16-16.5nm, it is moderate green-color blindness; when the spectrum shifts less than or equal to 14nm, it is mild green-color blindness.

[0027] Furthermore, the method further comprises:

[0028] S11: obtaining the expression level of the internal reference gene of the subject, and correcting the error caused by any one or more of the following factors during data processing based on the expression level of the internal reference gene: sequencing platform, probe, batch, DNA quality and sequencing depth;

[0029] The internal reference genes include any one or more of the following: PLP1, GAPDH, ACTB, HPRT1, RPL13A, TBP, PGK1, GUSB, PPIA and EIF2B1.

[0030] Furthermore, the method further comprises:

[0031] S12: obtaining DNA from the positive patient, and detecting the copy number of exon 5 of Gene_L and Gene_M by a molecular quantitative analysis method to obtain the measured copy number of Gene_L and the measured copy number of Gene_M; the molecular quantitative analysis method includes any one of the following: qPCR, dPCR, third-generation sequencing, long fragment-PCR, mass spectrometry, proteomics quantitative method and nuclear magnetic resonance;

[0032] S13: If the estimated copy number of Gene_L is equal to the measured copy number of Gene_L and the estimated copy number of Gene_M is equal to the measured copy number of Gene_M, then the methodology is reliable; if the estimated copy number of Gene_L is not equal to the measured copy number of Gene_L or the estimated copy number of Gene_M is not equal to the measured copy number of Gene_M, then another one or several molecular quantitative analysis methods are used for verification.

[0033] A data analysis system for red-green color vision abnormality, the system comprising:

[0034] An acquisition unit: used to acquire the sequencing data of the reference genome, the gene OPN1LW and the gene OPN1MW of the subject, wherein the gene OPN1LW is abbreviated as Gene_L, and the gene OPN1MW is abbreviated as Gene_M;

[0035] Single copy genome analysis unit: obtaining a single copy of Gene_L and a single copy of Gene_M based on the reference genome;

[0036] A copy number calculation unit is used to align the sequencing data to the genome of the single copy of Gene_L and the single copy of Gene_M, calculate the copy number of exon 5 of Gene_L and Gene_M, and obtain the estimated copy number of Gene_L and the estimated copy number of Gene_M;

[0037] Red-green color vision judgment unit: When the estimated copy number of Gene_L is equal to 0 or the estimated copy number of Gene_M is equal to 0, it indicates that the subject is a positive patient.

[0038] A data analysis device for red-green color vision abnormality, the device comprising: a memory and a processor;

[0039] The memory is used to store program instructions;

[0040] The processor is used to call program instructions, and when the program instructions are executed, it is used to execute the above-mentioned data analysis method for red-green color vision abnormality.

[0041] A computer-readable storage medium stores a computer program, which, when executed by a processor, implements the above-mentioned data analysis method for red-green color vision abnormality.

[0042] Any of the following applications:

[0043] The use of the system in newborn screening;

[0044] Application of the system in diagnosis of ophthalmic genetic diseases; the ophthalmic genetic diseases include any one or more of the following: retinitis pigmentosa, Leber optic atrophy, cone cell dystrophy, Stargard disease, age-related macular degeneration, diabetic retinitis pigmentosa and juvenile hereditary macular degeneration;

[0045] The use of the device in neonatal screening;

[0046] The device is used in the diagnosis of ophthalmic genetic diseases; the ophthalmic genetic diseases include any one or more of the following: retinitis pigmentosa, Leber optic atrophy, cone cell dystrophy, Stargard disease, age-related macular degeneration, diabetic retinitis pigmentosa and juvenile hereditary macular degeneration.

[0047] Advantages of the present invention:

[0048] 1. The method disclosed in the present application efficiently obtains the estimated copy number of the gene OPN1LW and the estimated copy number of the gene OPN1MW of the subject based on the genome and sequencing data of the single copy of the gene OPN1LW and the gene OPN1MW, thereby quickly screening out positive patients.

[0049] 2. The method disclosed in the present application separates the genes OPN1LW and OPN1MW aligned on the reference genome into first_Gene_L and redundant_Gene_L, and first_Gene_M and redundant_Gene_M in order of arrangement, and further sets the base sequences of redundant_Gene_L and redundant_Gene_M to N to obtain a single-copy genome, thereby solving the problem of being unable to analyze the copy numbers of genes OPN1LW and OPN1MW in conventional bioinformatics processing procedures and the problem of incorrect alignment due to the high similarity between the two genes, and improving the accuracy of estimated copy numbers.

[0050] 3. The method disclosed in the present application obtains sequencing data of the subject's genes OPN1LW and OPN1MW, and further analyzes whether the subject has a hotspot mutation, thereby helping researchers determine whether the subject is a green-blind or green-weak patient.

[0051] 4. The method disclosed in the present application obtains the displacement of the maximum wavelength of the absorption spectrum based on the mutation information of the light sensitivity site, thereby grading the severity of red- and green-blind patients into severe, moderate and mild, thereby achieving differentiation of the severity of color blindness.

[0052] 5. The method disclosed in the present application achieves calibration of the sequencing database between different subjects and genders by obtaining the expression level of the subject's internal reference gene, and can determine data anomalies caused by inconsistent other conditions in data processing, thereby improving the reliability of the analysis results.

[0053] 6. The method disclosed in the present application uses digital PCR to detect the measured copy numbers of genes OPN1LW and OPN1MW, and compares them with the corresponding estimated copy numbers to determine whether the positive patients are true positive patients, thereby proving the credibility of the analysis results of the method.

[0054] 7. The method disclosed in this application can be applied to the fields of newborn screening based on high-throughput sequencing data, analysis of the causes of color vision abnormalities in ophthalmic diseases, etc. Analysis of the genes OPN1LW and OPN1MW is added to newborn screening to identify whether the newborn has red-green color vision abnormalities, helping children with color vision abnormalities to receive adaptive treatment measures as early as possible to avoid being at a disadvantage in school teaching, entrance examinations, and career development; adding red-green color vision abnormality analysis to ophthalmic genetic high-throughput data analysis helps doctors better diagnose ophthalmic diseases, such as early-onset high myopia, achromatopsia, fundus diseases, etc., and provides guidance for formulating corresponding treatment plans.

[0055] 8. The method disclosed in this application is applicable to multiple genome versions and is applicable to the two commonly used reference genome versions, such as the hg19 / GRCh37 and hg38 / GRCh38 genomes. It can be widely used in different research and clinical practices, and covers redundant genes to provide more comprehensive information. BRIEF DESCRIPTION OF THE DRAWINGS

[0056] In order to more clearly illustrate the technical solutions in the embodiments of the present invention, the drawings required for use in the description of the embodiments will be briefly introduced below. Obviously, the drawings described below are only some embodiments of the present invention. For those skilled in the art, other drawings can be obtained based on these drawings without creative work.

[0057] Figure 1 A schematic diagram of a flow chart of a data analysis method for red-green color vision abnormality provided by an embodiment of the present invention;

[0058] Figure 2 is a schematic diagram of a data analysis system for red-green color vision abnormality provided by an embodiment of the present invention;

[0059] Figure 3 A schematic diagram of a data analysis device for red-green color vision abnormality provided by an embodiment of the present invention;

[0060] Figure 4 It is a schematic diagram of a data analysis system for red-green color vision abnormality provided by another embodiment of the present invention. DETAILED DESCRIPTION

[0061] In order to enable those skilled in the art to better understand the solutions of the present invention, the technical solutions in the embodiments of the present invention will be clearly and completely described below in conjunction with the accompanying drawings in the embodiments of the present invention.

[0062] In some of the processes described in the specification and claims of the present invention and the above-mentioned figures, multiple operations that appear in a specific order are included, but it should be clearly understood that these operations may not be executed in the order in which they appear in this article or executed in parallel. The sequence numbers of the operations, such as S101, S102, etc., are only used to distinguish between different operations, and the sequence numbers themselves do not represent any execution order. In addition, these processes may include more or fewer operations, and these operations may be executed in sequence or in parallel. It should be noted that the descriptions of "first", "second", etc. in this article are used to distinguish different messages, devices, modules, etc., do not represent the order of precedence, and do not limit the "first" and "second" to be different types.

[0063] The following will be combined with the drawings in the embodiments of the present invention to clearly and completely describe the technical solutions in the embodiments of the present invention. Obviously, the described embodiments are only part of the embodiments of the present invention, not all of the embodiments. Based on the embodiments of the present invention, all other embodiments obtained by those skilled in the art without creative work are within the scope of protection of the present invention.

[0064] Figure 1 A data analysis method for red-green color vision abnormality provided by an embodiment of the present invention comprises:

[0065] S1: Acquire the sequencing data of the reference genome, the gene OPN1LW and the gene OPN1MW of the subject, wherein the gene OPN1LW is abbreviated as Gene_L, and the gene OPN1MW is abbreviated as Gene_M;

[0066] In one embodiment, the reference genome includes but is not limited to any one or more of the following:

[0067] GRCh37 (UCSC version number hg19) released by the Genome Reference Consorium (GRC) in February 2009; GRCh38 (UCSC version number hg38) released by GRC in November 2013; hg16 released by NCBI in July 2003, hg17 in May 2004, and hg18 in March 2006; reference genomes including OPN1LW and OPN1MW assembled by other laboratories, research institutions or hospitals.

[0068] In one embodiment, the subjects include 150 males and 203 females from a college student cohort. The college student cohort samples are samples of color blindness that may exist in the questionnaire survey, and are not natural cohorts. Oral swabs were collected from all samples for whole exome sequencing. The subjects also include 830 males from Wenzhou Vocational and Technical School. Oral swabs were collected from all samples for whole exome sequencing.

[0069] S2: Based on the reference genome, a genome with a single copy of Gene_L and a single copy of Gene_M is obtained;

[0070] The analysis steps of S2 include:

[0071] S2.1: Align Gene_L and Gene_M with the reference genome to obtain aligned_Gene_L and aligned_Gene_M;

[0072] S2.2: Divide aligned_Gene_L into first_Gene_L and redundant_Gene_L according to their order of arrangement on the reference genome; divide aligned_Gene_M into first_Gene_M and redundant_Gene_M according to their order of arrangement on the reference genome;

[0073] The first_Gene_L refers to the aligned_Gene_L that appears for the first time on the reference genome, the first_Gene_M refers to the aligned_Gene_M that appears for the first time on the genome, the redundant_Gene_L refers to the aligned_Gene_L other than the first_Gene_L on the reference genome, and the redundant_Gene_M refers to the aligned_Gene_M other than the first_Gene_M on the reference genome;

[0074] S2.3: Replace the base sequences of redundant_Gene_L and redundant_Gene_M on the reference genome with N to obtain a genome with a single copy of Gene_L and a single copy of Gene_M.

[0075] In one embodiment, the reference genome (hg19) OPN1MW2 gene is covered: OPN1LW is 1 copy on the hg19 / GRCh37 reference genome; OPN1MW is 2 copies (OPN1MW and OPN1MW3) on the hg19 (GRCh37) reference genome. Therefore, the sequenced data is randomly aligned to OPN1MW or OPN1MW3 when aligned with the hg19 (GRCh37) reference genome. Therefore, genes with multiple copies on the reference genome are covered with N instead of the reference genome base. When the hg38 / GRCh38 genome is used, the redundant genes are also covered.

[0076] S3: aligning the sequencing data to the genome of the single copy of Gene_L and the single copy of Gene_M, calculating the copy numbers of exon 5 of Gene_L and Gene_M, and obtaining the estimated copy number of Gene_L and the estimated copy number of Gene_M;

[0077] In one embodiment, only exon 5 of OPN1LW and OPN1MW genes is analyzed: the functional difference between OPN1LW and OPN1MW genes is exon 5, and exon 5 can usually be stably aligned to the reference genome.

[0078] S4: When the estimated copy number of Gene_L is equal to 0 or the estimated copy number of Gene_M is equal to 0, it indicates that the subject is a positive patient;

[0079] S5: Obtain the sequencing data of Gene_L and Gene_M of the subject;

[0080] S6: obtaining the base sequences of Gene_L and Gene_M of the subject based on the sequencing data of Gene_L and Gene_M of the subject;

[0081] S7: Based on the base sequences of Gene_L and Gene_M of the subject, determine whether the subject has a hotspot mutation, wherein the hotspot mutation refers to when c.-112A>C occurs in the subject, and the subject is a green-blind or green-weak patient.

[0082] c.-112A>C means that in transcript NM_020061.6, the base at position -112 mutated from A to C;

[0083] S8: Based on the base sequences of Gene_L and Gene_M of the positive patient, the mutation information of the light-sensitive site is obtained, and the light-sensitive site includes any one or more of the following: p.S116T, p.S180A, p.I230T;

[0084] p.S116T means that the 116th amino acid of the encoded protein is replaced by threonine (Thr, T) from serine (Ser, S); p.S180A means that the 180th amino acid of the encoded protein is replaced by alanine (Ala, A); p.I230T means that the 230th amino acid of the encoded protein is replaced by isoleucine (Ile, I) from threonine (Thr, T).

[0085] Red-green color vision abnormalities include red-green color blindness, which is completely indistinguishable, and red-green color weakness, which is partially indistinguishable. In this patent application, red color blindness refers to red color blindness and red color weakness, and green color blindness refers to green color blindness and green color weakness.

[0086] Red-brown: Also known as primary color blindness, red-brown patients cannot distinguish between red, purple, blue, purple-red, and dark green. They see green as yellow, purple as blue, and green and blue as white. Green-brown: Also known as secondary color blindness, green-brown patients see green as gray. They cannot distinguish between light green and dark red, purple-red and gray, and purple and cyan-blue.

[0087] In one embodiment, the severity of color blindness is calculated based on the light sensitive site analysis as shown in Table 1:

[0088] Table 1 Color blindness severity grading results

[0089]

[0090] S9: obtaining a spectral shift based on the mutation information of the light sensitivity site; the spectral shift refers to a shift of the maximum wavelength of the absorption spectrum;

[0091] S10: Obtaining a color blindness severity grading result for a positive patient based on the spectral shift.

[0092] The positive patients include red-eye blind patients and green-eye blind patients, and the grading standards for the color blindness severity grading results of red-eye blind patients and green-eye blind patients include:

[0093] For patients with red-eye blindness: when the spectrum shifts by 20nm, it is severe red-eye blindness; when the spectrum shifts by 17nm, it is moderate red-eye blindness; when the spectrum shifts by 14nm or less, it is mild red-eye blindness;

[0094] For patients with green-color blindness: when the spectrum shifts 17.5-20nm, it is severe green-color blindness; when the spectrum shifts 16-16.5nm, it is moderate green-color blindness; when the spectrum shifts less than or equal to 14nm, it is mild green-color blindness.

[0095] In one embodiment, the color blindness severity grading standards are shown in Table 2 and Table 3:

[0096] Table 2 Red-color blindness grading standards

[0097]

[0098] Table 3 Green blindness grading standards

[0099]

[0100] In one embodiment, the copy number statistics of OPN1LW and OPN1MW genes are shown in Table 4:

[0101] Table 4 OPN1LW and OPN1MW gene copy number statistics

[0102]

[0103] Note: The range of values ​​is after the mean in brackets.

[0104] There are slight differences in the distribution between the Chinese population and the foreign population, indicating that the OPN1LW and OPN1MW genes in the Chinese population may be more suitable for screening (the number of copies is less than that in foreign countries, and the proportion of complex genetic conditions is low).

[0105] In one embodiment, the method further comprises:

[0106] S1: Acquire the sequencing data of the reference genome, the gene OPN1LW and the gene OPN1MW of the subject, wherein the gene OPN1LW is abbreviated as Gene_L, and the gene OPN1MW is abbreviated as Gene_M;

[0107] S2: Based on the reference genome, a genome with a single copy of Gene_L and a single copy of Gene_M is obtained;

[0108] S3: aligning the sequencing data to the genome of the single copy of Gene_L and the single copy of Gene_M, calculating the copy numbers of exon 5 of Gene_L and Gene_M, and obtaining the estimated copy number of Gene_L and the estimated copy number of Gene_M;

[0109] S4: When the estimated copy number of Gene_L is equal to 0 or the estimated copy number of Gene_M is equal to 0, it indicates that the subject is a positive patient;

[0110] S11: obtaining the expression level of the internal reference gene of the subject, and correcting the error caused by any one or more of the following factors during data processing based on the expression level of the internal reference gene: sequencing platform, probe, batch, DNA quality and sequencing depth;

[0111] The internal reference genes include any one or more of the following: PLP1, GAPDH, ACTB, HPRT1, RPL13A, TBP, PGK1, GUSB, PPIA and EIF2B1.

[0112] In one embodiment, the internal reference genes and male and female quality control data are shown in Tables 5 and 6:

[0113] Table 5 PLP1, the internal reference gene of the college student cohort

[0114]

[0115] Table 6 Reference gene PLP1 of the cohort of XXXX College

[0116]

[0117] Among them, 3 samples had abnormal internal references. After data verification, X chromosomes were duplicated and the karyotype may be 47,XXY.

[0118] PLP1 (Proteolipidprotein 1): The genomic location is Xq22.2, encoding myelin protein, which is one of the main components of myelin in the central nervous system. Its function is to promote the formation and maintenance of myelin sheaths in neuronal axons; GAPDH (Glyceraldehyde-3-phosphate dehydrogenase): The genomic location is 12p13, encoding uronic acid-3-phosphate dehydrogenase in the glycolysis pathway. GAPDH plays an important role in energy metabolism and participates in the decomposition of sugars in the glycolysis process to generate energy; ACTB (Beta-actin): The genomic location is 7p22.1, encoding β-actin protein, which is one of the most important components in the cytoskeleton system, participates in the maintenance of cell morphology and movement, and plays an important role in intracellular transport and the assembly of functional cytoskeleton; HPRT1 (Hypoxanthine phosphoribosyltransferase 1): The genomic location is 19q13.2, encoding ribosomal protein L13a, which is one of the proteins that build ribosomes and participates in the translation of protein synthesis with other ribosomal proteins; RPL13A (Ribosomal protein L13a): The genomic location is 19q13.2, encoding ribosomal protein L13a, which is one of the proteins that build ribosomes and participates in the translation of protein synthesis with other ribosomal proteins; TBP (TATA-box binding protein): The genomic location is 6q27, encoding TATA box binding protein, which is an important component of the transcription initiation complex, binds to DNA, and provides an essential gene for the transcription initiation mechanism; PGK1 (Phosphoglycerate kinase 1): The genomic location is Xq13.3, encoding phosphoglycerate kinase 1, which is involved in the phosphate transfer reaction in the glycolysis pathway to produce triglyceride; GUSB (Beta-glucuronidase): The genomic location is 7q11.21, encoding β-glucuronidase, which is involved in the degradation and metabolism of glucuronic acid esters; PPIA (Peptidylprolylisomerase A): The genomic location is 7p13, encoding collagen type A isomerase, which is involved in protein folding and regulation; EIF2B1 (Eukaryotic translation initiation factor 2B subunit 1): The genomic location is 12q24.31, encoding subunit 1 of eukaryotic translation initiation factor 2B, which is involved in the initial step of protein synthesis and regulates the rate and accuracy of translation.

[0119] In one embodiment, the method includes executing S1-S4, S11-S13, as described below:

[0120] S1: Acquire the sequencing data of the reference genome, the gene OPN1LW and the gene OPN1MW of the subject, wherein the gene OPN1LW is abbreviated as Gene_L, and the gene OPN1MW is abbreviated as Gene_M;

[0121] S2: Based on the reference genome, a genome with a single copy of Gene_L and a single copy of Gene_M is obtained;

[0122] S3: aligning the sequencing data to the genome of the single copy of Gene_L and the single copy of Gene_M, calculating the copy numbers of exon 5 of Gene_L and Gene_M, and obtaining the estimated copy number of Gene_L and the estimated copy number of Gene_M;

[0123] S4: When the estimated copy number of Gene_L is equal to 0 or the estimated copy number of Gene_M is equal to 0, it indicates that the subject is a positive patient;

[0124] S12: obtaining DNA from the positive patient, and detecting the copy number of exon 5 of Gene_L and Gene_M by a molecular quantitative analysis method to obtain the measured copy number of Gene_L and the measured copy number of Gene_M; the molecular quantitative analysis method includes any one of the following: qPCR, dPCR, third-generation sequencing, long fragment-PCR, mass spectrometry, proteomics quantitative method and nuclear magnetic resonance;

[0125] In one embodiment, the positive sample qPCR verification results are shown in Table 7:

[0126] Table 7 qPCR verification results of positive samples

[0127]

[0128] Note: The above samples are from a college student cohort, and the qPCR results are consistent with the bioinformatics analysis results, indicating that the suggested copy number deletion is true and reliable.

[0129] qPCR: Real-time quantitative polymerase chain reaction, a technique widely used for quantification of DNA and RNA molecules, which quantitatively analyzes the amount of initial template by measuring the intensity of the fluorescent signal generated during different PCR amplification cycles;

[0130] dPCR: Digital polymerase chain reaction, similar to qPCR, is also a technology used for quantification of DNA and RNA molecules. dPCR divides the sample into thousands to millions of small reaction vessels, each of which contains one or no molecule. The number of initial templates is inferred through statistical analysis of positive and negative reaction vessels.

[0131] Third-generation sequencing: SMRT (Single-Molecule Real Time Sequencing) sequencing technology represented by the Pacbio platform has the characteristics of high throughput and long read length.

[0132] Long fragment-PCR: Long PCR (long PCR) refers to PCR that can amplify DNA fragments with a length of more than 5kb. Conventional PCR can only amplify DNA fragments of hundreds to thousands of bases, which is not enough in many molecular genetic studies, such as gene map analysis, so the PCR method of long fragment DNA came into being.

[0133] Mass spectrometry: Mass-based analysis to quantify molecules in a sample. Different types of mass spectrometry include gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), etc.

[0134] Commonly used quantitative methods in proteomics research include: isotope labeling quantification (such as protein labeling and metabolic labeling quantification), labeling-independent quantification (such as SILAC and immunoprecipitation-mass spectrometry), parallel reaction monitoring quantification (PRM), etc.

[0135] Nuclear magnetic resonance (NMR) can be used to quantitatively analyze compounds in solution by analyzing the resonance signals of different nuclear spins in the sample to determine the concentration of specific molecules.

[0136] S13: If the estimated copy number of Gene_L is equal to the measured copy number of Gene_L and the estimated copy number of Gene_M is equal to the measured copy number of Gene_M, then the methodology is reliable; if the estimated copy number of Gene_L is not equal to the measured copy number of Gene_L or the estimated copy number of Gene_M is not equal to the measured copy number of Gene_M, then another one or several molecular quantitative analysis methods are used for verification.

[0137] In one embodiment, the method includes executing S1-S7, S11-S13, as described below:

[0138] S1: Acquire the sequencing data of the reference genome, the gene OPN1LW and the gene OPN1MW of the subject, wherein the gene OPN1LW is abbreviated as Gene_L, and the gene OPN1MW is abbreviated as Gene_M;

[0139] S2: Based on the reference genome, a genome with a single copy of Gene_L and a single copy of Gene_M is obtained;

[0140] S3: aligning the sequencing data to the genome of the single copy of Gene_L and the single copy of Gene_M, calculating the copy numbers of exon 5 of Gene_L and Gene_M, and obtaining the estimated copy number of Gene_L and the estimated copy number of Gene_M;

[0141] S4: When the estimated copy number of Gene_L is equal to 0 or the estimated copy number of Gene_M is equal to 0, it indicates that the subject is a positive patient;

[0142] S5: Obtain sequencing data of Gene_L and Gene_M of positive patients;

[0143] S6: obtaining the base sequences of Gene_L and Gene_M of the positive patient based on the sequencing data of Gene_L and Gene_M of the positive patient;

[0144] S7: Based on the base sequences of Gene_L and Gene_M of the subject, determine whether the subject has a hotspot mutation, wherein the hotspot mutation refers to when the subject has c.-112A>C, and the subject is a green blind or green weak patient;

[0145] S11: obtaining the expression level of the internal reference gene of the subject, and correcting the error caused by any one or more of the following factors during data processing based on the expression level of the internal reference gene: sequencing platform, probe, batch, DNA quality and sequencing depth;

[0146] S12: obtaining DNA from the positive patient, and detecting the copy number of exon 5 of Gene_L and Gene_M by a molecular quantitative analysis method to obtain the measured copy number of Gene_L and the measured copy number of Gene_M; the molecular quantitative analysis method includes any one of the following: qPCR, dPCR, third-generation sequencing, long fragment-PCR, mass spectrometry, proteomics quantitative method and nuclear magnetic resonance;

[0147] S13: If the estimated copy number of Gene_L is equal to the measured copy number of Gene_L and the estimated copy number of Gene_M is equal to the measured copy number of Gene_M, then the methodology is reliable; if the estimated copy number of Gene_L is not equal to the measured copy number of Gene_L or the estimated copy number of Gene_M is not equal to the measured copy number of Gene_M, then another one or several molecular quantitative analysis methods are used for verification.

[0148] In one embodiment, the method includes executing S1-S13, as described below:

[0149] S1: Acquire the sequencing data of the reference genome, the gene OPN1LW and the gene OPN1MW of the subject, wherein the gene OPN1LW is abbreviated as Gene_L, and the gene OPN1MW is abbreviated as Gene_M;

[0150] S2: Based on the reference genome, a genome with a single copy of Gene_L and a single copy of Gene_M is obtained;

[0151] S3: aligning the sequencing data to the genome of the single copy of Gene_L and the single copy of Gene_M, calculating the copy numbers of exon 5 of Gene_L and Gene_M, and obtaining the estimated copy number of Gene_L and the estimated copy number of Gene_M;

[0152] S4: When the estimated copy number of Gene_L is equal to 0 or the estimated copy number of Gene_M is equal to 0, it indicates that the subject is a positive patient;

[0153] S5: Obtain sequencing data of Gene_L and Gene_M of positive patients;

[0154] S6: obtaining the base sequences of Gene_L and Gene_M of the positive patient based on the sequencing data of Gene_L and Gene_M of the positive patient;

[0155] S7: Based on the base sequences of Gene_L and Gene_M of the positive patient, determine whether the positive patient has a hotspot mutation, wherein the hotspot mutation means that when c.-112A>C occurs in the positive patient, the positive patient is a green-blind patient, otherwise, the positive patient is a red-blind patient;

[0156] S8: Based on the base sequences of Gene_L and Gene_M of the positive patient, the mutation information of the light-sensitive site is obtained, and the light-sensitive site includes any one or more of the following: p.S116T, p.S180A, p.I230T;

[0157] S9: obtaining a spectral shift based on the mutation information of the light sensitivity site;

[0158] S10: obtaining a color blindness severity grading result of a positive patient based on the spectral shift;

[0159] S12: obtaining DNA from the positive patient, and detecting the copy number of exon 5 of Gene_L and Gene_M by a molecular quantitative analysis method to obtain the measured copy number of Gene_L and the measured copy number of Gene_M; the molecular quantitative analysis method includes any one of the following: qPCR, dPCR, third-generation sequencing, long fragment-PCR, mass spectrometry, proteomics quantitative method and nuclear magnetic resonance;

[0160] S13: If the estimated copy number of Gene_L is equal to the measured copy number of Gene_L and the estimated copy number of Gene_M is equal to the measured copy number of Gene_M, then the methodology is reliable; if the estimated copy number of Gene_L is not equal to the measured copy number of Gene_L or the estimated copy number of Gene_M is not equal to the measured copy number of Gene_M, then another one or several molecular quantitative analysis methods are used for verification.

[0161] Figure 2 A data analysis system for red-green color vision abnormality provided by an embodiment of the present invention comprises:

[0162] 101 acquisition unit: used to acquire the reference genome, and sequencing data of the gene OPN1LW and the gene OPN1MW of the subject, wherein the gene OPN1LW is abbreviated as Gene_L, and the gene OPN1MW is abbreviated as Gene_M;

[0163] 201 Single copy genome analysis unit: obtaining a single copy of Gene_L and a single copy of Gene_M based on the reference genome;

[0164] 301 copy number calculation unit: used for aligning the sequencing data to the genome of the single copy of Gene_L and the single copy of Gene_M, calculating the copy number of exon 5 of Gene_L and Gene_M, and obtaining the estimated copy number of Gene_L and the estimated copy number of Gene_M;

[0165] 401 Red-green color vision judgment unit: When the estimated copy number of Gene_L is equal to 0 or the estimated copy number of Gene_M is equal to 0, it indicates that the subject is a positive patient.

[0166] Figure 4 Another embodiment of the present invention provides a data analysis system for red-green color vision abnormality, the system comprising:

[0167] 501 a first acquisition unit: used to acquire sequencing data of Gene_L and Gene_M of the subject;

[0168] 601 A first processing unit: obtaining the base sequences of Gene_L and Gene_M of the subject based on the sequencing data of Gene_L and Gene_M of the subject;

[0169] 701 The second processing unit: based on the base sequences of Gene_L and Gene_M of the subject, determine whether the subject has a hotspot mutation, wherein the hotspot mutation refers to when c.-112A>C occurs in the subject, and the subject is a green-blind or green-weak patient.

[0170] Figure 3 A data analysis device for red-green color vision abnormality is provided in an embodiment of the present invention. The device comprises: a memory and a processor; the device may also comprise: an input device and an output device.

[0171] The memory, processor, input device and output device may be connected via a bus or other means. Figure 3 What is shown is a bus connection method as an example; wherein the memory is used to store program instructions; the processor is used to call the program instructions, and when the program instructions are executed, they are used to implement the above-mentioned eukaryotic typing method based on core genome multi-site sequences.

[0172] In some embodiments, the memory may be understood as any storage device for the program, and the processor may be understood as a device for using the program.

[0173] Any of the following applications:

[0174] The use of the system in newborn screening;

[0175] Application of the system in diagnosis of ophthalmic genetic diseases; the ophthalmic genetic diseases include any one or more of the following: retinitis pigmentosa, Leber optic atrophy, cone cell dystrophy, Stargard disease, age-related macular degeneration, diabetic retinitis pigmentosa and juvenile hereditary macular degeneration;

[0176] The use of the device in neonatal screening;

[0177] The device is used in the diagnosis of ophthalmic genetic diseases; the ophthalmic genetic diseases include any one or more of the following: retinitis pigmentosa, Leber optic atrophy, cone cell dystrophy, Stargard disease, age-related macular degeneration, diabetic retinitis pigmentosa and juvenile hereditary macular degeneration.

[0178] Color vision tests for children are best done before school age, because color vision is sometimes needed to learn mathematics or read pictures. Children's learning disabilities are sometimes caused by color vision disorders. High-throughput sequencing technology is increasingly used in newborn screening, and the cost of testing a single gene is reduced, which is the trend of newborn screening in the future. Parents often have no problems with children who are color blind or color weak. Color is widely used in early school teaching subjects. Children with color blindness, in particular, may be at a disadvantage if they are not accurately diagnosed and adapted. Therefore, it is particularly important to include color blindness analysis in high-throughput sequencing for newborn screening.

[0179] Many ophthalmic genetic diseases have a certain degree of color vision abnormality. Analyzing congenital color vision abnormality can help clinicians better diagnose eye abnormalities caused by congenital or acquired reasons. Color vision abnormalities related to eye diseases include: retinitis pigmentosa, Leber optic atrophy, cone cell dystrophy, Stargard disease, age-related macular degeneration, diabetic retinitis pigmentosa, juvenile hereditary macular degeneration, etc. In addition, some red and green color vision abnormalities are also easily misdiagnosed as blue cone monochromacy.

[0180] Retinitis Pigmentosa is a family of inherited eye diseases characterized by the gradual degeneration and loss of pigment in the retinal cells (rods and cones). This results in a gradual decrease in low-light vision and increasing night blindness. Later, central vision loss gradually occurs, resulting in a reduced visual field. There are many inherited forms of the disease, and the severity of symptoms and the rate of progression vary from individual to individual.

[0181] Leber's Hereditary Optic Neuropathy (LHON) is a rare, hereditary eye disease that primarily affects the optic nerve. Patients often experience a sudden and rapid loss of vision in both eyes during young adulthood, often with central visual impairment. The disease is primarily caused by mitochondrial genetic mutations, and males are at a higher risk than females.

[0182] Cone dystrophy is a group of inherited eye diseases that primarily affect cones. These cells are responsible for color and intermediate vision. Patients usually begin to experience night blindness during childhood or adolescence, and gradually develop reduced visual fields and abnormal color perception. The severity and speed of symptom development vary from person to person, but generally speaking, central vision is more often impaired.

[0183] Stargardt Disease is an autosomal recessive disease that primarily affects vision. It usually begins in childhood or adolescence with blurred central vision and blindness due to degeneration of cells in the macula region of the retina. Patients usually maintain relatively good peripheral vision but gradually develop central vision loss.

[0184] Age-related macular degeneration (AMD) is a progressive retinal disease that is more common in older people. It mainly affects central vision, causing damage to the function of cells in the macula, the front area of ​​the eye. Early AMD may have no obvious symptoms, but as the disease progresses, patients may experience blurred, distorted or lost central vision and difficulty distinguishing details.

[0185] Diabetic retinopathy is a type of retinal damage caused by diabetes. High blood sugar levels can cause damage to retinal blood vessels and abnormal new blood vessels, which affect the light-sensitive cells in the retina. Symptoms include blurred vision, floaters in the eyes, and decreased dark adaptation. If not controlled, this disease can lead to severe vision loss.

[0186] Juvenile Macular Degeneration is a group of rare, inherited retinal diseases that primarily affect the macula. The first symptoms usually appear in childhood or adolescence and include blurred, absent or distorted central vision and light sensitivity. The severity and rate of progression of the disease vary from individual to individual, but usually result in severe vision loss.

[0187] A computer-readable storage medium stores a computer program, which, when executed by a processor, implements the above-mentioned eukaryotic typing method based on core genome multi-site sequences.

[0188] Those skilled in the art can clearly understand that, for the convenience and brevity of description, the specific working processes of the systems, devices and units described above can refer to the corresponding processes in the aforementioned method embodiments and will not be repeated here.

[0189] In the several embodiments provided in the present application, it should be understood that the disclosed systems, devices and methods can be implemented in other ways. For example, the device embodiments described above are only schematic. For example, the division of the units is only a logical function division. There may be other division methods in actual implementation, such as multiple units or components can be combined or integrated into another system, or some features can be ignored or not executed. Another point is that the mutual coupling or direct coupling or communication connection shown or discussed can be an indirect coupling or communication connection through some interfaces, devices or units, which can be electrical, mechanical or other forms.

[0190] The units described as separate components may or may not be physically separated, and the components shown as units may or may not be physical units, that is, they may be located in one place or distributed on multiple network units. Some or all of the units may be selected according to actual needs to achieve the purpose of the solution of this embodiment.

[0191] In addition, each functional unit in each embodiment of the present invention may be integrated into one processing unit, or each unit may exist physically separately, or two or more units may be integrated into one unit. The above-mentioned integrated unit may be implemented in the form of hardware or in the form of software functional units.

[0192] A person of ordinary skill in the art can understand that all or part of the steps in the various methods of the above embodiments can be completed by instructing related hardware through a program, and the program can be stored in a computer-readable storage medium, and the storage medium may include: a read-only memory (ROM), a random access memory (RAM), a disk or an optical disk, etc.

[0193] The above is a detailed introduction to a computer device provided by the present invention. For a person skilled in the art, according to the concept of the embodiments of the present invention, there may be changes in the specific implementation method and application scope. In summary, the content of this specification should not be understood as limiting the present invention.

Claims

1. A data analysis system for red-green color vision abnormality, characterized in that: The system comprises: Acquisition unit: used to obtain the reference genome and the subject's genes OPN1LW and genes OPN1MW The sequencing data of the gene OPN1LW Abbreviated as Gene_L, the gene OPN1MW Abbreviated as Gene_M; Single copy genome analysis unit: obtaining a single copy of Gene_L and a single copy of Gene_M based on the reference genome; A copy number calculation unit is used to align the sequencing data to the genome of the single copy of Gene_L and the single copy of Gene_M, calculate the copy number of exon 5 of Gene_L and Gene_M, and obtain the estimated copy number of Gene_L and the estimated copy number of Gene_M; Red-green color vision judgment unit: when the estimated copy number of Gene_L is equal to 0 or the estimated copy number of Gene_M is equal to 0, it indicates that the subject is a positive patient; the positive patients include red-green color blind patients and green-green color blind patients; The first acquisition unit is used to acquire the sequencing data of Gene_L and Gene_M of the subject; The first processing unit: obtains the base sequences of Gene_L and Gene_M of the subject based on the sequencing data of Gene_L and Gene_M of the subject; Based on the base sequences of Gene_L and Gene_M of the subject, determine whether the subject has a hotspot mutation, wherein the hotspot mutation refers to when the subject has c.-112A>C, and the subject is a green blind or green weak patient; Based on the base sequences of Gene_L and Gene_M of the positive patient, the mutation information of the light-sensitive site is obtained, and the light-sensitive site includes any one or more of the following: p.S116T, p.S180A, p.I230T; A spectral shift is obtained based on the mutation information of the photosensitive site; a color blindness severity grading result of a positive patient is obtained based on the spectral shift; and the grading standards for the color blindness severity grading results of red-eye blind patients and green-eye blind patients include: for red-eye blind patients: severe red-eye blindness when the spectral shift is 20nm, moderate red-eye blindness when the spectral shift is 17nm, and mild red-eye blindness when the spectral shift is less than 14nm; for green-eye blind patients: severe green-eye blindness when the spectral shift is 17.5-20nm, moderate green-eye blindness when the spectral shift is 16-16.5nm, and mild green-eye blindness when the spectral shift is less than or equal to 14nm.

2. The data analysis system for red-green color vision abnormality according to claim 1, characterized in that: The analysis steps in the single copy genome analysis unit include: S2.1: Align Gene_L and Gene_M with the reference genome to obtain aligned_Gene_L and aligned_Gene_M; S2.2: Divide aligned_Gene_L into first_Gene_L and redundant_Gene_L according to their order of arrangement on the reference genome; divide aligned_Gene_M into first_Gene_M and redundant_Gene_M according to their order of arrangement on the reference genome; The first_Gene_L refers to the aligned_Gene_L that appears for the first time on the reference genome, the first_Gene_M refers to the aligned_Gene_M that appears for the first time on the genome, the redundant_Gene_L refers to the aligned_Gene_L other than the first_Gene_L on the reference genome, and the redundant_Gene_M refers to the aligned_Gene_M other than the first_Gene_M on the reference genome; S2.3: Replace the base sequences of redundant_Gene_L and redundant_Gene_M on the reference genome with N to obtain a genome with a single copy of Gene_L and a single copy of Gene_M.

3. The data analysis system for red-green color abnormality according to claim 1, characterized in that: The system further comprises: S11: obtaining the expression level of the internal reference gene of the subject, and correcting the error caused by any one or more of the following factors during data processing based on the expression level of the internal reference gene: sequencing platform, probe, batch, DNA quality and sequencing depth; The internal reference genes include any one or more of the following: PLP1, GAPDH, ACTB, HPRT1, RPL13A, TBP, PGK1, GUSB、PPIA and eIF2B1 .

4. The data analysis system for red-green color vision abnormality according to claim 1, characterized in that: The system further comprises: S12: obtaining DNA from the positive patient, and detecting the copy number of exon 5 of Gene_L and Gene_M by a molecular quantitative analysis method to obtain the measured copy number of Gene_L and the measured copy number of Gene_M; the molecular quantitative analysis method includes any one of the following: qPCR, dPCR, third-generation sequencing, long fragment-PCR, mass spectrometry; S13: If the estimated copy number of Gene_L is equal to the measured copy number of Gene_L and the estimated copy number of Gene_M is equal to the measured copy number of Gene_M, then the methodology is reliable; if the estimated copy number of Gene_L is not equal to the measured copy number of Gene_L or the estimated copy number of Gene_M is not equal to the measured copy number of Gene_M, then another one or several molecular quantitative analysis methods are used for verification.

5. A data analysis device for red-green color vision abnormality, characterized in that: The device comprises: a memory and a processor; the memory is used to store program instructions; the processor is used to call the program instructions, and when the program instructions are executed, it is used to perform the following analysis method: S1: Obtain the reference genome and the subject's genes OPN1LW and genes OPN1MW The sequencing data of the gene OPN1LW Abbreviated as Gene_L, the gene OPN1MW Abbreviated as Gene_M; S2: Based on the reference genome, a genome with a single copy of Gene_L and a single copy of Gene_M is obtained; S3: aligning the sequencing data to the genome of the single copy of Gene_L and the single copy of Gene_M, calculating the copy numbers of exon 5 of Gene_L and Gene_M, and obtaining the estimated copy number of Gene_L and the estimated copy number of Gene_M; S4: When the estimated copy number of Gene_L is equal to 0 or the estimated copy number of Gene_M is equal to 0, it indicates that the subject is a positive patient; the positive patients include red-blind patients and green-blind patients; S5: Obtain the sequencing data of Gene_L and Gene_M of the subject; S6: obtaining the base sequences of Gene_L and Gene_M of the subject based on the sequencing data of Gene_L and Gene_M of the subject; S7: Based on the base sequences of Gene_L and Gene_M of the subject, determine whether the subject has a hotspot mutation, wherein the hotspot mutation refers to when the subject has c.-112A>C, and the subject is a green blind or green weak patient; S8: Based on the base sequences of Gene_L and Gene_M of the positive patient, the mutation information of the light-sensitive site is obtained, and the light-sensitive site includes any one or more of the following: p.S116T, p.S180A, p.I230T; S9: obtaining a spectral shift based on the mutation information of the light sensitivity site; S10: Based on the spectral shift, the color blindness severity grading result of the positive patient is obtained; the grading standards for the color blindness severity grading results of the red-blind patients and the green-blind patients include: for red-blind patients: when the spectral shift is 20nm, it is severe red-blindness, when the spectral shift is 17nm, it is moderate red-blindness, and when the spectral shift is less than 14nm, it is mild red-blindness; for green-blind patients: when the spectral shift is 17.5-20nm, it is severe green-blindness, when the spectral shift is 16-16.5nm, it is moderate green-blindness, and when the spectral shift is less than or equal to 14nm, it is mild green-blindness.

6. The data analysis device for red-green color abnormality according to claim 5, characterized in that: The analysis steps of S2 include: S2.1: Align Gene_L and Gene_M with the reference genome to obtain aligned_Gene_L and aligned_Gene_M; S2.2: Divide aligned_Gene_L into first_Gene_L and redundant_Gene_L according to their order of arrangement on the reference genome; divide aligned_Gene_M into first_Gene_M and redundant_Gene_M according to their order of arrangement on the reference genome; The first_Gene_L refers to the aligned_Gene_L that appears for the first time on the reference genome, the first_Gene_M refers to the aligned_Gene_M that appears for the first time on the genome, the redundant_Gene_L refers to the aligned_Gene_L other than the first_Gene_L on the reference genome, and the redundant_Gene_M refers to the aligned_Gene_M other than the first_Gene_M on the reference genome; S2.3: Replace the base sequences of redundant_Gene_L and redundant_Gene_M on the reference genome with N to obtain a genome with a single copy of Gene_L and a single copy of Gene_M.

7. The data analysis device for red-green color abnormality according to claim 5, characterized in that: The method further comprises: S11: obtaining the expression level of the internal reference gene of the subject, and correcting the error caused by any one or more of the following factors during data processing based on the expression level of the internal reference gene: sequencing platform, probe, batch, DNA quality and sequencing depth; The internal reference genes include any one or more of the following: PLP1, GAPDH, ACTB, HPRT1, RPL13A, TBP, PGK1, GUSB、PPIA and eIF2B1 .

8. The data analysis device for red-green color abnormality according to claim 5, characterized in that: The method further comprises: S12: obtaining DNA from the positive patient, and detecting the copy number of exon 5 of Gene_L and Gene_M by a molecular quantitative analysis method to obtain the measured copy number of Gene_L and the measured copy number of Gene_M; the molecular quantitative analysis method includes any one of the following: qPCR, dPCR, third-generation sequencing, long fragment-PCR, mass spectrometry; S13: If the estimated copy number of Gene_L is equal to the measured copy number of Gene_L and the estimated copy number of Gene_M is equal to the measured copy number of Gene_M, then the methodology is reliable; if the estimated copy number of Gene_L is not equal to the measured copy number of Gene_L or the estimated copy number of Gene_M is not equal to the measured copy number of Gene_M, then another one or several molecular quantitative analysis methods are used for verification.

9. A computer-readable storage medium having a computer program stored thereon, characterized in that: When the computer program is executed by a processor, the following analysis method is implemented: S1: Obtain reference genome and subject's genes OPN1LW and genes OPN1MW The sequencing data of the gene OPN1LW Abbreviated as Gene_L, the gene OPN1MW Abbreviated as Gene_M; S2: Based on the reference genome, a genome with a single copy of Gene_L and a single copy of Gene_M is obtained; S3: aligning the sequencing data to the genome of the single copy of Gene_L and the single copy of Gene_M, calculating the copy numbers of exon 5 of Gene_L and Gene_M, and obtaining the estimated copy number of Gene_L and the estimated copy number of Gene_M; S4: When the estimated copy number of Gene_L is equal to 0 or the estimated copy number of Gene_M is equal to 0, it indicates that the subject is a positive patient; the positive patients include red-blind patients and green-blind patients; S5: Obtain the sequencing data of Gene_L and Gene_M of the subject; S6: obtaining the base sequences of Gene_L and Gene_M of the subject based on the sequencing data of Gene_L and Gene_M of the subject; S7: Based on the base sequences of Gene_L and Gene_M of the subject, determine whether the subject has a hotspot mutation, wherein the hotspot mutation refers to when the subject has c.-112A>C, and the subject is a green blind or green weak patient; S8: Based on the base sequences of Gene_L and Gene_M of the positive patient, the mutation information of the light-sensitive site is obtained, and the light-sensitive site includes any one or more of the following: p.S116T, p.S180A, p.I230T; S9: obtaining a spectral shift based on the mutation information of the light sensitivity site; S10: Based on the spectral shift, the color blindness severity grading result of the positive patient is obtained; the grading standards for the color blindness severity grading results of the red-blind patients and the green-blind patients include: for red-blind patients: when the spectral shift is 20nm, it is severe red-blindness, when the spectral shift is 17nm, it is moderate red-blindness, and when the spectral shift is less than 14nm, it is mild red-blindness; for green-blind patients: when the spectral shift is 17.5-20nm, it is severe green-blindness, when the spectral shift is 16-16.5nm, it is moderate green-blindness, and when the spectral shift is less than or equal to 14nm, it is mild green-blindness.

10. The computer-readable storage medium according to claim 9, wherein: The analysis steps of S2 include: S2.1: Align Gene_L and Gene_M with the reference genome to obtain aligned_Gene_L and aligned_Gene_M; S2.2: Divide aligned_Gene_L into first_Gene_L and redundant_Gene_L according to their order of arrangement on the reference genome; divide aligned_Gene_M into first_Gene_M and redundant_Gene_M according to their order of arrangement on the reference genome; The first_Gene_L refers to the aligned_Gene_L that appears for the first time on the reference genome, the first_Gene_M refers to the aligned_Gene_M that appears for the first time on the genome, the redundant_Gene_L refers to the aligned_Gene_L other than the first_Gene_L on the reference genome, and the redundant_Gene_M refers to the aligned_Gene_M other than the first_Gene_M on the reference genome; S2.3: Replace the base sequences of redundant_Gene_L and redundant_Gene_M on the reference genome with N to obtain a genome with a single copy of Gene_L and a single copy of Gene_M.

11. The computer-readable storage medium according to claim 9, wherein: The method further comprises: S11: obtaining the expression level of the internal reference gene of the subject, and correcting the error caused by any one or more of the following factors during data processing based on the expression level of the internal reference gene: sequencing platform, probe, batch, DNA quality and sequencing depth; The internal reference genes include any one or more of the following: PLP1, GAPDH, ACTB, HPRT1, RPL13A, TBP, PGK1, GUSB、PPIA and eIF2B1 .

12. The computer-readable storage medium according to claim 9, wherein: The method further comprises: S12: obtaining DNA from the positive patient, and detecting the copy number of exon 5 of Gene_L and Gene_M by a molecular quantitative analysis method to obtain the measured copy number of Gene_L and the measured copy number of Gene_M; the molecular quantitative analysis method includes any one of the following: qPCR, dPCR, third-generation sequencing, long fragment-PCR, mass spectrometry; S13: If the estimated copy number of Gene_L is equal to the measured copy number of Gene_L and the estimated copy number of Gene_M is equal to the measured copy number of Gene_M, then the methodology is reliable; if the estimated copy number of Gene_L is not equal to the measured copy number of Gene_L or the estimated copy number of Gene_M is not equal to the measured copy number of Gene_M, then another one or several molecular quantitative analysis methods are used for verification.

13. Use of the system according to any one of claims 1 to 4 in the preparation of a newborn screening product.

14. Use of the system according to any one of claims 1 to 4 in the preparation of ophthalmic genetic disease diagnostic products; the ophthalmic genetic diseases include any one or more of the following: retinitis pigmentosa, Leber optic atrophy, cone cell dystrophy, Stargard disease, age-related macular degeneration, diabetic retinitis pigmentosa and juvenile hereditary macular degeneration.

15. Use of the device according to any one of claims 5 to 8 in neonatal screening auxiliary diagnosis.

16. Use of the device according to any one of claims 5 to 8 in auxiliary diagnosis of ophthalmic genetic diseases; the ophthalmic genetic diseases include any one or more of the following: retinitis pigmentosa, Leber optic atrophy, cone cell dystrophy, Stargard's disease, age-related macular degeneration, diabetic retinitis pigmentosa and juvenile hereditary macular degeneration.

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