CN116732180A - Composition for detecting thyroid cancer and application thereof - Google Patents

Abstract

The application provides a composition for detecting thyroid cancer and application thereof, wherein the composition comprises the following components: the nucleic acid is used for detecting the methylation state of a target gene, wherein the target gene is one or more than two of MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene and SLC38A1 gene. The application also provides a kit comprising the composition and application of the composition in preparing a kit for detecting thyroid cancer in vitro.

Description

Composition for detecting thyroid cancer and application thereof

Technical Field

The application belongs to the field of molecular biology, relates to gene detection, and in particular relates to a nucleic acid composition for detecting thyroid cancer related gene methylation, and a corresponding kit and application thereof.

Background

Thyroid cancer includes four pathological types of papillary, follicular, undifferentiated and medullary cancers. Papillary cancers with low malignancy and better prognosis are most common, with the vast majority of thyroid cancers originating from follicular epithelial cells, except medullary cancers. The incidence rate has a certain relationship with the region, race and sex. The female disease is more, and the ratio of the male disease to the female disease is 1: (2-4). Onset can occur at any age, but is seen in young and strong years. Most thyroid cancers occur in the lateral thyroid gland lobes, often as a single tumor.

Recent studies have shown that epigenetics play an important role in the development and progression of cancer. As an important mechanism of epigenetic science, DNA methylation regulation of various cancers has been intensively studied. Study data showed that: regulation of gene methylation is related to biological mechanisms such as chromatin structure and gene expression regulation; changes in cellular gene methylation occur early in tumor formation and are throughout the course of cancer development and progression; methylation of cancer suppressor genes is an important molecular mechanism for the transformation of precancerous lesion tissues into malignant tumor cells. But currently there is a lack of detection techniques, methods and products for the detection of thyroid cancer methylation genes. Thus, there is a current need for methylation gene markers with high sensitivity and specificity for thyroid cancer detection.

For thyroid cancer detection, currently, a fine needle puncture biopsy and molecular detection are mostly adopted. The fine needle puncture biopsy is a gold standard for thyroid cancer screening and diagnosis, has high sensitivity, and is further beneficial to improving the detection rate of lesions. The thyroid nodule with benign and malignant characteristics can not be determined by puncture biopsy, and molecular marker detection such as BRAF mutation, RAS mutation, RET/PTC rearrangement and the like can be performed on a puncture specimen, so that the diagnosis rate can be improved. However, the fine needle puncture biopsy has invasiveness, the detection process has larger uncomfortable feeling, and the compliance of patients is lower; meanwhile, most thyroid nodules are found through thyroid palpation and neck ultrasonic examination during physical examination, but most thyroid nodules are benign, malignant tumors account for 5% -10%, and if puncture biopsy is performed on all the nodule patients, the population to be screened is huge, so that medical resources are wasted and the like. In addition, the gold standard method has complex detection flow and low flux, and can not be used for the implementation of early thyroid cancer screening.

The blood detection of traditional tumor markers thyroglobulin (Tg), calcitonin and carcinoembryonic antigen (CEA) can be used for auxiliary diagnosis, prognosis judgment, curative effect evaluation and the like of thyroid cancer to a certain extent clinically, and the accuracy of diagnosis, prognosis judgment and curative effect observation of medium-and-late-stage thyroid cancer can be improved. The biggest disadvantage of traditional tumor marker detection is the high false positive, and many benign diseases such as inflammation can be represented as abnormal tumor markers. Serum Tg assays lack specific value for identifying benign and malignant thyroid nodules. Thus, serum Tg determinations are not generally used clinically for preoperative diagnosis of DTCs. In the follow-up stage after treatment of DTC patients, serum Tg change is an important means for judging whether the patients have tumor recurrence, and the serum Tg can be used for monitoring recurrence and metastasis after DTC operation. For DTC patients who have cleared all thyroid tissue, an elevated serum Tg suggests a potential for tumor recurrence. MTC patients suggest simultaneous detection of serum calcitonin and CEA prior to treatment and periodic monitoring of serum level changes after treatment, and if they are beyond normal range and continue to increase, the progression or recurrence of the condition should be highly suspected. Serum calcitonin and CEA detection, and is helpful for efficacy evaluation and disease monitoring of patients with medullary cancer. In conclusion, the traditional tumor marker has low detection sensitivity and poor specificity, so that early cancers cannot be detected, and the method is not suitable for screening early cancers of large-scale people.

Disclosure of Invention

At present, early diagnosis of thyroid cancer mainly depends on traditional modes such as finding a nodule by an imaging means, further puncture examination of the nodule and the like, and has low examination efficiency and low detection sensitivity. For example, cervical ultrasound, while sensitive, has the ability to identify thyroid nodules is related to the clinical experience of the sonographer. CT is poorly observed for patients with nodules less than or equal to 5mm in maximum diameter and nodules combined with diffuse lesions. MRI is insensitive to calcification, and has long examination time and is easily affected by respiratory and swallowing actions. In conclusion, early thyroid cancer is small in size, the traditional method is not easy to find, the current examination efficiency is low, and the method is not suitable for large-scale popularization and screening. The methylation marker combination which can be detected in early cancer can be selected, so that the detection of early thyroid cancer can be greatly improved, in addition, for a patient who finds out a nodule in physical examination, the methylation marker of plasma thyroid cancer can be detected first, if the methylation marker combination shows high risk, puncture detection is considered (more than 90% of thyroid nodules are benign), and the unnecessary consumption of medical resources is reduced.

Based on the problems existing in the existing thyroid cancer detection, the application aims to provide a composition for detecting thyroid cancer in vitro, a kit and application thereof, a method for performing detection based on the kit and application for detecting thyroid cancer.

The specific technical scheme of the application is as follows:

1. a composition for detecting thyroid cancer in vitro, the composition comprising:

nucleic acid for detecting methylation status of a target gene,

wherein the methylation state of the target gene is characterized by methylation of a target sequence of the target gene,

wherein the target gene is one or more than two of MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene and SLC38A1 gene.

2. The composition of item 1, wherein the target sequence of the MIR578 gene is shown as SEQ ID NO. 1 or SEQ ID NO. 2 or SEQ ID NO. 3 or SEQ ID NO. 4 or the target sequence of the MIR578 gene comprises a sequence shown as SEQ ID NO. 1 or SEQ ID NO. 2 or SEQ ID NO. 3 or SEQ ID NO. 4.

3. The composition according to item 1, wherein the target sequence of the SNHG15 gene is shown as SEQ ID NO. 5 or SEQ ID NO. 6 or SEQ ID NO. 7 or SEQ ID NO. 8 or the target sequence of the SNHG15 gene comprises a sequence shown as SEQ ID NO. 5 or SEQ ID NO. 6 or SEQ ID NO. 7 or SEQ ID NO. 8.

4. The composition of item 1, wherein the target sequence of the IFFO1 gene is shown as SEQ ID NO. 9 or SEQ ID NO. 10 or SEQ ID NO. 11 or SEQ ID NO. 12 or the target sequence of the IFFO1 gene comprises a sequence shown as SEQ ID NO. 9 or SEQ ID NO. 10 or SEQ ID NO. 11 or SEQ ID NO. 12.

5. The composition of item 1, wherein the target sequence of the OSTM1 gene is shown as SEQ ID NO. 13 or SEQ ID NO. 14 or SEQ ID NO. 15 or SEQ ID NO. 16 or the target sequence of the OSTM1 gene comprises a sequence shown as SEQ ID NO. 13 or SEQ ID NO. 14 or SEQ ID NO. 15 or SEQ ID NO. 16.

6. The composition of item 1, wherein the target sequence of the SLC38A1 gene is shown as SEQ ID NO. 17 or SEQ ID NO. 18 or SEQ ID NO. 19 or SEQ ID NO. 20 or the target sequence of the SLC38A1 gene comprises a sequence shown as SEQ ID NO. 17 or SEQ ID NO. 18 or SEQ ID NO. 19 or SEQ ID NO. 20.

7. The composition according to any one of items 1 to 6, wherein the nucleic acid for detecting methylation status of a target gene comprises:

a primer that is a fragment of at least 9 nucleotides in a target sequence of the target gene, the fragment comprising at least one CpG dinucleotide sequence.

8. The composition according to any one of items 1 to 7, wherein the nucleic acid for detecting methylation status of a target gene comprises:

a probe which is a fragment of at least 15 nucleotides hybridised to the target sequence of the target gene under moderately stringent or stringent conditions,

The fragment comprises at least one CpG dinucleotide sequence.

9. The composition of any one of items 1-8, further comprising:

an agent that converts an unmethylated cytosine base at position 5 of a target sequence of a target gene into uracil.

10. The composition according to any one of items 1 to 9, wherein the nucleic acid for detecting methylation status of a target gene further comprises:

blocking agents that preferentially bind to target sequences in the unmethylated state.

11. The composition according to item 10, wherein,

the at least 9 nucleotide fragment is the sequence of SEQ ID NO. 21 and SEQ ID NO. 22, or it is the sequence of SEQ ID NO. 24 and SEQ ID NO. 25, or it is the sequence of SEQ ID NO. 27 and SEQ ID NO. 28, or it is the sequence of SEQ ID NO. 30 and SEQ ID NO. 31, or it is the sequence of SEQ ID NO. 33 and SEQ ID NO. 34;

the fragment of at least 15 nucleotides, which is the sequence of SEQ ID NO. 23, or the sequence of SEQ ID NO. 26, or the sequence of SEQ ID NO. 29, or the sequence of SEQ ID NO. 32, or the sequence of SEQ ID NO. 35.

12. An oligonucleotide for detecting thyroid cancer in vitro, comprising:

a fragment of at least 9 nucleotides of SEQ ID NO. 1 or SEQ ID NO. 2 or SEQ ID NO. 3 or SEQ ID NO. 4 or the complement thereof comprising at least one CpG dinucleotide sequence; and/or

A fragment of at least 9 nucleotides of said SEQ ID NO. 5 or SEQ ID NO. 6 or SEQ ID NO. 7 or SEQ ID NO. 8 or the complement thereof comprising at least one CpG dinucleotide sequence; and/or

A fragment of at least 9 nucleotides of said SEQ ID NO. 9 or SEQ ID NO. 10 or SEQ ID NO. 11 or SEQ ID NO. 12 or the complement thereof comprising at least one CpG dinucleotide sequence; and/or

A fragment of at least 9 nucleotides of said SEQ ID NO. 13 or SEQ ID NO. 14 or SEQ ID NO. 15 or SEQ ID NO. 16 or the complement thereof comprising at least one CpG dinucleotide sequence; and/or

The fragment of at least 9 nucleotides of SEQ ID NO. 17 or SEQ ID NO. 18 or SEQ ID NO. 19 or SEQ ID NO. 20 or the complement thereof comprising at least one CpG dinucleotide sequence.

13. The oligonucleotide of item 12, further comprising:

a fragment which hybridizes under moderately stringent or stringent conditions to at least 15 nucleotides of said SEQ ID NO. 1 or SEQ ID NO. 2 or SEQ ID NO. 3 or SEQ ID NO. 4 or the complement thereof and which comprises at least one CpG dinucleotide sequence; and/or

A fragment which hybridizes under moderately stringent or stringent conditions to at least 15 nucleotides of said SEQ ID NO. 5 or SEQ ID NO. 6 or SEQ ID NO. 7 or SEQ ID NO. 8 or the complement thereof and which comprises at least one CpG dinucleotide sequence; and/or

A fragment which hybridizes under moderately stringent or stringent conditions to at least 15 nucleotides of said SEQ ID NO. 9 or SEQ ID NO. 10 or SEQ ID NO. 11 or SEQ ID NO. 12 or the complement thereof and which comprises at least one CpG dinucleotide sequence; and/or

A fragment which hybridizes under moderately stringent or stringent conditions to at least 15 nucleotides of said SEQ ID NO. 13 or SEQ ID NO. 14 or SEQ ID NO. 15 or SEQ ID NO. 16 or the complement thereof and which comprises at least one CpG dinucleotide sequence; and/or

A fragment which hybridizes under moderately stringent or stringent conditions to at least 15 nucleotides of said SEQ ID NO. 17 or SEQ ID NO. 18 or SEQ ID NO. 19 or SEQ ID NO. 20 or the complement thereof and which comprises at least one CpG dinucleotide sequence.

14. The oligonucleotide of item 13, further comprising:

blocking agents that preferentially bind to target sequences in the unmethylated state.

15. An oligonucleotide for detecting thyroid cancer in vitro, comprising:

SEQ ID NO. 21 and SEQ ID NO. 22.

16. The oligonucleotide of item 15, further comprising:

SEQ ID NO. 23.

17. An oligonucleotide for detecting thyroid cancer in vitro, comprising:

SEQ ID NO. 24 and SEQ ID NO. 25.

18. The oligonucleotide of item 17, further comprising:

SEQ ID NO. 26.

19. An oligonucleotide for detecting thyroid cancer in vitro, comprising:

the sequences of SEQ ID NO. 27 and SEQ ID NO. 28.

20. The oligonucleotide of item 19, further comprising:

SEQ ID NO. 29.

21. An oligonucleotide for detecting thyroid cancer in vitro, comprising:

SEQ ID NO. 30 and SEQ ID NO. 31.

22. The oligonucleotide of item 21, further comprising:

SEQ ID NO. 32.

23. An oligonucleotide for detecting thyroid cancer in vitro, comprising:

SEQ ID NO. 33 and SEQ ID NO. 34.

24. The oligonucleotide of item 23, further comprising:

SEQ ID NO. 35.

25. A kit comprising the composition of any one of claims 1-11 or comprising the oligonucleotide of any one of claims 12-24.

26. The kit of item 25, further comprising at least one additional component selected from the group consisting of:

nucleoside triphosphates, DNA polymerase and buffers required for the function of the DNA polymerase.

27. The kit of item 25 or 26, wherein the sample for detection of the kit comprises: cell lines, histological sections, tissue biopsies/paraffin-embedded tissues, body fluids, faeces, colonic exudates, urine, plasma, serum, whole blood, isolated blood cells, cells isolated from blood, or combinations thereof.

28. The kit of any one of items 25 to 27, further comprising: and (3) a specification.

29. Use of the composition of any one of claims 1-11 or the oligonucleotide of any one of claims 12-24 for the preparation of a kit for detecting thyroid cancer in vitro.

30. The use of item 29, wherein the kit for in vitro detection of thyroid cancer detects thyroid cancer by a method comprising:

1) Isolating a DNA sample comprising a target sequence of a target gene or a fragment thereof from a biological sample to be tested;

2) Determining the methylation status of the target sequence of the target gene;

3) Judging the state of the biological sample according to the detection result of the methylation state of the target sequence of the target gene, thereby realizing the in vitro detection of thyroid cancer.

31. The use according to item 30, wherein the method comprises the steps of:

extracting genome DNA of a biological sample to be detected;

treating the extracted genomic DNA with a reagent to convert the unmethylated cytosine base at position 5 to uracil or other bases;

contacting the DNA sample treated by the reagent with a DNA polymerase and a primer of a target sequence of a target gene to perform DNA polymerization reaction;

Detecting the amplified product with a probe; and

determining the methylation status of at least one CpG dinucleotide of the target sequence of the target gene based on the presence or absence of the amplification product.

32. The use according to item 31, wherein the reagent is a bisulphite reagent.

The application has the following beneficial effects:

according to the application, 5 relevant markers capable of sensitively and specifically detecting thyroid cancer are screened out, and methylation areas of the relevant markers are determined. By detecting the target sequences of the methylation genes of the MIR578 gene, the SNHG15 gene, the IFFO1 gene, the OSTM1 gene and the SLC38A1 gene, the methylation state of the genes can be sensitively and specifically detected, so that the detection method can be used for detecting the free DNA of peripheral blood. The detection of peripheral blood samples of thyroid cancer patients and normal control individuals shows that: the composition and the detection method can sensitively and specifically detect thyroid cancer, thereby ensuring the correctness and reliability of detection results. Therefore, the application provides a composition, a kit and a detection method for detecting thyroid cancer in vitro, which can conveniently, rapidly and effectively detect thyroid cancer and have important clinical application value.

The application utilizes the epigenomic and bioinformatics technology to find a plurality of methylation genes related to thyroid cancer by analyzing genome methylation data of the thyroid cancer, determines a target sequence of methylation abnormality of the methylation genes of the thyroid cancer, and can sensitively and specifically detect the methylation state of the genes by the target sequence of the methylation genes, thereby being used for detecting free DNA of peripheral blood.

The composition is used for screening asymptomatic people in a non-invasive mode, reduces the harm caused by invasive detection, has higher sensitivity and accuracy, and can realize real-time monitoring.

Detailed Description

The present application will be described in detail below. While specific embodiments of the application are shown, it should be understood that the application may be embodied in various forms and should not be limited to the embodiments set forth herein. Rather, these embodiments are provided so that this disclosure will be thorough and complete, and will fully convey the scope of the application to those skilled in the art.

The practice of the present application will employ, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, biochemistry and genetics, which are within the skill of the art. Such techniques are described in detail in the literature as Molecular Cloning: A Laboratory Manual, second edition (Sambrook et al, 1989); oligonucleotide Synthesis (M.J.Gait, 1984); animal Cell Culture (R.I. Freshney, 1987); methods in Enzymology Cluster books (American academic Press Co., ltd.); current Protocols in Molecular Biology (F.M. Ausubel et al, 1987 edition, and periodic updates); PCR The Polymerase Chain Reaction (Mullis et al, 1994). Primers, probes, blockers and kits useful in the present application can be prepared using standard techniques well known in the art.

Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this application belongs.

Definition of the definition

"precancerous" in the present application means a cell at an early stage of or prone to be transformed into a cancer cell. Such cells may exhibit one or more phenotypic traits characteristic of cancer cells.

"stringent hybridization conditions" and "high stringency" in the present application refer to conditions under which a probe hybridizes to its target sequence, typically in a complex mixture of nucleic acids. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. For detailed guidance on nucleic acid hybridization, reference may be made to Tijssen, biochemical and molecular biological techniques-nucleic acid probe hybridization, "review of hybridization principles and nucleic acid assay strategies. Typically, stringent conditions are those about 5-10deg.C below the melting point (Tm) for a specific nucleic acid at a defined ionic strength pH. At Tm temperatures (at defined ionic strength, pH and nucleic acid concentration), 50% of the probes complementary to the target hybridize uniformly to the target sequence. Stringent conditions can also be achieved with the addition of destabilizing agents. For selective or specific hybridization, the positive signal is twice, preferably 10 times, that of the background hybridization. Exemplary stringent hybridization conditions are as follows: hybridization was performed at 42℃in a solution of 50% formamide, 5 XSSC and 1% SDS, or at 65℃in a solution of 5 XSSC and 1% SDS, followed by washing at 65℃in a solution of 0.2XSSC and 0.1% SDS.

Also, if the polypeptides encoded by the nucleic acids are substantially similar, the nucleic acids are substantially similar even if they are not capable of hybridizing under stringent conditions. In this case, the nucleic acid is typically hybridized under moderately stringent hybridization conditions. As an example, "moderately stringent hybridization conditions" include hybridization in a solution of 40% formamide, 1M sodium chloride and 1% SDS at 37 ℃ and washing in a solution of 1xSSC at 45 ℃. It will be apparent to one of ordinary skill in the art that guidance in achieving the conditions to achieve the same stringency is available in the prior art. For PCR, temperatures around 36℃are typically suitable for low stringency amplification, while annealing temperatures range between 32℃and 48℃based on the length of the primer. For highly stringent PCR amplification, it is typically at 62℃and the annealing temperature for highly stringent hybridization ranges between 50℃and 65℃based on the length and specificity of the primers. For cycling conditions of high stringency and low stringency amplification, typically, include: the denaturation phase is continued for 30 seconds to 2 minutes at 90-95 ℃, the annealing phase is continued for 30 seconds to 2 minutes, and the extension phase is continued for 1 to 2 minutes at about 72 ℃. Tools and guidelines for low and high stringency amplification reactions are available in the prior art.

"oligonucleotide" in the present application refers to a molecule consisting of two or more nucleotides, preferably three or more nucleotides, the exact size of which may depend on a number of factors, which in turn are determined by the ultimate function and use of the oligonucleotide. In certain embodiments, the oligonucleotide may comprise a length of 10 nucleotides to 100 nucleotides. In certain embodiments, the oligonucleotides may comprise a length of 10 nucleotides to 30 nucleotides, or may have lengths of 20 and 25 nucleotides. In some particular embodiments, oligonucleotides shorter than these lengths are also suitable.

"primer" according to the present application means an oligonucleotide capable of acting as a starting point for synthesis, whether it is naturally occurring in a purified restriction digest or synthetically produced, when placed under conditions that induce synthesis of a primer extension product complementary to a nucleic acid strand, i.e., in the presence of a nucleotide and an inducer such as a DNA or RNA polymerase and at a suitable temperature and pH. The primer may be single-stranded or double-stranded and must be long enough to prime the synthesis of the desired extension product in the presence of the primer. The exact length of the primer depends on a variety of factors, including temperature, primer source and method used. For example, for diagnostic and prognostic applications, an oligonucleotide primer will typically contain at least or more than about 9, 10, or 15, or 20, or 25 or more nucleotides, depending on the complexity of the target sequence, but it may contain fewer nucleotides or more nucleotides. Factors involved in determining the appropriate length of the primer are well known to those skilled in the art.

"primer pair" according to the present application means a primer pair which hybridizes to the opposite strand of a target DNA molecule or to a region of the target DNA flanked by nucleotide sequences to be amplified.

"primer site" in the present application refers to a region of target DNA or other nucleic acid to which a primer hybridizes.

The "probe" of the present application, when referring to a nucleic acid sequence, is used in its ordinary sense to denote a selected nucleic acid sequence that hybridizes to a target sequence under defined conditions and can be used to detect the presence of the target sequence. Those skilled in the art will appreciate that in some cases, probes may also be used as primers, and primers may be used as probes.

"DNA methylation" according to the application refers to the addition of a methyl group to the 5-position of cytosine (C), which is usually (but not necessarily) the case in CpG (cytosine followed by guanine) dinucleotides. As used herein, "increased degree of methylation" or "substantial degree of methylation" refers to the presence of at least one methylated cytosine nucleotide in a DNA sequence, wherein the corresponding C in a normal control sample (e.g., a DNA sample extracted from a non-cancerous cell or tissue sample or a DNA sample treated for methylation of DNA residues) is unmethylated, and in certain embodiments, at least 2, 3, 4, 5, 6, 7, 8, 9, 10, or more C can be methylated, wherein the C at these positions in the control DNA sample is unmethylated.

In embodiments, a variety of different methods may be used to detect DNA methylation changes. Methods for detecting DNA methylation include, for example, methylation-sensitive restriction endonuclease (MSRE) assays using southern or Polymerase Chain Reaction (PCR) assays, methylation-specific or methylation-sensitive PCR (MS-PCR), methylation-sensitive single nucleotide primer extension (MS-SnuPE), high Resolution Melting (HRM) assays, bisulfite sequencing, pyrosequencing, methylation-specific single strand conformation assays (MS-SSCA), combinatorial bisulfite restriction assays (COBRA), methylation-specific gradient gel electrophoresis (MS-DGGE), methylation-specific melting curve assays (MS-MCA), methylation-specific high performance liquid chromatography (MS-DHPLC), methylation-specific Microarray (MSO). These assays may be PCR assays, quantitative assays using fluorescent markers or southern blot assays.

"methylation determination" in the context of the present application refers to any determination of the methylation status of one or more CpG dinucleotide sequences within a DNA sequence.

"detecting" according to the present application means any process of observing a marker or a change in a marker (e.g. a change in the methylation state of a marker or the expression level of a nucleic acid or protein sequence) in a biological sample, whether or not the marker or the change in the marker is actually detected. In other words, the act of detecting the marker or a change in the marker of the sample is "detecting" even if the marker is determined to be absent or below the sensitivity level. The detection may be quantitative, semi-quantitative, or non-quantitative observation, and may be based on comparison to one or more control samples. It is to be understood that detecting thyroid cancer as disclosed herein includes detecting pre-cancerous cells that begin to develop into, or are about to develop into, thyroid cancer cells, or have an increased propensity to develop into thyroid cancer cells. Detecting thyroid cancer may also include detecting a possible probability of death or a possible prognosis of a disease condition.

"homology", "identity" and "similarity" in the present application refer to sequence similarity between 2 nucleic acid molecules. The positions in each sequence can be compared to determine "homology", "identity" or "similarity", and the sequences can be aligned for comparison purposes. When an equivalent position in the compared sequences is occupied by the same base, the molecules are identical at that position; when an equivalent site is occupied by the same or a similar amino acid (e.g., similar in steric or charged properties) residue, the molecule may be said to be homologous (similar) at that position. Expression of homology/similarity or percent identity refers to a function of the number of identical or similar amino acids at positions shared by the compared sequences. "unrelated" or "non-homologous" sequences share less than 40% identity, preferably less than 25% identity, with the sequences of the present application. The absence of residues (amino acids or nucleic acids) or the presence of redundant residues also reduces identity and homology/similarity when comparing 2 sequences. In particular embodiments, two or more sequences or subsequences are considered substantially or significantly homologous, similar or identical if their sequences are about 60% identical, or about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical over a defined region when compared and aligned for maximum correspondence over a comparison window or defined region, as determined using BLAST or BLAST 2.0 sequence comparison algorithms having default parameters described below, or as determined by manual alignment and visual inspection provided on-line by, for example, the national center for biotechnology information (National Center for Biotechnology Information (NCBI)). The definition also relates to or can be used to test the complement of a sequence. Thus, for example, if a nucleotide sequence can be predicted to occur naturally in a DNA duplex, or can occur naturally in the form of one or both of the complementary strands, the nucleotide sequence that is complementary to a specified target sequence or variant thereof is itself considered "similar" to the target sequence, and when reference is made to a "similar" nucleic acid sequence, includes single-stranded sequences, their complementary sequences, double-stranded strand complexes, sequences capable of encoding the same or similar polypeptide products, and any permissible variants of any of the foregoing, to the extent permitted by the context herein. The circumstances in which similarity must be limited to analysis of a single nucleic acid strand sequence may include, for example, detection and quantification of expression of a particular RNA sequence or coding sequence in a cell. The definition also includes sequences with deletions and/or additions, as well as sequences with substitutions. In embodiments, identity or similarity may be over a region of at least about 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 10, 21, 22, 23, 24, 25 or more nucleotides in length, or over a region of more than about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or more than about 100 nucleotides in length.

"amplification" according to the present application means the process of obtaining multiple copies from one specific locus of a nucleic acid, such as genomic DNA or cDNA. Amplification may be accomplished using any of a variety of known means including, but not limited to, polymerase Chain Reaction (PCR), transcription-based amplification, and Strand Displacement Amplification (SDA).

The "fluorescence-based real-time PCR" of the present application means a method of: and adding a fluorescent group into the PCR reaction system, monitoring the whole PCR process in real time by utilizing fluorescent signal accumulation, and finally quantitatively analyzing the unknown template through a standard curve. In this PCR technique, there is a very important concept, the cycle threshold, also called Ct value. C represents Cycle, t represents threshold, and Ct has the meaning of: the number of cycles that the fluorescent signal within each reaction tube experiences when reaching a set threshold. For example, the fluorescence threshold (threshold) is set as follows: the fluorescent signal of the first 15 cycles of the PCR reaction served as the fluorescent background signal, and the default (default) setting of the fluorescent threshold was 10 times the standard deviation of the fluorescent signal of 3-15 cycles.

The "cut off value of real-time PCR" of the present application means a critical Ct value for a biomarker that determines whether a sample is negative or positive. According to some embodiments of the present application, the "critical Ct value (Cut Off value) is obtained based on statistical processing from a certain number of sample data, and may be different depending on the required sensitivity or specificity requirements.

The "sensitivity" of the present application means the ratio of cancers detected from a certain cancer sample, and the calculation formula is: sensitivity= (detected cancer/all cancers), whereas "specificity" indicates the normal proportion detected in a certain normal human sample, the formula is specificity= (detected negative/total negative).

A "label" or "detectable moiety" according to the present application is a component that is detectable by spectroscopic, photochemical, biochemical, immunochemical, chemical or other physical means. For example, useful labels include 32P, fluorescent dyes, electron dense reagents, enzymes (e.g., enzymes commonly used in ELISA), biotin, digoxin, or haptens, and proteins that can be prepared to be detectable, e.g., by incorporating a radiolabel into the peptide or for detecting antibodies that specifically react with the peptide.

Nucleic acid molecules can be detected using a variety of different methods. Nucleic acid detection methods include, for example, PCR and nucleic acid hybridization (e.g., southern blot, northern blot, or in situ hybridization). In particular, oligonucleotides (e.g., oligonucleotide primers) capable of amplifying a target nucleic acid may be used in a PCR reaction. The PCR method generally comprises the steps of: obtaining a sample, isolating nucleic acids (e.g., DNA, RNA, or both) from the sample, and contacting the nucleic acids with one or more oligonucleotide primers that specifically hybridize to a template nucleic acid under conditions that enable amplification of the template nucleic acid to occur. In the presence of a template nucleic acid, amplification products are produced. Conditions for nucleic acid amplification and detection of amplification products are known to those skilled in the art. Various improvements to the basic PCR technique have been developed, including, but not limited to, anchored PCR, RACE PCR, RT-PCR, and Ligase Chain Reaction (LCR). The primer pairs in the amplification reaction must anneal to the opposite strand of the template nucleic acid and should be kept at a suitable distance from each other so that the polymerase can efficiently polymerize across the region and so that the amplified product can be easily detected, for example, using electrophoresis. For example, oligonucleotide primers may be designed using a computer program such as OLIGO (Molecular Biology Insights inc., cascades, colo.) to aid in designing primers with similar melting temperatures. Typically, the oligonucleotide primer is 9-30 or 40 or 50 nucleotides in length (e.g., 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 or 50 nucleotides in length), although the oligonucleotide primer may be longer or shorter as long as appropriate amplification conditions are used.

Detection of the amplification product or hybridization complex is typically accomplished using a detectable label. The term "label", when referring to a nucleic acid, is intended to include direct labeling of the nucleic acid by coupling (i.e., physically linking) a detectable substance to the nucleic acid, as well as indirect labeling of the nucleic acid by reaction with another reagent that directly labels the detectable substance. Detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase; examples of suitable prosthetic groups include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; examples of luminescent materials include luminol; examples of bioluminescent materials include luciferase, luciferin and aequorin. Examples of indirect labeling include end-labeling a nucleic acid with biotin such that the nucleic acid can be detected with fluorescently labeled streptavidin.

SUMMARY

In one aspect, the application provides a composition for detecting thyroid cancer in vitro, the composition comprising a nucleic acid for detecting methylation status within a target sequence of a target gene, wherein the methylation status of the target gene is characterized by methylation of the target sequence of the target gene, wherein the target gene is one or more of MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene, SLC38A1 gene.

The present application provides a set of target sequences of target genes that emit abnormal methylation in thyroid cancer, including one or more of MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene, SLC38A1 gene, the target sequence of MIR578 gene is shown as any one of SEQ ID NO:1-4 or includes a sequence shown as any one of SEQ ID NO:1-4, the target sequence of SNHG15 gene is shown as any one of SEQ ID NO:5-8 or includes a sequence shown as any one of SEQ ID NO:5-8, the target sequence of IFFO1 gene is shown as any one of SEQ ID NO:9-12 or includes a sequence shown as any one of SEQ ID NO:9-12, the target sequence of OSTM1 gene is shown as any one of SEQ ID NO:13-16 or includes a sequence shown as any one of SEQ ID NO:13-16, and the target sequence of SLC38A1 gene is shown as any one of SEQ ID NO:17-20 or includes a sequence shown as any one of SEQ ID NO: 17-20.

It will also be appreciated by those skilled in the art that the target sequences of the MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene, SLC38A1 gene are not limited to the specific sequences listed above. The target sequence of the MIR578 gene should encompass sequences which comprise one or two or more nucleotide mutations compared to the sequence shown in any of SEQ ID NO. 1-4, but which are substantially functionally identical thereto, as well as sequences which have 95%, 96%, 97%, 98% or 99% sequence identity compared to the sequence shown in any of SEQ ID NO. 1-4, as well as sequences which delete one or more nucleotides, add one or more nucleotides, or replace one or more nucleotides but which are 90%, 91%, 92%, 93%, 94%, 95% or 96% or 97% or 98% or 99% identity to the nucleotide sequence shown in any of SEQ ID NO. 1-4 on the basis of the nucleotide sequence shown in any of SEQ ID NO. 1-4. The target sequence of the SNHG15 gene should encompass sequences comprising one or two or more nucleotide mutations compared to the sequence shown in any of SEQ ID NO:5-8, but which are substantially functionally identical thereto, as well as sequences having 95%, 96%, 97%, 98% or 99% sequence identity compared to the sequence shown in any of SEQ ID NO:5-8, as well as sequences comprising one or more nucleotide deletions, one or more nucleotide additions, or one or more nucleotide substitutions but 90%, 91%, 92%, 93%, 94%, 95% or 96% or 97% or 98% or 99% identity to the nucleotide sequence shown in any of SEQ ID NO:5-8 on the basis of the nucleotide sequence shown in any of SEQ ID NO: 5-8. The target sequence of the IFFO1 gene should encompass sequences which comprise one or two or more nucleotide mutations compared to the sequence shown in any of SEQ ID NO:9-12, but which are substantially functionally identical thereto, as well as sequences which have 95%, 96%, 97%, 98% or 99% sequence identity compared to the sequence shown in any of SEQ ID NO:9-12, as well as sequences which delete one or more nucleotides, add one or more nucleotides, or replace one or more nucleotides but which are 90%, 91%, 92%, 93%, 94%, 95% or 96% or 97% or 98% or 99% identical to the nucleotide sequence shown in any of SEQ ID NO:9-12 on the basis of the nucleotide sequence shown in any of SEQ ID NO: 9-12. The target sequence of the OSTM1 gene should encompass sequences comprising one or two or more nucleotide mutations compared to the sequence shown in any of SEQ ID NO:13-16, but which are substantially functionally identical thereto, as well as sequences having 95%, 96%, 97%, 98% or 99% sequence identity compared to the sequence shown in any of SEQ ID NO:13-16, as well as sequences comprising one or more nucleotide deletions, one or more nucleotide additions, or one or more nucleotide substitutions but 90%, 91%, 92%, 93%, 94%, 95% or 96% or 97% or 98% or 99% identity to the nucleotide sequence shown in any of SEQ ID NO:13-16 on the basis of the nucleotide sequence shown in any of SEQ ID NO: 13-16. The target sequence of the SLC38A1 gene should encompass sequences comprising one or two or more nucleotide mutations compared to the sequence shown in any of SEQ ID NOS: 17-20, but which are substantially functionally identical thereto, as well as sequences having 95%, 96%, 97%, 98% or 99% sequence identity compared to the sequence shown in any of SEQ ID NOS: 17-20, as well as sequences comprising one or more nucleotide deletions, one or more nucleotide additions, or one or more nucleotide substitutions but 90%, 91%, 92%, 93%, 94%, 95% or 96% or 97% or 98% or 99% identity to the nucleotide sequence shown in any of SEQ ID NOS: 17-20.

The target sequences (5 '-3') of the MIR578 gene are as follows:

the sequence (5 '-3') of the target sequence of the MIR578 gene after bisulfite treatment is as follows:

the complement (5 '-3') of the target sequence of the MIR578 gene is as follows:

the sequence complementary to the target sequence of the MIR578 gene after bisulfite treatment (5 '-3') is as follows:

the target sequence (5 '-3') of the SNHG15 gene is as follows:

the sequence (5 '-3') of the target sequence of the SNHG15 gene after bisulfite treatment is as follows:

the complementary sequences (5 '-3') of the target sequence of the SNHG15 gene are as follows:

the sequence (5 '-3') of the complementary sequence of the target sequence of the SNHG15 gene after bisulfite treatment is as follows:

the target sequence (5 '-3') of the IFFO1 gene is as follows

The sequence (5 '-3') of the target sequence of the IFFO1 gene after bisulphite treatment is as follows:

the complement (5 '-3') of the target sequence of the IFFO1 gene is as follows:

the sequence (5 '-3') of the complementary sequence of the target sequence of the IFFO1 gene after bisulphite treatment is as follows:

the target sequence (5 '-3') of the OSTM1 gene is as follows:

the sequence (5 '-3') of the target sequence of the OSTM1 gene after bisulfite treatment is as follows:

the complementary sequences (5 '-3') of the target sequence of the OSTM1 gene are as follows:

the sequence (5 '-3') of the complementary sequence of the target sequence of the OSTM1 gene after bisulfite treatment is as follows:

The target sequence (5 '-3') of the SLC38A1 gene is as follows:

the target sequence of the SLC38A1 gene after bisulfite treatment (5 '-3') is as follows:

the complementary sequence (5 '-3') of the target sequence of the SLC38A1 gene is as follows:

the sequence complementary to the target sequence of the SLC38A1 gene after bisulfite treatment (5 '-3') is as follows:

target sequences of MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene, SLC38A1 gene and related sequences are shown in Table 1:

table 1: target sequence and related sequence of each gene

Target sequence name	Sequence number
		Target sequence of MIR578 gene	SEQ ID NO:1
Sequence of target sequence of MIR578 gene after bisulfite treatment	SEQ ID NO:2
		Complement of the target sequence of the MIR578 gene	SEQ ID NO:3
Sequence complementary to target sequence of MIR578 Gene after bisulfite treatment	SEQ ID NO:4
		Target sequence of SNHG15 gene	SEQ ID NO:5
Sequence of target sequence of SNHG15 gene after bisulfite treatment	SEQ ID NO:6
		Complementary sequence of target sequence of SNHG15 gene	SEQ ID NO:7
Sequence complementary to target sequence of SNHG15 Gene after bisulfite treatment	SEQ ID NO:8
		Target sequence of IFFO1 gene	SEQ ID NO:9
Target sequence of IFFO1 Gene after bisulfite treatment	SEQ ID NO:10
		Complement of the target sequence of the IFFO1 gene	SEQ ID NO:11
Sequence of the complement of the target sequence of the IFFO1 gene after bisulfite treatment	SEQ ID NO:12
		Target sequence of OSTM1 gene	SEQ ID NO:13
Sequence of target sequence of OSTM1 gene after bisulfite treatment	SEQ ID NO:14
		Complementary sequence to target sequence of OSTM1 gene	SEQ ID NO:15
Sequence complementary to the target sequence of the OSTM1 gene after bisulfite treatment	SEQ ID NO:16
		Target sequence of SLC38A1 gene	SEQ ID NO:17
Sequence of target sequence of SLC38A1 gene after bisulphite treatment	SEQ ID NO:18
		Complementary sequence of target sequence of SLC38A1 gene	SEQ ID NO:19
Sequence of complementary sequence of target sequence of SLC38A1 Gene after bisulfite treatment	SEQ ID NO:20

Preferably, the nucleic acid for detecting methylation status of a gene of interest comprises a fragment of at least 9 nucleotides in a target sequence of the gene of interest, wherein the fragment comprises at least one CpG dinucleotide sequence. In certain preferred embodiments, the nucleic acid for detecting methylation status of a target gene comprises a fragment of at least 9 nucleotides, preferably a fragment of at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 or more nucleotides in a sequence that has been bisulfite converted from a target sequence of the target gene, such as by using bisulfite to convert a sample DNA to be tested, wherein the fragment of a nucleotide comprises at least one CpG dinucleotide sequence.

More preferably, the nucleic acid for detecting methylation status of a gene of interest comprises a fragment of at least 15 nucleotides that hybridizes under moderate stringency or stringent conditions to a target sequence of said gene of interest, wherein said fragment of nucleotides comprises at least one CpG dinucleotide sequence. In certain preferred embodiments, the nucleic acid for detecting the methylation state of a target gene, such as by converting a test sample DNA using bisulfite, comprises a fragment of at least 15 nucleotides, preferably a fragment of at least 16, 17, 18, 19, 20, 21, 22 or more nucleotides, in a sequence following bisulfite conversion of a target sequence hybridized to the target gene under moderately stringent or stringent conditions, wherein the fragment of nucleotides comprises at least one CpG dinucleotide sequence.

Preferably, the composition further comprises an agent that converts an unmethylated cytosine base at position 5 of the target sequence of the target gene to uracil. More preferably, the reagent is bisulphite.

The nucleic acid used to detect the methylation state of a gene of interest can also include a blocking agent that preferentially binds to DNA in the unmethylated state.

Preferably, the composition comprises one or more of the primers, probes as shown in table 2:

TABLE 2 primer and probe sequences used in the present application

"F" in Table 2 represents a forward primer; "R" means the reverse primer; "P" means a probe.

Preferably, the fluorescent labeling patterns of the probe sequences used in the present application are shown in Table 3.

TABLE 3 fluorescent labelling of probe sequences for use in the present application

Sequence numbering	Sequence name	5' tag	3' tag
				SEQ ID NO:23	MIR578_1P	FAM	BHQ1
SEQ ID NO:26	SNHG15_1P	Cy5	BHQ3
				SEQ ID NO:29	IFFO1_1P	VIC	BHQ1
SEQ ID NO:32	OSTM1_1P	FAM	BHQ1
				SEQ ID NO:35	SLC38A1_1P	VIC	BHQ1

In certain embodiments, the composition further comprises an agent that converts an unmethylated cytosine base at position 5 of the gene to uracil. Preferably, the agent is bisulphite. Bisulfite modification of DNA is a known tool for assessing CpG methylation status. In eukaryotic DNA, 5-methylcytosine is the most common covalent base modification. 5-methylcytosine cannot be identified by sequencing because 5-methylcytosine has the same base pairing behavior as cytosine. Furthermore, the epigenetic information carried by 5-methylcytosine is completely lost during PCR amplification. The most commonly used method for analyzing DNA for the presence of 5-methylcytosine is based on the specific reaction of bisulfite with cytosine; after subsequent alkaline hydrolysis, unmethylated cytosines are converted to uracil which corresponds to thymine in pairing behavior; but under these conditions 5-methylcytosine remains unmodified. The original DNA is thus converted in such a way that the 5-methylcytosine, which was originally indistinguishable from cytosine in its hybridization behavior, can now be detected as the only cytosine remaining by conventional known molecular biological techniques, for example by amplification and hybridization. All of these techniques are now fully utilized based on different base pairing properties. Thus, typically, the present application provides for the use of bisulfite technology in combination with one or more methylation assays for determining the methylation status of CpG dinucleotide sequences within a target sequence of a gene of interest. Furthermore, the method of the application is suitable for analyzing heterogeneous biological samples, such as low concentrations of tumor cells in blood or stool. Thus, when analyzing the methylation status of CpG dinucleotide sequences in such samples, one skilled in the art can use quantitative assays to determine the methylation level (e.g., percentage, fraction, ratio, proportion or degree) of a particular CpG dinucleotide sequence, rather than the methylation status. Accordingly, the term methylation status or methylation status shall also be taken to mean a value reflecting the methylation status of a CpG dinucleotide sequence.

In another aspect, the application provides an oligonucleotide for detecting thyroid cancer in vitro, comprising: a fragment of at least 9 nucleotides of SEQ ID NO. 1 or SEQ ID NO. 2 or SEQ ID NO. 3 or SEQ ID NO. 4 or the complement thereof comprising at least one CpG dinucleotide sequence; and/or a fragment of at least 9 nucleotides of SEQ ID NO. 5 or SEQ ID NO. 6 or SEQ ID NO. 7 or SEQ ID NO. 8 or the complement thereof comprising at least one CpG dinucleotide sequence; and/or a fragment of at least 9 nucleotides of SEQ ID NO. 9 or SEQ ID NO. 10 or SEQ ID NO. 11 or SEQ ID NO. 12 or the complement thereof comprising at least one CpG dinucleotide sequence; and/or a fragment of at least 9 nucleotides of SEQ ID NO. 13 or SEQ ID NO. 14 or SEQ ID NO. 15 or SEQ ID NO. 16 or the complement thereof comprising at least one CpG dinucleotide sequence; and/or a fragment of at least 9 nucleotides of SEQ ID NO. 17 or SEQ ID NO. 18 or SEQ ID NO. 19 or SEQ ID NO. 20 or the complement thereof and comprising at least one CpG dinucleotide sequence.

Preferably the oligonucleotide for in vitro detection of thyroid cancer comprises: a fragment of at least 9 nucleotides of the sequence after bisulfite conversion of SEQ ID NO. 1 or SEQ ID NO. 2 or SEQ ID NO. 3 or SEQ ID NO. 4 or the complement thereof; and/or a fragment of at least 9 nucleotides of the sequence after bisulfite conversion of SEQ ID NO. 5 or SEQ ID NO. 6 or SEQ ID NO. 7 or SEQ ID NO. 8 or the complement thereof and comprising at least one CpG dinucleotide sequence; and/or a fragment of at least 9 nucleotides of the sequence after bisulfite conversion of SEQ ID NO. 9 or SEQ ID NO. 10 or SEQ ID NO. 11 or SEQ ID NO. 12 or the complement thereof and comprising at least one CpG dinucleotide sequence; a fragment of at least 9 nucleotides of the sequence after bisulfite conversion of SEQ ID NO. 13 or SEQ ID NO. 14 or SEQ ID NO. 15 or SEQ ID NO. 16 or the complement thereof; and/or a fragment of at least 9 nucleotides of the sequence after bisulfite conversion of SEQ ID NO. 17 or SEQ ID NO. 18 or SEQ ID NO. 19 or SEQ ID NO. 20 or the complement thereof and comprising at least one CpG dinucleotide sequence.

The oligonucleotide for detecting thyroid cancer in vitro of the present application further comprises: a fragment which hybridizes under moderately stringent or stringent conditions to at least 15 nucleotides of SEQ ID NO. 1 or SEQ ID NO. 2 or SEQ ID NO. 3 or SEQ ID NO. 4 or the complement thereof and which comprises at least one CpG dinucleotide sequence; and/or a fragment which hybridizes under moderately stringent or stringent conditions to at least 15 nucleotides of SEQ ID NO. 5 or SEQ ID NO. 6 or SEQ ID NO. 7 or SEQ ID NO. 8 or the complement thereof and which comprises at least one CpG dinucleotide sequence; and/or a fragment which hybridizes under moderately stringent or stringent conditions to at least 15 nucleotides of SEQ ID NO. 9 or SEQ ID NO. 10 or SEQ ID NO. 11 or SEQ ID NO. 12 or the complement thereof and which comprises at least one CpG dinucleotide sequence; and/or a fragment which hybridizes under moderately stringent or stringent conditions to at least 15 nucleotides of SEQ ID NO. 13 or SEQ ID NO. 14 or SEQ ID NO. 15 or SEQ ID NO. 16 or the complement thereof and which comprises at least one CpG dinucleotide sequence; and/or a fragment which hybridizes under moderately stringent or stringent conditions to at least 15 nucleotides of SEQ ID NO. 17 or SEQ ID NO. 18 or SEQ ID NO. 19 or SEQ ID NO. 20 or the complement thereof and which comprises at least one CpG dinucleotide sequence.

Preferably the oligonucleotide for in vitro detection of thyroid cancer comprises: a fragment which hybridizes under moderately stringent or stringent conditions to at least 15 nucleotides of the sequence after bisulfite conversion of SEQ ID NO. 1 or SEQ ID NO. 2 or SEQ ID NO. 3 or SEQ ID NO. 4 or the complement thereof and which comprises at least one CpG dinucleotide sequence; and/or a fragment which hybridizes under moderately stringent or stringent conditions to at least 15 nucleotides of the sequence after bisulfite conversion of SEQ ID NO. 5 or SEQ ID NO. 6 or SEQ ID NO. 7 or SEQ ID NO. 8 or the complement thereof and which comprises at least one CpG dinucleotide sequence; and/or a fragment which hybridizes under moderately stringent or stringent conditions to at least 15 nucleotides of the sequence after bisulfite conversion of SEQ ID NO. 9 or SEQ ID NO. 10 or SEQ ID NO. 11 or SEQ ID NO. 12 or the complement thereof and which comprises at least one CpG dinucleotide sequence; and/or a fragment which hybridizes under moderately stringent or stringent conditions to at least 15 nucleotides of the sequence after bisulfite conversion of SEQ ID NO. 13 or SEQ ID NO. 14 or SEQ ID NO. 15 or SEQ ID NO. 16 or the complement thereof and which comprises at least one CpG dinucleotide sequence; and/or a fragment which hybridizes under moderately stringent or stringent conditions to at least 15 nucleotides of the sequence after bisulfite conversion of SEQ ID NO. 17 or SEQ ID NO. 18 or SEQ ID NO. 19 or SEQ ID NO. 20 or the complement thereof and which comprises at least one CpG dinucleotide sequence.

The oligonucleotide for detecting thyroid cancer in vitro of the present application may further comprise: blocking agents that preferentially bind to DNA in the unmethylated state.

In a specific embodiment, an oligonucleotide for detecting thyroid cancer in vitro, comprising: SEQ ID NO. 21 and SEQ ID NO. 22. It also includes: SEQ ID NO. 23.

In another specific embodiment, an oligonucleotide for detecting thyroid cancer in vitro, comprising: SEQ ID NO. 24 and SEQ ID NO. 25. It also includes: SEQ ID NO. 26.

In another specific embodiment, an oligonucleotide for detecting thyroid cancer in vitro, comprising: the sequences of SEQ ID NO. 27 and SEQ ID NO. 28, further comprising: SEQ ID NO. 29.

In another specific embodiment, an oligonucleotide for detecting thyroid cancer in vitro, comprising: the sequences of SEQ ID NO. 30 and SEQ ID NO. 31, further comprising: SEQ ID NO. 32.

In another specific embodiment, an oligonucleotide for detecting thyroid cancer in vitro, comprising: the sequences of SEQ ID NO. 33 and SEQ ID NO. 34, further comprising: SEQ ID NO. 35.

In another aspect, the application provides a kit comprising the composition. The kit further comprises at least one additional component selected from the group consisting of: nucleoside triphosphates, DNA polymerase and buffers required for the function of the DNA polymerase.

Typically, the kit further comprises a container for holding a biological sample of a patient. And, the kit also includes instructions for use and interpretation of the test results.

The application also relates to the application of the composition and the oligonucleotide in preparing a kit for detecting thyroid cancer in vitro.

The application also relates to application of one or more than two of MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene and SLC38A1 gene in preparing a kit for detecting thyroid cancer in vitro.

Wherein the MIR578 gene is an RNA gene and belongs to miRNA class. mirnas are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of mRNA stability and translation by affecting gene expression in multicellular organisms.

The SNHG15 gene (micronucleolar RNA host gene 15) is an RNA gene, belongs to the lncRNA class, and diseases related to SNHG15 include hereditary hemorrhagic telangiectasia and pancreatic cancer.

The IFFO1 gene is a member of a middle filament family, the middle filament is a protein main component of a cytoskeleton and a nuclear membrane, and the coded protein interacts with a nuclear layer component LMNA to promote fixation of a broken terminal and prevent chromosome translocation.

The protein encoded by the OSTM1 gene may be involved in the degradation of G protein by the ubiquitin-dependent proteasome pathway. The protein has a central ring finger domain and E3 ubiquitin ligase activity. This protein is highly conserved from flies to humans, and a deficiency in this gene may lead to malignant osteosclerosis in infants inherited by autosomal recessions.

The SLC38A1 gene encodes an amino acid transporter that plays an important role in nutrient uptake, energy production, chemical metabolism, detoxification, and neurotransmitter circulation. SLC38A1 is an important transporter of glutamine, an intermediate for ammonia detoxification and urea production, and in addition glutamine is a precursor of synaptic transmitter glutamate.

In yet another aspect, the present application provides a method for detecting thyroid cancer in vitro, the method comprising the steps of:

1) Isolating a target sequence of a target gene or a fragment thereof in a biological sample to be tested;

2) Determining the methylation status of the target sequence of the target gene;

3) Judging the state of the biological sample according to the detection result of the methylation state of the target sequence of the target gene, thereby realizing the in vitro detection of thyroid cancer.

According to certain preferred embodiments, the method further comprises the steps of:

1) Extracting genome DNA of a biological sample to be detected;

2) Treating the DNA sample obtained in step 1) with a reagent to convert the 5-unmethylated cytosine base into uracil or another base, i.e., the 5-unmethylated cytosine base of the target sequence of the target gene into uracil or another base, the converted base being different from the 5-unmethylated cytosine base in hybridization performance and being detectable;

3) Contacting the DNA sample treated in step 2) with a DNA polymerase and primers for the target sequence of the target gene such that the target sequence of the treated target gene is amplified to produce amplified products or not; the target sequence of the treated target gene produces amplified products if DNA polymerization occurs; the target sequence of the treated target gene is not amplified if DNA polymerization does not occur;

4) Detecting the amplified product with a probe; and

5) Determining the methylation status of at least one CpG dinucleotide of the target sequence of the target gene based on the presence or absence of the amplification product.

Preferably, typical primers comprise fragments of the target sequence of the target gene comprising fragments of at least 9 nucleotides which are identical to, complementary to or hybridise under moderate stringency or stringent conditions to a sequence selected from any one of SEQ ID NOS: 1 to 4, any one of SEQ ID NOS: 5 to 8, any one of SEQ ID NOS: 9 to 12, any one of SEQ ID NOS: 13 to 16, any one of SEQ ID NOS: 17 to 20, respectively.

Preferably, a typical probe comprises a fragment of the target sequence of the target gene comprising a fragment of at least 15 nucleotides which is identical to, complementary to or hybridizes under moderately stringent or stringent conditions to a sequence selected from any one of SEQ ID NOS: 1-4, any one of SEQ ID NOS: 5-8, any one of SEQ ID NOS: 9-12, any one of SEQ ID NOS: 13-16, any one of SEQ ID NOS: 17-20, respectively.

Preferably, one or more of the primers, probes are as set forth in table 2 above.

And, the contacting or amplifying comprises using at least one of the following methods: using a thermostable DNA polymerase as the amplification enzyme, using a polymerase lacking 5'-3' exonuclease activity, using Polymerase Chain Reaction (PCR), producing an amplification product nucleic acid molecule with a detectable label.

Preferably, the methylation status is determined by means of PCR, such as "fluorescence-based real-time PCR technique", methylation sensitive single nucleotide primer extension reaction (Ms-SNuPE), methylation Specific PCR (MSP), and methylation CpG island amplification (MCA), etc., is used to determine the methylation status of at least one CpG dinucleotide of the target sequence of the gene of interest. Among these, the "fluorescence-based real-time PCR" assay is a high throughput quantitative methylation assay that uses fluorescence-based real-time PCR (TaqMan) techniques, requiring no further manipulation after the PCR step. Briefly, the "fluorescence-based real-time PCR" method starts with a mixed sample of genomic DNA that is converted into a mixed pool of methylation-dependent sequence differences in a sodium bisulfite reaction according to standard procedures. Fluorescence-based PCR was then performed in an "offset" (biased) reaction (using PCR primers overlapping known CpG dinucleotides). Sequence differences can be produced at the amplification level and at the fluorescence detection amplification level. The "fluorescence-based real-time PCR" assay can be used as a quantitative test for methylation status in genomic DNA samples, where sequence discrimination occurs at the level of probe hybridization. In this quantitative format, the PCR reaction provides methylation specific amplification in the presence of fluorescent probes that overlap specific CpG dinucleotides. An unbiased control for the amount of starting DNA is provided by the following reaction: wherein neither the primer nor the probe covers any CpG dinucleotide. The "fluorescence-based real-time PCR" method can be used with any suitable probe, such as "TaqMan", "Lightcycler", etc. The TaqMan probe is double labeled with a fluorescent reporter (RTSP ULT 5 rter) and a Quencher (Quencher) and is designed to be specific for a relatively high GC content region such that it melts at a temperature about 10℃higher than the forward or reverse primer during the PCR cycle. This allows the TaqMan probe to remain fully hybridized during the PCR annealing/extension step. When Taq polymerase enzymatically synthesizes a new strand in PCR, it eventually encounters an annealed TaqMan probe. Taq polymerase 5 'to 3' endonuclease activity will then displace the TaqMan probe by digesting it, thereby releasing the fluorescent reporter molecule for quantitative detection of its now unquenched signal using a real-time fluorescent detection system. Typical reagents for "fluorescence-based real-time PCR" analysis may include, but are not limited to: target sequence PCR primers for the target gene; a non-specific amplification blocker; taqMan or Lightcycler probes; optimized PCR buffers and deoxynucleotides; taq polymerase, and the like.

In certain preferred embodiments, the methylation status of at least one CpG dinucleotide in the target sequence of the target gene is determined from the critical Ct value of the real-time PCR reaction. The method for analyzing DNA in the biological sample by utilizing the real-time PCR reaction can conveniently realize the detection of the methylation state of the target sequence of the target gene, and can rapidly and conveniently judge whether the detected sample is positive according to the critical Ct value of the PCR reaction, thereby providing a noninvasive and rapid thyroid cancer in-vitro detection method.

The biological sample is selected from the group consisting of a cell line, a histological section, a tissue biopsy/paraffin-embedded tissue, a body fluid, stool, a colonic outflow, urine, plasma, serum, whole blood, isolated blood cells, cells isolated from blood, or a combination thereof. A preferred biological sample is plasma.

The inventors found that there was a significant difference between the methylation status of the target sequences of the MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene, SLC38A1 gene, and the methylation status of the target sequences of the genes of normal tissue in thyroid cancer tissue: in thyroid cancer tissues, the target sequences of MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene, SLC38A1 gene are methylated, whereas in normal tissues, the target sequences of MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene, SLC38A1 gene are not methylated. Therefore, the application provides a method for detecting thyroid cancer in vitro by detecting methylation status of one or more gene target sequences of MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene and SLC38A1 gene in a sample, and the method provided by the application can detect thyroid cancer noninvasively and rapidly.

Examples

The materials used in the test and the test methods are described generally and/or specifically in the examples which follow,% represents wt%, i.e. weight percent, unless otherwise specified. The reagents or apparatus used were conventional reagent products commercially available without the manufacturer's knowledge.

Example 1 primer and Probe test

First, sites of low methylation level were screened in the second generation sequencing information of 340 healthy human WBC samples and 102 healthy human plasma cfDNA samples. Next, plasma and thyroid cancer tissue analyses were performed on the screened hypomethylation level sites, and sites that were different in 103 cases of thyroid cancer plasma and 102 cases of normal human plasma and were different in 56 cases of thyroid cancer tissue and 56 cases of paracancerous tissue were screened as candidate markers. Then, plasma tracing is carried out on the candidate markers. Finally, five specific markers of MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene and SLC38A1 gene are determined through thyroid cancer tissue and normal human blood plasma sensitivity and specificity verification.

Primers and probes were designed based on the target sequences of the five genes, and the designed primer probe sequences are shown in Table 2.

The cell line DNA of normal human leukocytes is normally in a low/unmethylated state and can be used as a negative control, with an amount of 15.75 ng/reaction in this embodiment; the total methylated DNA was in a high/total methylated state and served as a positive control, and the amount of DNA used in this embodiment was 200 pg/reaction. Firstly, bisulphite conversion is carried out on a DNA sample, and real-time PCR amplification is carried out by using the converted BisDNA as a template and using the primer probe. The beta Actin (ACTB) gene is used as an internal reference, a beta actin gene amplicon is created by using a primer complementary to the beta actin gene sequence, and the beta actin gene amplicon is detected with a specific probe. Each sample is subjected to at least one real-time PCR, and in some embodiments, two or three real-time PCR assays are performed. The PCR system for the primer probe test is shown in Table 4 below.

TABLE 4 PCR System for primer probe test

	Volume (mu L)	Final concentration
			Taq DNA Polymerase(Biochain)	1.2	/
4.2×buffer(Biochain)	11.9	1×
			Forward primer F (10. Mu.M)	1.0	200nM
Reverse primer R (10. Mu.M)	1.0	200nM
			Probe P (10 mu M)	1.0	200nM
ACTB_F(10μM)	0.5	100nM
			ACTB_R(10μM)	0.5	100nM
ACTB_P(10μM)	0.375	75nM
			BisDNA	4.0	/
H 2 O	19.05	/
			Total	50.0	/

Note that: "F" represents a forward primer; "R" means the reverse primer; "P" means a probe.

The PCR amplification procedure used was: 94 ℃ for 20min; (93 ℃,30s;57 ℃,35 s-read fluorescent signal) 45 cycles; 40℃for 5s.

As shown in Table 5, when the bisDNA of the total methylated DNA was used as a template, MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene and SLC38A1 gene were amplified efficiently; when the bisDNA of WBC is used as the template, the target genes except the reference gene ACTB are not amplified.

TABLE 5 results of primer probe test for each Gene

Where "No Ct" indicates that No Ct value is detected.

Example 2

30 thyroid cancer tissue samples (10 ng/reaction) and 20 normal human plasma samples (3.5 mL) were selected, genomic DNA was extracted and converted to BisDNA by bisulfite, and methylation of MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene and SLC38A1 gene was detected according to the PCR reaction system shown in Table 4 and the reaction procedure in example 1. The threshold value of each marker was set at 41, and finally Ct values of real-time PCR of 30 thyroid cancer tissues and 20 normal human plasma for target sequences of the target genes were measured. The results are shown in tables 6 and 7.

Table 6 sensitivity detection of genes in thyroid cancer tissue and normal human plasma

Table 7 specific detection of genes in thyroid cancer tissue and normal human plasma

The results in Table 6 show that the sensitivity of thyroid cancer tissue detection using MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene, SLC38A1 gene was 83%, 80%, 73%, 77%, respectively. The results in Table 7 show that the target sequence of the target gene has good specificity in methylation, and that the specificity of the MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene, and SLC38A1 gene in normal human plasma is 95%, 100%, and 95%, respectively.

Among the 5 markers related to thyroid cancer, the tissue sensitivity was 70% or more from the results of the detection of the tissue. From the detection result of normal human blood plasma, the blood plasma specificity is above 95%. Under small sample size validation conditions, plasma specificity up to 80% is a relatively reasonable and high index level. Thus, the above experimental results indicate that the 5 target genes selected in the present application are potential markers for detecting thyroid cancer methylation.

Example 3

40 thyroid cancer plasma samples (3.5 mL) and 32 normal human plasma samples (3.5 mL) were selected, genomic DNA was extracted, bisulphite-converted to BisDNA, and methylation was detected in combination with MIR578, SNHG15, IFFO1, OSTM1, SLC38A1 genes according to the PCR reaction system of example 1. Finally, ct values of real-time PCR of 40 thyroid cancer plasma samples and 32 normal human plasma samples on target sequences of target genes are measured. The critical values of the Ct values of the five genes all select ct=38. The experimental results are shown in table 8.

Sensitivity/specificity detection of genes in thyroid cancer plasma and normal human plasma

The results in Table 8 show that the sensitivity of detection of thyroid cancer by MIR578, SNHG15, IFFO1, OSTM1, SLC38A1 genes alone was 77.5%, 72.5%, 70%, 67.5%, 62.5%, respectively.

The above experimental results show that the methylated DNA of the target sequence of the target gene is a marker of thyroid cancer. The detection of the target sequence methylated DNA of the target gene can realize noninvasive detection of thyroid cancer in vitro and can improve the detection rate of thyroid cancer.

In summary, the composition, the nucleic acid sequence, the kit and the application thereof and the detection method realize in vitro detection of thyroid cancer by using the target sequence methylation biomarker of the target gene by detecting the target sequence of the target gene and the methylated nucleic acid sequence of the fragment thereof, thereby effectively improving the sensitivity and the specificity of in vitro detection of thyroid cancer.

The above description is only a preferred embodiment of the present application, and is not intended to limit the application in any way, and any person skilled in the art may make modifications or alterations to the disclosed technical content to the equivalent embodiments. However, any simple modification, equivalent variation and variation of the above embodiments according to the technical substance of the present application still fall within the protection scope of the technical solution of the present application.

Claims (10)

1. A composition for detecting thyroid cancer in vitro, the composition comprising:

nucleic acid for detecting methylation status of a target gene,

wherein the methylation state of the target gene is characterized by methylation of a target sequence of the target gene,

wherein the target gene is one or more than two of MIR578 gene, SNHG15 gene, IFFO1 gene, OSTM1 gene and SLC38A1 gene.

2. The composition of claim 1, wherein the target sequence of the MIR578 gene is shown as SEQ ID No. 1 or SEQ ID No. 2 or SEQ ID No. 3 or SEQ ID No. 4 or the target sequence of the MIR578 gene comprises the sequence shown as SEQ ID No. 1 or SEQ ID No. 2 or SEQ ID No. 3 or SEQ ID No. 4.

3. The composition of claim 1, wherein the target sequence of the SNHG15 gene is shown as SEQ ID NO. 5 or SEQ ID NO. 6 or SEQ ID NO. 7 or SEQ ID NO. 8 or the target sequence of the SNHG15 gene comprises a sequence shown as SEQ ID NO. 5 or SEQ ID NO. 6 or SEQ ID NO. 7 or SEQ ID NO. 8.

4. The composition of claim 1, wherein the target sequence of the IFFO1 gene is as shown in SEQ ID No. 9 or SEQ ID No. 10 or SEQ ID No. 11 or SEQ ID No. 12 or the target sequence of the IFFO1 gene comprises a sequence as shown in SEQ ID No. 9 or SEQ ID No. 10 or SEQ ID No. 11 or SEQ ID No. 12.

5. The composition of claim 1, wherein the target sequence of the OSTM1 gene is as shown in SEQ ID No. 13 or SEQ ID No. 14 or SEQ ID No. 15 or SEQ ID No. 16 or the target sequence of the OSTM1 gene comprises a sequence as shown in SEQ ID No. 13 or SEQ ID No. 14 or SEQ ID No. 15 or SEQ ID No. 16.

6. The composition of claim 1, wherein the target sequence of the SLC38A1 gene is shown as SEQ ID NO. 17 or SEQ ID NO. 18 or SEQ ID NO. 19 or SEQ ID NO. 20 or the target sequence of the SLC38A1 gene comprises a sequence shown as SEQ ID NO. 17 or SEQ ID NO. 18 or SEQ ID NO. 19 or SEQ ID NO. 20.

7. The composition of any one of claims 1 to 6, wherein the nucleic acid for detecting methylation status of a target gene comprises:

a primer which is a fragment of at least 9 nucleotides in a target sequence of the target gene,

the fragment comprises at least one CpG dinucleotide sequence.

8. The composition of any one of claims 1-7, wherein the nucleic acid for detecting methylation status of a target gene comprises:

a probe which is a fragment of at least 15 nucleotides hybridised to the target sequence of the target gene under moderately stringent or stringent conditions,

The fragment comprises at least one CpG dinucleotide sequence.

9. The composition of any one of claims 1-8, further comprising:

an agent that converts an unmethylated cytosine base at position 5 of a target sequence of a target gene into uracil.

10. The composition of any one of claims 1-9, wherein the nucleic acid for detecting methylation status of a target gene further comprises:

blocking agents that preferentially bind to target sequences in the unmethylated state.