CN112608925B - Pathogenic gene COL2A1 mutation of bone dysplasia disease and detection reagent thereof - Google Patents

Abstract

The invention discloses pathogenic mutation of osteogenesis imperfecta and a detection reagent thereof. A novel mutant COL2A1 gene features that the mutant COL2A1 gene is single-point mutation c.3944G > A (chr12:48368588), the heterozygosis mutation is pathogenic, and its site mutation can change the structure of collagen type II in articular cartilage and cause collagen type II disease. A kit for detecting osteogenesis imperfecta comprising: a reagent for detecting the 3944bp site of CDS of the COL2A1 gene; or a reagent for detecting the 1315 th amino acid site of the COL2A1 protein. The invention obtains the pathogenic mutation (c.3944G > A on COL2A1 gene) of the osteogenesis imperfecta disease, and the diagnosis of the osteogenesis imperfecta disease can be carried out by detecting the mutation.

Description

Pathogenic gene COL2A1 mutation of bone dysplasia disease and detection reagent thereof

Technical Field

The invention belongs to the fields of biomedicine and genetics, and relates to a pathogenic gene COL2A1 mutation of an abnormal bone development disease and a detection reagent thereof.

Background

Skeletal dysplasia, also known as dwarfism, is a general term for a group of diseases of short stature caused by abnormal bone or cartilage, and although most of the patients have normal intelligence, the diseases affect normal development of bone and cartilage tissues, sometimes cause bone deformation and even affect other systems of the body. At present, more than 200 kinds of bone dysplasia diseases are reported, many congenital bone dysplasias are caused by mutation of a genetic gene, the condition of the bone dysplasia is generally diagnosed and evaluated through examination such as an x-ray film and nuclear magnetic resonance, after symptoms generally appear, because the genetic disease cannot be treated once, heavy burden is brought to the society and families, and the only measure is early diagnosis and informed selection, so that pathogenic sites of the genetic disease are searched and verified, a gene diagnosis method of the bone dysplasia is established, prenatal gene diagnosis is carried out, the birth of the sick children is avoided, the burden of the society and families of patients is reduced, the prenatal and postnatal care is realized, and the quality of the population in China is improved.

More than ten years ago, for the diagnosis of genetic diseases, the diagnosis is generally carried out by examining a body, carrying out biochemical and mass spectrometric examination, then carrying out nuclear magnetism, CT and other auxiliary examinations, and finally carrying out targeted gene detection, so prenatal diagnosis cannot be realized. The advent of high throughput sequencing (NGS) provides a good solution to the above-mentioned problems. NGS is fast in speed, high in flux and high in operation automation degree, DNA samples can detect all related genes of diseases once only 8-9 hours from preparation of libraries and on-computer sequencing to data analysis, the diagnosis efficiency of the genetic diseases is greatly improved, particularly, the occurrence of whole exon sequencing greatly increases the detection rate of pathogenic mutation of the genetic diseases, the technology can detect about 2 ten thousand exon regions of genes in a human genome at one time, wherein the coverage rate reaches more than 95 percent of gene factors of 18105, and the technology reads 4000 genes which include definite pathogenic relations in an OMIM database, more than 5000 diseases and detects 68 microdeletion microdrop syndromes. The kit is particularly suitable for ultrasonic prompt of skeletal systems in pregnancy, but no family (new variation) exists, the acquisition of clinical representation in the fetal period is limited, and pathogenic mutation sites can be quickly, accurately and widely searched (all exons) by sequencing all exons of fetal parents and fetuses.

Based on the emergence of NGS, clinical diagnosis strategies for monogenic genetic diseases have changed greatly, and different detection schemes have emerged for 3 clinical detection needs: (1) for definite single diseases, a Sanger sequencing method, a qPCR method or a Panel single disease detection is used, a detection platform is first-generation sequencing, MLPA or NGS, the advantages and the limitations of the method are that a character or a disease gene is amplified, point mutation and deletion repetition are detected, new mutation is found, but new gene cannot be found; (2) for objects with definite single clinical phenotype, family history or other obvious genetic factors and higher requirements on diagnosis period and efficiency, a panel disease combination or full panel detection is adopted, the detection platform is NGS, the advantages and the limitations of the detection platform lie in detecting related gene combinations, the detection result has definite clinical significance, the result is easy to explain, the period is short, the cost performance is high, new mutation can be found, but new genes cannot be found; (3) for difficult cases with complex clinical representation or unknown disease directions, or negative panel detection results, or clinical scientific researches based on a plurality of disease families, the NGS-based whole exome sequencing detection is adopted, the whole exome is captured and sequenced, point mutation and deletion repetition are discovered, 75-85% pathogenic mutation can be detected, new genes are discovered, but mutation with unknown clinical significance can be discovered, and the explanation is difficult; the whole genome sequencing detection based on NGS can also be adopted, the whole genome of human can be detected, the whole genome is sequenced, point mutation and deletion repetition, structural variation and dynamic mutation can be found, the mitochondrial variation can be detected simultaneously, and new genes can be found, but the mutation with unknown clinical significance can be found possibly and is difficult to explain.

The COL2A1 gene is located at the position 12q13.11-q13.2 of the long arm of chromosome 12, and the gene is 31.538kb long, and has 54 exons and 53 introns and codes for 1487 amino acids. The COL2a1 gene encodes the pre- α 1(II) chain of collagen type II, which adds structure and strength to the connective tissue supporting the muscles, joints, organs and skin of the body, and is mainly present in cartilage, most of which is subsequently converted into bone, and is involved in the regulatory process of intrabony and intrachondral osteogenesis. Type II collagen has a homotrimeric structure and consists of three triple helical alpha polypeptides folded into a rod. The collagen regions are composed of a plurality of amino acid sequences that are repeated in a Gly-X-Y pattern (Gly being glycine, X typically representing proline and Y typically representing hydroxyproline). Many exons of COL2A1 gene are reported, so far, more than one hundred mutations have been reported, COL2A1 gene-related diseases include Torrance type vertebral body flat lethal skeletal dysplasia, chondrogenesis imperfecta type 2, congenital spondyloepiphysis dysplasia, Kniest dysplasia, Strudwick type spondyloepiphysis metaphysis dysplasia and the like (https:// mistor. OMIM. org/entry/120140), and COL2A1 gene-related diseases shown by OMIM are all normal chromosome dominant inheritance, however, COL2A1 gene c.3944G > A (p.Cys1315Tyr) mutation (detected by NGS technology based on the above strategies) causes osteogenesis imperfecta (Osteogenesis imperfecta, OI) never reported and proved.

Disclosure of Invention

The invention aims to provide a COL2A1 mutation gene causing bone dysplastic diseases and a detection reagent thereof aiming at the defects.

Another object of the present invention is to provide the use of such pathogenic mutations.

The purpose of the invention can be realized by the following technical scheme:

a mutated COL2a1 gene for detecting osteogenesis imperfecta disease, the mutated COL2a1 being heterozygous or homozygous mutation c.3944g > a, the wild type COL2a1 gene having the gene numbering in NCBI database of: NM-001844.4, the nucleotide of 3944bp of CDS is mutated from G to A, and the rest is the same as wild type. The CDS sequence of the wild-type COL2A1 gene is shown in SEQ ID NO. 1.

A mutant COL2a1 protein, wild-type COL2a1 protein, having the gene transcript number in NCBI database: NP-001835.3, mutant COL2A1 protein was mutated from cysteine to tyrosine at amino acid 1315 of the wild-type protein, and the rest was identical to the wild-type protein. The amino acid sequence of the wild type COL2A1 protein is shown in SEQ ID NO.2,

the application of the reagent for detecting the mutant COL2A1 gene or the mutant COL2A1 protein in preparing a detection reagent or detection equipment for the osteogenesis imperfecta disease.

The detection reagent is preferably selected from one or more of primers or primer pairs, probes, antibodies, or nucleic acid chips, high-throughput sequencing and Sanger sequencing.

The primer pair preferably consists of SEQ ID NO.3 and SEQ ID NO. 4.

The detection device preferably comprises a gene chip containing COL2A1 gene for detecting mutation, a high-throughput sequencing platform and a Sanger sequencing platform.

A kit for detecting osteogenesis imperfecta disease, said kit comprising:

(1) a reagent for detecting nucleotide 3944bp of CDS of COL2A1 gene; or a reagent for detecting the 1315 th amino acid site of the COL1A1 protein;

(2) the product use instruction contains the clear record that the nucleotide at 3944bp of CDS of COL2A1 gene is mutated from G to A, or the amino acid site at 1315 position of COL2A1 protein is mutated from C to Y to cause osteogenesis imperfecta.

Wherein the reagent is preferably selected from a primer or primer pair, a probe, an antibody, or a nucleic acid chip.

Preferably, the reagent is a gene chip hybridization probe based on deep sequencing as a platform.

The reagent is further preferably a primer pair for detecting nucleotide 3944bp of CDS of COL21A1 gene; still further preferred is a primer pair consisting of 5'-TGGACTTAGCTCATGCAGAT-3' (SEQ ID NO.3) and 5'-TGGATTGGGGTAGACGC-3' (SEQ ID NO. 4).

The gene chip hybridization probe sequence for detecting the nucleotide at 3944bp of CDS of COL2A1 gene in the kit is preferably shown as SEQ ID NO. 5.

A method for screening new mutations of COL2A1 genes in OI patients by taking deep sequencing as a platform and verifying the gene mutations into pathogenic gene mutations by combining a zebra fish mutation model with SIFT and Polyphen protein function prediction is disclosed: comprises the following steps:

(1) for families with fetal ultrasound showing skeletal dysplasia (+/-with other abnormalities) or with OI genetic disease history, collecting clinical data and DNA-containing specimens such as blood, tissues and the like, and extracting genomic DNA;

(2) a series of genes involved in the detection of bone dysplasia, including genes ADAMTSL2, AGPS, ANKH, ARSE, CCDC8, CHST3, COL10a1, COL2a1, COL9a1, COMP, CTSK, CUL 1, DLL 1, EBP, EVC 1, FBN1, FGFR1, FLNB, GNAS, GNPAT, HES 1, LFNG, LMNA, MATN 1, MESP 1, OBSL1, PEX 1, PTH 11, ROR 1, RUNX 1, SLC26 a1, SLC35D1, smarccal 1, SOST, SOX 1, TGFB1, TNFRS, ppf 11, trac 1, trx 1, ntb 1, ptx 1, pctfb 1, ptb 1, ptx 1, spb 1, ptx 1, spb 1, ptx 1, spb 1, spx 1, spf 1, spx 1, spf 1, spx 1, spf 1, spp 1, spf; or directly carrying out whole exon detection, wherein the detection mutation comprises point mutation of about 2 ten thousand genes and small fragment deletion insertion mutation within 20 bp.

(3) And breaking DNA and preparing a library, capturing and enriching a target gene coding region or a whole exon region and near-sheared DNA through a chip, and finally performing mutation detection by using a high-throughput sequencing platform.

(4) And (3) performing optimized bioinformatics analysis on the sequencing result, and screening a new OI pathogenic mutation to COL2A1. Cys1315Tyr. The mutation is located in chromosome 12, and the base with the physical position of 48368588(NCBI database) is mutated from G to A; protein level: the 1315 th amino acid of protein coded by COL2A1 gene is mutated from cysteine to tyrosine.

(5) The high-throughput sequencing in the step (3) is carried out, wherein the length of a target region based on whole exon sequencing is 58682415bp, the coverage of the target region reaches at least 99.91%, the average depth of the target region is at least 83.48X, and the proportion of sites with the average depth of the target region being more than 30X is at least 98.70%.

(6) Protein function prediction was performed on the new mutation site COL2A1.Cys1315Tyr with SIFT and Polyphen.

(7) The zebra fish model is used for verifying that the c.3944G > A point mutation on the COL2A1 gene influences skeletal development, the gene COL2a1a (ENSDARG00000069093) which is highly similar to the human COL2A1 gene is found in an ENSEMBL database, dominant expression in a human body is simulated by expressing the COL2a1a isopoint mutation gene in wild zebra fish, and the skeletal development condition of the zebra fish embryo is observed to verify that the new mutation site COL2A1.c.3944G > A causes skeletal development abnormality OI.

(8) Based on the detection result of the Trio family complete exon detection, the source of the mutation is identified to be a new mutation or a hereditary mutation, and if the mutation is the hereditary mutation, whether the mutation is the gonad chimeric mutation or not is also distinguished according to the mutation ratio of a parent side.

(9) If the mutation is new, the next pregnancy can be selected from natural conception and prenatal diagnosis, and the probability of suffering from the same mutation again is very low; if genetic mutation, test tube infants can be selected + pre-implantation genetic diagnosis + prenatal diagnosis, and implanted embryos are excluded from being inherited with the same mutation COL2A1.c.3944G > A.

Advantageous effects

1. The invention reports a new mutation site in an OI pathogenic gene COL2A1.c.3944G > A for the first time, which is pathogenic for autosomal dominant hereditary diseases, whether heterozygous mutation or homozygous mutation, and the invention provides a new pathogenic site for the diagnosis of the disease.

2. Provides a new idea for searching and verifying clinical new mutation, carries out Trio whole exon sequencing on difficult and complicated cases with complex clinical characteristics or unknown disease directions, analyzes the harmfulness of the new mutation by bioinformatics of families, carries out verification on animal models such as zebra fish and the like, combines diagnosis before implantation of tube-fed infants under the condition of informed consent, transplants and eliminates the embryo of the mutation COL2A1.c.3944G > A, thereby obtaining normal children without clinical abnormal bone development characteristics.

3. The method can be expanded to diagnosis and analysis of difficult cases with complex clinical characteristics or unknown disease directions in other fields except for bone dysplasia, and provides an effective platform for searching new mutation sites and even new mutant genes for clinic.

Drawings

FIG. 1 fetal ultrasound results chart

FIG. 2 family Sanger sequencing results

FIG. 3 conservation of human COL2A1 Gene to the site of homologous Gene mutation in Zebra fish, the mutation site described in the present invention (G3944A) and its counterpart in Zebra fish are indicated by boxes

FIG. 4 nucleotide and amino acid map of the sequence of the mutant site of zebra fish

FIG. 5 construction of zebra fish transcription and microinjection plasmids

Fig. 6 SIFT prediction results for the new locus in each database.

FIG. 7 the prediction of polyphen at the new site in each database.

FIG. 8 wild type zebra fish and COL2A1 gene c.3944G > A mutant zebra fish

FIG. 9 fetal Sanger sequencing results

FIG. 10 PGT-M fetal ultrasound results plot

Detailed Description

The present inventors have extensively and intensively studied and found that a novel mutation site of COL2A1, a gene related to OI, can be used for diagnosing the above-mentioned diseases and for developing a gene therapeutic drug effective for the above-mentioned diseases.

In detecting the variation at the relevant site, the detection may be directed to genomic DNA, to cDNA or mRNA, or to a protein. The mutation can be detected by using known techniques such as Western blotting, Southern blotting, DNA sequencing, PCR and in situ hybridization.

Various techniques can be used to detect the presence of a G to A mutation at position 3944 of the wild-type COL2A1 gene (SEQ ID NO.1), and are encompassed by the present invention. For example, gene chips and high throughput sequencing capture probes are prepared based on the relevant sites. In addition, PCR can be performed using primers specific to the relevant site for identification; or probes that specifically bind can be designed for identification based on the relevant sites; or may be identified using specific restriction enzymes.

As an optional mode, a single base extension technology based on a PCR technology can be adopted to detect the mutation site, and the principle is to design a primer which is positioned at the upstream of the mutation site to be detected, and the 3' end of the primer is one base away from the mutation site. Adding different fluorescently-labeled ddNTPs for reaction, or adding dNTP and related reaction enzyme through pyrosequencing, wherein the primer is extended only when the added ddNTP or dNTP is complementary with the base of the mutation site. The type of mutation can be determined by detecting fluorescence emitted from the extended base or visible light emitted from a series of enzyme reactions in pyrosequencing.

The invention also includes reagents for detecting the presence of the mutation site (presence of a G to A mutation at position 3944 of CDS of COL2A 1) in an analyte. The reagents are, for example: primers specific to the relevant mutation sites, wherein the amplified product contains a base corresponding to 3944 th site of the COL1A1 gene; a probe specific to the relevant mutation site, capable of specifically binding to the mutated region but not to the non-mutated region, and carrying a detectable signal; or a restriction enzyme specific for the relevant mutation site.

The kit may also include various reagents required for DNA extraction, RNA extraction, hybridization, color development, and the like, including but not limited to: an extraction solution, an amplification solution, a hybridization solution, an enzyme, a control solution, a color development solution, a washing solution, and the like.

In addition, the kit can also comprise instructions for use, nucleic acid sequence analysis software and the like.

The invention will be further illustrated with reference to the following specific examples.

Example 1

A fetus with abnormal bone development prompted by ultrasound is subjected to genetic detection.

The experimental method comprises the following steps:

1. for the husband chromosome 46, XY, inv (1) (p11q12), the collection of serial ultrasonic results of IVF-ET (PGT-A) pregnant single embryo transplantation pregnant women, and the case data collection: collecting umbilical cord tissue of the induced fetus and collecting peripheral blood of parents of the fetus for genetic diagnosis. Genomic DNA was extracted from blood and tissue samples of each member of the family using a blood genomic DNA extraction kit (Tiangen Biochemical technology Co., Ltd.).

2. Adopting a high-throughput sequencing technology to mine pathogenic mutation of the family: the detection of deletion and repeat syndrome of over 100kb of the whole genome and the detection of mutation of 1bp in the whole exon range are detected by the line CNV-seq. Clinical whole exome detection-exo detection region exome regions of about 2 ten thousand genes in the human genome, the detection strategy was an analysis of 3583 genes individually for all clear pathogenic relationships contained in the OMIM database involved in clinical complaints of subjects.

And 3, carrying out Trio full exon information analysis, namely filtering out joints, low-quality bases and undetected bases from original off-line data, then comparing the filtered data with a reference genome, carrying out SNP (single nucleotide polymorphism) detection and InDel or CNV (continuous nucleotide polymorphism) analysis, then annotating through a database, and screening harmful sites or genes related to diseases according to three analysis strategies based on variation harmfulness, sample family conditions and gene functional phenotypes on the variation detection result.

4. Through Sanger sequencing verification, the pathogenic genes are identified: the PCR method respectively amplifies the screened mutation sites and adjacent DNA sequences in corresponding families, the Primer sequences are designed by adopting Primer 5 Primer design software, and the sequences of the Primer pairs for detecting the pathogenic mutation are shown as SEQ ID NO.3 and SEQ ID NO. 4. The reaction system for the PCR used (50. mu.l system) was: 10 buffer 5. mu.l, 25mM MgCl ₂ 3μl，Taq DNA polymerase 5U, dNTP mix 2mM, forward and reverse primers 1.2. mu.M each, sterile distilled water to 50. mu.l. Placing into a PCR instrument, and heating at 94 deg.C for 3 min; (94 ℃, 25 s; 55 ℃, 25 s; 72 ℃, 20s)35 cycles; 7min at 72 ℃; storing at 4 deg.C. And (3) detecting by using a gel imager after 2% agarose electrophoresis, adding a Marker to judge the size of the fragment, carrying out Sanger sequencing on a sample with a single band and the fragment size meeting the size, and judging whether the site is mutated or not or judging whether the chimeric condition exists according to the mutation peak height.

The experimental results are as follows:

1. the ultrasonic department main and conception department carries out ultrasonic detection on the fetus in the abdomen of the pregnant woman, finds that the fetus has congenital dysplasia, fetal cervical lymphadenocystis cystoma, fetal edema, short and small development of limbs (namely, long bones of the limbs are in short strip-like echoes), the head and the trunk of the fetus are wrapped in cocoon-like shapes, the thorax is narrow and small, the abdomen is bulged (figure 1), the possibility of lethal dysplasia is preliminarily judged, and members with similar symptoms do not appear in the family.

2. After CNV-seq detection and whole exon detection are carried out on the DNA of a fetal induced delivery tissue sample, the fact that a c.3944G > A mutation exists on COL2A1 gene of a fetus, the mutation is VOUS mutation, namely the mutation with unknown clinical significance, other suspected pathogenic gene mutation sites are not found, and the result of whole exon secondary sequencing shows that the father of the fetus has low-proportion chimeric mutation sites at the same mutation sites, and the same mutation is not found in the peripheral blood DNA of the mother of the fetus. Sanger sequencing verification proves that the mutation of the gene locus is heterozygous mutation in a fetal sample, low-proportion chimeric mutation exists in the father peripheral blood, no mutation is found in the maternal peripheral blood, and the result is consistent with the result of second-generation sequencing (figure 2). The father is suspected to be gonadal chimerism, and children with the same mutation can be avoided by pre-implantation diagnosis of the test-tube infant.

3. According to the design scheme of the invention, the detected c.3944G > A mutation of the COL2A1 gene is successfully proved to be a new OI pathogenic site.

Example 2:

functional studies and knockout animal model studies were performed on the pathogenic gene detected in example 1, which is exemplified by the detected new mutation c.3944G > A in COL2A1 gene.

The experimental method comprises the following steps:

1. conservative analysis: the frequency of occurrence of the site in each database was evaluated.

2. And predicting the pathogenic capability of the mutation according to SIFT and polyphen values.

3. The animal model of gene knockout proves that the mutation site is a pathogenic mutation site.

(1) Analyzing the homologous genes and the point mutation positions of the COL2A1 in the zebra fish, and selecting the correct homologous genes in the zebra fish for preparing the point mutation; a gene which is highly similar to the human COL2A1 gene is found in the ENSEMBL website, namely ENSDARG00000069093, and the conservation of mutation positions is analyzed, as shown in figure 3. The comparison result shows that the site is conserved in the zebra fish gene, and the importance of the site function is suggested. To verify that mutation at this site in zebrafish results in a similar phenotype, the gene COL2a1a (ENSDARG00000069093) with higher similarity to human COL2A1 in zebrafish was selected for experiment.

(2) Method for verifying COL2A1(G3944A) point mutation function: in humans, COL2a1(G3944A) exhibits dominant skeletal dysplastic phenotype at embryonic stage, and thus can be verified by expressing COL2a1 a-like point mutant gene in wild-type zebrafish to simulate dominant expression in human body, and further by observing skeletal development of zebrafish embryos. Using the sequence of the transcript ENSDARG00000069093 of the col2a1a gene as a reference, primers were designed to clone the full length of the gene and construct the col2a1a (G3944A) point mutation, and the nucleotide and amino acid mapping of the sequence at the mutation site is shown in FIG. 4.

(3) Construction of a plasmid for expressing col2a1a (G3944A) in zebrafish: mutation points: G3944A, mutant primer: original plasmid is taken as a template, a promoter region is amplified, primers col2a1a-F1(5'-CCT CTG ACA CCT GAT GCC AAT TGC-3') and col2a1a-R1(5'-ATG CAG GTC CTA AGG GGT GAA AGT CG-3') are selected, zebra fish genome DNA is taken as the template, and three pairs of primers are used for amplifying col2a1a mutant fragments, namely col2a1a-M1F1(5'-ATG TTC AGA TTG CTG GAT TCA CG-3') and col2a1a-CDSR4(5'-GCC AAT TGG ACC AGT CAA ACC T-3'), col2a1a-F4(5'-AAG AGG TTT GAC TGG TCC AAT-3') and col2a1a-mutR (5'-CCA TGT TGT AGA AAA CTT TGA TGG CAT CAG CAG-3'), and col2a1a-mut (5' -GCC ATC AAA GTT TTC TAC AAC ATG GAG ACC GGA GAG ACC T2 a-mutR) (5'-CCA TGT TGT AGA AAA CTT TGA TGG CAT CAG CAG-3') -3') and col2a1a-CDSR5(5'-CAA GAA GCA GAC TGC GCC AAT GTC-3'). Synthesizing a plasmid by using a homologous recombination method, sending the plasmid to a sequencing company for sequencing after the plasmid is constructed, and analyzing a sequencing result to ensure that the plasmid is constructed correctly; strain preservation, plasmid extraction and purification. The concentration after plasmid purification was 400 ng/. mu.L. The method for expressing col2a1a (G3944A) selects DNA microinjection (using tol2 transposase to mediate high-efficiency transgenes), and uses the overexpression plasmid (figure 5) constructed by microinjection and transposase mRNA overexpression to confirm whether the influence is caused by phenotype.

(4) Phenotypic observations after expression of col2a1a (G3944A): after microinjection, the development of the overall morphology is continuously observed, and the development of trunk skeletons (with or without bending) is particularly concerned.

The experimental results are as follows:

COL2a 1; NM-001844.4; c.3944G > A; p.cys1315tyr | p.c 1315y; EX 52; CDS 52: missense mutation, and related literature reports of the pathogenicity of the site are temporarily absent. Protein function prediction was performed with SIFT and Polyphen, and the results were both harmful, and the probability of this site occurring in normal humans was very low (fig. 6-7). The Torrance type vertebral body flat lethal skeletal dysplasia, chondrogenesis imperfecta type 2, congenital spondyloepiphyseal dysplasia, Kniest dysplasia and Strudwick type spondyloepiphyseal dysplasia related to COL2A1 are all autosomal dominant inheritance, that is, the existence of a harmful mutation on an allele can cause diseases.

2. Injection of col2a1a plasmid resulted in spinal column curvature in zebrafish as shown by spinal curvature phenotypic analysis (fig. 8).

Example 3:

making an assisted reproduction strategy, and selecting an assisted reproduction line implantation diagnosis PGT-M and a prenatal diagnosis experiment method by the informed consent of the couples:

the embryos remaining after the transplantation in example 1 are subjected to PGT-M detection, embryos (with normal chromosome CNV) without the mutation are selected for transplantation, the embryo is subjected to pregnancy at 18 weeks +, amniotic fluid puncture karyotype analysis, and COL2A1 gene c.3944G > A (p.Cys1315Tyr) mutation detection to further determine that no mutation exists at the site, genomic DNA is directly extracted from peripheral blood, tissues or amniotic fluid of a subject, a fragment of COL2A1 gene exon 52 c.3944G > A (p.Cys1315Tyr) is subjected to PCR amplification and Sanger sequencing, and the sequencing result is compared with a reference sequence (NM _001844) of the COL2A1 gene. Ultrasonic follow-up visit, and postnatal follow-up visit.

The experimental results are as follows:

1. from the gene level, the fetus (M3944, II-2) was not suggested to carry the COL2A1 gene c.3944G > A (p.Cys1315Tyr) variation (FIG. 9).

2. Ultrasound suggests no abnormality, normal newborn development after birth, no skeletal deformity, etc. (fig. 10).

Sequence listing

<110> Huanghuan

<120> pathogenic gene COL1A2 mutation of bone dysplastic disease and detection reagent thereof

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gggactgcct ggtgctcctg gtctgagggg tcttcctggc aaagatggtg agacaggtgc 2100

tgcaggaccc cctggccctg ctggacctgc tggtgaacga ggcgagcagg gtgctcctgg 2160

gccatctggg ttccagggac ttcctggccc tcctggtccc ccaggtgaag gtggaaaacc 2220

aggtgaccag ggtgttcccg gtgaagctgg agcccctggc ctcgtgggtc ccaggggtga 2280

acgaggtttc ccaggtgaac gtggctctcc cggtgcccag ggcctccagg gtccccgtgg 2340

cctccccggc actcctggca ctgatggtcc caaaggtgca tctggcccag caggcccccc 2400

tggggctcag ggccctccag gtcttcaggg aatgcctggc gagaggggag cagctggtat 2460

cgctgggccc aaaggcgaca ggggtgacgt tggtgagaaa ggccctgagg gagcccctgg 2520

aaaggatggt ggacgaggcc tgacaggtcc cattggcccc cctggcccag ctggtgctaa 2580

tggcgagaag ggagaagttg gacctcctgg tcctgcagga agtgctggtg ctcgtggcgc 2640

tccgggtgaa cgtggagaga ctgggccccc cggaccagcg ggatttgctg ggcctcctgg 2700

tgctgatggc cagcctgggg ccaagggtga gcaaggagag gccggccaga aaggcgatgc 2760

tggtgcccct ggtcctcagg gcccctctgg agcacctggg cctcagggtc ctactggagt 2820

gactggtcct aaaggagccc gaggtgccca aggccccccg ggagccactg gattccctgg 2880

agctgctggc cgcgttggac ccccaggctc caatggcaac cctggacccc ctggtccccc 2940

tggtccttct ggaaaagatg gtcccaaagg tgctcgagga gacagcggcc cccctggccg 3000

agctggtgaa cccggcctcc aaggtcctgc tggaccccct ggcgagaagg gagagcctgg 3060

agatgacggt ccctctggtg ccgaaggtcc accaggtccc cagggtctgg ctggtcagag 3120

aggcatcgtc ggtctgcctg ggcaacgtgg tgagagagga ttccctggct tgcctggccc 3180

gtcgggtgag cccggcaagc agggtgctcc tggagcatct ggagacagag gtcctcctgg 3240

ccccgtgggt cctcctggcc tgacgggtcc tgcaggtgaa cctggacgag agggaagccc 3300

cggtgctgat ggcccccctg gcagagatgg cgctgctgga gtcaagggtg atcgtggtga 3360

gactggtgct gtgggagctc ctggagcccc tgggccccct ggctcccctg gccccgctgg 3420

tccaactggc aagcaaggag acagaggaga agctggtgca caaggcccca tgggaccctc 3480

aggaccagct ggagcccggg gaatccaggg tcctcaaggc cccagaggtg acaaaggaga 3540

ggctggagag cctggcgaga gaggcctgaa gggacaccgt ggcttcactg gtctgcaggg 3600

tctgcccggc cctcctggtc cttctggaga ccaaggtgct tctggtcctg ctggtccttc 3660

tggccctaga ggtcctcctg gccccgtcgg tccctctggc aaagatggtg ctaatggaat 3720

ccctggcccc attgggcctc ctggtccccg tggacgatca ggcgaaaccg gccctgctgg 3780

tcctcctgga aatcctggac cccctggtcc tccaggtccc cctggccctg gcatcgacat 3840

gtccgccttt gctggcttag gcccgagaga gaagggcccc gaccccctgc agtacatgcg 3900

ggccgaccag gcagccggtg gcctgagaca gcatgacgcc gaggtggatg ccacactcaa 3960

gtccctcaac aaccagattg agagcatccg cagccccgag ggctcccgca agaaccctgc 4020

tcgcacctgc agagacctga aactctgcca ccctgagtgg aagagtggag actactggat 4080

tgaccccaac caaggctgca ccttggacgc catgaaggtt ttctgcaaca tggagactgg 4140

cgagacttgc gtctacccca atccagcaaa cgttcccaag aagaactggt ggagcagcaa 4200

gagcaaggag aagaaacaca tctggtttgg agaaaccatc aatggtggct tccatttcag 4260

ctatggagat gacaatctgg ctcccaacac tgccaacgtc cagatgacct tcctacgcct 4320

gctgtccacg gaaggctccc agaacatcac ctaccactgc aagaacagca ttgcctatct 4380

ggacgaagca gctggcaacc tcaagaaggc cctgctcatc cagggctcca atgacgtgga 4440

gatccgggca gagggcaata gcaggttcac gtacactgcc ctgaaggatg gctgcacgaa 4500

acataccggt aagtggggca agactgttat cgagtaccgg tcacagaaga cctcacgcct 4560

ccccatcatt gacattgcac ccatggacat aggagggccc gagcaggaat tcggtgtgga 4620

catagggccg gtctgcttct tgtaaaaacc tgaacccaga aacaacacaa tccgttgcaa 4680

acccaaagga cccaagtact ttccaatctc agtcactcta ggactctgca ctgaatggct 4740

gacctgacct gatgtccatt catcccaccc tctcacagtt cggacttttc tcccctctct 4800

ttctaagaga cctgaactgg gcagactgca aaataaaatc tcggtgttct atttatttat 4860

tgtcttcctg taagaccttc gggtcaaggc agaggcagga aactaactgg tgtgagtcaa 4920

atgccccctg agtgactgcc cccagcccag gccagaagac ctcccttcag gtgccgggcg 4980

caggaactgt gtgtgtccta cacaatggtg ctattctgtg tcaaacacct ctgtattttt 5040

taaaacatca attgatatta aaaatgaaaa gattattgga aagtaca 5087

<210> 2

<211> 1487

<212> PRT

<213> human (Homo sapiens)

<400> 2

Met Ile Arg Leu Gly Ala Pro Gln Thr Leu Val Leu Leu Thr Leu Leu

1 5 10 15

Val Ala Ala Val Leu Arg Cys Gln Gly Gln Asp Val Gln Glu Ala Gly

20 25 30

Ser Cys Val Gln Asp Gly Gln Arg Tyr Asn Asp Lys Asp Val Trp Lys

35 40 45

Pro Glu Pro Cys Arg Ile Cys Val Cys Asp Thr Gly Thr Val Leu Cys

50 55 60

Asp Asp Ile Ile Cys Glu Asp Val Lys Asp Cys Leu Ser Pro Glu Ile

65 70 75 80

Pro Phe Gly Glu Cys Cys Pro Ile Cys Pro Thr Asp Leu Ala Thr Ala

85 90 95

Ser Gly Gln Pro Gly Pro Lys Gly Gln Lys Gly Glu Pro Gly Asp Ile

100 105 110

Lys Asp Ile Val Gly Pro Lys Gly Pro Pro Gly Pro Gln Gly Pro Ala

115 120 125

Gly Glu Gln Gly Pro Arg Gly Asp Arg Gly Asp Lys Gly Glu Lys Gly

130 135 140

Ala Pro Gly Pro Arg Gly Arg Asp Gly Glu Pro Gly Thr Pro Gly Asn

145 150 155 160

Pro Gly Pro Pro Gly Pro Pro Gly Pro Pro Gly Pro Pro Gly Leu Gly

165 170 175

Gly Asn Phe Ala Ala Gln Met Ala Gly Gly Phe Asp Glu Lys Ala Gly

180 185 190

Gly Ala Gln Leu Gly Val Met Gln Gly Pro Met Gly Pro Met Gly Pro

195 200 205

Arg Gly Pro Pro Gly Pro Ala Gly Ala Pro Gly Pro Gln Gly Phe Gln

210 215 220

Gly Asn Pro Gly Glu Pro Gly Glu Pro Gly Val Ser Gly Pro Met Gly

225 230 235 240

Pro Arg Gly Pro Pro Gly Pro Pro Gly Lys Pro Gly Asp Asp Gly Glu

245 250 255

Ala Gly Lys Pro Gly Lys Ala Gly Glu Arg Gly Pro Pro Gly Pro Gln

260 265 270

Gly Ala Arg Gly Phe Pro Gly Thr Pro Gly Leu Pro Gly Val Lys Gly

275 280 285

His Arg Gly Tyr Pro Gly Leu Asp Gly Ala Lys Gly Glu Ala Gly Ala

290 295 300

Pro Gly Val Lys Gly Glu Ser Gly Ser Pro Gly Glu Asn Gly Ser Pro

305 310 315 320

Gly Pro Met Gly Pro Arg Gly Leu Pro Gly Glu Arg Gly Arg Thr Gly

325 330 335

Pro Ala Gly Ala Ala Gly Ala Arg Gly Asn Asp Gly Gln Pro Gly Pro

340 345 350

Ala Gly Pro Pro Gly Pro Val Gly Pro Ala Gly Gly Pro Gly Phe Pro

355 360 365

Gly Ala Pro Gly Ala Lys Gly Glu Ala Gly Pro Thr Gly Ala Arg Gly

370 375 380

Pro Glu Gly Ala Gln Gly Pro Arg Gly Glu Pro Gly Thr Pro Gly Ser

385 390 395 400

Pro Gly Pro Ala Gly Ala Ser Gly Asn Pro Gly Thr Asp Gly Ile Pro

405 410 415

Gly Ala Lys Gly Ser Ala Gly Ala Pro Gly Ile Ala Gly Ala Pro Gly

420 425 430

Phe Pro Gly Pro Arg Gly Pro Pro Gly Pro Gln Gly Ala Thr Gly Pro

435 440 445

Leu Gly Pro Lys Gly Gln Thr Gly Glu Pro Gly Ile Ala Gly Phe Lys

450 455 460

Gly Glu Gln Gly Pro Lys Gly Glu Pro Gly Pro Ala Gly Pro Gln Gly

465 470 475 480

Ala Pro Gly Pro Ala Gly Glu Glu Gly Lys Arg Gly Ala Arg Gly Glu

485 490 495

Pro Gly Gly Val Gly Pro Ile Gly Pro Pro Gly Glu Arg Gly Ala Pro

500 505 510

Gly Asn Arg Gly Phe Pro Gly Gln Asp Gly Leu Ala Gly Pro Lys Gly

515 520 525

Ala Pro Gly Glu Arg Gly Pro Ser Gly Leu Ala Gly Pro Lys Gly Ala

530 535 540

Asn Gly Asp Pro Gly Arg Pro Gly Glu Pro Gly Leu Pro Gly Ala Arg

545 550 555 560

Gly Leu Thr Gly Arg Pro Gly Asp Ala Gly Pro Gln Gly Lys Val Gly

565 570 575

Pro Ser Gly Ala Pro Gly Glu Asp Gly Arg Pro Gly Pro Pro Gly Pro

580 585 590

Gln Gly Ala Arg Gly Gln Pro Gly Val Met Gly Phe Pro Gly Pro Lys

595 600 605

Gly Ala Asn Gly Glu Pro Gly Lys Ala Gly Glu Lys Gly Leu Pro Gly

610 615 620

Ala Pro Gly Leu Arg Gly Leu Pro Gly Lys Asp Gly Glu Thr Gly Ala

625 630 635 640

Ala Gly Pro Pro Gly Pro Ala Gly Pro Ala Gly Glu Arg Gly Glu Gln

645 650 655

Gly Ala Pro Gly Pro Ser Gly Phe Gln Gly Leu Pro Gly Pro Pro Gly

660 665 670

Pro Pro Gly Glu Gly Gly Lys Pro Gly Asp Gln Gly Val Pro Gly Glu

675 680 685

Ala Gly Ala Pro Gly Leu Val Gly Pro Arg Gly Glu Arg Gly Phe Pro

690 695 700

Gly Glu Arg Gly Ser Pro Gly Ala Gln Gly Leu Gln Gly Pro Arg Gly

705 710 715 720

Leu Pro Gly Thr Pro Gly Thr Asp Gly Pro Lys Gly Ala Ser Gly Pro

725 730 735

Ala Gly Pro Pro Gly Ala Gln Gly Pro Pro Gly Leu Gln Gly Met Pro

740 745 750

Gly Glu Arg Gly Ala Ala Gly Ile Ala Gly Pro Lys Gly Asp Arg Gly

755 760 765

Asp Val Gly Glu Lys Gly Pro Glu Gly Ala Pro Gly Lys Asp Gly Gly

770 775 780

Arg Gly Leu Thr Gly Pro Ile Gly Pro Pro Gly Pro Ala Gly Ala Asn

785 790 795 800

Gly Glu Lys Gly Glu Val Gly Pro Pro Gly Pro Ala Gly Ser Ala Gly

805 810 815

Ala Arg Gly Ala Pro Gly Glu Arg Gly Glu Thr Gly Pro Pro Gly Pro

820 825 830

Ala Gly Phe Ala Gly Pro Pro Gly Ala Asp Gly Gln Pro Gly Ala Lys

835 840 845

Gly Glu Gln Gly Glu Ala Gly Gln Lys Gly Asp Ala Gly Ala Pro Gly

850 855 860

Pro Gln Gly Pro Ser Gly Ala Pro Gly Pro Gln Gly Pro Thr Gly Val

865 870 875 880

Thr Gly Pro Lys Gly Ala Arg Gly Ala Gln Gly Pro Pro Gly Ala Thr

885 890 895

Gly Phe Pro Gly Ala Ala Gly Arg Val Gly Pro Pro Gly Ser Asn Gly

900 905 910

Asn Pro Gly Pro Pro Gly Pro Pro Gly Pro Ser Gly Lys Asp Gly Pro

915 920 925

Lys Gly Ala Arg Gly Asp Ser Gly Pro Pro Gly Arg Ala Gly Glu Pro

930 935 940

Gly Leu Gln Gly Pro Ala Gly Pro Pro Gly Glu Lys Gly Glu Pro Gly

945 950 955 960

Asp Asp Gly Pro Ser Gly Ala Glu Gly Pro Pro Gly Pro Gln Gly Leu

965 970 975

Ala Gly Gln Arg Gly Ile Val Gly Leu Pro Gly Gln Arg Gly Glu Arg

980 985 990

Gly Phe Pro Gly Leu Pro Gly Pro Ser Gly Glu Pro Gly Lys Gln Gly

995 1000 1005

Ala Pro Gly Ala Ser Gly Asp Arg Gly Pro Pro Gly Pro Val Gly Pro

1010 1015 1020

Pro Gly Leu Thr Gly Pro Ala Gly Glu Pro Gly Arg Glu Gly Ser Pro

1025 1030 1035 1040

Gly Ala Asp Gly Pro Pro Gly Arg Asp Gly Ala Ala Gly Val Lys Gly

1045 1050 1055

Asp Arg Gly Glu Thr Gly Ala Val Gly Ala Pro Gly Ala Pro Gly Pro

1060 1065 1070

Pro Gly Ser Pro Gly Pro Ala Gly Pro Thr Gly Lys Gln Gly Asp Arg

1075 1080 1085

Gly Glu Ala Gly Ala Gln Gly Pro Met Gly Pro Ser Gly Pro Ala Gly

1090 1095 1100

Ala Arg Gly Ile Gln Gly Pro Gln Gly Pro Arg Gly Asp Lys Gly Glu

1105 1110 1115 1120

Ala Gly Glu Pro Gly Glu Arg Gly Leu Lys Gly His Arg Gly Phe Thr

1125 1130 1135

Gly Leu Gln Gly Leu Pro Gly Pro Pro Gly Pro Ser Gly Asp Gln Gly

1140 1145 1150

Ala Ser Gly Pro Ala Gly Pro Ser Gly Pro Arg Gly Pro Pro Gly Pro

1155 1160 1165

Val Gly Pro Ser Gly Lys Asp Gly Ala Asn Gly Ile Pro Gly Pro Ile

1170 1175 1180

Gly Pro Pro Gly Pro Arg Gly Arg Ser Gly Glu Thr Gly Pro Ala Gly

1185 1190 1195 1200

Pro Pro Gly Asn Pro Gly Pro Pro Gly Pro Pro Gly Pro Pro Gly Pro

1205 1210 1215

Gly Ile Asp Met Ser Ala Phe Ala Gly Leu Gly Pro Arg Glu Lys Gly

1220 1225 1230

Pro Asp Pro Leu Gln Tyr Met Arg Ala Asp Gln Ala Ala Gly Gly Leu

1235 1240 1245

Arg Gln His Asp Ala Glu Val Asp Ala Thr Leu Lys Ser Leu Asn Asn

1250 1255 1260

Gln Ile Glu Ser Ile Arg Ser Pro Glu Gly Ser Arg Lys Asn Pro Ala

1265 1270 1275 1280

Arg Thr Cys Arg Asp Leu Lys Leu Cys His Pro Glu Trp Lys Ser Gly

1285 1290 1295

Asp Tyr Trp Ile Asp Pro Asn Gln Gly Cys Thr Leu Asp Ala Met Lys

1300 1305 1310

Val Phe Cys Asn Met Glu Thr Gly Glu Thr Cys Val Tyr Pro Asn Pro

1315 1320 1325

Ala Asn Val Pro Lys Lys Asn Trp Trp Ser Ser Lys Ser Lys Glu Lys

1330 1335 1340

Lys His Ile Trp Phe Gly Glu Thr Ile Asn Gly Gly Phe His Phe Ser

1345 1350 1355 1360

Tyr Gly Asp Asp Asn Leu Ala Pro Asn Thr Ala Asn Val Gln Met Thr

1365 1370 1375

Phe Leu Arg Leu Leu Ser Thr Glu Gly Ser Gln Asn Ile Thr Tyr His

1380 1385 1390

Cys Lys Asn Ser Ile Ala Tyr Leu Asp Glu Ala Ala Gly Asn Leu Lys

1395 1400 1405

Lys Ala Leu Leu Ile Gln Gly Ser Asn Asp Val Glu Ile Arg Ala Glu

1410 1415 1420

Gly Asn Ser Arg Phe Thr Tyr Thr Ala Leu Lys Asp Gly Cys Thr Lys

1425 1430 1435 1440

His Thr Gly Lys Trp Gly Lys Thr Val Ile Glu Tyr Arg Ser Gln Lys

1445 1450 1455

Thr Ser Arg Leu Pro Ile Ile Asp Ile Ala Pro Met Asp Ile Gly Gly

1460 1465 1470

Pro Glu Gln Glu Phe Gly Val Asp Ile Gly Pro Val Cys Phe Leu

1475 1480 1485

<210> 3

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 3

tggacttagc tcatgcagat 20

<210> 4

<211> 17

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 4

tggattgggg tagacgc 17

<210> 5

<211> 21

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 5

aaggttttct gcaacatgga g 21

Claims (2)

1. The application of a reagent for detecting the mutant COL2A1 gene in preparing a detection reagent for the osteogenesis imperfecta disease; the mutant COL2a1 is either a heterozygous or homozygous mutation c.3944g > a, and the gene numbering of the wild-type COL2a1 gene in the NCBI database is: NM-001844.4, the nucleotide of 3944bp of CDS is mutated from G to A, and the rest is the same as wild type.

2. The use according to claim 1, wherein the reagent for detecting the mutant COL2A1 gene is selected from one or more of a probe and a primer for detecting the mutant COL2A1 gene.

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