Patent Application
20170226584
The present disclosure belongs to the field of medical diagnosis, which relates to a product for diagnosing diseases and application thereof, and particularly relates to a product for diagnosing congenital scoliosis and application thereof.
Array-comparative genomic hybridization (Array-CGH) is a high-throughput analytical technology developed on the basis of traditional CGH. With this technology, BAC cloned DNA or oligonucleotides are made into a microarray for replacing metaphase chromosomes taken as a hybridization target for detection in the traditional CGH detection, which not only improves resolution but also provides precise localization. Meanwhile, each chromosome can be recognized by computer software, which overcomes the limitation that experienced staff are required for chromosome identification, thus providing a relatively ideal method for the rapid and comprehensive analysis of changes in DNA copy numbers and the instability detection of chromosomes. In this technology, after the genomic DNA is extracted from tissue cells, non-specific repetitive sequences of same amount of different fluorescently labeled samples and reference DNA are sealed by human Cot-1 DNA, and the labeled samples and reference DNA are hybridized simultaneously to the microarray composed of DNA or oligonucleotides. Changes in the copy numbers of the genomic DNA to be detected in corresponding sequences or genes are reflected by the fluorescence ratio of two types of signals on each target spot of the microarray. Since the first article about utilizing the gene chip technology to study gene levels issued in the journal Science by Schena et al. from Stanford University in 1995, this technology has been applied to the screening of genes and diagnostic indicators with respect to the occurrence and development of various congenitally handicapped and neoplastic diseases, especially has been applied to the studies on molecular subtyping of various malignant tumors and prediction of therapeutic response, tumors metastasis and recurrence and prognosis, and great achievements have been made. The main contents of the study include changes in tumor gene copy number, specific gene region analysis and a series of clinical application related research, such as assisting in pathological type diagnosis, screening tumor prognosis related markers and so on.
Congenital scoliosis (CS) is a common spinal disease, the neonatal morbidity is 0.5-1%. The clinical manifestation of CS is a scoliosis of more than 10 degrees, which is due to the spinal longitudinal growth imbalance caused by the spinal deformity (such as hemivertebrae deformity, segmental disorder, butterfly vertebrae, fused ribs, etc.) during the embryonic development process. CS can affect the physical and mental health, and has become a major factor in adolescent disability.
In the past, it is believed that most of the congenital scoliosis is not hereditary but caused by environmental factors in the development process of the embryo. In recent years, studies show that genetic factors are involved in the pathogenesis of CS. Previous genetic manipulation experiments in animal models show that genetic defects lead to spinal abnormalities. Interestingly, it is shown that some mutations in human genes (e.g., DLL3, HEST, MESP2 and T) are involved in the CS process; however, these mutations can be inherited from phenotypically normal family members. Phenotypic differences caused by identical mutations within the family are indicative of the complexities of human CS genetic variation. Interactions between genes and the environment are proposed to explain the above phenomena.
Several studies have reported that patients with a human chromosome 16p11.2 microdeletion have a CS phenotype, so we hypothesize that genetic modifying factors and cofactors may be another mechanism for CS genetic variation. About 0.6 Mb deletion of human chromosome 16p11.2 is a rare human mutation, the mutation frequency is about 0.02%. This deletion can cause neurodevelopmental related diseases (e.g., autism and obesity). Interestingly, the phenotype of CS has recently been found in a small number of patients with the 16p11.2 microdeletions, which suggests that 16p11.2 microdeletion may be involved in the pathogenesis of CS. In addition, the low penetrance of 16p11.2 microdeletion in CS also highlights the complexity of the human CS genetic mechanism.
Although CS is often found in infants or early childhood, it is not manifested until their adolescence for many children. Due to the lack of diagnostic knowledge and diagnostic means and other reasons, the lesion is often ignored by parents and doctors, and not found until after the obvious development of deformity. Now, the usual methods of diagnosing congenital scoliosis include X-ray, MRI, and so on, but these methods are only applicable to patients with obvious lesions, and not applicable to those potential patients who have not yet an obvious phenotype, therefore, the development of a sensitive method capable of diagnosing the congenital scoliosis in early stage is a problem need to be solved.
The object of the present disclosure is to provide a product for diagnosing congenital scoliosis, and compared with the detection by using medical instruments traditionally, the detection by using the product is more sensitive, and is suitable for the early diagnosis of congenital scoliosis. The present disclosure also provides a method for diagnosing congenital scoliosis.
The object of the present disclosure is achieved by the following technical solutions:
In one aspect, the present disclosure provides a product for diagnosing congenital scoliosis, and the product can detect whether there is a mutation in a chromosome 16p11.2 region or not. The product for diagnosing congenital scoliosis provided by the present disclosure may be a diagnostic kit, and the diagnostic kit includes a reagent capable of detecting whether a mutation exists in the chromosome 16p11.2 region or not.
Mutations in the chromosome 16p11.2 region include nucleotide deletions, nucleotide insertions, and nucleotide mutations. The nucleotide microdeletion in the chromosome 16p11.2 region is a deletion of a nucleotide sequence with a length of 0.6 Mb in the chromosome 16p11.2 region, referred to as a 16p11.2 microdeletion. In an implementation, the reagent in the kit for diagnosing congenital scoliosis provided by the present disclosure comprises a reagent capable of detecting whether the 16p11.2 microdeletion exists or not, the reagent comprises primers for amplifying a nucleotide sequence having a length of 0.6 Mb located between 29.5 Mb and 30.1 Mb in the chromosome 16p11.2 region, and the sequences of the primers are as follows: P1 site forward primer 5′-GGGGAAGGAACTTACATGAC-3′, P1 site reverse primer 5′-TCGTGTTTCCCTGTTGTACC-3′, PA site forward primer 5′-GGTCTAAGCCACACACTAAC-3′, PA site reverse primer 5′-TGAGTTTAGGGACCAATCTA-3′, PB site forward primer 5′-GCTGCCAGTATGTGACCGAGA-3′, PB site reverse primer 5′-GGGTGGAGGAGAGGATAGGG-3′.
As an alternative embodiment, the reagent in the kit for diagnosing congenital scoliosis provided by the present disclosure comprises a reagent capable of detecting the genotypes of the TBX6 gene rs3809624 site and/or rs3809627 site in the chromosome 16p11.2 region. The reagent capable of detecting the genotypes of the TBX6 gene rs3809624 site and/or rs3809627 site in the chromosome 16p11.2 region comprises primers for constructing a recombinant vector containing the TBX6 gene, the sequences of the primers are as follows: T7 reverse primer 5′-TCGCCCTATAGTGAGTCGTATTACA-3′, SP6 reverse primer 5′-GTATTCTATAGTGTCACCTAAATAG-3′, CS forward primer 5′-GACTCACTATAGGGCGAGGGGAAGGGAGCGGGAGGTTTGTG-3′, CS reverse primer 5′-GGTGACACTATAGAATACGCGCTGAGCCTGCCGGGAAGTGTAGT-3′. Preferably, the reagent capable of detecting the genotypes of the TBX6 gene rs3809624 site and/or rs3809627 site in the chromosome 16p11.2 region further comprises primers for the nucleotide sequence sequencing of the TBX6 gene, the sequences of the primers are as follows:
As an alternative embodiment, the reagent in the kit for diagnosing congenital scoliosis provided by the present disclosure comprises a reagent capable of detecting whether a TBX6 gene nucleotide frameshift mutation exists in the chromosome 16p11.2 region or not, the above-mentioned reagent comprises primers for amplifying the TBX6 gene, and the sequences of the primers are as follows: forward primer 5′-TAGGGAGAGGGCTCTGTTCTCATGG-3′, reverse primer 5′-GCGTCCCAGGGAGGCAACCG-3′. Preferably, the reagent capable of detecting whether the TBX6 gene nucleotide frameshift mutation exists in the chromosome 16p11.2 region or not further comprises primers for the nucleotide sequence sequencing of the TBX6 gene, and the sequences of the primers are as follows:
As an alternative embodiment, the reagent in the kit for diagnosing congenital scoliosis provided by the present disclosure comprises a reagent capable of detecting whether the 16p11.2 microdeletion exists or not, and a reagent capable of detecting the genotypes of the TBX6 gene rs3809624 site and/or rs3809627 site in the chromosome 16p11.2 region. The reagent capable of detecting whether the 16p11.2 microdeletion exists or not comprises primers for amplifying a nucleotide sequence having a length of 0.6 Mb of the chromosome 16p11.2 region, and the sequences of the primers are as follows: P1 site forward primer 5′-GGGGAAGGAACTTACATGAC-3′, P1 site reverse primer 5′-TCGTGTTTCCCTGTTGTACC-3′, PA site forward primer 5′-GGTCTAAGCCACACACTAAC-3′, PA site reverse primer 5′-TGAGTTTAGGGACCAATCTA-3′, PB site forward primer 5′-GCTGCCAGTATGTGACCGAGA-3′, PB site reverse primer 5′-GGGTGGAGGAGAGGATAGGG-3′. The reagent capable of detecting the genotypes of the TBX6 gene rs3809624 site and/or rs3809627 site in the chromosome 16p11.2 region comprises primers for constructing a recombinant vector containing the TBX6 gene, and the sequences of the primers are as follows: T7 reverse primer 5′-TCGCCCTATAGTGAGTCGTATTACA-3′, SP6 reverse primer 5′-GTATTCTATAGTGTCACCTAAATAG-3′, CS forward primer 5′-GACTCACTATAGGGCGAGGGGAAGGGAGCGGGAGGTTTGTG-3′, CS reverse primer 5′-GGTGACACTATAGAATACGCGCTGAGCCTGCCGGGAAGTGTAGT-3′. Preferably, the reagent capable of detecting the genotypes of the TBX6 gene rs3809624 site and/or rs3809627 site in the chromosome 16p11.2 region also comprises primers for the nucleotide sequence sequencing of the TBX6 gene, and the sequences of the primers are as follows:
As an alternative embodiment, the reagent in the kit for diagnosing congenital scoliosis provided by the present disclosure comprises a reagent capable of detecting whether a TBX6 gene nucleotide frameshift mutation exists in the chromosome 16p11.2 region or not and a reagent capable of detecting the genotypes of the TBX6 gene rs3809624 site and/or rs3809627 site in the chromosome 16p11.2 region. The reagent capable of detecting whether the TBX6 gene nucleotide frameshift mutation exists in the chromosome 16p11.2 region or not comprises primers for amplifying the TBX6 gene, and the sequences of the primers are as follows: forward primer 5′-TAGGGAGAGGGCTCTGTTCTCATGG-3′, reverse primer 5′-GCGTCCCAGGGAGGCAACCG-3′. Preferably, the reagent capable of detecting whether the TBX6 gene nucleotide frameshift mutation exists in the chromosome 16p11.2 region or not further comprises primers for the nucleotide sequence sequencing of the TBX6 gene, and the sequences of the primers are as follows: 5′-CTCGAAGGGGTCCGAGAGG-3′, 5′-CTCCTTCCATAGCTCCCGGT-3′, 5′-GTTGCATACTGATCCCGAAT-3′, 5′-CTGCCCGAACTAGGTGTATG-3′, 5′-AATGGCTTCCTAACAGATGAC-3′, 5′-GAGCGGGAGGTTTGTGATG-3′, 5′-GGCAGCTGGAAACACAGGT-3′. The reagent capable of detecting the genotypes of the TBX6 gene rs3809624 site and/or rs3809627 site in the chromosome 16p11.2 region comprises primers for constructing a recombinant vector containing the TBX6 gene, and the sequences of the primers are as follows: T7 reverse primer 5′-TCGCCCTATAGTGAGTCGTATTACA-3′, SP6 reverse primer 5′-GTATTCTATAGTGTCACCTAAATAG-3′, CS forward primer 5′-GACTCACTATAGGGCGAGGGGAAGGGAGCGGGAGGTTTGTG-3′, CS reverse primer 5′-GGTGACACTATAGAATACGCGCTGAGCCTGCCGGGAAGTGTAGT-3′. Preferably, the reagent capable of detecting the genotypes of the TBX6 gene rs3809624 site and/or rs3809627 site in the chromosome 16p11.2 region further comprises primers for the nucleotide sequence sequencing of the TBX6 gene, and the sequences of the primers are as follows:
As an alternative embodiment, the reagent in the kit for diagnosing congenital scoliosis provided by the present disclosure comprises a reagent capable of detecting whether a 16p11.2 microdeletion exists or not, and a reagent capable of detecting whether a TBX6 gene nucleotide frameshift mutation exists in the chromosome 16p11.2 region or not. The reagent capable of detecting whether the 16p11.2 microdeletion exists or not comprises primers for amplifying a nucleotide sequence having a length of 0.6 Mb of the chromosome 16p11.2 region, and the sequences of the primers are as follows: P1 site forward primer 5′-GGGGAAGGAACTTACATGAC-3′, P1 site reverse primer 5′-TCGTGTTTCCCTGTTGTACC-3′, PA site forward primer 5′-GGTCTAAGCCACACACTAAC-3′, PA site reverse primer 5′-TGAGTTTAGGGACCAATCTA-3′, PB site forward primer 5′-GCTGCCAGTATGTGACCGAGA-3′, PB site reverse primer 5′-GGGTGGAGGAGAGGATAGGG-3′. The reagent capable of detecting whether the TBX6 gene nucleotide frameshift mutation exists in the chromosome 16p11.2 region or not comprises primers for amplifying the TBX6 gene, and the sequences of the primers are as follows: forward primer 5′-TAGGGAGAGGGCTCTGTTCTCATGG-3′, reverse primer 5′-GCGTCCCAGGGAGGCAACCG-3′. Preferably, the reagent capable of detecting whether the TBX6 gene nucleotide frameshift mutation exists in the chromosome 16p11.2 region or not also comprises primers for the nucleotide sequence sequencing of the TBX6 gene, and the sequences of the primers are as follows: 5′-CTCGAAGGGGTCCGAGAGG-3′, 5′-CTCCTTCCATAGCTCCCGGT-3′, 5′-GTTGCATACTGATCCCGAAT-3′, 5′-CTGCCCGAACTAGGTGTATG-3′, 5′-AATGGCTTCCTAACAGATGAC-3′, 5′-GAGCGGGAGGTTTGTGATG-3′, 5′-GGCAGCTGGAAACACAGGT-3′.
As an alternative embodiment, the reagent in the kit for diagnosing congenital scoliosis provided by the present disclosure comprises a reagent capable of detecting whether a 16p11.2 microdeletion exists or not, a reagent capable of detecting whether a TBX6 gene nucleotide frameshift mutation exists in the chromosome 16p11.2 region or not, and a reagent capable of detecting the genotypes of the TBX6 gene rs3809624 site and/or rs3809627 site in the chromosome 16p11.2 region. The reagent capable of detecting whether the 16p11.2 microdeletion exists or not comprises primers for amplifying a nucleotide sequence having a length of 0.6 Mb of the chromosome 16p11.2 region, and the sequences of the primers are as follows: P1 site forward primer 5′-GGGGAAGGAACTTACATGAC-3′, P1 site reverse primer 5′-TCGTGTTTCCCTGTTGTACC-3′, PA site forward primer 5′-GGTCTAAGCCACACACTAAC-3′, PA site reverse primer 5′-TGAGTTTAGGGACCAATCTA-3′, PB site forward primer 5′-GCTGCCAGTATGTGACCGAGA-3′, PB site reverse primer 5′-GGGTGGAGGAGAGGATAGGG-3′. The reagent capable of detecting whether the TBX6 gene nucleotide frameshift mutation exists in the chromosome 16p11.2 region or not comprises primers for amplifying the TBX6 gene, and the sequences of the primers are as follows: forward primer 5′-TAGGGAGAGGGCTCTGTTCTCATGG-3′, reverse primer 5′-GCGTCCCAGGGAGGCAACCG-3′. Preferably, the reagent capable of detecting whether the TBX6 gene nucleotide frameshift mutation exists in the chromosome 16p11.2 region or not also comprises primers for the nucleotide sequence sequencing of the TBX6 gene, and the sequences of the primers are as follows: 5′-CTCGAAGGGGTCCGAGAGG-3′, 5′-CTCCTTCCATAGCTCCCGGT-3′, 5′-GTTGCATACTGATCCCGAAT-3′, 5′-CTGCCCGAACTAGGTGTATG-3′, 5′-AATGGCTTCCTAACAGATGAC-3′, 5′-GAGCGGGAGGTTTGTGATG-3′, 5′-GGCAGCTGGAAACACAGGT-3′. The reagent capable of detecting the genotypes of the TBX6 gene rs3809624 site and/or rs3809627 site in the chromosome 16p11.2 region comprises primers for constructing a recombinant vector containing the TBX6 gene, and the sequences of the primers are as follows: T7 reverse primer 5′-TCGCCCTATAGTGAGTCGTATTACA-3′, SP6 reverse primer 5′-GTATTCTATAGTGTCACCTAAATAG-3′, CS forward primer 5′-GACTCACTATAGGGCGAGGGGAAGGGAGCGGGAGGTTTGTG-3′, CS reverse primer 5′-GGTGACACTATAGAATACGCGCTGAGCCTGCCGGGAAGTGTAGT-3′. Preferably, the reagent capable of detecting the genotypes of the TBX6 gene rs3809624 site and/or rs3809627 site in the chromosome 16p11.2 region also comprises primers for the nucleotide sequence sequencing of the TBX6 gene, and the sequences of the primers are as follows:
Preferably, the diagnostic kit of the present disclosure further comprises an extraction reagent for genomic DNA. More preferably, the DNA extraction reagent comprises phenol, chloroform, isopropanol, and ethanol.
In another aspect, the present disclosure provides a use of the above-mentioned diagnostic product in the preparation of a product for diagnosing congenital scoliosis and/or a product for treating congenital scoliosis.
In yet another aspect, the present disclosure provides a method for detecting a mutation in a chromosome 16p11.2 region, the method comprising a method for detecting a chromosome 16p11.2 microdeletion. Preferably, the method for detecting the chromosome 16p11.2 microdeletion comprises using high-density oligonucleotide comparative genomic hybridization microarrays. More preferably, the method of detecting the chromosome 16p11.2 microdeletion comprises using QPCR for primary screening and using the high-density oligonucleotide comparative genomic hybridization microarray for confirmation.
The specific operation of the QPCR is: selecting two detection sites PA and PB in the 16p11.2 microdeletion region, selecting a reference site P1 outside the 16p11.2 microdeletion region, designing primers by utilizing the combination of P1 and PA or P1 and PB to amplify different fragments, and detecting the existing amount of the fragments by a conventional QPCR method. In an implementation, the sequences of the above-mentioned primers are as follows: P1 site forward primer 5′-GGGGAAGGAACTTACATGAC-3′, P1 site reverse primer 5′-TCGTGTTTCCCTGTTGTACC-3′, PA site forward primer 5′-GGTCTAAGCCACACACTAAC-3′, PA site reverse primer 5′-TGAGTTTAGGGACCAATCTA-3′, PB site forward primer 5′-GCTGCCAGTATGTGACCGAGA-3′, PB site reverse primer 5′-GGGTGGAGGAGAGGATAGGG-3′.
As an alternative embodiment, a method for detecting a mutation in a chromosome 16p11.2 region of the present disclosure comprises a method for detecting a TBX6 gene frameshift mutation and/or a method for detecting the genotypes of the rs3809624 site and/or the rs3809627 site in a TBX6 gene. The method for detecting a TBX6 gene frameshift mutation comprises: (1) designing reasonable primers for amplifying a TBX6 gene coding region and an upstream regulatory region of nearly 1 kb; (2) sequencing the amplified fragments in step (1) by using sequencing primers. Preferably, the sequences of the amplification primers are as follows: forward primer 5′-TAGGGAGAGGGCTCTGTTCTCATGG-3′; reverse primer 5′-GCGTCCCAGGGAGGCAACCG-3′. The sequences of the sequencing primers are as follows: 5′-CTCGAAGGGGTCCGAGAGG-3′, 5′-CTCCTTCCATAGCTCCCGGT-3′, 5′-GTTGCATACTGATCCCGAAT-3′, 5′-CTGCCCGAACTAGGTGTATG-3′, 5′-AATGGCTTCCTAACAGATGAC-3′, 5′-GAGCGGGAGGTTTGTGATG-3′, 5′-GGCAGCTGGAAACACAGGT-3′. The method for detecting the genotypes of the rs3809624 site and/or the rs3809627 site in the TBX6 gene comprises: (1) amplifying a vector and inserted DNA fragments, connecting and constructing a recombinant vector of the TBX6 gene; (2) transforming the recombinant vector into competent cells of Escherichia coli; (3) selecting clones, designing sequencing primers and detecting sequences by sanger sequencing. Preferably, the vector is pGEM-T. The sequences of the primers required for constructing the recombinant vector of the TBX6 gene are as follows: T7 reverse primer 5′-TCGCCCTATAGTGAGTCGTATTACA-3′, SP6 reverse primer 5′-GTATTCTATAGTGTCACCTAAATAG-3′, CS forward primer 5′-GACTCACTATAGGGCGAGGGGAAGGGAGCGGGAGGTTTGTG-3′, CS reverse primer 5′-GGTGACACTATAGAATACGCGCTGAGCCTGCCGGGAAGTGTAGT-3′. Preferably, the sequences of the sequencing primers are as follows: 5′-CTCGAAGGGGTCCGAGAGG-3′, 5′-CTCCTTCCATAGCTCCCGGT-3′, 5′-GTTGCATACTGATCCCGAAT-3′, 5′-CTGCCCGAACTAGGTGTATG-3′, 5′-AATGGCTTCCTAACAGATGAC-3′, 5′-GAGCGGGAGGTTTGTGATG-3′, 5′-GGCAGCTGGAAACACAGGT-3′.
As an alternative embodiment, a method for detecting a mutation in a chromosome 16p11.2 region of the present disclosure comprises a method for detecting a chromosome 16p11.2 microdeletion and a method for detecting a frameshift mutation in a TBX6 gene, and/or a method for detecting the genotypes of the rs3809624 site and/or the rs3809627 site in the TBX6 gene. Preferably, the method for detecting the chromosome 16p11.2 microdeletion comprises using a high-density oligonucleotide comparative genomic hybridization microarray. More preferably, the method for detecting the chromosome 16p11.2 microdeletion comprises using QPCR for primary screening and using the high-density oligonucleotide comparative genomic hybridization microarray for verification. The specific operation of the QPCR is: selecting two detection sites PA and PB in the 16p11.2 microdeletion region, selecting a reference site P1 outside the 16p11.2 microdeletion region, designing primers by utilizing P1 and PA or P1 and PB combination to amplify different fragments, and detecting the existing amount of the fragments by a conventional QPCR method. In an implementation, the sequences of the above-mentioned primers are as follows: P1 site forward primer 5′-GGGGAAGGAACTTACATGAC-3′, P1 site reverse primer 5′-TCGTGTTTCCCTGTTGTACC-3′; PA site forward primer 5′-GGTCTAAGCCACACACTAAC-3′, PA site reverse primer 5′-TGAGTTTAGGGACCAATCTA-3′; PB site forward primer 5′-GCTGCCAGTATGTGACCGAGA-3′, PB site reverse primer 5′-GGGTGGAGGAGAGGATAGGG-3′. The method for detecting a frameshift mutation in the TBX6 gene comprises: (1) designing proper primers to amplify a TBX6 gene coding region and an upstream regulatory region of nearly 1 kb; (2) sequencing the amplified fragments in step (1) by using sequencing primers. Preferably, the sequences of the amplification primers are as follows: forward primer 5′-TAGGGAGAGGGCTCTGTTCTCATGG-3′; reverse primer 5′-GCGTCCCAGGGAGGCAACCG-3′. The sequences of the sequencing primers are as follows: 5′-CTCGAAGGGGTCCGAGAGG-3′, 5′-CTCCTTCCATAGCTCCCGGT-3′, 5′-GTTGCATACTGATCCCGAAT-3′, 5′-CTGCCCGAACTAGGTGTATG-3′, 5′-AATGGCTTCCTAACAGATGAC-3′, 5′-GAGCGGGAGGTTTGTGATG-3′, 5′-GGCAGCTGGAAACACAGGT-3′. The method for detecting the genotypes of the rs3809624 site and/or the rs3809627 site in the TBX6 gene comprises: (1) amplifying a vector and inserted DNA fragments, connecting and constructing a recombinant vector of the TBX6 gene; (2) transforming the recombinant vector into competent cells of Escherichia coli; (3) selecting clones, designing sequencing primers and detecting sequences by sanger sequencing. Preferably, the vector is pGEM-T. The sequences of the primers required for constructing the recombinant vector of the TBX6 gene are as follows: T7 reverse primer 5′-TCGCCCTATAGTGAGTCGTATTACA-3′, SP6 reverse primer 5′-GTATTCTATAGTGTCACCTAAATAG-3′, CS forward primer 5′-GACTCACTATAGGGCGAGGGGAAGGGAGCGGGAGGTTTGTG-3′, CS reverse primer 5′-GGTGACACTATAGAATACGCGCTGAGCCTGCCGGGAAGTGTAGT-3′. Preferably, the sequences of the sequencing primers are as follows: 5′-CTCGAAGGGGTCCGAGAGG-3′, 5′-CTCCTTCCATAGCTCCCGGT-3′, 5′-GTTGCATACTGATCCCGAAT-3′, 5′-CTGCCCGAACTAGGTGTATG-3′, 5′-AATGGCTTCCTAACAGATGAC-3′, 5′-GAGCGGGAGGTTTGTGATG-3′, 5′-GGCAGCTGGAAACACAGGT-3′.
Preferably, the method for detecting the mutation in the chromosome 16p11.2 region provided by the present disclosure further comprises a method for extracting genomic DNA.
In yet another aspect, the present disclosure provides a method for diagnosing congenital scoliosis, the method comprises the following steps:
(1) extracting genomic DNA from an individual to be diagnosed;
(2) detecting whether a mutation exists in the chromosome 16p11.2 region or not. Preferably, the detecting whether a 16p11.2 mutation exists in the chromosome 16p11.2 region or not comprises: detecting whether a microdeletion exists in the chromosome 16p11.2 region or not, detecting the haplotype of two SNP sites of rs3809624-rs3809627 in the TBX6 gene located on the homologous chromosome without 16p11.2 microdeletions. When a 16p11.2 microdeletion exists in the chromosome 16p11.2 region, meanwhile the haplotype of two SNP sites of rs3809624-rs3809627 in the TBX6 gene located on the homologous chromosome without 16p11.2 microdeletion is C-A, an individual is diagnosed as a patient with congenital scoliosis.
Preferably, the detecting whether a mutation exists in the chromosome 16p11.2 region or not comprises: detecting whether a nucleotide frameshift mutation exists in the TBX6 gene within the chromosome 16p11.2 region or not, detecting the haplotype of two SNP sites of rs3809624-rs3809627 in the TBX6 gene located on the homologous chromosome without TBX6 gene nucleotide frameshift mutations. When one or more of nucleotide frameshift mutations caused by the following single nucleotide insertions and a double nucleotide deletion: insertion of T at C1248 site, insertion of C at C263 site, insertion of G at C697 site, insertion of C at C1167 site, double deletion of AG at C1179 site exist in the TBX6 gene in the chromosome 16p11.2 region, meanwhile the haplotype of two SNP sites of rs3809624-rs3809627 in the TBX6 gene located on the homologous chromosome without TBX6 gene nucleotide frameshift mutation is C-A, an individual is diagnosed as a patient with congenital scoliosis.
Preferably, the genomic DNA is extracted from peripheral leukocytes. The extraction of the genomic DNA from an individual to be tested is carried out by conventional techniques which are well known to those skilled in the art.
The method for detecting a chromosome 16p11.2 microdeletion comprises using a high-density oligonucleotide comparative genomic hybridization microarray and QPCR. Preferably, in the present disclosure, a QPCR method is used for the primary screening of the chromosome 16p11.2 microdeletion, and then the comparative genomic hybridization microarray is used for verification. The comparative genomic hybridization microarray includes a genome-wide genomic hybridization microarray and a targeted genomic hybridization microarray designed by a customer, the latter is prepared via designing oligonucleotides according to a selected target region by the customer.
Principles of using QPCR to detect the chromosome 16p11.2 microdeletion are: selecting two detection sites (named as PA and PB) in the chromosome 16p11.2 microdeletion region, selecting a reference site (named as P1) outside the chromosome 16p11.2 microdeletion region, designing primers by utilizing P1 and PA or P1 and PB combination to amplify different fragments, and detecting the existing amount of the fragments by QPCR.
An implementation of detecting the haplotype of two SNP sites of rs3809624-rs3809627 in the TBX6 gene located on the homologous chromosome without 16p11.2 microdeletions is: using a ClonExpress One Step Cloning Kit (Vazyme) to detect a halotype of a common TBX6 gene variant; using a pGEM-T vector as a template for the amplification of the vector to amplify the vector and inserted DNA fragments respectively, and connecting; transforming the recombinant vector into competent cells of Escherichia coli; selecting clones, and detecting sequences by Sanger sequencing.
The method for detecting the nucleotide frameshift mutation in the TBX6 gene comprises the following steps: (1) amplifying a full-length TBX6 gene; (2) sequencing by Sanger.
In an implementation of the present disclosure, a frameshift mutation caused by nucleotide insertion occurs in the TBX6 gene. TBX6 gene expression amount is reduced when the frameshift mutation occurs, and of course presence of other frameshift mutations which also affect TBX6 gene expression is not excluded.
Experiments in the present disclosure prove that TBX6 gene expression is down-regulated when the haplotype of rs3809624-rs3809627 sites is C-A. Detailed operation steps for the demonstration are: (1) amplifying a 1120 bp DNA fragment of an upstream regulatory element of the TBX6 gene, and constructing a normal DNA fragment, a DNA fragment with only rs3809624 site mutated to C, a DNA fragment with only rs3809627 site mutated to A, a DNA fragment with rs3809624 site and rs3809627 site mutated at the same time onto a pGL3-Basic vector respectively; (2) transfecting recombinant vectors into HEK293T, HepG2, Hela cells cultured in vitro; (3) after transfection for a certain period of time, lysing the cells and obtaining supernatants to detect the activity of luciferase by using a Dual-Luciferase Reporter Gene Assay system.
In an implementation of the present disclosure, human cells are HEK293T, HepG2, and Hela. Preferably, the vector with a luciferase reporter gene used in the present disclosure is pGL3-Basic vector, and a control vector is pRL-TK.
By utilizing QPCR and a high-density oligonucleotide comparative genomic hybridization technique, the present disclosure identifies 12 individuals with the chromosome 16p11.2 microdeletion from a population of 161 patients who are not related to each other and suffer from congenital scoliosis. Four individuals with the TBX6 gene frameshift mutation caused by single nucleotide insertion are simultaneously identified from the above population of patients by utilizing a DNA sequencing technique. Four cases of the single nucleotide insertion are: insertion of A at C1248 site, insertion of G at C263 site, insertion of C at C697 site, and insertion of G at C1167 site. The Chromosome deletion and the frameshift mutation are collectively referred to as nonsense mutations. 16 individuals from the population of 161 patients are identified to have a nonsense mutation, and the probability of the nonsense mutation in CS is 10.6%. By the same techniques, the present disclosure re-collects a population of 76 patients who are not related to each other and suffer from congenital scoliosis, and 5 individuals with the chromosome 16p11.2 microdeletion are identified. One individual with the TBX6 gene frameshift mutation caused by double nucleotide deletions is simultaneously identified from the above population. The case of double nucleotide deletions is: double deletion of AG at C1179 site. 6 individuals from the population of 76 patients are identified to have the nonsense mutation, and the probability of the nonsense mutation in CS is 7.9%. Combined with the results of the two experiments, it is found that the probability of the nonsense mutation in CS is between 7.9%-10.6%.
Two families with the chromosome 16p11.2 microdeletion are selected as objects of study, and the phenotype of each individual is analyzed. Although father or siblings of an individual with CS have a 16p11.2 microdeletion, they do not have the CS phenotype. It has been hypothesized that other factors assist and involve in the manifestation of the CS phenotype. When analyzing the haplotype of the TBX6 gene located on the homologous chromosome without the 16p11.2 microdeletion, it is found that when the haplotype of three SNP sites of rs2289292-rs3809624-rs3809627 is T-C-A, the individual with the chromosome 16p11.2 microdeletion exhibits CS, otherwise the individual does not exhibit CS even having the chromosome 16p11.2 microdeletion. When simultaneously detecting the haplotypes of three SNP sites of rs2289292-rs3809624-rs3809627 in the TBX6 gene located on another normal chromosome of the 16 individuals with nonsense mutations identified from the population of 161 patients and the 6 individuals with nonsense mutations identified from the population of 76 patients, it is found that haplotypes of the three SNP sites all are T-C-A. The mutation of rs2289292 of the three SNP sites does not alter protein encoding of the TBX6 gene. And rs3809624 and rs3809627 locate within the upstream regulatory sequence of the TBX6 gene, effects of the mutations of the rs3809624 and rs3809627 sites on gene expression are tested by a luciferase reporter system, and the results show that gene expression is inhibited when both rs3809624 and rs3809627 sites mutate. Since mutation at rs2289292 site does not affect the protein encoding of the TBX6 gene, and it has been reported that rs2289292 site and rs3809624 site are in a linkage disequilibrium region, the haplotype of rs2289292 site is T when the haplotype of the rs3809624 and rs3809627 sites is determined to be C-A.
Accordingly, the present disclosure discloses criteria for judging congenital scoliosis:
(1) when a chromosome 16p11.2 microdeletion exists, and the haplotype of two SNP sites of rs3809624-rs3809627 in the TBX6 gene located on the homologous chromosome without the 16p11.2 microdeletion is C-A, an individual is diagnosed as a patient with congenital scoliosis.
(2) when one or more of nucleotide frameshift mutations caused by the following single nucleotide insertions and a double nucleotide deletion: insertion of T at C1248 site, insertion of C at C263 site, insertion of G at C697 site, insertion of C at C1167 site, double deletion of AG at C1179 site exist in the TBX6 gene within the chromosome 16p11.2 region, and the haplotype of two SNP sites of rs3809624-rs3809627 in the TBX6 gene located on the homologous chromosome without frameshift mutations is C-A, an individual is diagnosed as a patient with congenital scoliosis.
Based on the above theory, the present disclosure develops a product for diagnosing congenital scoliosis. The product is capable of detecting whether the chromosome 16p11.2 is micro-deleted or not, detecting whether a TBX6 gene frameshift mutation exists or not, and determining the haplotype of two SNP sites of rs3809624-rs3809627 in the TBX6 gene located on the homologous chromosome without nonsense mutations.
Advantages and benefit effects of the present disclosure are as follows: this is the first time to reveal the genetic basis of human congenital scoliosis, and to diagnose congenital scoliosis through detecting deletions or nucleotide frameshift mutations in a gene and single nucleotide polymorphisms of a gene of an individual. A diagnostic kit for diagnosing congenital scoliosis prepared according to the above principle is sensitive and suitable for diagnosis of congenital scoliosis in early stage, and is capable of buying best time for early intervention for a patient.
The present disclosure is further described below with reference to implementations. It should be understood that these embodiments are used for construing the present disclosure only, but not limiting its scope. The experimental methods without specific conditions in the following embodiments are usually in accordance with the conventional conditions, or the manufacturer recommended conditions. Unless otherwise noted, the experimental methods used in the following examples are conventional methods. Unless otherwise noted, materials, reagents and the like used in the following examples are commercially available.
Supervision of the study: inventors of the present disclosure ensure the integrity and accuracy of data and analysis. The present disclosure has been approved by Ethics Committee of Chinese Academy of Medical Sciences & Peking Union Medical College, Institutes of Biomedical Sciences Fudan University, and Capital Institute of Pediatrics. All patients or family members thereof have provided handwritten informed consents to participate in the present disclosure.
Information of the objects of the study: 237 Han Chinese who are not related to each other and suffer from congenital scoliosis were recruited. All patients are recruited from patients with congenital scoliosis confirmed by imaging examination in Chinese Academy of Medical Sciences & Peking Union Medical College Hospital from October 2010 to June 2014. Patients with known syndromes such as Alagille syndrome, Goldenhar's syndrome, hemifacial microsomia, Klippel-Feil syndrome, spondylocostal dysostosis and VACTERL syndrome are excluded. Two families which have 16p11.2 microdeletions but exhibit different phenotypes within the family are recruited from Affiliated Children's Hospital of Capital Institute of Pediatrics. Informed consents are obtained from all family members. A total of 166 healthy Han Chinese, who do not suffer from congenital scoliosis and do not have a genetic deficiency, are randomly selected as control.
1. Blood Sampling and Extraction of Genomic DNA
5 ml morning fasting peripheral venous blood is collected from each object by using vacuum blood collection tubes containing EDTA anticoagulants, centrifugated at 3000 rpm/min for 10 min, and then the plasma, the leucocyte layer and erythrocytes are separated. If possible, granulocytes can be further extracted by using a lymphocyte separation medium. If impossible, the leucocyte layer can be directly subpackaged in 2 ml freezing tubes and frozen for storage at −80° C. for subsequent use.
The genomic DNA is extracted by a phenol-chloroform method, purity of the DNA is determined by ultraviolet spectrophotometry (OD260/280 ratio), and concentration of the DNA is determined by OD260, and after unified standardization the DNA is stored at −20° C. for subsequent use. Detailed steps are as follows:
(1) transferring the leucocyte suspension into a 5 ml centrifuge tube, adding a hemolytic reagent, centrifuging at 4000 rpm/min for 10 min after uniformly mixing by oscillating, then discarding the supernatant, and repeating the above process one time;
(2) adding 1 ml of extraction liquid into the precipitate, adding 8 μl of proteinase K after uniformly mixing, and keeping in water bath at 37° C. overnight;
(3) slightly cooling after taking out, then adding 1 ml of Tris-saturated phenol, inverting the tube up and down for 15 min to mix uniformly, and centrifuging at 4000 rpm/min for 10 min;
(4) carefully pipetting the supernatant, adding 60 μl of 3 M sodium acetate of pH 5.0, then adding isoamyl alcohol as equal volume of the supernatant, a flocculent white precipitate can be seen after gently shaking, and centrifuging at 10000 rpm/min for 2 min;
(5) adding about 1 ml of 75% alcohol into the precipitate, centrifuging at 8000 rpm/min for 2 min, and discarding the supernatant;
(6) adding about 1 ml of anhydrous alcohol into precipitate, centrifuging at 8000 rpm/min for 2 min, and drying after discarding the supernatant;
(7) dissolving the dried product in 100 μl of TE buffer, determining the purity of the DNA by measuring OD260/280 and OD260/230 ratios, estimating the average size of the gDNA by 1% agarose gel electrophoresis, and storing the DNA at −20° C. after unified standardization; and
(8) the criteria for quality control of the DNA are: bands are obvious, with a length greater than 10 kb and without apparent degradations; the OD260/280 is between 1.8 and 2.0, and the OD260/230 is greater than 1.5, the criteria for detection are met.
2. Detection of Chromosome 16p11.2 Microdeletions in Small Samples
20 cases are selected from genomes of the 161 Han Chinese who are not related to each other and suffer from congenital scoliosis for oligonucleotide comparative genomic hybridization detection. DNA shearing, microarray processing and data analysis are performed according to the operational steps in the product instruction by using an Agilent's oligonucleotide comparative genomic hybridization microarray. Reference DNA is purchased from Promega.
3. Primary Screening in Large Samples by QPCR
Two detection sites (named as PA and PB) in the 16p11.2 microdeletion region and a reference site (named as P1) outside the 16p11.2 microdeletion region are selected. Different fragments are amplified by using P1 and PA or P1 and PB combination, and existing amount of the fragments is detected by a conventional QPCR method. The sequences of the primers used in the QPCR experiments are shown in Table 1:
4. Confirmation of the Results of the Primary Screening in Large Samples by QPCR
DNA samples with chromosome 16p11.2 microdeletions obtained from the primary screening in step (3) are confirmed according to the method described in step (1).
Results: genomes of 12 individuals of the 161 Han Chinese who are not related to each other and suffer from congenital scoliosis, have chromosome 16p11.2 microdeletions (the first 12 microdeletions shown in
The common mechanism of nucleotide deletion related diseases is haploinsufficiency, such as the presence of copy of only one key gene is insufficient for an individual's physiological demands. Taking into account that haploinsufficiency of the TBX6 gene is a factor for the occurrence of CS, it may be considered that other factors which can lead to haploinsufficiency of the TBX6 gene may also be the factors leading to the occurrence of CS. Gene mutation is a common cause of diseases. Then, DNA of the TBX6 gene is sequenced to study whether the mutation exists or not.
1. Amplification of the Gene
The entire TBX6 gene coding regions and upstream regulatory regions of nearly 1 kb of 149 CS patients who are not related to each other and have no 16p11.2 microdeletion and 166 randomly selected normal individuals are amplified. The sequences of the primers are: forward primer 5′-TAGGGAGAGGGCTCTGTTCTCATGG-3′; reverse primer 5′-GCGTCCCAGGGAGGCAACCG-3′. The PCR amplification conditions are as follows:
PCR Amplification System (50 μl):
2. Sequencing
Determination of the TBX6 gene sequence is carried out by sequencing techniques which are well known to those skilled in the art. The sequencing primers are shown in Table 2:
3. Results
As shown in
1. Repeated detection of chromosome 16p11.2 microdeletions
Object of study: 76 Han Chinese who are not related to each other and suffer from congenital scoliosis.
Method: the same as in Embodiment 1.
Result: the genomes of 5 of 76 Han Chinese who are not related to each other and suffer from congenital scoliosis have chromosome 16p11.2 microdeletions (the last five deletions in
2. Repeated Detection of Mutations in the TBX6 Gene
Object of study: 71 Han Chinese who are not related to each other, have no chromosome 16p11.2 microdeletion and suffer from congenital scoliosis.
Method: the same as in Embodiment 2.
Result: 1 of 71 Han Chinese who are not related to each other, have no chromosome 16p11.2 microdeletion and suffer from congenital scoliosis has a double nucleotide deletion, i.e. deletion of AG at C1179 (as shown in
The phenotypes of the parents and siblings of members suffering from CS of two families SE1 and SE2 with 16p11.2 microdeletions are investigated, and it is found that some relatives of CS patients have 16p11.2 microdeletions but their phenotypes are normal, so the 16p11.2 microdeletions are not enough to cause the occurrence of CS, and other influence factors are involved, gene mutations are common factors leading to diseases, thus which genetic alteration of the TBX gene are present in the genomes of CS patients with 16p11.2 microdeletions is studied in the following.
Taking the members of the families SE1 and SE2 as objects of the study, the haplotypes of three SNP sites rs2289292-rs3809624-rs3809627 in the TBX6 gene on a chromosome without 16p11.2 microdeletion are detected. The specific operation is: using a ClonExpress One Step Cloning Kit (Vazyme) to detect the haplotypes of common TBX6 gene variants; using a pGEM-T vector as a template for the amplification of the vector to amplify the vector and inserted DNA fragments respectively, connecting; transforming the recombinant vector into competent cells of Escherichia coli; selecting clones, and detecting sequence by using sanger sequencing. The primer sequences used in the experiments are shown in Table 3:
The haplotypes of the three SNP sites rs2289292-rs3809624-rs3809627 of the TBX6 gene on a normal chromosome of the 22 individuals selected in Embodiments 1 to 3 with genetically defective genomes are detected and it is found that the haplotypes of the three SNP sites rs2289292-rs3809624-rs3809627 of 22 patients are all T-C-A.
Experimental Steps:
(1) Amplifying a 1120 bp DNA fragment of an upstream regulatory element of the TBX 6 gene, and constructing a normal DNA fragment, a DNA fragment with only rs3809624 site mutated to C, a DNA fragment with only rs3809627 site mutated to A and a DNA fragment with rs3809624 site and rs3809627 site mutated at the same time onto a pGL3-Basic vector respectively (construction mode is shown in
(2) Transfecting recombinant vectors into HEK293T, HepG2, Hela cells cultured in vitro.
(3) After transfection for a certain period of time, lysing the cells and obtaining supernatants to detect the activity of luciferase by using a Dual-Luciferase Reporter Gene Assay system.
The results are shown in
While embodiments of the present disclosure have been shown and described, it would be understood by those of skilled in the art that various changes, modifications, substitutions and alterations can be made in these embodiments without departing from the principles and objects of the present disclosure, the scope of the present disclosure is defined by the claims and their equivalents.
| Number | Date | Country | Kind |
|---|---|---|---|
| 201410284657.5 | Jun 2014 | CN | national |
| 201410572962.4 | Oct 2014 | CN | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CN2015/076692 | 4/16/2015 | WO | 00 |
