Patent Application
20150307942
This application claims the benefit of priority to Chinese Patent Application No. CN 201410174277.6, filed on Apr. 23, 2014, the entire contents of which are incorporated herein by reference.
The present invention relates to genetic diagnosis field. More specifically, the present invention is directed to a method for detecting fetal deafness pathogenic gene mutations. The present invention also relates to a kit and uses thereof for detecting fetal deafness pathogenic gene mutations.
Deafness is a common disease resulting in disability and affecting health in humans, and is also one of the most common genetic diseases in clinic. According to statistics, there is one with dysaudia among every 1000 new-born babies over the world (Steel K P., “New interventions in hearing impairment,” BMJ, 2000, 320(4):622-625). Many reasons can result in deafness, while the genetic factor is the main one. Hearing disability occurred at the time of born or before 3 years old is called pre-lingual hearing impairment, at least half of which is caused by genetic deficiency. In a large number of patients with delayed hearing loss, many patients developed said disease due to their genetic deficiency, or due to increased susceptibility to the environment caused by genetic deficiency and polymorphism. It is estimated that there are totally more than 100 non-syndrome genetic deafness genes globally. In view of the domestic research progress, most of the pathogenicity loci found in China are on GJB2, GJB3, SLC26A4 and mitochondria 12SrRNA.
Brief introductions of GJB2, GJB3, and SLC26A4 are provided herein for better understanding. GJB2 gene: this gene is located on autosomal 13q11-12 region, and the DNA full length is 4804 bp, including 2 exons. The coding region is 678 bp, and encodes a connexion Connexin26 consisting of 266 amino acid residues, which belongs to beta-2 protein that is part of the potassium circulation pathway. GJB2 gene mutation is the most common cause for genetic deafness, and the deafness resulted from GJB2 gene mutation is pre-lingual, bilateral, and symmetric deafness, which varies a lot in terms of the degree of hearing loss. It may range from mild to extremely severe, while most is severe or extremely severe deafness. In Chinese population, the main types of GJB2 gene mutation are 235delC, 299-300delAT, 176-191del16 and the like, accounting for over 80% of the populations with GJB2 gene mutation. GJB3 gene: this gene is located on autosomal 1q33-35 region, has 2 exons, and encodes a connexion Connexin 31 comprising 270 amino acids. GJB3 gene mutation can lead to autosomal genetic non-syndrome deafness, dominant or recessive, and is considered to be associated with high frequency hearing loss. SLC26A1 gene is located on autosomal 7q31 region, has 21 exons, and encodes a multipass transmembrane protein Pendrin consisting of 780 amino acid residues, which belongs to the transporter family that mainly relates with iodine/chloride ion transportation and plays an important role in maintaining the balance of the body ion compositions. Recently, many studies abroad demonstrate that SLC26A4 is close related with Pendred syndrome (enlarged vestibular aqueduct or accompanied with nerve deafness of inner ear malformation and goiter) and large vestibular aqueduct syndrome (LVAS). Among the numerous mutations, many are presented in both Pendred syndrome and LVAS. Thus, mutations at the same loci may result in different clinic performances. There are many types of SLC26A4 gene mutations, while the mutation frequencies of 281C>T, 589G>A, IVS7-2A>G, 1174A>T(N392Y), 1226G>A, 1229C>T(T410M), 1975G>C, 2027T>A(L676Q), 2168A>G(HIS723ARG) and IVS15+5G>A are as high as 82.51%.
With the development of science and technology, many deafness patients of new-born babies are diagnosed using methods of Sanger sequencing, gene chip and protein detection. There is also prenatal detection based on invasive diagnosis of fetal deafness pathogenic genes. However, non-invasively detection of fetal deafness pathogenic genes has not been achieved yet.
The inventor explored a method for detecting fetal deafness pathogenic gene mutations (genotype) using fragment DNA from venous blood of a pregnant woman based on the second generation high-throughput sequencing technology. After the discovery of embryo DNA in maternal blood, it is possible to non-invasively diagnose and detecting fetal chromosomal abnormalities and gene mutations directly (Lo Y M et al., (1997) “Presence of fetal DNA in maternal plasma and serum,” Lancet, 350:485-487). The Illumina products are the best among the second generation high-throughput sequencing technologies, in which two representative products are Miseq and Hiseq, one is known for sequencing length, and the other is known for sequencing throughput. Miseq sequencer is used in the present invention. However, the amount of embryo DNA in blood is low, and how to determine the related fetal genotypes quickly and accurately is still a technical problem to be solved.
The technical problem to be solved in the present invention is how to non-invasively detecting the genotypes of fetal deafness pathogenic genes using the venous blood of a pregnant woman. Accordingly, the first object of the present invention is to provide a method that is capable of effectively detecting gene mutations of pre-determined mutation loci on deafness pathogenic genes in a fetus through the use of plasma DNA samples, comprising the following steps:
According to one preferred embodiment of the invention, the pre-determined locus is at least one gene mutation selected from the 22 loci of GJB2 gene, GJB3 gene and SLC26A4 gene.
According to one preferred embodiment of the invention, the primers are a pair of primers that are backward extended.
According to one preferred embodiment of the invention, the backward extended pair of primers is designed to aim at exon 2 of GJB2, exon 2 of GJB3, or exon 3, exon 5, exon 7, intron 7, exon 8, exon 10, exon 17 or exon 19 of SLC26A4.
According to one preferred embodiment of the invention, the backward extended pair of primers consist of backward extended pair of primers that are adjacent to a group of disease detection loci (e.g. high frequency mutation loci).
According to one preferred embodiment of the invention, the backward extended pair of primers contains universal primer region suitable for different high-throughput sequencing platforms.
According to another preferred embodiment of the invention, the sequences of the backward extended pair of primers are as follows respectively:
According to one preferred embodiment of the invention, one pair of the backward extended pair of primers detects one or more loci.
According to one preferred embodiment of the invention, detection of the 22 loci of GJB2 gene, GJB3 gene and SLC26A4 gene is accomplished in one PCR using 9 pairs of primers.
According to one preferred embodiment of the invention, the linkers are barcode (multiple sequence labelled) linkers.
According to one preferred embodiment of the invention, there are at least two base differences between the linkers.
According to one preferred embodiment of the invention, the linkers are partially matched Y-type linkers.
According to one preferred embodiment of the invention, the method used in the cyclization of step c) is a splint cyclization, wherein single stand DNAs complementary to both ends of the pre-amplified DNA are used as splints; and close of the ring is completed by a heat-resistant Taq ligase.
According to one preferred embodiment of the invention, the cyclization of step c) is multiple reactions of a single system circulation consisting of DNA denaturation, splint DNA annealing and connecting.
According to one preferred embodiment of the invention, the method of the invention further comprises digesting the uncyclized linear DNA.
According to one preferred embodiment of the invention, the method of the invention detects the genotype of fetal deafness pathogenic genes using fragment DNA from venous blood of a pregnant woman.
According to one preferred embodiment of the invention, the deafness pathogenic genes have insertion, deletion, substitution or gene fusion mutations.
The second object of the present invention is to provide a kit for non-invasively detecting fetal deafness pathogenic gene mutations, comprising:
reagents for extracting plasma DNAs, a DNA cyclase, primers and reagents for amplifying target DNAs.
According to one preferred embodiment of the invention, the kit further comprises primers and reagents for pre-amplifying pre-determined loci of deafness pathogenic genes.
According to one preferred embodiment of the invention, the kit further comprises reagents for high throughput sequencing.
According to one preferred embodiment of the invention, the plasma DNAs are connected with linkers, wherein the linkers are barcode (multiple sequence labelled) linkers.
The third object of the present invention is to provide a use of primers designed against pre-determined loci of deafness pathogenic genes in the preparation of diagnosing reagents or kits for non-invasively detecting fetal deafness pathogenic gene mutations, characterized in that the diagnosing reagents or kits are applicable to a method for non-invasively detecting fetal deafness pathogenic gene mutations comprising the following steps:
The first object of the present invention is to provide a method for detecting gene mutations of pre-determined mutation loci of deafness pathogenic genes in a fetus through the use of plasma DNA samples, comprising the following steps:
Traditional methods for detecting fragment DNA are mainly performed by PCR amplifying the regions to be tested before detection. As the PCR primers are on both ends of the regions to be tested, the regions to be tested are required to be complete. However, the regions to be tested in most fragment DNAs are incomplete, as the fragment DNAs are produced by random cleavage. Accordingly, the number of fragment DNAs that can be used as amplification templates is few, and is difficult to be detected. In the invention, the adaptation range of the primer amplification and the effective amount of templates are largely increased by cyclizing the fragment DNAs, thereby improving the detection sensitivity of the fragment DNA dramatically. A more important aspect of the invention is to label the initial template using the start and terminal positions of the fragment DNA as well as the 6 different bases on 3′ end of the linker while improving the utility of the template. Thus, whether the pre-determined loci in mother and fetus have been mutated as well as the type of mutations can be effectively determined. Another important aspect of the invention is to detect multiple loci to be tested simultaneously, e.g., to detect the 22 high frequency pathogenic loci in a sample to be tested at one time using the Multi-PCR technology.
The detection method of the invention can be used to detect fragment DNA comprising mutations, such as homozygous mutation and heterozygous mutation; or base deletion, insertion or substitution. “Fragment DNA” of the invention refers to short fragment DNA with the length of about 166 bp that is formed by random cleavage of the genome DNA of an organism.
In sum, template cyclization of the invention makes the available DNA templates more than that of conventional PCR, thereby improving detection sensitivity. Labelling initial templates using the start and terminal positions of the fragment DNA as well as the 6 different bases of Barcode on 3′ end of the linker makes it possible to effectively reduce the sequence to a template sequence through sequencing before PCR amplification, thus decreasing the sequence bias resulted from PCR amplification, and determining whether the pre-determined loci in mother and fetus have been mutated as well as the type of mutations more accurately. Meanwhile, 9 pairs of backward extended primers are designed and optimized against high frequency mutation loci of the deafness pathogenic genes GJB2, GJB3, and SLC26A4, and the 22 high frequency pathogenic loci in a sample to be tested are detected at one time using the Multi-PCR technology.
To achieve the detection of mutation genotypes of the pre-determined loci of fetal deafness pathogenic genes in maternal venous blood, the mutation of the pre-determined loci of the invention is at least one gene mutation selected from the 22 loci of GJB2 gene, GJB3 gene, and SLC26A4 gene, preferably, the mutation of GJB2 gene is at least one mutation selected from 35delG, 109G>A(VAL37ILE)167delT, 176-191del16, 235delC and 299—300delAT; the mutation of GJB3 gene is at least one mutation selected from 421A>G(ILE141VAL), 421-423delATT, 497A-G(ASN166SER), 538C>T(ARG180TER), 547G>A(GLU183LYS) and 580G>A(ALA194THR); and the mutation of SCL26A4 gene is at least one mutation selected from 281C>T, 589G>A, IVS7-2A>G, 1174A>T(N392Y), 1226G>A, 1229C>T(T410M), 1975G>C, 2027T>A(L676Q), 2162C>T(T721M), 2168A>G(HIS723ARG) and IVS15+5G>A. The tested loci do not include mitochondria C1494T and A1555G mutation loci, as the amount of mitochondria DNA in plasma is very low. More preferably, the pairs of primers are designed to extend backward for detection of pre-determined mutation loci, and the F-end primer is closer to the tested loci, as shown in
Backward extended amplification primers in the target region aimed at exon 2 of GJB2.
Backward extended amplification primers in the target region aimed at exon 2 of GJB3.
Backward extended amplification primers in the target region aimed at exon 3 of SLC26A4.
Backward extended amplification primers in the target region aimed at exon 5 of SLC26A4.
Backward extended amplification primers in the target region aimed at exon 7, intron 7 and exon 8 of SLC26A4.
Backward extended amplification primers in the target region aimed at exon 10 of SLC26A4.
Backward extended amplification primers in the target region aimed at exon 17 of SLC26A4.
Backward extended amplification primers in the target region aimed at exon 19 of SLC26A4.
To achieve quantified template detection of the loci of the deafness pathogenic genes, the invention employed barcode (multiple sequence labelled) linkers to label the sequences of plasma DNA. The labelling is obtained using the start and terminal positions of the fragment DNA as well as the 6 different bases on 3′ end of the linker. The above labelling achieves two objectives: one is to quantitatively label the initial templates of the tested loci; the other is to exclude contamination between different samples in the same batch. To achieve the first objective, the number of combination types of a group of barcode linkers has to be much bigger than the maximal number of the templates with the same start and same terminal positions. For instance, in 1 ml plasma, the maximal number of the templates with the same start and same terminal positions is approximately 10, and the number of combination types of each group of barcode linkers of the invention is 10, thus the number of random combinations of upstream and downstream of the linkers is 100. The combination number of 100 is much bigger than the template number of 10, thus each template is ensured to link to different type of barcode linkers. To achieve the second objectives, various combinations of barcode linkers are designed in the invention. There are totally 16 groups of barcode linkers without repetition between each group of linkers, thus a maximal of 16 samples can be detected in one experiment. More preferably, there are at least two base differences between different barcode linkers, thus to reduce the possibility of mistake. Correction function of the barcode linkers achieves quantification and eliminates contamination. Thus, whether the pre-determined loci in mother and fetus have been mutated as well as the type of mutations can be effectively determined. The specific linker and primer sequences are as follows:
Linker design, need to be annealed to a double strand:
wherein N can be any amino acid.
pre-library amplification primers:
Traditional methods for detecting fragment DNA are mainly performed by PCR amplifying the regions to be tested before detection. As the PCR primers are designed on both ends of the regions to be tested, the regions to be tested are required to be complete. However, the regions to be tested in most fragment DNAs are incomplete, as the fragment DNAs are produced by random cleavage. Accordingly, the number of fragment DNAs that can be used as amplification templates is few, and is difficult to be detected by PCR. The invention uses plasma DNA fragment (about 166 bp) to achieve quantified template detection of the loci on the deafness pathogenic genes. First, the fragment DNA is cyclized. As long as the cleavage point is not in the template of the backward extended primers, the amplification can be conducted. Thus, the adaptation range of the primer amplification and the effective amount of templates are increased, and the detection sensitivity of the fragment DNA is also improved dramatically. After connection of the plasma DNA and linkers, the pre-library is amplified and is subsequently cyclized. Cyclization of the pre-library can be auto-connection to a ring. The invention selects single strand splint cyclization with specific auxiliary sequences. Preferably, the linkers connected to plasma fragment DNA are partially matched Y-type linkers, wherein the length of matched base that next to barcode is 9 bp, and the length of unmatched base is 7 bp. Preferably, a single strand DNA that is complementary to the Y-type linkers is used in assisting the cyclization. The linkers and auxiliary sequences are complementary to each other to form double strands, wherein the length of the auxiliary sequence is 32 bp. Preferably, the ends between the linker sequences are connected by Taq DNA Ligase (MO208L) from NEB.
Plasma DNA was extracted from 1-2 ml plasma by QIAamp Circulating Nucleic Acid Kit (CAT No. 55114). DNA was eluted in 45 μl elution buffer, wherein 2 μl is used for concentration detection by Qubit.
The reaction mixture was prepared as shown in Table 1.
4° C.: maintain
The product with A addition was purified on a column, dissolved in 25 μl Buffer EB, and eluted twice.
3. Connection with the Linkers
The reaction mixture was prepared as shown in Table 2.
4° C.: maintain
4.1 PCR (100 μl system), the reaction mixture was prepared as shown in Table 3.
6.1 Components as Shown in Table 7 were Added in the Reaction System of Step 5 in Order.
The detection of the 22 loci of GJB2 gene, GJB3 gene and SLC26A4 gene was performed in one PCR using 9 pairs of primers by means of Multi-PCR, which solve multi-point detection.
After PCR reaction, the product was immediately purified using 90 μl XP Beads (0.9×), and then dissolved in 26 μl Buffer EB.
8.2 PCR Reaction Conditions were as Shown in Table 12
After PCR reaction, 10 μl product was analysed by electrophoresis on 2% agarose gel, while other products were purified and recycled using 0.8× XP Beads, and were finally dissolved in 22 μl EB Buffer, which were used in a subsequent Q-PCR as the final library. The size of the final library is 320 bp (used in calculating QPCR concentration), and it should mix with Read1 Sequencing Primer from NEXTERA for sequencing. 300 bp double-end sequencing was performed using Miseq from Illumina.
The sample was plasma from a pregnant woman. Preferably, the mutation of the pre-determined loci is at least one gene mutation selected from the 22 loci of GJB2 gene, GJB3 gene, and SLC26A4 gene. More preferably, the mutation of GJB2 gene is at least one mutation selected from 35delG, 109G>A(VAL37ILE)167delT, 176-191del16, 235delC and 299—300 delAT; the mutation of GJB3 gene is at least one mutation selected from 421A>G(ILE141VAL), 421-423delATT, 497A-G(ASN166SER), 538C>T(ARG180TER), 547G>A(GLU183LYS) and 580G>A(ALA194THR); and the mutation of SCL26A4 gene is at least one mutation selected from 281C>T, 589G>A, IVS7-2A>G, 1174A>T(N392Y), 1226G>A, 1229C>T(T410M), 1975G>C, 2027T>A(L676Q), 2162C>T(T721M), 2168A>G(HIS723ARG) and IVS15+5G>A. For convenience of description, the above mutation loci tested by primer combinations are summarized as shown in Table 13.
1Mutated templates: the number of templates of the corresponding mutated loci in the non-invasive prenatal detection.
2Total templates: the total number of templates of the corresponding loci in the non-invasive prenatal detection.
Main reagents include: QIAamp Circulating Nucleic Acid Kit, T4 DNA phosphorylation buffer (10×), 10 μM dNTP mixture, T4 DNA polymerase, T4 DNA phosphorylase, dATP solution, Quick ligation buffer (5×), Y-type DNA double strand linkers, T4 DNA Ligase(HC), Quick T4 DNA ligase (NEB), Phusion DNA polymerase (Phusion DNA polymerase mixture), pre-amplification primers, Ultra-pure water, 10× Taq ligase Buffer, Taq ligase, 10× NEBuffer 1, Exo III.
The data standard for the conclusion of the experiment results:
According to an internal statistics, the average amount of fetal plasma DNA in a pregnant woman at gestational age of 12-26 weeks is around 10% based on the amount of plasma DNA of the pregnant woman. Deafness gene disorder is autosomal inherited, and thus the data standard of various combinations of maternal and fetal pathogenic genotypes can be obtained based on the laws of inheritance. The experiment conclusion is deduced based on the genotype data of the tested pathogenic genotypes.
| Number | Date | Country | Kind |
|---|---|---|---|
| 201410174277.6 | Apr 2014 | CN | national |
