Method for evaluating quality of body fluid sample
Technical field
[0001]
　The present invention relates to a method for evaluating the quality of a body fluid sample based on the abundance of a specific miRNA contained in the body fluid sample.
Background technology
[0002]
　miRNA (microRNA) is transcribed from genomic DNA as RNA (pre-mRNA) with a hairpin-like structure. This precursor is cleaved by a dsRNA cleavage enzyme (Drosha, Dicer) having a specific enzyme RNase III cleavage activity, then changes to a double-stranded form, and then becomes single-stranded. Then, one of the antisense strands is incorporated into a protein complex called RISC, which is thought to be involved in the suppression of mRNA translation. As described above, since miRNA has a different mode at each stage after transcription, usually, when miRNA is to be detected, various forms such as a hairpin structure, a double-stranded structure, and a single-stranded structure are used. Need to consider. miRNA consists of 15 to 25 bases of RNA, and its existence has been confirmed in various organisms.
[0003]
　In recent years, miRNAs are abundant not only in cells but also in body fluids such as serum, plasma, urine, and cerebrospinal fluid, which are cell-free samples, and their abundance is found in various diseases including cancer. It has been suggested that it may be a biomarker. As of June 2018, there are more than 2,600 types of miRNAs in humans, and when a measurement system such as a highly sensitive DNA microarray is used, the expression of more than 1000 types of miRNAs is detected simultaneously in serum and plasma. It is possible. Therefore, biomarker search research targeting body fluids such as serum / plasma, urine, and cerebrospinal fluid is being conducted using the DNA microarray method, and it is expected to develop into biomarker tests that can detect diseases at an early stage. ..
[0004]
　On the other hand, RNA is a substance that is easily decomposed by various physical and chemical factors such as heat, degrading enzymes, and freeze-thaw, and when gene expression analysis is performed using a DNA microarray, RNA degradation is abundant. It is known to affect the measurement. In tests that measure the abundance of miRNA contained in body fluids as a biomarker of a disease, if the test / diagnosis is made based on the measured value of the abundance with uncertainty, an appropriate treatment opportunity will be missed. Or, applying the wrong medical care will impose an unnecessary financial and physical burden on the patient. Therefore, in order to accurately measure the abundance, it is extremely important to use a sample in which the miRNA to be tested is not degraded for the test.
[0005]
　Conventionally, electrophoresis is generally used as a method for measuring the degree of RNA degradation. For example, it can be measured from the concentration ratio (28S / 18S) of a band derived from 28S ribosomal RNA and a band derived from 18S ribosomal RNA. .. As another method, Patent Document 1 proposes a method of quantitatively evaluating the degree of RNA degradation based on the difference in RNA segment length. Here, the segment length becomes shorter when nucleotides are degraded. It utilizes the characteristics of long RNA.
[0006]
　However, when measuring the abundance of miRNA, short-chain fractional RNA is often used, and in this case, long-chain RNA is not included. Therefore, the conventional method as described above measures the degree of RNA degradation. It cannot be an effective method for doing so. It is possible to measure the degree of degradation of the RNA used from the correlation coefficient of all genes in the gene expression analysis result, but data on all genes is required, which takes time and effort. Therefore, a method has been developed that focuses on the degraded fragments derived from long RNA and evaluates the degree of degradation of miRNA in the short chain fraction using the degraded fragment mixed in the short chain fraction as an index (Patent Document 2). .. Further, Patent Document 3 discloses a method for evaluating the quality by measuring the degree of decomposition of miRNA contained in a body fluid sample.
Prior art literature
Patent documents
[0007]
Patent Document 1: Japanese
Patent Application Laid-Open No. 2015-519045: Japanese Patent Application Laid-Open No. 2008-35779
Patent Document 3: International Publication No. 2017/146033
Outline of the invention
Problems to be solved by the invention
[0008]
　As described above, in order to accurately measure the abundance of target RNA, it is important to measure the degree of degradation of RNA in the sample to evaluate the sample quality. However, the methods of Patent Document 1 and Patent Document 2 described above are methods using ribosomal RNA and long RNA. Ribosomal RNA and long-chain RNA are RNAs that are present in the nucleus and cytoplasm, and are rarely present in body fluid samples such as serum, plasma, urine, and cerebrospinal fluid. Therefore, it was not possible to accurately measure the degree of degradation of miRNA contained in body fluid samples and evaluate the quality by these methods.
[0009]
　On the other hand, Patent Document 3 discloses a plurality of types of miRNAs whose abundance changes with the decomposition of miRNAs contained in body fluids. Specifically, we have selected miRNAs that degrade when left at 4 ° C for 0 hours to 2 weeks in the serum state, but their presence is present only after standing for 6 hours compared to the 0 hour condition. There is almost no change in the amount, and even if it is left to stand for 24 hours, the fluctuation of its abundance is about 10%. If it is desired to determine whether or not the quality of the sample has deteriorated by allowing it to stand at 4 ° C. for 24 hours, a slight variation in the abundance of 10% may not be detected due to the variation in the measurement system. Judgment is difficult by the described method. In addition, when performing gene expression analysis using a DNA microarray, quality deterioration of the sample within a short period of several hours to one day after the sample is collected may affect the measurement and diagnostic results. If it has been confirmed, a sensitive index or method for detecting the deterioration of the quality of the sample in a short period of time and determining whether or not the measurement is possible is required.
[0010]
　An object of the present invention is to find a method for evaluating the quality by measuring the degree of degradation of miRNA contained in a body fluid sample, and in particular, the quality of the body fluid sample occurring in a short time of several hours to one day after the collection of the body fluid sample. Finding a method to detect deterioration sensitively.
Means to solve problems
[0011]
　In order to solve the above problems, the present inventors have prepared miRNA whose abundance varies depending on the deterioration of the body fluid sample for several hours to one day after the collection of the body fluid sample (hereinafter referred to as "reference miRNA"). We have found that the quality of a body fluid sample can be evaluated by measuring its abundance as a reference, and completed the present invention. That is, in the present invention, one or more of the miRNAs shown in SEQ ID NOs: 1 to 16 and 37 to 61 is used as a reference miRNA, and the abundance of the reference miRNA contained in the body fluid sample and a predetermined threshold value are set. It is a method of evaluating the quality of a body fluid sample by comparison, and includes the following aspects.
[0012]
(1) A method for evaluating the quality of a body fluid sample,
　in which one or a plurality of reference miRNAs selected from miRNAs consisting of the base sequences shown in SEQ ID NOs: 1 to 16 and 37 to 61 are present in the body fluid sample. The measurement step of measuring the amount; and the
　index value calculated from the abundance of the one or more reference miRNAs obtained in the measurement step or the abundance of the plurality of reference miRNAs are arbitrarily determined in advance. The
method comprising a determination step; determining the quality of a body fluid sample by comparison with a threshold .
(2) The method according to (1), wherein the index value is the difference or ratio of the abundances of two arbitrarily selected reference miRNAs.
(3) The miRNA consisting of the base sequences shown in SEQ ID NOs: 1, 5 and 7 has poor quality of the body fluid sample when the abundance in the body fluid sample exceeds the first threshold value or falls below the second threshold value. The miRNA indicating that there is, and the miRNA consisting of the base sequences shown by SEQ ID NOs: 2, 3, 4, 6, 11, 37 to 43, 45, 46, 49, 51, 52, 54, 58 is contained in the body fluid sample. It is a miRNA indicating that the quality of the body fluid sample is poor when the abundance of the above exceeds the threshold value, and is a miRNA of SEQ ID NO: 8, 9, 10, 12 to 16, 44, 47, 48, 50, 53, 55 to 57, The miRNA consisting of the base sequences shown by 59 to 61 is a miRNA indicating that the quality of the body fluid sample is poor when the abundance in the body fluid sample is below the threshold value, according to (1) or (2). Method.
(4) The measurement step comprises a probe for capturing one or more reference miRNAs selected from miRNAs consisting of the nucleotide sequences represented by SEQ ID NOs: 1 to 16 and 37 to 61 immobilized on the support. , (1) to (3), which are steps of contacting a nucleic acid sample derived from a body fluid sample labeled with a labeling substance and performing hybridization to measure the abundance of the one or more reference miRNAs in the body fluid sample. The method according to any one of the above.
(5) The determination step is carried out using the corrected abundance value, further including a correction step for correcting the measured value of the abundance of the one or more reference miRNAs obtained in the measurement step. The method according to any one of (1) to (4).
(6) The measurement step includes measuring the abundance of one or more reference miRNAs in the body fluid sample and simultaneously measuring the abundance of the target miRNA in the body fluid sample (1) to (5). The method according to any one of the above.
(7) One or more of the measurement steps selected from a probe for capturing the target miRNA immobilized on the support and a miRNA consisting of the nucleotide sequences shown in SEQ ID NOs: 1 to 16 and 37 to 61. The probe for capturing the reference miRNA and the nucleic acid sample derived from the body fluid sample labeled with the labeling substance are brought into contact with each other for hybridization, and the abundance of the target miRNA and the one or more reference miRNAs in the body fluid sample is determined, respectively. The method according to (6), which is a step of measuring.
(8) A correction step for correcting the measured value of the abundance of the target miRNA in the body fluid sample obtained in the measuring step and the measured value of the abundance of the one or more reference miRNAs is further included (6). Or the method described in (7).
(9) The method according to any one of (1) to (8), wherein the body fluid sample is whole blood, serum or plasma.
(10) From the
　base sequences shown by SEQ ID NOs: 1 to 16 and 37 to 61, which were measured using RNA samples prepared from body fluid samples on one or more computers in order to evaluate the quality of the body fluid samples. Amount of one or more reference miRNAs selected from these miRNAs in a body fluid sample. Measurement value acquisition step;
　Absence of one or more reference miRNAs, or presence of multiple reference miRNAs.
A program for executing a determination step of determining the quality of a body fluid sample by comparing an index value calculated from the amount with a threshold value arbitrarily determined in advance .
(11) A computer-readable recording medium on which the program described in (10) is recorded.
(12) For miRNA quality evaluation, which comprises a support on which a probe for capturing one or more reference miRNAs selected from miRNAs consisting of the nucleotide sequences shown in SEQ ID NOs: 1 to 16 and 37 to 61 is immobilized. Chip.
Effect of the invention
[0013]
　INDUSTRIAL APPLICABILITY According to the present invention, it is possible to evaluate the degree of quality deterioration of a body fluid sample with high accuracy and easily. In particular, in a short period of several hours to one day after collecting a body fluid sample, which was difficult with conventional methods. It is possible to evaluate whether or not deterioration of sample quality (mainly decomposition of miRNA) has occurred. Further, according to the present invention, it is possible to easily and accurately evaluate whether or not the body fluid sample has a quality suitable for gene expression analysis using, for example, miRNA, and thus the abundance of biomarkers in the body fluid sample. It is possible to obtain more accurate test results in the test of diseases using the above as an index.
A brief description of the drawing
[0014]
[Fig. 1] Fig. 1 is a conceptual diagram regarding setting of a threshold value.
[Fig. 2] Fig. 2 is a conceptual diagram in which a threshold value is set in consideration of measurement variation, sample variation, and the like.
FIG. 3 shows the change in the abundance of hsa-miR-204-3p when the coagulation temperature in the whole blood state was changed (7 conditions in total) detected by the DNA microarray in Example 1.
FIG. 4 shows the change in the abundance of hsa-miR-4730 when the coagulation time at room temperature in the whole blood state was changed (4 conditions in total) detected by the DNA microarray in Example 1.
[Fig. 5] Changes in the abundance of hsa-miR-204-3p and hsa-miR-4730 when the coagulation temperature in the whole blood state was changed (total of 2 conditions) detected by the DNA microarray in Example 2. Is shown.
[Fig. 6] Difference in abundance of hsa-miR-204-3p and hsa-miR-4730 when the coagulation temperature in the whole blood state was changed (total of 2 conditions) detected by the DNA microarray in Example 2 Shows the change of.
FIG. 7 shows changes in the abundance of hsa-miR-4800-3p detected by a DNA microarray in Example 3 when the standing time and standing temperature in the serum state were changed (total of 8 conditions). ..
FIG. 8 shows the change in the abundance of hsa-miR-135a-3p when the standing time at room temperature in the serum state was changed (6 conditions in total) detected by the DNA microarray in Example 3.
[Fig. 9] Abundance of hsa-miR-204-3p and hsa-miR-4800-3p detected by DNA microarray in Example 4 when the standing time in the serum state was changed (total of 2 conditions). Shows the change of.
[Fig. 10] Abundance of hsa-miR-204-3p and hsa-miR-4800-3p detected by DNA microarray in Example 4 when the standing time in the serum state was changed (total of 2 conditions). Shows the change in the difference between.
FIG. 11 shows changes in the abundance of hsa-miR-3648 detected by a DNA microarray in Example 5 when the coagulation temperature and coagulation time in the whole blood state were changed (7 conditions in total).
FIG. 12 shows changes in the abundance of hsa-miR-4632-5p when the coagulation temperature and coagulation time in the whole blood state were changed (7 conditions in total) detected by the DNA microarray in Example 5.
[Fig. 13] Changes in the abundance of hsa-miR-3648 and hsa-miR-6780b-5p when the coagulation time in the whole blood state was changed (total of 2 conditions) detected by the DNA microarray in Example 6 Is shown.
[Fig. 14] Difference in abundance of hsa-miR-3648 and hsa-miR-6780b-5p when the coagulation time in the whole blood state was changed (total of 2 conditions) detected by the DNA microarray in Example 6 Shows the change of.
FIG. 15 shows changes in the abundance of hsa-miR-4497 detected by a DNA microarray in Example 7 when the standing time and the standing temperature in the serum state were changed (8 conditions in total).
FIG. 16 shows changes in the abundance of hsa-miR-744-5p detected by a DNA microarray in Example 7 when the standing time and standing temperature in the serum state were changed (8 conditions in total). ..
[Fig. 17] Changes in the abundance of hsa-miR-4497 and hsa-miR-744-5p when the standing time in the serum state was changed (total of 2 conditions) detected by the DNA microarray in Example 8. Is shown.
[Fig. 18] Difference in abundance of hsa-miR-4497 and hsa-miR-744-5p when the standing time in the serum state was changed (total of 2 conditions) detected by the DNA microarray in Example 8 Shows the change of.
FIG. 19 shows the change in the abundance of hsa-miR-204-3p when the standing time in the serum state was changed (total of 2 conditions) detected by quantitative RT-PCR in Example 9.
Mode for carrying out the invention
[0015]
　The present invention is a method for evaluating the quality of a body fluid sample, wherein one or a plurality of miRNAs selected from miRNAs consisting of the base sequences shown in SEQ ID NOs: 1 to 16 and 37 to 61 are used as reference miRNAs. The measurement step of measuring the reference miRNA contained in the above, the abundance of the one or more reference miRNAs obtained in the measurement step, or the index value calculated from the abundance of the plurality of reference miRNAs can be arbitrarily set in advance. This method includes a determination step of determining the quality of a body fluid sample by comparing it with a predetermined threshold value.
[0016]
　The method of the present invention is to evaluate the quality of miRNA contained in a body fluid sample in advance in gene expression analysis, for example, analysis using an array chip such as a microarray, or analysis by a polymerase chain reaction (PCR) method or a sequence method. , Can be used to determine the suitability of performing these analyzes. For gene expression analysis, for example, each miRNA is labeled with a miRNA in body fluid and uses a support on which a probe for capturing one or more target miRNAs and a probe for capturing a reference miRNA are fixed. To measure the abundance of a target miRNA, etc., to perform an amplification reaction using a probe for amplifying one or more target miRNAs and a probe for amplifying a reference miRNA, and the like. In addition, these results are used to analyze and test gene expression, for example, to measure gene expression in clinical specimens in order to understand the pathological condition.
[0017]
　“MiRNA” is a type of non-coding RNA (ncRNA) that means a short RNA having a chain length of about 15 to 25 bases produced in vivo, and is considered to have a function of regulating the expression of mRNA. miRNAs are transcribed from genomic DNA as RNAs (pre-mRNA) with a hairpin-like structure. This precursor is cleaved by a dsRNA cleavage enzyme (Drosha, Dicer) having a specific enzyme RNase III cleavage activity, then changes to a double-stranded form, and then becomes single-stranded. Then, one of the antisense strands is incorporated into a protein complex called RISC, which is thought to be involved in the suppression of mRNA translation. As described above, since miRNA has a different mode at each stage after transcription, usually, when miRNA is targeted (detection target), a hairpin structure, a double-stranded structure, a single-stranded structure, or the like is used. It is necessary to consider various forms. The existence of miRNA has been confirmed in various organisms.
[0018]
　The body fluid sample to which the present invention can be applied is a body fluid sample separated from the living body, and examples thereof include body fluids such as blood (whole blood, serum, plasma), urine, spinal fluid, saliva, wipes, and various tissue fluids. It can, but is not limited to these. The type of organism from which the body fluid sample is derived is not particularly limited and includes various species, but is typically a mammal, particularly a human.
[0019]
　Various biomolecules are contained in the body fluid sample. For example, proteins, peptides, nucleic acids such as DNA and RNA, metabolites and the like can be mentioned. These biomolecules are suitable as biomarkers for various diseases.
[0020]
　Deterioration of the quality of a body fluid sample means that the abundance of the biomolecule changes from the time of sample collection, and mainly means that RNA including miRNA is decomposed. Possible causes include not only temperature and heat, but also external forces such as vibrations and ultrasonic waves against body fluids, and various direct and indirect physical forces including electric and magnetic fields, but the causes of quality deterioration are possible. Is not limited to these.
[0021]
　In the present invention, RNA can be extracted from these samples, and the abundance of miRNA can be measured using this RNA. For RNA extraction, known methods (eg, the method of Favaloro et al. (Favaloro et.al., Methods Enzymol.65: 718 (1980)), etc.) and various commercially available kits for RNA extraction (eg, E.g.) Qiagen's miRNeasy, Toray's "3D-Gene" RNA extraction reagent from liquid sample, etc.) can be applied.
[0022]
　 In the
　present invention, the abundance of one or more reference miRNAs selected from the miRNAs consisting of the nucleotide sequences represented by SEQ ID NOs: 1 to 16 and 37 to 61 contained in the body fluid sample is measured. Further, the abundance of the target miRNA may be measured at the same time as the abundance of the reference miRNA contained in the body fluid sample. The target miRNA is defined as the miRNA to be measured according to each purpose among the miRNAs contained in the body fluid sample.
[0023]
　The miRNA consisting of the nucleotide sequences represented by SEQ ID NOs: 1 to 16 and 37 to 61, which can be used as the reference miRNA in the present invention, is a miRNA whose abundance changes depending on the change in the quality of the body fluid sample. It is a miRNA found by et al. When the quality of a body fluid sample changes (deteriorates), the abundance of individual gene RNA contained in the sample changes. In this case, in all the genes detected by gene expression analysis, RNA in the body fluid sample (deteriorated body fluid sample) intentionally deteriorated by heating or the like and the freshest body fluid sample (standard body fluid sample) that has not deteriorated. Correlation with the RNA inside is reduced. The degree of deterioration of the quality of the deteriorated body fluid sample is evaluated using, for example, a value that is twice the standard deviation (2SD) of the abundance ratio (FCi) of each miRNA that can be calculated by the following formulas 1 and 2. it can. In the present invention, this 2SD value is referred to as an overall fluctuation index value. When the overall fluctuation index value is 1.5 or more, it means that the degree of fluctuation in the abundance of each miRNA measured in the deteriorated body fluid sample is large, and therefore the degree of quality deterioration of the deteriorated body fluid sample is large. The reference miRNA used in the present invention is a miRNA whose abundance fluctuates in correlation with such an overall variation in RNA.
[0024]
[Number 1]

[0025]
[Number 2]

[0026]
　Here, in Formulas 1 and 2,
　miRNA i_control represents the abundance of the i-th miRNA in the standard body fluid sample as a logarithm with a base of 2, and
　miRNA i_sample is the degraded body fluid of the i-th miRNA. which bottom the abundance in the sample was expressed as 2 log,
　FC averages are abundance ratio of n miRNA (miRNA I_control - miRNA I_sample average value of)
a.
[0027]
　When serum (blood) is used as a body fluid sample, as the reference miRNA used in the present invention, select a miRNA whose abundance changes depending on the whole blood state after blood collection or the storage time and storage temperature in the serum state. Can be done. The miRNA whose abundance changes depending on the storage time in the whole blood state is stored, for example, in the whole blood state immediately after blood collection under a certain temperature condition (for example, room temperature (22 ° C to 24 ° C)). It can be selected by separating the serum 0 hour, 3 hours, 6 hours, and 9 hours after the start of storage, measuring the abundance of miRNA in the serum, and comparing the degree of change. In the actual test of clinical specimens, if the period of storing the whole blood as whole blood is longer, the storage time may be extended to, for example, 12 hours or 24 hours according to the period. The abundance of miRNA may be measured and compared. In this way, the abundance of miRNAs obtained from sera with different storage times in the whole blood state can be compared between different storage conditions, and different miRNAs can be selected. In general, in the measurement of DNA microarrays, fluctuations in abundance of 2 times are considered to be sufficient differences, so it is preferable to select miRNAs having a difference of 2 times or more between different storage conditions. For miRNA whose abundance changes depending on the storage time of serum, for example, a serum sample prepared after blood collection is stored in a refrigerator (for example, 4 ° C), and storage is started 0 hours, 6 hours, and 12 hours. After that, it can be selected by measuring the abundance of miRNA in serum after 24 hours and comparing the degree of change. Similarly, miRNAs whose abundance changes depending on the storage temperature in the whole blood state or the serum state were also stored for a certain period of time in the whole blood state or the serum state immediately after blood collection under the required temperature conditions. Later, it can be selected by measuring the abundance of miRNA in each sample and comparing the degree of change.
[0028]
　In the measurement step of the present invention, the abundance of one or more reference miRNAs selected from miRNAs consisting of the nucleotide sequences represented by SEQ ID NOs: 1 to 16 and 37 to 61 contained in the body fluid sample is measured.
[0029]
　Hereinafter, the reference miRNA and the probe for capturing the target miRNA are generally referred to as "capture probe" or simply "probe".
[0030]
　The abundance of miRNA can be measured, for example, by a hybridization assay using an array chip such as a microarray in which a probe that specifically binds to the miRNA of interest is immobilized on a support. In the present invention, an array chip containing a support on which a "reference miRNA capture probe" for capturing one or more reference miRNAs is immobilized can be used. Alternatively, an array chip containing a support on which a "target miRNA capture probe" for capturing the target miRNA is further immobilized may be used.
[0031]
　The "capture probe" or "probe for capture" means a substance capable of directly or indirectly, preferably directly and selectively binding to the miRNA to be captured, as a typical example. , Nucleic acids, proteins, sugars and other antigenic compounds. In the present invention, a nucleic acid probe can be preferably used. As the nucleic acid, in addition to DNA and RNA, nucleic acid derivatives such as PNA (peptide nucleic acid) and LNA (Locked Nucleic Acid) can be used. Here, in the case of a nucleic acid, the derivative is a derivative labeled with a fluorescent group or the like, a modified nucleotide (for example, an alkyl such as halogen or methyl, an alkoxy such as methoxy, a nucleotide containing a group such as thio or carboxymethyl, and a re-base. It means a chemically modified derivative such as a derivative containing (such as a nucleotide having undergone composition, saturation of a double bond, deaminoization, substitution of an oxygen molecule with a sulfur molecule, etc.).
[0032]
　The chain length of the nucleic acid probe is preferably longer than the length of the miRNA to be detected from the viewpoint of ensuring the stability and specificity of hybridization. Usually, if the strand length is about 17 to 25 bases, the probe can sufficiently exert the selective binding property to the target miRNA. Such an oligonucleic acid probe having a short chain length can be easily prepared by a well-known chemical synthesis method or the like.
[0033]
　Stringency during hybridization is known to be a function of temperature, salt concentration, probe chain length, probe nucleotide sequence GC content and the concentration of chaotropic agents in the hybridization buffer. As stringent conditions, for example, the conditions described in Sambrook, J. et al. (1998) Molecular Cloning: A Laboratory Manual (2nd ed.), Cold Spring Harbor Laboratory Press, New York can be used. .. Stringent temperature conditions are above about 30 ° C. Other conditions include hybridization time, concentration of cleaning agent (for example, SDS), presence / absence of carrier DNA, and the like, and various stringencies can be set by combining these conditions. One of ordinary skill in the art can appropriately determine the conditions for obtaining the function as a capture probe prepared for the detection of the desired sample RNA.
[0034]
　Although the nucleic acid probe is the complementary strand of the miRNA to be captured, it is clear to those in the same industry that there are sequences other than those to be captured that are bound by cross-hybridization. That is, in the present invention, the abundance of miRNA is measured using the complementary strand of the reference miRNA shown in SEQ ID NOs: 1 to 16 and 37 to 61 as a probe, but the change in the abundance of miRNA due to deterioration is a cross-hybrid other than the reference miRNA. It can also include changes in the abundance of RNA.
[0035]
　When the deterioration of the sample progresses and the degradation of RNA in the sample progresses, the degradation of miRNA also progresses, but the progress of degradation may increase the number of molecules cross-hybrid to the reference miRNA capture probe in the sample. .. In addition, in the case of blood samples, by leaving them in a whole blood state, miRNAs may be secreted from blood cells over time, and miRNAs that cross-hybride with the reference miRNA itself or the reference miRNA capture probe may increase in the sample. Obtain (Koberle V. et al., (2016) Translational Res. 169: 40-46). Therefore, the "change in miRNA abundance due to deterioration" detected by the capture probe includes not only a decrease in the miRNA abundance but also an increase in the abundance.
[0036]
　MiRNA sequence information can be obtained from databases such as GenBank (http://www.ncbi.nlm.nih.gov/genbank/) and the miRBase website (http://www.mirbase.org/). it can. Reference miRNA capture probes and target miRNA capture probes can be designed based on the sequence information available from these sites.
[0037]
　The number of miRNA capture probes immobilized on the support is not particularly limited. For example, the abundance of miRNA may be measured using a number of miRNA capture probes immobilized on a support that covers all known miRNAs whose sequences have been identified, or for testing purposes, etc. Depending on the situation, a desired number of miRNA capture probes immobilized on a support may be used.
[0038]
　As the support on which the capture probe is aligned and immobilized, the same support as that used in known microarrays, macroarrays and the like can be used, and for example, slide glass, membranes, beads and the like can be used. it can. It is also possible to use a support having a shape having a plurality of convex portions on the surface, which is described in Japanese Patent No. 4244788 and the like. The material of the support is not particularly limited, and examples thereof include inorganic materials such as glass, ceramics, and silicon; polymers such as polyethylene terephthalate, cellulose acetate, polycarbonate, polystyrene, polymethylmethacrylate, and silicone rubber.
[0039]
　As a method of immobilizing the capture probe on the support, a method of synthesizing an oligo DNA on the surface of the support and a method of dropping and immobilizing the oligo DNA synthesized in advance on the surface of the support are known.
[0040]
　Examples of the former method include the method of Ronald et al. (US Pat. No. 5,705,610), the method of Michel et al. (US Pat. No. 6,142,266), and the method of Francesco et al. (US Pat. No. 7037659). .. Since an organic solvent is used in the DNA synthesis reaction in these methods, it is desirable that the support is made of a material resistant to the organic solvent. Further, in the method of Francesco et al., Since DNA synthesis is controlled by irradiating light from the back surface of the support, the support is preferably made of a translucent material.
[0041]
　Examples of the latter method include the method of Hirota et al. (Patent No. 3922454) and the method using a spotter. Examples of the spot method include a pin method by mechanically contacting the tip of a pin with a solid phase, an inkjet method using the principle of an inkjet printer, and a capillary method using a capillary tube. After the spot treatment, post-treatment such as cross-linking by UV irradiation and surface blocking is performed as necessary. In order to immobilize the oligo DNA by covalent bond on the surface of the surface-treated support, a functional group such as an amino group or an SH group is introduced at the end of the oligo DNA. The surface modification of the support is usually performed by a silane coupling agent treatment having an amino group or the like.
[0042]
　For hybridization with each miRNA capture probe immobilized on the support, a nucleic acid sample labeled with a labeling substance (nucleic acid sample derived from the sample) is prepared from RNA extracted from the sample, and this labeled nucleic acid sample is probed. It is carried out by contacting with. The "nucleic acid sample derived from a sample" includes RNA extracted from the sample, and cDNA and cRNA prepared from the RNA by a reverse transcription reaction. The nucleic acid sample derived from the labeled sample may be a sample RNA directly or indirectly labeled with a labeling substance, or a cDNA or cRNA prepared from the sample RNA may be directly or indirectly labeled with a labeling substance. It may be labeled.
[0043]
　As a method of binding the labeling substance to the nucleic acid sample derived from the sample, a method of binding the labeling substance to the 3'end of the nucleic acid sample, a method of binding the labeling substance to the 5'end, and a nucleotide to which the labeling substance is bound are incorporated into the nucleic acid. There are ways to make it. An enzymatic reaction can be used in the method of binding the labeling substance to the 3'end and the method of binding the labeling substance to the 5'end. For the enzymatic reaction, T4 RNA Ligase, Terminal Deoxitidil Transferase, Poly A polymerase and the like can be used. For any of the labeling methods, the methods described in "Shao-Yao Ying ed., MiRNA Experiment Protocol, Yodosha, 2008" can be referred to. In addition, various kits for directly or indirectly binding a labeling substance to the end of RNA are commercially available. For example, as a kit for directly or indirectly binding a labeling substance to the 3'end, "3D-Gene" miRNA labeling kit (manufactured by Toray Industries, Inc.), miRCURY miRNA HyPower labeling kit (exicon), NCode miRNA Labeling system (Life Technologies), FlashTag Biotin RNA Labeling Kit (Genifia), etc. can be exemplified.
[0044]
　In addition, as in the conventional method, cDNA or cDNA incorporating the labeling substance is prepared by synthesizing cDNA or cDNA from the sample RNA in the presence of the labeled deoxyribonucleotide or labeled ribonucleotide, and the cDNA or cRNA incorporating the labeling substance is prepared and arrayed. It is also possible to hybridize with the above probe.
[0045]
　Examples of the labeling substance that can be used in the present invention include various labeling substances that are also used in known microarray analysis. Specific examples thereof include, but are not limited to, fluorescent dyes, phosphorescent dyes, enzymes, and radioisotopes. Fluorescent dyes that are easy to measure and easy to detect are preferred. Specifically, cyanine (cyanine 2), aminomethylcoumarin, fluorosane, indocarbocyanine (cyanine 3), cyanine 3.5, tetramethyllodamine, rhodamine red, Texas red, indocarbocyanine (cyanine 5), cyanine. Known fluorescent dyes such as 5.5, cyanine 7, and oyster can be mentioned, but are not limited thereto.
[0046]
　Further, as the labeling substance, semiconductor fine particles having luminescence may be used. Examples of such semiconductor fine particles include cadmium selenium (CdSe), cadmium telluride (CdTe), indium gallium phosphide (InGaP), and silver indium zinc sulfide (AgInZnS).
[0047]
　The nucleic acid sample derived from the sample labeled as described above is brought into contact with the miRNA capture probe on the support to hybridize the nucleic acid sample and the probe. This hybridization step can be performed in exactly the same manner as before. The reaction temperature and time are appropriately selected according to the chain length of the nucleic acid to be hybridized, but in the case of nucleic acid hybridization, it is usually about 30 ° C. to 70 ° C. for 1 minute to a dozen hours. Hybridization is performed, and after washing, the signal intensity from the labeling substance in each probe-immobilized region on the support is detected. The signal intensity is detected by using an appropriate signal reader according to the type of labeling substance. When a fluorescent dye is used as a labeling substance, a fluorescence microscope, a fluorescence scanner, or the like may be used.
[0048]
　The measured fluorescence intensity measured is compared to ambient noise. Specifically, the measured values ​​obtained from the probe-immobilized region are compared with the measured values ​​obtained from other positions, and the case where the former value is exceeded is regarded as detected (valid judgment positive). ..
[0049]
　If the detected measured value contains background noise, the background noise may be subtracted. Ambient noise can also be subtracted from the detected measurements as background noise. In addition, the method described in "Kou Fujibuchi, Katsuhisa Horimoto, Microarray Data Statistical Analysis Protocol, Yodosha, 2008" may be used.
[0050]
In the
　present invention, the measured value of the abundance of the reference miRNA obtained in the measurement step may be used as it is in the determination step described later, but for example, the gene expression analysis of the target miRNA contained in the body fluid sample is performed. In this case, the measured value may be corrected by various methods illustrated below to obtain a corrected abundance value, which may be used in the determination step.
[0051]
　As the correction method, a conventional method can be used, and examples thereof include a global normalization method and a quantum normalization method in which correction is performed using the measured values ​​of all detected miRNAs. It may also be corrected using housekeeping RNAs such as U1 snoRNA, U2 snoRNA, U3 snoRNA, U4 snoRNA, U5 snoRNA, U6 snoRNA, 5S rRNA, 5.8S rRNA, or specific correction endogenous miRNAs, or RNA. It may be corrected by using an external standard nucleic acid added at the time of extraction or labeling. By "endogenous" is meant to be naturally present in the specimen, rather than being artificially added to the specimen. For example, the term "endogenous miRNA" refers to a miRNA that is naturally present in a sample and is derived from the organism that provided the sample. When the gene expression analysis of the target miRNA contained in the body fluid sample is performed by applying the method of the present invention, it is preferable to use a correction method using an external standard nucleic acid such as spike control that does not depend on the sample.
[0052]

　The determination step of the present invention is an index value calculated from the abundance of one or more reference miRNAs in the body fluid sample obtained in the measurement step, or the corrected abundance of a plurality of reference miRNAs. Is a step of comparing with a threshold value arbitrarily determined in advance and determining the quality of the body fluid sample based on the magnitude relationship between the two. The reference miRNA consisting of the nucleotide sequences shown in SEQ ID NOs: 1 to 16 and 37 to 61 changes to a high value when the quality of the body fluid sample is poor (for example, hsa- consisting of the nucleotide sequence shown in SEQ ID NO: 2). There are both miR-4730) and those that change to low values ​​(for example, hsa-miR-4800-3p consisting of the nucleotide sequence shown in SEQ ID NO: 8). That is, since there are both cases where it can be determined to be defective when the abundance of the reference miRNA exceeds an arbitrarily set threshold value and cases where it can be determined to be defective when it falls below the threshold value, the reference miRNA used for determination is used. It is necessary to change the judgment criteria depending on the situation. In Tables 3, 5, 7, and 9 below, when the body fluid sample is a blood sample, 41 reference miRNAs consisting of the nucleotide sequences shown in SEQ ID NOs: 1 to 16 and 37 to 61 are shown, respectively. It shows which type it belongs to. The miRNA consisting of the nucleotide sequences shown by SEQ ID NOs: 2, 3, 4, 6, 11, 37 to 43, 45, 46, 49, 51, 52, 54, 58 is a miRNA that changes to a high value in the deteriorated body fluid sample. Yes, miRNAs consisting of the nucleotide sequences shown by SEQ ID NOs: 8, 9, 10, 12 to 16, 44, 47, 48, 50, 53, 55 to 57, 59 to 61 remain low in the degraded body fluid sample. MiRNA to be used. The miRNA consisting of the nucleotide sequences shown in SEQ ID NOs: 1, 5 and 7 is a miRNA that changes to a low value or a high value depending on which step of the sample processing the deterioration occurs.
[0053]
　In the determination step, the abundance of one or more reference miRNAs obtained in the measurement step may be converted into a logarithm, and the determination may be made using the logarithm. When performing logarithm conversion, it is common to convert to a logarithm with a base of 2.
[0054]
　For the threshold used as the criterion for judgment, prepare a standard body fluid sample and a deteriorated body fluid sample, measure the abundance of the reference miRNA contained in those body fluid samples, and based on the results, depending on the purpose of evaluation and the required accuracy. It can be set arbitrarily.
[0055]
　The setting of the threshold value will be described with reference to the conceptual diagrams shown in FIGS. 1 and 2. FIGS. 1 and 2 schematically show the abundance when the reference miRNA contained in the standard body fluid sample and the deteriorated body fluid sample 2 conditions (deteriorated samples 1 and 2) is measured, and due to the deterioration of the quality of the sample. It is a conceptual diagram in the example in which the abundance of the reference miRNA changes to a high value. The deteriorated sample 2 is a sample having a greater degree of deterioration than the deteriorated sample 1.
[0056]
　In FIG. 1, the boundary values ​​1 to 3 are the abundance of the reference miRNA of each sample. If you want to judge whether the sample quality is good or bad between the standard body fluid sample and the deteriorated sample 1, you can set a threshold value between the boundary values ​​1 and 2. A threshold value can be set to the boundary value 1 when the quality deterioration is to be determined severely, and to the boundary value 2 when the quality deterioration is to be determined loosely. When it is desired to judge whether the sample quality is good or bad between the deteriorated sample 1 and the deteriorated sample 2, a threshold value can be set between the boundary values ​​2 and 3. A threshold value can be set at the boundary value 2 when the quality deterioration is to be determined severely, and at the boundary value 3 when the quality deterioration is to be determined loosely.
[0057]
　If there are some variations such as variations in repeated measurements and variations between samples, the threshold value can be set in consideration of these variations. In FIG. 2, the average value of the abundance of the reference miRNA in each sample is shown by a bar graph, the standard deviation (SD) is schematically shown by the error bar, and the boundary values ​​4 to 9 are above and below the error bar of each condition. The value of. If you want to judge the quality of the sample between the standard body fluid sample and the deteriorated sample 1, you can set a threshold value between the boundary values ​​5 and 6. A boundary value of 5 can be set as a threshold value when quality deterioration is to be determined severely, and a boundary value 6 can be set as a threshold value when a loose judgment is desired. If it is desired to judge whether the sample quality is good or bad between the deteriorated sample 1 and the deteriorated sample 2, a threshold value can be set between the boundary values ​​7 and 8. A boundary value of 7 can be set as a threshold when quality deterioration is to be determined severely, and a boundary value of 8 can be set as a threshold when a loose determination is desired. Further, the boundary value 4 can be set as the threshold value when the quality is judged to be the most rigorous, and the boundary value 9 can be set as the threshold value when the quality is judged to be the loosest. 1SD, 2SD, or more may be used for setting the threshold value, which can be selected according to the purpose. Furthermore, although FIGS. 1 and 2 exemplify the method of setting the threshold value using the standard deviation, the method generally used for evaluating the variation in statistics such as the standard error, the confidence interval, and the prediction interval is used. The threshold value may be set.
[0058]
　As shown in Tables 3, 5, 7, and 9 below, the sequences are shown by SEQ ID NOs: 2, 3, 4, 6, 11, 37 to 43, 45, 46, 49, 51, 52, 54, 58. The miRNA consisting of the nucleotide sequence is a miRNA that changes to a high value in the deteriorated body fluid sample regardless of which step of the sample processing the deterioration occurs, and when the abundance in the body fluid sample exceeds the threshold value, the body fluid is concerned. It can be determined that the quality of the sample is poor. When these miRNAs are used as reference miRNAs, it is possible to determine whether the quality is good or bad by setting one threshold value for each miRNA.
[0059]
　In which step of sample processing did the miRNA consisting of the nucleotide sequences represented by SEQ ID NOs: 8, 9, 10, 12-16, 44, 47, 48, 50, 53, 55-57, 59-61 deteriorate? Regardless of this, it is a miRNA that changes to a low value in the deteriorated body fluid sample, and when the abundance in the body fluid sample is below the threshold value, it can be determined that the quality of the body fluid sample is poor. When these miRNAs are used as reference miRNAs, it is possible to determine whether the quality is good or bad by setting one threshold value for each miRNA.
[0060]
　The miRNA consisting of the nucleotide sequences shown in SEQ ID NOs: 1, 5 and 7 is a miRNA that changes to a low value or a high value depending on which step of the sample processing the deterioration occurs. Specifically, these miRNAs were allowed to stand for several hours (for example, 6 hours or more) under conditions where the temperature of the serum sample was higher than room temperature (for example, 28 ° C. or higher) in the whole blood state before serum separation. If it has been deteriorated by, it will change to a low value, and if it has been deteriorated in the serum state after serum separation, it will change to a high value. Therefore, when evaluating the quality of any clinical fluid sample using these miRNAs as reference miRNAs, there are two thresholds for each reference miRNA, that is, if this value is exceeded, the quality is judged to be poor. It is preferable to set a "threshold value of 1" and a "second threshold value" that is judged to be poor quality if the value falls below this value. When the abundance of these reference miRNAs in the serum sample exceeds the first threshold value or falls below the second threshold value, it can be determined that the quality of the sample is poor. When the abundance of the reference miRNA in the serum sample exceeds the first threshold value, it is estimated that the serum state has deteriorated, and when it falls below the second threshold value, it is in the whole blood state. It is presumed that deterioration had occurred. When the abundance of the reference miRNA in the serum sample is between the first threshold value and the second threshold value, the quality of the sample can be judged to be good.
[0061]
　When a plurality of reference miRNAs among the miRNAs consisting of the nucleotide sequences shown by SEQ ID NOs: 1 to 16 and 37 to 61 are used as the reference miRNAs, the abundance in the body fluid sample for each reference miRNA and each miRNA It is possible to compare the magnitude relationship with a predetermined threshold, make a judgment according to the judgment criteria for each reference miRNA, and comprehensively judge the quality of the body fluid sample. In this case, it is preferable to set further judgment criteria by prioritizing or weighting individual judgments by a plurality of reference miRNAs.
[0062]
　Specifically, for example, in the determination for each reference miRNA, when the number of reference miRNAs determined to be good exceeds the number of reference miRNAs determined to be poor or an arbitrary predetermined number, the miRNAs contained in the body fluid sample. The quality of can be judged to be good. On the contrary, when the number of the reference miRNAs determined to be defective exceeds the number of the reference miRNAs determined to be good or a predetermined number, the quality of the miRNA contained in the sample can be determined to be defective. Further, in the case of performing a more rigorous or highly accurate evaluation, if the determination result of one specific reference miRNA is defective, the quality of the miRNA contained in the body fluid sample may be determined to be defective.
[0063]
　Alternatively, when a plurality of reference miRNAs among the miRNAs consisting of the nucleotide sequences represented by SEQ ID NOs: 1 to 16 and 37 to 61 are used as the reference miRNAs, the index is based on the abundance of the plurality of reference miRNAs in the body fluid sample. It is also possible to calculate a value and determine the quality of the body fluid sample based on the magnitude relationship between this index value and a predetermined threshold value. As the index value, the difference or ratio between the two reference miRNAs can be used.
[0064]
　In the case of a combination in which the abundances approach each other due to deterioration (for example, the combination of hsa-miR-204-3p and hsa-miR-4730 shown in FIG. 5), the index value (difference) becomes smaller as the deterioration of the body fluid sample progresses. .. Therefore, in the case of such a combination, if the index value (difference) is less than a predetermined threshold value, it can be determined that the quality is poor. Further, when the ratio is used as the index value in such a combination, the determination may be made as follows. The reference miRNA (hsa-miR-204-3p in the example of FIG. 5) having the higher abundance in the standard body fluid sample that has not deteriorated is defined as A, and the reference miRNA having the lower abundance in the body fluid sample (Fig. 5). In the example, assuming that the abundance of hsa-miR-4730) in the body fluid sample is B, when A / B is used as the index value, the A / B value decreases as the deterioration progresses, so it falls below a predetermined threshold. In this case, the body fluid sample can be determined to be of poor quality. When B / A is used as an index value, the B / A value rises as the deterioration progresses, so that the body fluid sample can be judged to be of poor quality when it exceeds a predetermined threshold value.
[0065]
　In the case of a combination in which the abundances are separated from each other due to deterioration (for example, the combination of hsa-miR-204-3p and hsa-miR-4800-3p shown in FIG. 9), the index value (difference) increases as the deterioration of the body fluid sample progresses. growing. Therefore, in the case of such a combination, if the index value (difference) exceeds a predetermined threshold value, it can be determined that the quality is poor. Further, when the ratio is used as the index value in such a combination, the determination may be made as follows. The reference miRNA (hsa-miR-204-3p in the example of FIG. 9) having the higher abundance in the standard body fluid sample that has not deteriorated is defined as A, and the reference miRNA having the lower abundance in the body fluid sample (Fig. 9). In the example, assuming that the abundance of hsa-miR-4800-3p) in the body fluid sample is B, when A / B is used as the index value, the A / B value rises as the deterioration progresses, so a predetermined threshold value If it exceeds, the body fluid sample can be judged to be of poor quality. When B / A is used as an index value, the B / A value decreases as the deterioration progresses, so that the body fluid sample can be judged to be of poor quality when it falls below a predetermined threshold value.
[0066]
　When three or more types of reference miRNAs are used and a judgment is made based on index values, two types of reference miRNAs are selected and combined so that the abundances approach each other due to deterioration or are separated from each other. Just make. The index value may be calculated using all of the three or more types of reference miRNAs used, or the index value may be calculated using only a part of the three or more types of reference miRNAs. For example, when four types of reference miRNAs A, B, C, and D are used, the difference or ratio between A and B is calculated as the index value 1, and the difference or ratio between A and C is calculated as the index value 2, respectively. Compare the magnitude relationship with the threshold value of, and D compare the magnitude relationship with the threshold value for D (furthermore, A, B, and C also independently compare the magnitude relationship with each threshold value for A, B, and C. (Relationships may be compared), the result is judged comprehensively, or the difference or ratio between A and B is calculated as the index value 1, and the difference or ratio between C and D is calculated as the index value 2, respectively. It is also possible to compare the magnitude relationship with the threshold value of and comprehensively judge the result.
[0067]
　When one reference miRNA is used, one miRNA may be arbitrarily selected from the miRNAs shown in SEQ ID NOs: 1 to 16 and 37 to 61, but the abundance changes remarkably depending on the storage time. It is preferable to select. Among the miRNAs shown in Tables 2, 4, 6 and 8 below, the miRNAs whose abundance changes by 3 times or more compared to the reference conditions, that is, by 1.6 or more with the value of log 2 , are hsa-miR. -204-3p (SEQ ID NO: 1), hsa-miR-4730 (SEQ ID NO: 2), hsa-miR-4800-3p (SEQ ID NO: 8), hsa-miR-744-5p (SEQ ID NO: 9), hsa-miR -6511a-5p (SEQ ID NO: 10), hsa-miR-135a-3p (SEQ ID NO: 11), hsa-miR-940 (SEQ ID NO: 12), hsa-miR-3648 (SEQ ID NO: 38), hsa-miR-4497 (SEQ ID NO: 40), hsa-miR-4745-5p (SEQ ID NO: 41), hsa-miR-92a-2-5p (SEQ ID NO: 43), hsa-miR-6132 (SEQ ID NO: 57). And one of these can be preferably selected. Furthermore, among these, miRNAs whose abundance changes significantly depending on the storage time are defined as miRNAs that change 3.6 times or more compared to the reference conditions, that is , 1.85 or more at the log 2 value, hsa-miR-204-. There are seven types: 3p, hsa-miR-4730, hsa-miR-4800-3p, hsa-miR-744-5p, hsa-miR-135a-3p, hsa-miR-940, hsa-miR-4497. And any of these can be selected particularly preferably.
[0068]
　Even when a plurality of reference miRNAs are used, it is preferable to select from the above 12 types of miRNAs. By using a plurality of reference miRNAs, more rigorous or highly accurate evaluation can be performed. It is also preferable to make a judgment using the difference or ratio of two reference miRNAs, in which case the abundance changes to a high value with deterioration, hsa-miR-204-3p, hsa-miR-4730, hsa. -One type from the miRNA group consisting of miR-135a-3p, hsa-miR-3648, hsa-miR-4497, hsa-miR-4745-5p, hsa-miR-92a-2-5p, which changes to a low value. One type from the miRNA group consisting of hsa-miR-204-3p, hsa-miR-4800-3p, hsa-miR-744-5p, hsa-miR-6511a-5p, hsa-miR-940, hsa-miR-6132 It is preferable to select and combine.
[0069]
　Furthermore, it is more preferable to select a plurality of miRNAs from the seven types of reference miRNAs in which the change in abundance due to the above-mentioned deterioration is particularly large. When making a judgment using the difference or ratio of two reference miRNAs, as described above, the abundance changes to a high value with deterioration, hsa-miR-204-3p, hsa-miR-4730, hsa- One type from the miRNA group consisting of miR-135a-3p and hsa-miR-4497, and hsa-miR-204-3p, hsa-miR-4800-3p, hsa-miR-744-5p, hsa that change to low values. It is preferable to select and combine one of the miRNA groups consisting of -miR-940. For example, the combination of hsa-miR-204-3p and hsa-miR-4730, the combination of hsa-miR-204-3p and hsa-miR-4800-3p, hsa-miR-744-5p and hsa-miR-4497. A combination or the like can be preferably used. As for hsa-miR-204-3p, as described above, it is a miRNA whose abundance changes to a low value or a high value depending on which step of the sample processing the deterioration occurs. .. When you want to evaluate the deterioration of serum samples caused by standing for several hours (for example, 6 hours or more) under conditions where the temperature is higher than room temperature (for example, 28 ° C or more) in the whole blood state using the miRNA. As a miRNA whose abundance changes to a low value due to deterioration, it is necessary to select it as a miRNA whose abundance changes to a high value when it is desired to evaluate the deterioration received in the serum state after serum separation.
[0070]
　Some of the reference miRNAs change their abundance even with slight deterioration of the body fluid sample, or some of them change their abundance after the degree of deterioration becomes large. Therefore, select the reference miRNA according to the purpose. Is preferable.
[0071]
　If you want to evaluate the deterioration in a short period of time up to several hours (for example, 6 hours) when preparing the sample, hsa-miR-204-3p, hsa-miR-4730, hsa-miR-4800-3p, It is preferable to select a combination of two types from hsa-miR-744-5p, hsa-miR-940, and hsa-miR-4497.
[0072]
　If you want to evaluate the deterioration of the sample preparation from several hours (for example, 6 hours) to one day, hsa-miR-204-3p, hsa-miR-4730, hsa-miR-4800-3p , Hsa-miR-744-5p, hsa-miR-135a-3p, hsa-miR-940, it is preferable to select a combination of two types.
[0073]
　Further, for example, when the purpose is gene expression analysis and the target miRNA in the analysis corresponds to any of the miRNAs shown in SEQ ID NOs: 1 to 16 and 37 to 61, the miRNA excluding the target miRNA is used as a reference. You can choose miRNA.
[0074]
　The present invention also relates
　to a sequence measured using an RNA sample prepared from a body fluid sample on one or more computers in order to evaluate the quality of the body fluid sample according to the above-mentioned method for evaluating the quality of a body fluid sample. Measurement value acquisition step of acquiring the abundance measurement value of one or more reference miRNAs selected from the miRNA consisting of the base sequences shown by Nos. 1 to 16 and 37 to 61 in the body fluid sample;
　one or more kinds By comparing the index value calculated from the abundance of the reference miRNA or the abundance of a plurality of types of reference miRNA with a threshold value arbitrarily determined in advance, a determination step
of determining the quality of the body fluid sample is executed. To provide a program (ie, including an instruction to cause one or more computers to perform each of the above steps), and a computer-readable recording medium on which the program is recorded.
[0075]
　For example, the program is incorporated into a device for analyzing the expression level of miRNA, and in the measurement value acquisition step, a reference in a body fluid sample measured by an expression measuring unit included in the device or an expression measuring device separate from the device. A measured value of the abundance of miRNA may be obtained and each step may be carried out using the measured value. The measured value to be acquired may be a corrected measured value. In addition, the program may include an instruction to cause a computer to execute a process of correcting the acquired measured value. The details of each step are as described above with respect to the quality evaluation method of the body fluid sample of the present invention.
[0076]
　A "program" is a data processing method described in any language or description method, regardless of the format such as source code or binary code. The "program" is not necessarily limited to a single program, but is distributed as multiple modules or libraries, or in cooperation with a separate program represented by an OS (Operating System). Including those that achieve the function. A well-known configuration or procedure can be used for a specific configuration for reading the recording medium, a reading procedure, an installation procedure after reading, and the like.
[0077]
　The "recording medium" can be any "portable physical medium" (non-transient recording medium) such as a flexible disk, magneto-optical disk, ROM, EPROM, EEPROM, CD-ROM, MO, DVD or the like. Alternatively, it may be a "communication medium" that holds the program in a short period of time, such as a communication line or a carrier wave when the program is transmitted via a network represented by LAN, WAN, or the Internet.
[0078]
　The present invention also comprises a miRNA quality including a probe-immobilized support for capturing one or more reference miRNAs selected from miRNAs consisting of the nucleotide sequences set forth in SEQ ID NOs: 1-16 and 37-61. An evaluation chip is provided. Further, the present invention includes a probe for capturing a target miRNA and a probe for capturing one or more reference miRNAs selected from miRNAs consisting of the nucleotide sequences represented by SEQ ID NOs: 1 to 16 and 37 to 61. A chip for miRNA expression analysis including an immobilized support is provided. Here, the target miRNA, one or more reference miRNAs selected from the miRNAs consisting of the nucleotide sequences represented by SEQ ID NOs: 1 to 16 and 37 to 61, probes for capturing these, and these capture probes are fixed. The support to be converted is as described above.
[0079]
　The miRNA expression analysis chip of the present invention is for capturing correction nucleic acids such as housekeeping RNA used in the correction step, specific correction endogenous miRNA, and external standard nucleic acid to be added, particularly correction endogenous miRNA. The probe may be further immobilized on the support.
[0080]
　Hereinafter, known information and the like will be described for miRNAs consisting of the nucleotide sequences represented by SEQ ID NOs: 1 to 16 and 37 to 61, which can be used as reference miRNAs in the present invention.
[0081]
　As used herein, the term "miR-204-3p gene" or "miR-204-3p" refers to the hsa-miR-204-3p gene (miRBase Accession No) described in SEQ ID NO: 1, which is a human gene. . MIMAT0022693) and homologs or orthologs of other species are included. The hsa-miR-204-3p gene can be obtained by the method described in Lim LP et al., 2003, Science, Vol. 299, p1540. Further, as a precursor of "hsa-miR-204-3p", "hsa-mir-204" (miRBase Accession No. MI0000284, SEQ ID NO: 17) having a hairpin-like structure is known.
[0082]
　As used herein, the term "miR-4730 gene" or "miR-4730" includes the hsa-miR-4730 gene (miRBase Accession No. MIMAT0019852) described in SEQ ID NO: 2, which is a human gene, and others. Includes homologs or orthologs of species. The hsa-miR-4730 gene can be obtained by the method described in Persson H et al., 2011, Cancer Res, Vol. 71, p78-86. Further, as a precursor of "hsa-miR-4730", "hsa-mir-4730" (miRBase Accession No. MI0017367, SEQ ID NO: 18) having a hairpin-like structure is known.
[0083]
　The term "miR-128-2-5p gene" or "miR-128-2-5p" used herein refers to the hsa-miR-128-2- given in SEQ ID NO: 3, which is a human gene. The 5p gene (miRBase Accession No. MIMAT0031095) and homologs or orthologs of other species are included. The hsa-miR-128-2-5p gene can be obtained by the method described in Lagos-Quintana M et al., 2002, Curr Biol, Vol. 12, p735-739. Further, as a precursor of "hsa-miR-128-2-5p", "hsa-mir-128-2" (miRBase Accession No. MI0000727, SEQ ID NO: 19) having a hairpin-like structure is known.
[0084]
　As used herein, the term "miR-4649-5p gene" or "miR-4649-5p" refers to the hsa-miR-4649-5p gene (miRBase Accession No) described in SEQ ID NO: 4, which is a human gene. . MIMAT0019711) and homologs or orthologs of other species are included. The hsa-miR-4649-5p gene can be obtained by the method described in Persson H et al., 2011, Cancer Res, Vol. 71, p78-86. Further, as a precursor of "hsa-miR-4649-5p", "hsa-mir-4649" (miRBase Accession No. MI0017276, SEQ ID NO: 20) having a hairpin-like structure is known.
[0085]
　The term "miR-6893-5p gene" or "miR-6893-5p" used herein refers to the hsa-miR-6893-5p gene (miRBase Accession No) described in SEQ ID NO: 5, which is a human gene. . MIMAT0027686) and homologs or orthologs of other species are included. The hsa-miR-6893-5p gene can be obtained by the method described in Ladwig E et al., 2012, Genome Res, Vol. 22, p1634-1645. Further, as a precursor of "hsa-miR-6893-5p", "hsa-mir-6893" (miRBase Accession No. MI0022740, SEQ ID NO: 21) having a hairpin-like structure is known.
[0086]
　As used herein, the term "miR-187-5p gene" or "miR-187-5p" refers to the hsa-miR-187-5p gene (miRBase Accession No) described in SEQ ID NO: 6, which is a human gene. . MIMAT0004561) and homologs or orthologs of other species are included. The hsa-miR-187-5p gene can be obtained by the method described in Lim LP et al., 2003, Science, Vol. 299, p1540. Further, as a precursor of "hsa-miR-187-5p", "hsa-mir-187" (miRBase Accession No. MI0000274, SEQ ID NO: 22) having a hairpin-like structure is known.
[0087]
　As used herein, the term "miR-6076" or "miR-6076" includes the hsa-miR-6076 gene (miRBase Accession No. MIMAT0023701) described in SEQ ID NO: 7, which is a human gene, and others. Includes homologs or orthologs of species. The hsa-miR-6076 gene can be obtained by the method described in Voellenkle C et al., 2012, RNA, Vol. 18, p472-484. Further, as a precursor of "hsa-miR-6076", "hsa-mir-6076" (miRBase Accession No. MI0020353, SEQ ID NO: 23) having a hairpin-like structure is known.
[0088]
　The term "miR-4800-3p gene" or "miR-4800-3p" as used herein refers to the hsa-miR-4800-3p gene (miRBase Accession No) described in SEQ ID NO: 8, which is a human gene. . MIMAT0019979) and homologs or orthologs of other species are included. The hsa-miR-4800-3p gene can be obtained by the method described in Persson H et al., 2011, Cancer Res, Vol. 71, p78-86. Further, as a precursor of "hsa-miR-4800-3p", "hsa-mir-4800" (miRBase Accession No. MI0017448, SEQ ID NO: 24) having a hairpin-like structure is known.
[0089]
　As used herein, the term "miR-744-5p gene" or "miR-744-5p" refers to the hsa-miR-744-5p gene (miRBase Accession No) described in SEQ ID NO: 9, which is a human gene. . MIMAT0004945) and homologs or orthologs of other species are included. The hsa-miR-744-5p gene can be obtained by the method described in Berezikov E et al., 2006, Genome Res, Vol. 16, p1289-1298. Further, as a precursor of "hsa-miR-744-5p", "hsa-mir-744" (miRBase Accession No. MI0005559, SEQ ID NO: 25) having a hairpin-like structure is known.
[0090]
　As used herein, the term "miR-6511a-5p gene" or "miR-6511a-5p" refers to the hsa-miR-6511a-5p gene (miRBase Accession No) according to SEQ ID NO: 10, which is a human gene. . MIMAT0025478) and homologs or orthologs of other species are included. The hsa-miR-6511a-5p gene can be obtained by the method described in Joyce CE et al., 2011, Hum Mol Genet, Vol. 20, p4025-4040. In addition, as a precursor of "hsa-miR-6511a-5p", "hsa-mir-6511a-1, hsa-mir-6511a-2, hsa-mir-6511a-3, hsa-mir-" which has a hairpin-like structure. 6511a-4 ”(miRBase Accession No. MI0022223, MI0023564, MI0023565, MI0023566, SEQ ID NOs: 26-29) is known.
[0091]
　As used herein, the term "miR-135a-3p gene" or "miR-135a-3p" refers to the hsa-miR-135a-3p gene (miRBase Accession No) according to SEQ ID NO: 11, which is a human gene. . MIMAT0004595) and homologs or orthologs of other species are included. The hsa-miR-135a-3p gene can be obtained by the method described in Lagos-Quintana M et al., 2002, Curr Biol, Vol. 12, p735-739. Further, as a precursor of "hsa-miR-135a-3p", "hsa-mir-135a" (miRBase Accession No. MI0000452, SEQ ID NO: 30) having a hairpin-like structure is known.
[0092]
　As used herein, the term "miR-940 gene" or "miR-940" includes the hsa-miR-940 gene (miRBase Accession No. MIMAT0004983) described in SEQ ID NO: 12, which is a human gene, and others. Includes homologs or orthologs of species. The hsa-miR-940 gene can be obtained by the method described in Lui WO et al., 2007, A Cancer Res., Vol. 67, p6031-6043. Further, as a precursor of "hsa-miR-940", "hsa-mir-940" (miRBase Accession No. MI0005762, SEQ ID NO: 31) having a hairpin-like structure is known.
[0093]
　As used herein, the term "miR-4429 gene" or "miR-4429" includes the hsa-miR-4429 gene (miRBase Accession No. MIMAT0018944) described in SEQ ID NO: 13, which is a human gene, and others. Includes homologs or orthologs of species. The hsa-miR-4429 gene can be obtained by the method described in Jima DD et al., 2010, Blood, Vol. 116, e118-e127. Further, as a precursor of "hsa-miR-4429", "hsa-mir-4429" (miRBase Accession No. MI0016768, SEQ ID NO: 32) having a hairpin-like structure is known.
[0094]
　As used herein, the term "miR-6068 gene" or "miR-6068" includes the hsa-miR-6068 gene (miRBase Accession No. MIMAT0023693) described in SEQ ID NO: 14, which is a human gene, and others. Includes homologs or orthologs of species. The hsa-miR-6068 gene can be obtained by the method described in Voellenkle C et al., 2012, RNA, Vol. 18, p472-484. Further, as a precursor of "hsa-miR-6068", "hsa-mir-6068" (miRBase Accession No. MI0020345, SEQ ID NO: 33) having a hairpin-like structure is known.
[0095]
　As used herein, the term "miR-6511b-5p gene" or "miR-6511b-5p" refers to the hsa-miR-6511b-5p gene (miRBase Accession No) according to SEQ ID NO: 15, which is a human gene. . MIMAT0025847) and homologs or orthologs of other species are included. The hsa-miR-6511b-5p gene can be obtained by the method described in Li Y et al., 2012, Gene, Vol. 497, p330-335. In addition, as a precursor of "hsa-miR-6511b-5p", "hsa-mir-6511b-1, hsa-mir-6511b-2" having a hairpin-like structure (miRBase Accession No. MI0022552, MI0023431, SEQ ID NO: 34) , 35) are known.
[0096]
　As used herein, the term "miR-885-3p gene" or "miR-885-3p" refers to the hsa-miR-885-3p gene (miRBase Accession No) according to SEQ ID NO: 16, which is a human gene. . MIMAT0004948) and homologs or orthologs of other species are included. The hsa-miR-885-3p gene can be obtained by the method described in Berezikov E et al., 2006, Genome Res, Vol. 16, p1289-1298. Further, as a precursor of "hsa-miR-885-3p", "hsa-mir-885" (miRBase Accession No. MI0005560, SEQ ID NO: 36) having a hairpin-like structure is known.
[0097]
　As used herein, the term "miR-3619-3p gene" or "miR-3619-3p" refers to the hsa-miR-3619-3p gene (miRBase Accession No. MIMAT0019219) set forth in SEQ ID NO: 37 and others. Includes species homologs or orthologs. The hsa-miR-3619-3p gene can be obtained by the method described in Witten D et al., 2010, BMC Biol, Vol. 8, p58. In addition, "hsa-mir-3619" (miRBase Accession No. MI0016009, SEQ ID NO: 62), which has a hairpin-like structure as a precursor of "hsa-miR-3619-3p", is known.
[0098]
　As used herein, the term "miR-3648 gene" or "miR-3648" refers to the hsa-miR-3648 gene (miRBase Accession No. MIMAT0018068) set forth in SEQ ID NO: 38 and other species homologs or orthologs. Is included. The hsa-miR-3648 gene can be obtained by the method described in Meiri E et al., 2010, Nucleic Acids Res, Vol. 38, p6234-6246. Further, as a precursor of "hsa-miR-3648", "hsa-mir-3648-1" (miRBase Accession No. MI0016048, SEQ ID NO: 63) having a hairpin-like structure is known.
[0099]
　As used herein, the term "miR-4485-5p gene" or "miR-4485-5p" refers to the hsa-miR-4485-5p gene (miRBase Accession No. MIMAT0032116) set forth in SEQ ID NO: 39 and others. Includes species homologs or orthologs. The hsa-miR-5p gene can be obtained by the method described in Jima DD et al., 2010, Blood, Vol. 116, e118-e127. Further, as a precursor of "hsa-miR-4485-5p", "hsa-mir-4485" (miRBaseAccession No. MI0016846, SEQ ID NO: 64) having a hairpin-like structure is known.
[0100]
　As used herein, the term "miR-4497 gene" or "miR-4497" refers to the hsa-miR-4497 gene (miRBase Accession No. MIMAT0019032) set forth in SEQ ID NO: 40 and other species homologs or orthologs. Including. The hsa-miR-4497 gene can be obtained by the method described in Jima DD et al., 2010, Blood, Vol. 116, e118-e127. Further, as a precursor of "hsa-miR-4497", "hsa-mir-4497" (miRBaseAccession No. MI0016859, SEQ ID NO: 65) having a hairpin-like structure is known.
[0101]
　As used herein, the term "miR-4745-5p gene" or "miR-4745-5p" refers to the hsa-miR-4745-5p gene (miRBase Accession No. MIMAT0019878) set forth in SEQ ID NO: 41 and others. Includes species homologs or orthologs. The hsa-miR-4745-5p gene can be obtained by the method described in Persson H et al., 2011, Cancer Res, Vol. 71, p78-86. Further, as a precursor of "hsa-miR-4745-5p", "hsa-mir-4745" (miRBase Accession No. MI0017384, SEQ ID NO: 66) having a hairpin-like structure is known.
[0102]
　As used herein, the term "miR-663b gene" or "miR-663b" refers to the hsa-miR-663b gene (miRBase Accession No. MIMAT0005867) set forth in SEQ ID NO: 42 and other species homologs or orthologs. Including. The hsa-miR-663b gene can be obtained by the method described in Takada S et al., 2008, Leukemia, Vol. 22, p1274-1278. Further, as a precursor of "hsa-miR-663b", "hsa-mir-663b" (miRBase Accession No. MI0006336, SEQ ID NO: 67) having a hairpin-like structure is known.
[0103]
　The terms "miR-92a-2-5p gene" or "miR-92a-2-5p" as used herein refer to the hsa-miR-92a-2-5p gene (miRBase Accession) set forth in SEQ ID NO: 43. No. MIMAT0004508) and other species such as homologs or orthologs. The hsa-miR-92a-2-5p gene can be obtained by the method described in Mourelatos Z et al., 2002, Genes Dev, Vol. 16, p720-728. Further, as a precursor of "hsa-miR-92a-2-5p", "hsa-miR-92a-2" (miRBaseAccession No. MI0000094, SEQ ID NO: 68) having a hairpin-like structure is known.
[0104]
　As used herein, the term "miR-1260b gene" or "miR-1260b" includes the hsamiR-1260b gene (miRBase Accession No. MIMAT0015041) set forth in SEQ ID NO: 44 and other species homologs or orthologs. To do. The hsa-miR-1260b gene can be obtained by the method described in Stark MS et al., 2010, PLoS One, Volume 5, e9685. Further, as a precursor of "hsa-miR-1260b", "hsa-mir-1260b" (miRBase Accession No. MI0014197, SEQ ID NO: 69) having a hairpin-like structure is known.
[0105]
　As used herein, the term "miR-3197 gene" or "miR-3197" refers to the hsa-miR-3197 gene (miRBase Accession No. MIMAT0015082) set forth in SEQ ID NO: 45 and other species homologs or orthologs. Including. The hsa-miR-3197 gene can be obtained by the method described in Stark MS et al., 2010, PLoS One, Volume 5, e9685. Further, as a precursor of "hsa-miR-3197", "hsa-mir-3197" (miRBase Accession No. MI0014245, SEQ ID NO: 70) having a hairpin-like structure is known.
[0106]
　The terms "miR-3663-3p gene" or "miR-3663-3p" used herein refer to the hsa-miR-3663-3p gene (miRBase Accession No. MIMAT0018085) set forth in SEQ ID NO: 46 and others. Includes species homologs or orthologs. The hsa-miR-3663-3p gene can be obtained by the method described in Liao JY et al., 2010, PLoS One, Volume 5, e10563. Further, as a precursor of "hsa-miR-3663-3p", "hsa-mir-3663" (miRBase Accession No. MI0016064, SEQ ID NO: 71) having a hairpin-like structure is known.
[0107]
　As used herein, the term "miR-4257 gene" or "miR-4257" refers to the hsa-miR-4257 gene (miRBase Accession No. MIMAT0016878) set forth in SEQ ID NO: 47 and other species homologs or orthologs. Including. The hsa-miR-4257 gene can be obtained by the method described in Goff LA et al., 2009, PLoS One, Volume 4, e7192. Further, as a precursor of "hsa-miR-4257", "hsa-mir-4257" (miRBase Accession No. MI0015856, SEQ ID NO: 72) having a hairpin-like structure is known.
[0108]
　As used herein, the term "miR-4327 gene" or "miR-4327" refers to the hsa-miR-4327 gene (miRBase Accession No. MIMAT0016889) set forth in SEQ ID NO: 48 and other species homologs or orthologs. Including. The hsa-miR-4327 gene can be obtained by the method described in Goff LA et al., 2009, Plos One, Volume 4, e7192. Further, as a precursor of "hsa-miR-4327", "hsa-mir-4327" (miRBaseAccession No. MI0015867, SEQ ID NO: 73) having a hairpin-like structure is known.
[0109]
　As used herein, the term "miR-4476 gene" or "miR-4476" refers to the hsa-miR-4476 gene (miRBase Accession No. MIMAT0019003) set forth in SEQ ID NO: 49 and other species homologs or orthologs. Including. The hsa-miR-4476 gene can be obtained by the method described in Jima DD et al., 2010, Blood, Vol. 116, e118-e127. Further, as a precursor of "hsa-miR-4476", "hsa-mir-4476" (miRBaseAccession No. MI0016828, SEQ ID NO: 74) having a hairpin-like structure is known.
[0110]
　As used herein, the term "miR-4505 gene" or "miR-4505" refers to the hsa-miR-4505 gene (miRBase Accession No. MIMAT0019041) set forth in SEQ ID NO: 50 and other species homologs or orthologs. Including. The hsa-miR-4505 gene can be obtained by the method described in Jima DD et al., 2010, Blood, Vol. 116, e118-e127. Further, as a precursor of "hsa-miR-4505", "hsa-mir-4505" (miRBaseAccession No. MI0016868, SEQ ID NO: 75) having a hairpin-like structure is known.
[0111]
　As used herein, the term "miR-4532 gene" or "miR-4532" refers to the hsa-miR-4532 gene (miRBase Accession No. MIMAT0019071) set forth in SEQ ID NO: 51 and other species homologs or orthologs. Including. The hsa-miR-4532 gene can be obtained by the method described in Jima DD et al., 2010, Blood, Vol. 116, e118-e127. Further, as a precursor of "hsa-miR-4532", "hsa-mir-4532" (miRBase Accession No. MI0016899, SEQ ID NO: 76) having a hairpin-like structure is known.
[0112]
　As used herein, the term "miR-4674 gene" or "miR-4674" refers to the hsa-miR-4674 gene (miRBase Accession No. MIMAT0019756) set forth in SEQ ID NO: 52 and other species homologs or orthologs. Including. The hsa-miR-4674 gene can be obtained by the method described in Persson H et al., 2011, Cancer Res, Vol. 71, p78-86. Further, as a precursor of "hsa-miR-4674", "hsa-mir-4674" (miRBase Accession No. MI0017305, SEQ ID NO: 77) having a hairpin-like structure is known.
[0113]
　As used herein, the term "miR-4690-5p gene" or "miR-4690-5p" refers to the hsa-miR-4690-5p gene (miRBase Accession No. MIMAT0019779) set forth in SEQ ID NO: 53 and others. Includes species homologs or orthologs. The hsa-miR-4690-5p gene can be obtained by the method described in Persson H et al., 2011, Cancer Res, Vol. 71, p78-86. Further, as a precursor of "hsa-miR-4690-5p", "hsa-mir-4690" (miRBase Accession No. MI0017323, SEQ ID NO: 78) having a hairpin-like structure is known.
[0114]
　As used herein, the term "miR-4792 gene" or "miR-4792" refers to the hsa-miR-4792 gene (miRBase Accession No. MIMAT0019964) set forth in SEQ ID NO: 54 and other species homologs or orthologs. Including. The hsa-miR-4792 gene can be obtained by the method described in Persson H et al., 2011, Cancer Res, Vol. 71, p78-86. Further, as a precursor of "hsa-miR-4792", "hsa-mir-4792" (miRBase Accession No. MI0017439, SEQ ID NO: 79) having a hairpin-like structure is known.
[0115]
　As used herein, the term "miR-5001-5p gene" or "miR-5001-5p" refers to the hsa-miR-5001-5p gene (miRBase Accession No. MIMAT0021021) set forth in SEQ ID NO: 55 and others. Includes species homologs or orthologs. The hsa-miR-5001-5p gene can be obtained by the method described in Hansen TB et al., 2011, RNA Biol, Vol. 8, p378-383. Further, as a precursor of "hsa-miR-5001-5p", "hsa-mir-5001" (miRBase Accession No. MI0017867, SEQ ID NO: 80) having a hairpin-like structure is known.
[0116]
　As used herein, the term "miR-6075 gene" or "miR-6075" refers to the hsa-miR-6075 gene (miRBase Accession No. MIMAT0023700) set forth in SEQ ID NO: 56 and other species homologs or orthologs. Including. The hsa-miR-6075 gene can be obtained by the method described in Voellenkle C et al., 2012, RNA, Vol. 18, p472-484. Further, as a precursor of "hsa-miR-6075", "hsa-mir-6075" (miRBase Accession No. MI0020352, SEQ ID NO: 81) having a hairpin-like structure is known.
[0117]
　As used herein, the term "miR-6132 gene" or "miR-6132" refers to the hsa-miR-6132 gene (miRBase Accession No. MIMAT0024616) set forth in SEQ ID NO: 57 and other species homologs or orthologs. Including. The hsa-miR-6132 gene can be obtained by the method described in Dannemann M et al., 2012, Genome Biol Evol, Vol. 4, p552-564. Further, as a precursor of "hsa-miR-6132", "hsa-mir-6132" (miRBase Accession No. MI0021277, SEQ ID NO: 82) having a hairpin-like structure is known.
[0118]
　As used herein, the term "miR-6885-5p gene" or "miR-6885-5p" refers to the hsa-miR-6885-5p gene (miRBase Accession No. MIMAT0027670) set forth in SEQ ID NO: 58 and others. Includes species homologs or orthologs. The hsa-miR-6885-5p gene can be obtained by the method described in Ladwig E et al., 2012, Genome Res, Vol. 22, p1634-1645. In addition, "hsa-mir-6885" (miRBase Accession No. MI0022732, SEQ ID NO: 83), which has a hairpin-like structure as a precursor of "hsa-miR-6885-5p", is known.
[0119]
　As used herein, the term "miR-6780b-5p gene" or "miR-6780b-5p" refers to the hsa-miR-6780b-5p gene (miRBase Accession No. MIMAT0027572) set forth in SEQ ID NO: 59 and others. Includes species homologs or orthologs. The hsa-miR-6780b-5p gene can be obtained by the method described in Ladwig E et al., 2012, Genome Res, Vol. 22, p1634-1645. Further, as a precursor of "hsa-miR-6780b-5p", "hsa-mir-6780b" (miRBase Accession No. MI0022681, SEQ ID NO: 84) having a hairpin-like structure is known.
[0120]
　The terms "miR-4723-5p gene" or "miR-4723-5p" as used herein refer to the hsa-miR-4723-5p gene (miRBase Accession No. MIMAT0019838) set forth in SEQ ID NO: 60 and others. Includes species homologs or orthologs. The hsa-miR-4723-5p gene can be obtained by the method described in Persson H et al., 2011, Cancer Res, Vol. 71, p78-86. Further, as a precursor of "hsa-miR-4723-5p", "hsa-mir-4723" (miRBase Accession No. MI0017359, SEQ ID NO: 85) having a hairpin-like structure is known.
[0121]
　As used herein, the term "miR-5100 gene" or "miR-5100" refers to the hsa-miR-5100 gene (miRBase Accession No. MIMAT0022259) set forth in SEQ ID NO: 61 and other species homologs or orthologs. Including. The hsa-miR-5100 gene can be obtained by the method described in Tandon M et al., 2012, Oral Dis, Vol. 18, p127-131. Further, as a precursor of "hsa-miR-5100", "hsa-mir-5100" (miRBase Accession No. MI0019116, SEQ ID NO: 86) having a hairpin-like structure is known.
Example
[0122]
　Hereinafter, the process of selecting the reference miRNA that varies depending on the quality of the RNA of the present invention will be described in more detail. However, the present invention is not limited to the following examples.
[0123]
(Collection of serum sample) In the
　examples, serum was selected as an example of the body fluid sample, and the contents related to the quality evaluation of the body fluid sample were described. The process of obtaining serum consists of three steps: (1) blood is collected from the subject, (2) coagulated in a whole blood state, (3) centrifuged, and separated into serum. Of these, for (2) standing at the time of coagulation and (3) standing after separation into serum until cryopreservation, multiple standing times or temperature conditions were set, and based on these. The following experiments were performed using the prepared serum samples.
[0124]
　Among Examples 1 to 8, the above-mentioned (2) Examples relating to standing still during coagulation are Examples 1, 2, 5, 6, and (3) Examples relating to standing standing from serum separation to cryopreservation are Examples. 3, 4, 7, 8. Further, Examples 5 to 8 were experiments in which the standing time at the time of sample preparation was shorter than that of Examples 1 to 4, and Examples 5 and 6 were described in Examples 1 and 2 and Example 7. , 8 correspond to Examples 3 and 4. Table 1 shows the sample preparation conditions of Examples 1 to 8.
[0126]
(DNA microarray) The
　following experiments of Examples 1 to 8 were carried out using a "3D-Gene" human miRNA oligo chip (corresponding to miRBase release 21) manufactured by Toray Industries, Inc.
[0127]
Selection of a reference miRNA that can detect deterioration in whole blood coagulation
(sample preparation for detection of deterioration due to temperature influence)
　Blood was collected from 3 healthy subjects by 7 blood collection tubes each, and 7 in the whole blood state. One of the books was allowed to stand at room temperature (23 ° C) for 0.5 hours (using this as a reference condition), and the remaining 6 books were 4 ° C, 18 ° C, 20 ° C, room temperature (23 ° C), 28 ° C, It was allowed to stand at each temperature of 30 ° C. for 6 hours. After the time was reached, centrifugation was performed each time, and 300 μL of the obtained serum was dispensed within 10 minutes after centrifugation and stored in a freezer at -80 ° C.
[0128]
(Preparation of specimens for detection of deterioration by standing for a long time at room temperature)
　Blood was collected from 3 healthy subjects by 4 blood collection tubes, and one of the 4 blood samples was collected at room temperature (23 ° C). It was allowed to stand for 0.5 hours (using this as a reference condition), and the remaining 3 bottles were also allowed to stand at room temperature (23 ° C.) for 3 hours, 6 hours, and 9 hours, respectively. After the time was reached, centrifugation was performed each time, and 300 μL of the obtained serum was dispensed within 10 minutes after centrifugation and stored in a freezer at -80 ° C.
[0129]
(Preparation of sample RNA and measurement of miRNA abundance)
　The serum prepared as described above and stored in the freezer was simultaneously thawed, and RNA contained in the serum sample (hereinafter referred to as sample RNA) was extracted. A “3D-Gene” RNA extraction reagent from liquid sample kit (manufactured by Toray Industries, Inc.) was used for extraction. For purification, RNeasy 96 QIAcube HT kit (QIAGEN) was used.
[0130]
　The obtained sample RNA was labeled using a "3D-Gene" miRNA labeling kit (manufactured by Toray Industries, Inc.). At the time of labeling, an external standard nucleic acid was added to correct the miRNA measurements. The labeled sample RNA was hybridized using a "3D-Gene" miRNA chip (manufactured by Toray Industries, Inc.) according to the standard protocol. The DNA microarray after hybridization was subjected to a microarray scanner (manufactured by Toray Industries, Inc.) to measure the fluorescence intensity. The scanner was set to 100% laser output, and the voltage setting of the photo multiplier was set to AUTO.
[0131]
　Each miRNA contained in the sample RNA under each condition was measured with a DNA microarray. The measured values ​​of each detected miRNA were converted to a logarithm with a base of 2, and appropriate corrections were made to standardize the data between samples to obtain the miRNA abundance of each serum sample.
[0132]
(Selection of reference miRNA)
　By comparing the miRNA abundance of each serum sample obtained as described above, and extracting a large miRNA whose abundance varies depending on the standing time and the standing temperature. , Criteria miRNA were selected.
[0133]
　Table 2 shows the average variation values ​​of 8 types of reference miRNAs (SEQ ID NOs: 1 to 8) and the abundance of each condition from the reference conditions among individuals, and among the samples obtained by the above formulas 1 and 2. The overall variation index value of miRNA is shown. The abundance of the miRNA is such that the miRNA is allowed to stand at room temperature for a long time, or is allowed to stand at a temperature of 28 ° C. or higher, that is, the miRNA in serum is stored in a relatively unstable state. It fluctuated more than twice (more than 1 due to the logarithmic difference of the base 2). In general, doubling the abundance is considered a sufficient difference in measurements on DNA microarrays. In addition, the overall fluctuation index value shows a higher value of 1.5 or more as the standing temperature (coagulation temperature) of whole blood is higher or the standing time at room temperature is longer, and the degree of deterioration of sample quality is. It was confirmed that it was high. From this, it was confirmed that the miRNA can be used as a miRNA index whose abundance varies depending on the quality of the body fluid sample. That is, it was found that the quality of the body fluid sample can be known by measuring the abundance of the reference miRNA shown in Table 2.
[0135]
　FIG. 3 shows the abundance of hsa-miR-204-3p (SEQ ID NO: 1) under the reference condition and the condition in which the coagulation temperature under the whole blood state was changed (7 conditions in total). The abundance of hsa-miR-204-3p became sharply low after the solidification condition of 28 ° C. For example, when determining the deterioration of body fluid sample quality due to being allowed to stand at 28 ° C or higher in a whole blood state, the abundance amount 12 of hsa-miR-204-3p is set as a threshold value and is used in a certain body fluid sample. If the abundance of hsa-miR-204-3p is lower than that value, it can be determined that the sample is deteriorated, that is, the sample is of poor quality.
[0136]
　In addition, FIG. 4 shows the abundance of hsa-miR-4730 (SEQ ID NO: 2) under the reference condition and the condition in which the room temperature standing time in whole blood was changed (4 conditions in total). The abundance of hsa-miR-4730 remained higher as the room temperature standing time in whole blood increased. For example, when determining the deterioration of body fluid sample quality due to standing for 6 hours or more in a whole blood state, the abundance amount 11 of hsa-miR-4730 is set as a threshold value, and hsa-miR in a certain body fluid sample is set. -4730 If the abundance exceeds that value, it can be determined that the sample is deteriorated, that is, the sample is of poor quality.
[0137]
　Specific examples of the threshold values ​​of the eight types of reference miRNAs shown in Table 2 that can be set from the results of this Example 1 are shown in Table 3 below together with the average value of the abundance under the reference conditions. These thresholds are thresholds that can be used as thresholds for detecting deterioration that occurs in a whole blood state such as when whole blood is stored. For example, it took time to separate serum from a clinical blood sample. In some cases, these thresholds can be preferably used. If you measure the reference miRNA in the body fluid sample for which you want to evaluate the quality, convert the measured value to a logarithm with a base of 2, and make appropriate corrections to standardize the data between samples, and compare the values ​​with these thresholds. Good. Depending on how strict the determination is, the threshold value ± α (α is an arbitrary numerical value, for example, about 0.5 to 3) shown in Table 3 may be set as the threshold value.
[0139]
Detection of deterioration during whole blood coagulation with a plurality of miRNAs
　It is also possible to judge deterioration of body fluid sample quality by combining any two types of reference miRNAs instead of a single miRNA.
[0140]
　The abundance of hsa-miR-204-3p (SEQ ID NO: 1) and hsa-miR-4730 (SEQ ID NO: 2) under the reference conditions of Example 1 and the conditions of standing at 30 ° C. for 6 hours with whole blood was used. .. The individual abundances of these miRNAs under each condition are as shown in FIG. 5, and the difference in abundance of these two types of miRNAs under each condition was calculated as shown in FIG. As shown in Table 3 and FIG. 5, hsa-miR-204-3p is a miRNA that changes to a low value due to deterioration of the sample that occurs in the whole blood state, and hsa-miR-4730 is the deterioration of the sample that occurs in the whole blood state. It is a miRNA that changes to a higher value due to the above, and the abundance in the undegraded sample is higher in hsa-miR-204-3p than in hsa-miR-4730. In the body fluid sample in good quality (reference conditions), the difference between the abundance of hsa-miR-204-3p and the abundance of hsa-miR-4730 is large, but the quality deteriorates due to standing at 30 ° C. In the body fluid sample, the difference between the abundances of the two is small. When determining the deterioration of body fluid sample quality due to standing at 30 ° C in the whole blood state, for example, the threshold value of the difference in the abundance of these two types of miRNA is set to 1, and in a certain body fluid sample, these are set. If the difference in the abundance of miRNA is less than that value, it can be determined that the sample is deteriorated, that is, the sample is of poor quality.
[0141]
　When the same determination is made with a combination other than the combination of hsa-miR-204-3p (SEQ ID NO: 1) and hsa-miR-4730 (SEQ ID NO: 2), the two reference miRNAs are shown in Table 3. Among the reference miRNAs, one type may be selected from the reference miRNAs that change to a low value, and one type may be selected from the reference miRNAs that change to a high value. In the case where the abundance of the reference miRNA that changes to a low value under the reference condition is higher than the abundance of the reference miRNA that changes to a high value under the reference condition and the abundance of both approaches due to deterioration, FIG. As in the example, when the difference in abundance falls below an arbitrarily determined threshold value, it can be determined that the quality is poor. On the contrary, in the case of a combination in which the abundance of the reference miRNA that changes to a low value under the reference condition is lower than the abundance of the reference miRNA that changes to a high value under the reference condition, and the abundance of both is separated due to deterioration. When the difference in abundance exceeds an arbitrarily determined threshold value, it can be determined that the quality is poor.
[0142]
　When the abundance of the reference miRNA that changes to a low value under the reference condition is higher than the abundance of the reference miRNA that changes to a high value under the reference condition, the degree of deterioration is very large and the presence of the former reference miRNA The amount may fall below the latter reference miRNA abundance, and the abundance difference may begin to open again. Therefore, in general, there are two types of combinations in which the abundance of the reference miRNA that changes to a low value under the reference condition is lower than the abundance of the reference miRNA that changes to a high value under the reference condition, and the abundance of both is separated by deterioration. It is more preferable to select the reference miRNA of. However, the combination is not limited to the combination of the reference miRNAs described in this example, and a plurality of reference miRNAs that change to a low value or a plurality of reference miRNAs that change to a high value are selected and combined from Table 3. It is also possible to judge the quality of the body fluid sample by integrating the judgment results of each standard miRNA.　
[0143]
Selection of standard miRNA that can detect deterioration in
serum state (Sample preparation for detection of deterioration by standing at 4 ° C for a long time in serum state (preparation 1))
　Blood collection tubes from 3 healthy subjects Four blood samples were collected, all of which were allowed to stand at room temperature (23 ° C.) for 0.5 hours, and then centrifuged to obtain serum. For one bottle, 300 μL of the obtained serum was dispensed within 10 minutes after centrifugation and stored in a freezer at -80 ° C (this is the standard condition). For the remaining 3 sera, the obtained serum was allowed to stand at 4 ° C. for 12 hours, 21 hours, and 24 hours, and when the time was reached, 300 μL of serum was dispensed and stored in a freezer at -80 ° C.
[0144]
(Sample preparation for detection of deterioration by
　standing in the serum state (preparation 2)) Blood was collected from 3 healthy subjects by 7 blood collection tubes, and all were allowed to stand at room temperature (23 ° C) for 0.5 hours, and then centrifuged. Serum was obtained by separation. For one bottle, 300 μL of the obtained serum was dispensed within 10 minutes after centrifugation and stored in a freezer at -80 ° C (this is the standard condition). For the remaining 6 serums, the obtained serum was allowed to stand at room temperature (23 ° C) for 0.5 hour, 1 hour, 2 hours, 3 hours, 6 hours, and 4 ° C for 6 hours, respectively, and after reaching the time, 300 μL of serum was added. It was dispensed one by one and stored in a freezer at -80 ° C.
[0145]
(Sample preparation to detect deterioration due to temperature influence in serum state (preparation 3))
　Blood was collected from 3 healthy subjects by 4 blood collection tubes, and all were allowed to stand at room temperature (23 ° C) for 0.5 hours. Serum was obtained by centrifugation. For one, 300 μL of the obtained serum was dispensed within 10 minutes after centrifugation and stored in a freezer at -80 ° C (this is the standard condition). The remaining 3 sera were allowed to stand at 4 ° C, 10 ° C, and 14 ° C for 21 hours, and then 300 μL of each was dispensed and stored in a freezer at -80 ° C.
[0146]
(Preparation of sample RNA and measurement of miRNA abundance)
　Serum prepared as described above and placed in a freezer was simultaneously thawed, and RNA contained in the serum sample (hereinafter referred to as sample RNA) was extracted. A “3D-Gene” RNA extraction reagent from liquid sample kit (manufactured by Toray Industries, Inc.) was used for extraction. For purification, RNeasy 96 QIAcube HT kit (QIAGEN) was used.
[0147]
　The obtained sample RNA was labeled using a "3D-Gene" miRNA labeling kit (manufactured by Toray Industries, Inc.). At the time of labeling, an external standard nucleic acid was added to correct the miRNA measurements. The labeled sample RNA was hybridized using a "3D-Gene" miRNA chip (manufactured by Toray Industries, Inc.) according to the standard protocol. The DNA microarray after hybridization was subjected to a microarray scanner (manufactured by Toray Industries, Inc.) to measure the fluorescence intensity. The scanner was set to 100% laser output, and the voltage setting of the photo multiplier was set to AUTO.
[0148]
　Each miRNA contained in the sample RNA under each condition was measured with a DNA microarray. The measured values ​​of each detected miRNA were converted to a logarithm with a base of 2, and appropriate corrections were made to standardize the data between samples to obtain the miRNA abundance of each serum sample.
[0149]
(Selection of reference miRNA)
　By comparing the miRNA abundance of each serum sample obtained as described above and extracting a large miRNA whose abundance varies depending on the standing time and temperature, the reference is obtained. The miRNA was selected.
[0150]
　Table 4 shows the average variation values ​​of 15 types of miRNAs that can detect deterioration in serum standing and the abundance of each condition from the reference conditions, and the values ​​obtained by the above formulas 1 and 2 respectively. The overall variation index value of miRNA in the sample is shown. The 15 types of miRNAs (SEQ ID NOs: 1 to 5, 7 to 16) are allowed to stand for a long time at room temperature or at a temperature of 10 ° C. or higher after serum separation, that is, serum. Under the condition that the miRNA inside was stored in a relatively unstable state, the abundance fluctuated more than twice (1 or more by the logarithmic difference of the base 2). Generally, in the measurement on DNA microarray, the fluctuation of abundance twice is considered as a sufficient difference. In addition, the overall fluctuation index value shows a higher value of 1.5 or more as the serum standing temperature is higher, or as the standing temperature is lower than the refrigerating temperature (4 ° C) or at room temperature, and the standing time is longer. It was confirmed that the degree of quality deterioration was high. From this, it was confirmed that the miRNA can be used as a miRNA index whose abundance varies depending on the quality of the body fluid sample. That is, it was found that the quality of body fluid samples can be known by measuring the abundance of the 15 types of miRNAs shown in Table 4.
[0152]
　FIG. 7 shows the abundance of hsa-miR-4800-3p (SEQ ID NO: 8) under the reference condition and the condition in which the standing time and temperature under the serum state were changed (8 conditions in total). The abundance of hsa-miR-4800-3p (SEQ ID NO: 8) remained low as the degree of deterioration increased. For example, when determining the deterioration of sample quality when the sample is left at 4 ° C for 6 hours or more, or at 10 ° C or higher for 21 hours, the abundance of hsa-miR-4800-3p is 6.2. It is set as a threshold value, and when the abundance of hsa-miR-4800-3p in a certain body fluid sample is lower than that value, it can be determined that the sample is deteriorated, that is, the sample is of poor quality.
[0153]
　In addition, FIG. 8 shows the abundance of hsa-miR-135a-3p (SEQ ID NO: 11) under the reference condition and the condition in which the room temperature standing time under the serum state was changed (6 conditions in total). The abundance of hsa-miR-135a-3p (SEQ ID NO: 11) remained higher as the room temperature standing time in serum increased. For example, when determining the deterioration of the quality of a body fluid sample due to being left to stand at room temperature for 3 hours or more with serum, the abundance of hsa-miR-135a-3p of 7.7 is set as a threshold, and the content of the body fluid sample is set as a threshold. If the abundance of hsa-miR-135a-3p exceeds that value, it can be determined that the sample is deteriorated, that is, the sample is of poor quality.
[0154]
　Specific examples of the threshold values ​​of the 15 types of reference miRNAs shown in Table 4 that can be set from the results of this Example 3 are shown in Table 5 below together with the average value of the abundance in the reference sample. These thresholds are thresholds that can be used as thresholds for detecting deterioration that occurs in the serum state such as during serum storage. For example, after separating serum from a clinical blood sample, until it is cryopreserved, or until it is cryopreserved. These thresholds can be preferably used when it takes time to store the product without freezing and perform expression analysis. If you measure the reference miRNA in the body fluid sample for which you want to evaluate the quality, convert the measured value to a logarithm with a base of 2, and make appropriate corrections to standardize the data between samples, and compare the values ​​with these thresholds. Good. The threshold value ± α (α is an arbitrary numerical value, for example, about 0.5 to 3) shown in Table 5 may be set as the threshold value depending on how strict the determination is.
[0156]
Detection of serum deterioration with a plurality of miRNAs It
　is also possible to determine the quality deterioration of a body fluid sample by combining any two types of miRNAs rather than a single miRNA.
[0157]
　The abundance of hsa-miR-204-3p (SEQ ID NO: 1) and hsa-miR-4800-3p (SEQ ID NO: 8) under the reference conditions of Example 3 and the conditions of standing at 4 ° C. for 24 hours with serum was used. did. The individual abundances of these miRNAs under each condition are as shown in FIG. 9, and the difference in abundance of these two types of miRNAs under each condition was calculated as shown in FIG. As shown in Table 5 and FIG. 9, hsa-miR-204-3p is a miRNA that changes to a high value due to deterioration of the sample caused by the serum state, and hsa-miR-4800-3p is caused by deterioration of the sample caused by the serum state. It is a miRNA that changes to a low value, and the abundance in the undegraded sample is higher in hsa-miR-204-3p than in hsa-miR-4800-3p. In the body fluid sample in good quality (reference conditions), the difference between the abundance of hsa-miR-204-3p and the abundance of hsa-miR-4800-3p is small, but it deteriorates after standing at 4 ° C for 24 hours. In the body fluid sample in this state, the difference in the abundance between the two becomes large. When determining the deterioration of body fluid sample quality due to standing at 4 ° C for 24 hours, for example, the threshold value of the difference in the abundance of these two types of miRNA is set to 8, and in a certain body fluid sample, these miRNAs are used. If the abundance difference exceeds that value, it can be determined that the sample is deteriorated, that is, the sample is of poor quality.
[0158]
　When the same determination is made with a combination other than the combination of hsa-miR-204-3p (SEQ ID NO: 1) and hsa-miR-4800-3p (SEQ ID NO: 8), the two reference miRNAs are shown in Table 5. Among the indicated reference miRNAs, one type may be selected from the reference miRNAs that change to a low value, and one type may be selected from the reference miRNAs that change to a high value. In the case of a combination in which the abundance of the reference miRNA that changes to a low value under the reference condition is lower than the abundance of the reference miRNA that changes to a high value under the reference condition and the abundance of both increases due to deterioration, FIG. As in the example, when the difference in abundance exceeds an arbitrarily determined threshold value, it can be determined that the quality is poor. On the contrary, in the case of a combination in which the abundance of the reference miRNA that changes to a low value under the reference condition is higher than the abundance of the reference miRNA that changes to a high value under the reference condition, and the abundance of both approaches due to deterioration. If the difference in abundance falls below an arbitrarily determined threshold value, it can be determined that the quality is poor.
[0159]
　As described in Example 2, in general, the abundance of the reference miRNA that changes to a low value under the reference condition is lower than the abundance of the reference miRNA that changes to a high value under the reference condition, and the abundance of both is due to deterioration. It is more preferable to select two reference miRNAs in a combination that moves away from each other. However, the combination is not limited to the combination of the reference miRNAs described in this example, and a plurality of reference miRNAs that change to a low value or a plurality of reference miRNAs that change to a high value are selected and combined from Table 5. It is also possible to determine the quality of the body fluid sample (whether or not deterioration has occurred in the serum state) by integrating the judgment results based on the individual reference miRNAs.
[0160]
Selection of criteria miRNA that can detect deterioration in whole blood coagulation
(sample preparation)
　Seven blood collection tubes were collected from each of three healthy subjects, and one of the seven blood samples was at room temperature (in a whole blood state). Let stand for 0.5 hours under the condition of 24 ℃ (using this as the reference condition), and the remaining 6 bottles are at room temperature (24 ℃), room temperature (24 ℃), 26 ℃, 28 ℃ for 1 hour. It was allowed to stand at 24 ° C. for 3 hours. After the time was reached, centrifugation was performed each time, and 300 μL of the obtained serum was dispensed within 10 minutes after centrifugation and stored in a freezer at -80 ° C.
[0161]
(Preparation of sample RNA, measurement of miRNA abundance, and selection of reference miRNA)
　The procedure was the same as in Example 1. However, UNIFILTER 96Well (GE Healthcare) was used for purification.
[0162]
　Table 6 shows the 12 types of reference miRNAs (SEQ ID NOs: 1 to 4, 37 to 43, 59), the average variation value of the abundance of each condition from the reference condition, and the above-mentioned formulas 1 and 2 as well. The overall variation index value of miRNA in each sample obtained by is shown. In addition, for comparison with the reference miRNA, three types of miRNA whose abundance does not change due to deterioration of the sample are shown in the same table. The reference miRNA is twice as high in abundance under the condition of 3 hours, which is the longest standing time at room temperature, that is, the condition where the miRNA in serum is stored in a relatively unstable state. Above (1 or more due to the difference in logarithmic value of base 2), those that remained low fluctuated 1.5 times (0.6 or more due to the difference in logarithmic value of bottom 2). In general, doubling the abundance is considered a sufficient difference in measurements on DNA microarrays. In addition, the overall fluctuation index value shows a higher value under the condition that the standing temperature (coagulation temperature) of whole blood is higher or the standing time at room temperature is longer, and it is confirmed that the degree of deterioration of sample quality is higher. Was done. From this, it was confirmed that the miRNA can be used as a miRNA index whose abundance varies depending on the quality of the body fluid sample. That is, it was found that the quality of the body fluid sample can be known by measuring the abundance of the reference miRNA shown in Table 6.
[0164]
　FIG. 11 shows the abundance of hsa-miR-3648 (SEQ ID NO: 38) under the reference condition and the condition in which the coagulation temperature and time under the whole blood state were changed (7 conditions in total). The abundance of hsa-miR-3648 increased as the solidification temperature increased and as the solidification time increased. For example, when determining the deterioration of body fluid sample quality due to standing for 3 hours or more in a whole blood state, the abundance of hsa-miR-3648 of 11.6 is set as a threshold value, and hsa-miR in a certain body fluid sample is set. If the abundance of -3648 exceeds that value, it can be determined that the sample is deteriorated, that is, the sample is of poor quality.
[0165]
　FIG. 12 shows the abundance of hsa-miR-4632-5p (Comparison 3) under the reference condition and the condition in which the coagulation temperature and time under the whole blood state were changed (7 conditions in total). It is difficult to set the threshold because the fluctuation of the abundance due to the deterioration of the sample is very small. Therefore, such miRNAs are inappropriate for detecting sample degradation.
[0166]
　Specific examples of the threshold values ​​of the 12 types of reference miRNAs shown in Table 6 that can be set from the results of Example 5 are shown in Table 7 below together with the average value of the abundance under the reference conditions. These thresholds are thresholds that can be used as thresholds for detecting deterioration that occurs in a whole blood state such as when whole blood is stored. For example, it took time to separate serum from a clinical blood sample. In some cases, these thresholds can be preferably used. If you measure the reference miRNA in the body fluid sample for which you want to evaluate the quality, convert the measured value to a logarithm with a base of 2, and make appropriate corrections to standardize the data between samples, and compare the values ​​with these thresholds. Good. Depending on how strict the determination is, the threshold value ± α (α is an arbitrary numerical value, for example, about 0.5 to 3) shown in Table 7 may be set as the threshold value.
[0168]
Detection of deterioration during whole blood coagulation with a plurality of miRNAs
　It is also possible to determine deterioration of body fluid sample quality by combining any two types of reference miRNAs instead of a single miRNA.
[0169]
　Abundance of hsa-miR-3648 (SEQ ID NO: 38) and hsa-miR-6780b-5p (SEQ ID NO: 59) under the reference conditions of Example 5 and the conditions of standing at room temperature (24 ° C.) for 3 hours with whole blood. It was used. The individual abundances of these miRNAs under each condition are as shown in FIG. 13, and the difference in abundance of these two types of miRNAs under each condition was calculated as shown in FIG. As shown in Table 7 and FIG. 13, hsa-miR-3648 is a miRNA that changes to a high value due to deterioration of the sample that occurs in the whole blood state, and hsa-miR-6780b-5p is due to deterioration of the sample that occurs in the whole blood state. It is a miRNA that changes to a low value. The abundance in the non-deteriorated sample of hsa-miR-6780b-5p is higher than that of hsa-miR-3648, but as it deteriorates, the abundance is reversed and that of hsa-miR-3648 is higher. For body fluid samples in good quality (reference conditions), subtracting the abundance of hsa-miR-6780b-5p from the abundance of hsa-miR-3648 gives a negative value, but leave it at room temperature. In the body fluid sample whose quality has deteriorated due to the above, the difference in the abundance between the two increases to a positive value. When determining the deterioration of body fluid sample quality due to standing at room temperature for 3 hours or more in a whole blood state, for example, the threshold value of the difference in the abundance of these two types of miRNA is set to 1, and a certain body fluid sample is used. If the difference in the abundance of these miRNAs exceeds that value, it can be determined that the sample is deteriorated, that is, the sample is of poor quality.
[0170]
　When similar determinations are made with combinations other than those of hsa-miR-3648 (SEQ ID NO: 38) and hsa-miR-6780b-5p (SEQ ID NO: 59), the two reference miRNAs are shown in Table 7. Among the reference miRNAs, one type may be selected from the reference miRNAs that change to a low value, and one type may be selected from the reference miRNAs that change to a high value. However, it is not limited to the combination of the reference miRNAs described in this example, and only a plurality of reference miRNAs that change to high values ​​are selected and combined from Table 7, and the judgment results of the individual reference miRNAs are integrated into the body fluid. It is also possible to determine the quality of the sample (whether or not deterioration has occurred in a short period of time in the whole blood state).
[0171]
Selection of reference miRNA that can detect deterioration in serum status
(sample preparation)
　Eight blood collection tubes were collected from each of three healthy subjects, and all were allowed to stand at room temperature (23 ° C) for 0.5 hours, and then allowed to stand for 0.5 hours. Serum was obtained by centrifugation. For one, 300 μL of the obtained serum was dispensed within 10 minutes after centrifugation and stored in a freezer at -80 ° C (this is the standard condition). For the remaining 7 sera, the obtained serum was used at room temperature (24 ° C) for 0.5 hours, 20 ° C, 22 ° C, room temperature (24 ° C), 26 ° C, 28 ° C for 1 hour, and room temperature (24 ° C) for 2 hours, respectively. After allowing to stand for a certain period of time, 300 μL of serum was dispensed and stored in a freezer at -80 ° C.
[0172]
(Preparation of sample RNA, measurement of miRNA abundance, and selection of reference miRNA)
　The procedure was the same as in Example 3. However, UNIFILTER 96Well (GE Healthcare) was used for purification.
[0173]
　Table 8 shows the 34 types of reference miRNAs (SEQ ID NOs: 1-5, 8-10, 12, 13, 16, 37, 38, 40-58, 60, 61) and the abundance of each condition from the reference conditions. The average variation value between individuals and the overall variation index value of miRNA in each sample obtained by the above formulas 1 and 2 are shown. The abundance of the miRNA is such that the miRNA is allowed to stand at room temperature for a long time, or is allowed to stand at a temperature of 28 ° C. or higher, that is, the miRNA in serum is stored in a relatively unstable state. It fluctuated more than twice (more than 1 due to the logarithmic difference of the base 2). In general, doubling the abundance is considered a sufficient difference in measurements on DNA microarrays. In addition, the overall fluctuation index value shows a higher value under the condition that the standing temperature (coagulation temperature) of whole blood is higher or the standing time at room temperature is longer, and it is confirmed that the degree of deterioration of sample quality is higher. Was done. From this, it was confirmed that the miRNA can be used as a miRNA index whose abundance varies depending on the quality of the body fluid sample. That is, it was found that the quality of the body fluid sample can be known by measuring the abundance of the reference miRNA shown in Table 8.
[0175]
　FIG. 15 shows the abundance of hsa-miR-4497 (SEQ ID NO: 40) under the reference condition and the condition in which the standing time and temperature under the serum state were changed (8 conditions in total). The abundance of hsa-miR-4497 (SEQ ID NO: 40) remained high as the degree of deterioration increased. For example, when determining the deterioration of sample quality when the sample is left at 28 ° C for 1 hour or more, or when it is left at 24 ° C for 2 hours, the abundance of hsa-miR-4497 of 13.6 is set as a threshold value. However, if the abundance of hsa-miR-4497 in a certain body fluid sample exceeds that value, it can be determined that the sample is deteriorated, that is, the sample is of poor quality.
[0176]
　In addition, FIG. 16 shows the abundance of hsa-miR-744-5p (SEQ ID NO: 9) under the reference condition and the condition in which the standing time and temperature under the serum state were changed (8 conditions in total). The abundance of hsa-miR-744-5p (SEQ ID NO: 9) remained high as the degree of deterioration increased. For example, when determining the deterioration of the quality of a body fluid sample caused by allowing serum to stand at room temperature for 2 hours or more, the abundance amount 8.1 of hsa-miR-744-5p is set as a threshold value, and the abundance of hsa-miR-744-5p is set as a threshold value in a certain body fluid sample. If the abundance of hsa-miR-744-5p is lower than that value, it can be determined that the sample is deteriorated, that is, the sample is of poor quality.
[0177]
　Specific examples of the threshold values ​​of the 34 types of reference miRNAs shown in Table 8 that can be set from the results of this Example 7 are shown in Table 9 below together with the average value of the abundance in the reference sample. These thresholds are thresholds that can be used as thresholds for detecting deterioration that occurs in the serum state such as during serum storage. For example, after separating serum from a clinical blood sample, until it is cryopreserved, or until it is cryopreserved. These thresholds can be preferably used when it takes time to store the product without freezing and perform expression analysis. If you measure the reference miRNA in the body fluid sample for which you want to evaluate the quality, convert the measured value to a logarithm with a base of 2, and make appropriate corrections to standardize the data between samples, and compare the values ​​with these thresholds. Good. Depending on how strict the determination is, the threshold value ± α (α is an arbitrary numerical value, for example, about 0.5 to 3) shown in Table 9 may be set as the threshold value.
[0179]
Detection of deterioration of serum in a short time with a plurality of miRNAs
　It is also possible to determine the deterioration of body fluid sample quality by combining any two types of reference miRNAs instead of a single miRNA.
[0180]
　The abundance of hsa-miR-4497 (SEQ ID NO: 40) and hsa-miR-744-5p (SEQ ID NO: 9) under the reference conditions of Example 7 and the conditions of allowing the serum to stand at room temperature (24 ° C.) for 2 hours. used. The individual abundances of these miRNAs under each condition are as shown in FIG. 17, and the difference in abundance of these two types of miRNAs under each condition was calculated as shown in FIG. As shown in Table 9 and FIG. 17, hsa-miR-4497 has a high value due to deterioration of the sample caused by the serum state, and hsa-miR-744-5p has a low value due to the deterioration of the sample caused by the serum state. The abundance of hsa-miR-4497 in the undegraded sample is higher than that of hsa-miR-744-5p. In the body fluid sample in good quality (reference conditions), the difference between the abundance of hsa-miR-4497 and the abundance of hsa-miR-744-5p is small, but it was allowed to stand at 24 ° C for 2 hours. In the body fluid sample in a deteriorated state, the difference in the abundance between the two becomes large. When determining the deterioration of body fluid sample quality due to standing at 24 ° C in the serum state, for example, the threshold value of the difference in the abundance of these two types of miRNA is set to 4, and in a certain body fluid sample, these If the difference in the abundance of miRNA exceeds that value, it can be determined that the sample is deteriorated, that is, the sample is of poor quality.
[0181]
　When similar determinations are made with combinations other than the combination of hsa-miR-4497 (SEQ ID NO: 40) and hsa-miR-744-5p (SEQ ID NO: 9), the two reference miRNAs are shown in Table 9. Among the reference miRNAs, one type may be selected from the reference miRNAs that change to a low value, and one type may be selected from the reference miRNAs that change to a high value. In the case where the abundance of the reference miRNA that changes to a low value under the reference condition is higher than the abundance of the reference miRNA that changes to a high value under the reference condition and the abundance of both approaches due to deterioration, FIG. As in the example, when the difference in abundance falls below an arbitrarily determined threshold value, it can be determined that the quality is poor. On the contrary, in the case of a combination in which the abundance of the reference miRNA that changes to a low value under the reference condition is lower than the abundance of the reference miRNA that changes to a high value under the reference condition, and the abundance of both is separated due to deterioration. When the difference in abundance exceeds an arbitrarily determined threshold value, it can be determined that the quality is poor. However, the combination is not limited to the combination of the reference miRNAs described in this example, and a plurality of reference miRNAs that change to a low value or a plurality of reference miRNAs that change to a high value are selected and combined from Table 9. It is also possible to determine the quality of the body fluid sample (whether or not deterioration has occurred in a short period of time in the serum state) by integrating the judgment results based on the individual reference miRNAs.
[0182]
Deterioration of serum sample detected by quantitative RT-PCR
(sample preparation for detection of deterioration by standing at 4 ° C for a long time in serum state)
　Blood was collected from two healthy subjects, two blood collection tubes each. All of them were allowed to stand at room temperature (24 ° C.) for 0.5 hours, and then centrifuged to obtain serum. For one, 300 μL of the obtained serum was dispensed within 10 minutes after centrifugation and stored in a freezer at -80 ° C (this is the standard condition). For the remaining one, the obtained serum was allowed to stand at 4 ° C. for 24 hours, and after the time was reached, 300 μL of serum was dispensed and stored in a freezer at −80 ° C.
[0183]
(Preparation of sample RNA and measurement of miRNA abundance)
　The serum prepared as described above and stored in the freezer was simultaneously thawed, and RNA contained in the serum sample (hereinafter referred to as sample RNA) was extracted. A “3D-Gene” RNA extraction reagent from liquid sample kit (manufactured by Toray Industries, Inc.) was used for extraction. UNIFILTER 96Well (GE Healthcare) was used for purification.
[0184]
　The abundance of hsa-miR-204-3p (SEQ ID NO: 1) was measured using TaqMan® Small RNA Assays (Life Technologies) for RNA under two conditions for each of the two individuals according to the company's protocol. In addition, a dilution series was created with the standard substance of hsa-miR-204-3p, and a calibration curve was created. The concentration of hsa-miR-204-3p under each condition was calculated from the obtained Ct value and its calibration curve.
[0185]
　FIG. 19 shows the abundance of hsa-miR-204-3p (SEQ ID NO: 1) under the conditions of standing at 4 ° C. for 24 hours under the reference conditions and the serum state. The abundance of hsa-miR-204-3p remained high as the degree of deterioration increased. For example, when determining the deterioration of sample quality when the sample is allowed to stand at 4 ° C for 24 hours or more, the abundance of hsa-miR-204-3p of 0.002 atto mole / μL is set as a threshold value in a certain body fluid sample. If the abundance of hsa-miR-204-3p exceeds that value, it can be determined that the sample is deteriorated, that is, the sample is of poor quality.
The scope of the claims
[Claim 1]
　A method for evaluating the quality
　of a body fluid sample, in which the abundance of one or more reference miRNAs selected from miRNAs consisting of the base sequences shown by SEQ ID NOs: 1 to 16 and 37 to 61 in the body fluid sample is measured. The measurement step; and the
　index value calculated from the abundance of the one or more reference miRNAs obtained in the measurement step or the abundance of the plurality of reference miRNAs are compared with a predetermined threshold value. The
method for determining the quality of a body fluid sample, which comprises a determination step;
[Claim 2]
　The method of claim 1, wherein the index value is the difference or ratio of the abundance of two arbitrarily selected reference miRNAs.
[Claim 3]
　When the abundance of the miRNA consisting of the base sequences shown in SEQ ID NOs: 1, 5 and 7 exceeds the first threshold value or falls below the second threshold value, the quality of the body fluid sample is poor. The miRNA shown is the abundance of the miRNA consisting of the base sequences shown by SEQ ID NOs: 2, 3, 4, 6, 11, 37 to 43, 45, 46, 49, 51, 52, 54, and 58 in the body fluid sample. Is a miRNA indicating that the quality of the body fluid sample is poor when the value exceeds the threshold value, and SEQ ID NOs: 8, 9, 10, 12 to 16, 44, 47, 48, 50, 53, 55 to 57, 59 to 61. The method according to claim 1 or 2, wherein the miRNA consisting of the base sequence shown by is a miRNA indicating that the quality of the body fluid sample is poor when the abundance in the body fluid sample is below the threshold value.
[Claim 4]
　The measurement step is a probe for capturing one or more reference miRNAs selected from miRNAs consisting of the nucleotide sequences represented by SEQ ID NOs: 1 to 16 and 37 to 61 immobilized on the support, and a labeling substance. Any one of claims 1 to 3, which is a step of measuring the abundance of the one or more reference miRNAs in the body fluid sample by contacting the nucleic acid sample derived from the body fluid sample labeled with (1) and performing hybridization. The method described in.
[Claim 5]
　Claim 1 further includes a correction step of correcting the measured value of the abundance of the one or a plurality of reference miRNAs obtained in the measurement step, and the determination step is carried out using the corrected abundance value. The method according to any one of 4 to 4.
[Claim 6]
　Any one of claims 1 to 5, which comprises measuring the abundance of one or more reference miRNAs in the body fluid sample and simultaneously measuring the abundance of the target miRNA in the body fluid sample in the measurement step. The method described in.
[Claim 7]
　The measurement step selects one or more reference miRNAs selected from a probe for capturing the target miRNA immobilized on the support and a miRNA consisting of the nucleotide sequences shown in SEQ ID NOs: 1 to 16 and 37 to 61. A step of contacting a probe for capture with a nucleic acid sample derived from a body fluid sample labeled with a labeling substance to perform hybridization, and measuring the abundance of the target miRNA and the one or more reference miRNAs in the body fluid sample, respectively. The method according to claim 6.
[Claim 8]
　6. The claim 6 or 7, further comprising a correction step of correcting the measured value of the abundance of the target miRNA in the body fluid sample obtained in the measuring step and the measured value of the abundance of the one or a plurality of reference miRNAs. the method of.
[Claim 9]
　The method according to any one of claims 1 to 8, wherein the body fluid sample is whole blood, serum or plasma.
[Claim 10]
　From
　miRNA consisting of the base sequences shown by SEQ ID NOs: 1 to 16 and 37 to 61, measured using RNA samples prepared from body fluid samples on one or more computers in order to evaluate the quality of body fluid samples. Amount of one or more selected reference miRNAs abundance in a body fluid sample A measurement value acquisition step;
　calculated from the abundance of one or more reference miRNAs or the abundance of multiple reference miRNAs
A program for executing a determination step of determining the quality of a body fluid sample by comparing the index value to be measured with a threshold value arbitrarily determined in advance .
[Claim 11]
　A computer-readable recording medium on which the program according to claim 10 is recorded.
[Claim 12]
　A chip for evaluating miRNA quality, which comprises a support on which a probe for capturing one or more reference miRNAs selected from miRNAs consisting of the nucleotide sequences shown in SEQ ID NOs: 1 to 16 and 37 to 61 is immobilized.