WO2025141758A1 - Procédé d'inspection d'échantillon et système d'inspection d'échantillon - Google Patents
Procédé d'inspection d'échantillon et système d'inspection d'échantillon Download PDFInfo
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- WO2025141758A1 WO2025141758A1 PCT/JP2023/046907 JP2023046907W WO2025141758A1 WO 2025141758 A1 WO2025141758 A1 WO 2025141758A1 JP 2023046907 W JP2023046907 W JP 2023046907W WO 2025141758 A1 WO2025141758 A1 WO 2025141758A1
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- blood
- gdna
- amount
- blood collection
- nucleic acid
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
Definitions
- the concentration and amount of nucleic acid and the amount of impurities are measured by measuring absorbance using a spectrophotometer or by staining the nucleic acid with a fluorescent dye and measuring the fluorescence intensity.
- Indicators of good chemical purity of DNA are an A260/A280 value of 1.8-2.0 and an A260/A230 value of greater than 1.0.
- a variety of specialized blood collection tubes are manufactured and sold to prevent blood cells from breaking down. However, at present, all of them have a limit of how long they can preserve blood cells, at around two weeks.
- the present invention can provide more accurate and rapid results than conventional methods by reducing the time required to obtain test results and the amount of material required for testing. Problems, configurations, and effects other than those described above will become clear from the description of the examples below.
- FIG. 1 is a diagram showing an overview of a specimen testing system according to a first embodiment.
- 4 is a flowchart illustrating a process performed by a management system in the sample testing system of the first embodiment.
- FIG. 1 is a graph showing the relationship between the gDNA concentration in plasma and the number of days since blood was collected from a sample in a certain blood collection tube.
- FIG. 4 is a graph showing the relationship between the gDNA concentration in plasma and the number of days elapsed since blood was collected from a sample in a blood collection tube different from that in FIG. 3 .
- FIG. 5 is a graph showing the relationship between the gDNA concentration in plasma and the number of days elapsed since blood was collected from a sample in a blood collection tube different from that in FIGS.
- FIG. 4 is a graph showing the relationship between the number of days elapsed since blood was collected from the blood collection tube in FIG. 3 and the absorbance of plasma.
- FIG. 5 is a graph showing the relationship between the number of days elapsed since blood was collected from the blood collection tube in FIG. 4 and the absorbance of plasma.
- FIG. 6 is a graph showing the relationship between the number of days elapsed since blood was collected from the blood collection tube in FIG. 5 and the absorbance of plasma.
- FIG. 13 is a graph showing an example of the correlation between absorbance and the amount of gDNA mixed in for each type of blood collection tube.
- FIG. 13 is a graph showing the relationship between saturation and gDNA amount of a plasma sample in a blood collection tube.
- FIG. 13 is a graph showing the relationship between the brightness of a plasma sample in a blood collection tube and the amount of gDNA.
- FIG. 13 is a diagram showing an overview of a specimen testing system according to a second embodiment.
- FIG. 1 shows sample conditions used to investigate the effect of gDNA contamination on mutation detection.
- FIG. 1 shows the results of evaluating the difference in mutation rate (VAF) relative to the amount of gDNA contamination.
- FIG. 1 shows the results of evaluating the difference in mutation rate (VAF) relative to the amount of gDNA contamination.
- FIG. 13 shows the results of evaluating the difference in mutation rate (VAF) relative to the amount of gDNA contamination.
- FIG. 13 is a diagram showing an overview of a specimen testing system according to a third embodiment.
- FIG. 13 is a diagram showing an example of a consumables order screen in the sample testing
- Example 1 A sample testing method and a sample testing system according to a first embodiment of the present invention will be described with reference to Figs. 1 to 11 .
- FIG. 1 is a diagram showing an overview of the specimen testing system of the first embodiment.
- the specimen testing system 1 shown in FIG. 1 is a system for testing specimens made of blood, and includes a plasma fractionation section 11, a blood condition confirmation section 14, a nucleic acid extraction section 17, a nucleic acid extraction QC section 20, an assay setup section 23, a post-setup QC section 26, a measurement section 29, a data analysis section 32, and a management system 35.
- This specimen testing system 1 solves the problem of unnecessary NGS and nucleic acid extraction being performed because gDNA is mixed in during cfDNA extraction, reducing the sensitivity of mutation detection and making it impossible to detect.
- the state of hemolysis in which red blood cells in the blood are destroyed and the hemoglobin (blood pigment) is eluted, is measured using color information such as red, green, and blue in an image, or color information such as saturation, hue, and brightness, and the absorbance of hemoglobin at around 410 to 430 nm.
- color information such as red, green, and blue in an image, or color information such as saturation, hue, and brightness
- absorbance of hemoglobin at around 410 to 430 nm is measured using color information such as red, green, and blue in an image, or color information such as saturation, hue, and brightness, and the absorbance of hemoglobin at around 410 to 430 nm.
- gDNA leakage due to the destruction of white blood cells is indirectly detected, and the amount of unnecessary gDNA contained during nucleic acid extraction and the unnecessary components that will be given to the enzyme reaction after nucleic acid extraction are calculated, thereby determining whether or not to perform the nucleic acid extraction step and NGS step, thereby solving the above-ment
- the plasma collection unit 11 is a mechanism for collecting plasma from blood, and is composed of, for example, various mechanisms capable of collecting liquids. This plasma collection unit 11 is preferably the entity that performs the plasma collection step of collecting plasma from blood.
- data on the number of days since blood collection and the amount of gDNA contamination after nucleic acid extraction are obtained as known data for each type of blood collection tube. Since the recommended storage conditions differ depending on the type of blood collection tube due to differences in the ingredients of the additives that protect each blood cell component, it is necessary to accumulate data for each type of blood collection tube in advance. This data is accumulated by the manufacturer that provides this management system 35 and may be provided to the user, or the user may perform it independently. Since the storage conditions, transportation conditions of the blood collection tube, and the performance of the nucleic acid extraction reagent differ depending on each user, more accurate management is possible by performing it by the user himself.
- the management system 35 calculates the amount of gDNA from the known data and the blood condition measurement results based on the absorbance measurement results and the data described above in S110 (S135), and proceeds to step S140.
- gDNA is used as the quality to be checked, but this is not limited to these.
- the quantity, length, purity, and structural integrity may be used as indicators for judgment. If the amount of nucleic acid is insufficient, the length is short, the purity is low, and the structural integrity is low, the expected results will not be obtained in the subsequent steps. Therefore, appropriate values for such indicators are determined in step 0).
- the quality information of the nucleic acid obtained here can be combined with information on the type of blood collection tube and blood condition such as hemolysis, etc., shown in Figures 3 to 11, and correlated information can be accumulated to accumulate data and update existing data.
- nucleic acid quality confirmation step it is desirable to further include an improvement step of calculating the amount of gDNA contained in the sample and adding and correcting data used in the prediction step that indicates the relationship between the result obtained in the blood condition confirmation step and the amount of gDNA contained in the blood. It is also desirable to further include an accumulation step of executing the improvement step on a per-test community basis and accumulating data, which uses the data to calculate correlation and makes it possible to calculate the presence of gDNA even in unknown cfDNA collection tubes.
- the calculated gDNA amount is compared with the gDNA amount predicted in the prediction step, and if it is determined that the difference is equal to or exceeds a certain threshold, it is possible that inappropriate processing may have occurred in the steps following the plasma collection step.
- nucleic acid extraction is performed after aspirating the buffy coat, which is mainly composed of white blood cells, or the layer of red blood cells, which is the lower layer
- gDNA can be mixed in from the white blood cells.
- Possible causes of this include, for example, a fault in the CCD camera used as the liquid level detection mechanism, the lighting used for image detection, or a fault in the pressure sensor or capacitance sensor.
- the mechanism for separating plasma or serum such as it not working in the correct position, the dispensing tip not being inserted correctly, or the aspirating speed being inappropriate.
- the management system 35 executes assay setup and measurement using NGS and dPCR by the assay setup unit 23, post-setup QC unit 26, measurement unit 29, and data analysis unit 32 (measurement step for measuring nucleic acids).
- the nucleic acids whose quality has been confirmed are prepared for analysis using measuring devices such as next-generation DNA sequencers (NGS) and digital PCR.
- NGS next-generation DNA sequencers
- digital PCR digital PCR
- nucleic acid extract QC unit 20 when preparation is performed, appropriate confirmation is made through steps performed by the above-mentioned nucleic acid extract QC unit 20 to ensure that the preparation has been performed appropriately. For example, it is confirmed whether there is an appropriate amount of nucleic acid before the amplification of the gene sequence, whether there is an appropriate amount of nucleic acid after amplification, whether there is an appropriate amount of nucleic acid when an adapter is attached and brought into various measuring devices, etc. If the amount is not appropriate, the previous process may be repeated as appropriate or the process may be interrupted, and the management system may be used to control the process so that the analysis is reliably performed by the measuring device.
- the specimen testing method of the first embodiment of the present invention described above includes a prediction step of predicting the amount of gDNA that will be mixed into the collected blood based on data showing the relationship between the number of days since blood collection and the amount of gDNA contained in the blood and the number of days since blood collection, depending on the type of at least one blood collection tube, and a determination step of determining a processing step for the collected blood based on the amount of gDNA that will be mixed in predicted in the prediction step.
- the specimen testing system 1 for testing specimens consisting of blood includes a plasma collection unit 11 for collecting plasma from blood, a nucleic acid extraction unit 17 for extracting nucleic acid from plasma, a measurement unit 29 for measuring the nucleic acid, a data analysis unit 32 for analyzing the measurement results of the measurement unit 29, and a management system 35 for managing the specimen testing system.
- the management system 35 predicts the amount of gDNA that will be mixed into the collected blood based on data showing the relationship between the number of days since blood collection and the amount of gDNA contained in the blood and the number of days since blood collection according to the type of at least one blood collection tube, and determines the processing step in at least one of the plasma collection unit 11 and the nucleic acid extraction unit 17 based on the predicted amount of gDNA that will be mixed in.
- the system also includes a blood condition confirmation step for confirming the condition of the blood, and in the prediction step, the number of days since the pseudo blood collection is calculated from data showing the relationship between the results obtained in the blood condition confirmation step for each type of blood collection tube and the amount of gDNA contained in the blood, and the number of days since the pseudo blood collection is used to predict the amount of gDNA.
- a blood condition confirmation step for confirming the condition of the blood
- the prediction step the number of days since the pseudo blood collection is calculated from data showing the relationship between the results obtained in the blood condition confirmation step for each type of blood collection tube and the amount of gDNA contained in the blood, and the number of days since the pseudo blood collection is used to predict the amount of gDNA.
- the processing step has a setting step for setting a threshold value for the amount of gDNA contained in the blood, and in the determination step, the amount of gDNA mixed in, predicted in the prediction step, is compared with the threshold value to determine the processing step, making it possible to make decisions in accordance with the processing in the subsequent measurement step, and realizing measurements suited to the user environment.
- processing steps including plasma collection processing in the plasma collection unit 11 and nucleic acid extraction processing in the nucleic acid extraction unit 17, and further having a correction step of subtracting the effect of the gDNA amount predicted using the number of days since the pseudo blood collection from the mutation detection value calculated by NGS or dPCR, the accuracy of the decision as to whether or not to carry out subsequent processing steps and what type of processing steps to carry out can be improved with each test, making it possible to construct a testing method and testing system that can realize daily improvements in testing accuracy.
- Example 3 A sample testing method and a sample testing system according to a third embodiment of the present invention will be described with reference to Figs. 17 and 18.
- specimen testing systems 1 and 1A and specimen testing methods of Examples 1 and 2 examples were shown in which a series of testing steps were performed in a system located within a single analytical facility, but the specimen testing system 1B and specimen testing method of this embodiment show a form in which a series of testing steps are performed across multiple facilities.
- FIG. 17 is a diagram showing an overview of the specimen testing system of Example 3.
- the plasma fractionation section 11, blood condition confirmation section 14, nucleic acid extraction section 17, nucleic acid extraction QC section 20, and part of the management system 35B are provided at a sample site 43 of a hospital or the like, and the assay setup section 23, post-setup QC section 26, measurement section 29, data analysis section 32, and part of the management system 35B are provided at a test site 40 of a testing business or the like, in a form in which some processes are concentrated at the test site 40.
- Sample sites 46, 49 have the same configuration as sample site 43 or have more or less.
- the management system 35B shares the start and results of work at sample sites 43, 46, and 49 in multiple hospitals, etc., over a network for the process up to nucleic acid extract QC, and executes consumables management such as analysis planning and forecasting of consumables to be used at the test site 40.
- management system 35B in a cloud or server format, it can be connected via a network to sample sites 43, 46, 49, test site 40, and manufacturer site 52 that manufactures and sells consumables such as reagents and various test parts.
- FIG. 18 is a diagram showing an example of an order screen for consumables in the specimen testing system of Example 3.
- the user selects the selection area 363 of target display area 360 such as the target reagent or container while checking the number in remaining amount display area 366, enters the required number in order amount display area 370, and presses "Order" in instruction area 373, thereby making it possible to order consumables on the cloud.
- manufacturer site 52 can deliver the ordered consumables to test site 40 and sample sites 43, 46, 49 before they are needed.
- the management system 35B can also set flags based on trends in the results (QC results) of each process. This allows for the execution of a warning step in which a flag is set based on trends in the relationship between any two of the plasma fractionation step, blood condition confirmation step, nucleic acid extraction step, measurement step, nucleic acid quality confirmation step, prediction step, and nucleic acid amount calculation step.
- patient information clinical information, results of other tests (tumor markers), blood collection tube, blood collection date, blood collection tube transportation date
- QC results nucleic acid extraction results
- a flag can be raised and the analyst informed. This will enable further improvements in testing accuracy.
- a correlation is found between a blood collection tube and poor QC results, it is possible to detect poor compatibility between the blood collection tube and the nucleic acid extraction reagent, or a faulty lot number for the nucleic acid extraction reagent or blood collection tube lot number. This allows the testing of the blood specimen in question to be suspended or monitored closely, and resampling, etc. to be performed promptly.
- the specimen testing method and specimen testing system of the third embodiment of the present invention also provide substantially the same effects as those of the specimen testing method and specimen testing system of the first embodiment described above.
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Abstract
Le procédé d'inspection d'échantillon selon l'invention comprend : une étape de prédiction qui consiste à prédire la quantité d'ADNg mélangée dans du sang prélevé sur la base du nombre de jours écoulés depuis le prélèvement sanguin, et de données indiquant la relation entre le nombre de jours écoulés depuis le prélèvement sanguin et la quantité d'ADNg compris dans le sang selon le type d'au moins un tube de prélèvement sanguin ; et une étape de détermination qui consiste à déterminer une étape de traitement du sang prélevé sur la base de la quantité d'ADNg à mélanger, prédite dans l'étape de prédiction. L'invention permet ainsi de fournir un procédé d'inspection d'échantillon et un système d'inspection d'échantillon qui permettent d'obtenir des résultats précis et rapides par rapport à l'état de la technique, en réduisant la durée d'obtention d'un résultat d'inspection ainsi que la quantité de substances requises pour une inspection par rapport à l'état de la technique.
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| PCT/JP2023/046907 WO2025141758A1 (fr) | 2023-12-27 | 2023-12-27 | Procédé d'inspection d'échantillon et système d'inspection d'échantillon |
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| PCT/JP2023/046907 WO2025141758A1 (fr) | 2023-12-27 | 2023-12-27 | Procédé d'inspection d'échantillon et système d'inspection d'échantillon |
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