Method and apparatus for analyzing gene mutations specific to the site of a tumor.

Abstract

This invention provides a method for analyzing tumor-specific gene mutations in subjects with multiple tumors, based on gene mutation information identified by ctDNA testing. [Solution] A step of obtaining first gene mutation information identified by ctDNA testing of the subject, second gene mutation information output by analyzing images of a first target area in the subject, and third gene mutation information output by analyzing images of a second target area in the subject that is different from the first target area, and A step of determining whether a tumor-specific gene mutation included in the first gene mutation information is related to a gene mutation in the first target site for imaging included in the second gene mutation information, or a gene mutation in the second target site for imaging included in the third gene mutation information. A method for analyzing gene mutations, comprising the following:

Description

Technical Field

[0001] The embodiments disclosed in this specification and the drawings relate to a method and an apparatus for analyzing gene mutations specific to the site where a tumor is present.

Background Art

[0002] As tumors grow and evade the immune system, they usually accumulate gene mutations. Certain cancers, such as lung cancer, bladder cancer, breast cancer, and melanoma, may contain more than 500 mutations. There are specific genomic loci that are known to frequently mutate in various cancers, which are generally called "hotspots". For example, the KRAS gene mutations commonly observed in colorectal cancer and lung cancer, and other "long-tail" hotspot mutations in various cancer genes. Other genes associated with a concentration of mutation hotspots include BRAF found in 50% of melanoma patients (90% of this mutation is V600E), the BCR / Abl translocation found in 95% of CML patients, IDH1 found in 70% - 90% of glioma / glioblastoma patients, and p53 mutations found in many cancers. By detecting these gene mutations, it becomes possible to easily and highly accurately perform targeted drug delivery, treatment monitoring, early cancer screening, etc.

[0003] As a method for detecting this gene mutation, liquid biopsy, which is a diagnostic method using a patient's body fluid, has attracted attention and can be applied to the selection of diverse treatment methods and early detection. Liquid biopsy can be repeatedly collected with less invasiveness instead of surgically collecting biopsy specimens from the primary tumor or metastatic tumor, which requires invasive procedures. Therefore, it has the advantage of being able to grasp the changes in tumor characteristics in real time due to treatment and can also cover "tumor heterogeneity". In liquid biopsy, various components can be the measurement targets, but from the perspective of enabling highly accurate detection, ctDNA (circulating tumor DNA) is often selected as the measurement target.

[0004] Circulating tumor DNA (ctDNA) refers to tumor DNA that is present in bodily fluids such as blood and cerebrospinal fluid and is released outside of cells. ctDNA is usually mixed with free DNA derived from normal cells in the blood, also known as cfDNA (cellfree DNA). ctDNA can be easily obtained from blood and other sources, enabling minimally invasive acquisition of tumor-derived DNA and allowing for highly accurate prediction of gene mutations.

[0005] On the other hand, when a patient has multiple tumors, necrotic cells from multiple tumors are mixed in bodily fluids, including blood. Even if ctDNA testing is performed on this bodily fluid as a sample and tumor gene mutations can be identified, it can be difficult to determine which tumor the gene mutation originates from. Furthermore, metastatic tumors generally have the same gene mutations as the primary tumor in the early stages, but acquire their own unique gene mutations as they worsen and progress. Therefore, even when a tumor has metastasized, it can be difficult to determine which tumor the gene mutation originates from. Consequently, when a patient has multiple tumors, ctDNA testing alone cannot accurately identify gene mutations specific to each tumor. This raises concerns that this may result in disadvantages for the patient, such as the inability to present them with medications that are specifically effective against each tumor. [Prior art documents] [Patent Documents]

[0006] [Patent Document 1] Special Publication No. 2022-502343 [Overview of the project] [Problems that the invention aims to solve]

[0007] Traditionally, a method called radiogenomics has been known, which uses image features extracted from radiographic images of tumors to determine the presence or absence of gene mutations in tumors. However, this method has low accuracy, and in particular, the reliability of the results in determining gene mutations originating from tumors in subjects with multiple tumors is low.

[0008] One of the problems that the embodiments disclosed herein and in the drawings aim to solve is to enable the analysis of tumor-specific gene mutations in subjects with multiple tumors, based on gene mutation information identified by ctDNA testing. However, the problems that the embodiments disclosed herein and in the drawings aim to solve are not limited to the above problem. Problems corresponding to the effects of each configuration shown in the embodiments described later can also be positioned as other problems. [Means for solving the problem]

[0009] The method for analyzing gene mutations according to the embodiment includes the steps of obtaining first gene mutation information identified by a ctDNA test of a subject, second gene mutation information output by analyzing an image of a first target site in the subject, and third gene mutation information output by analyzing an image of a second target site in the subject that is different from the first target site, and determining whether a tumor-specific gene mutation included in the first gene mutation information is related to a gene mutation in the first target site included in the second gene mutation information, or a gene mutation in the second target site included in the third gene mutation information.

[0010] The apparatus for analyzing gene mutations according to the embodiment includes: an acquisition unit that acquires first gene mutation information identified by a ctDNA test of a subject; second gene mutation information output by analyzing an image of a first target site in the subject; and third gene mutation information output by analyzing an image of a second target site in the subject that is different from the first target site; and a determination unit that determines whether a tumor-specific gene mutation included in the first gene mutation information is related to a gene mutation in the first target site included in the second gene mutation information, or a gene mutation in the second target site included in the third gene mutation information. [Brief explanation of the drawing]

[0011] [Figure 1] Figure 1 shows an example of a flow chart of a method for analyzing gene mutations according to the first embodiment. [Figure 2] Figure 2 shows the results obtained by performing the gene mutation analysis method according to the first embodiment on patients suffering from lung cancer and pancreatic cancer. [Figure 3] Figure 3 shows the results obtained by performing the gene mutation analysis method according to the first embodiment on patients suffering from lung cancer, pancreatic cancer, and other undiscovered tumors. [Figure 4] Figure 4 shows the results of evaluating the therapeutic effect of a drug on patients with tumors by performing a gene mutation analysis method according to the first embodiment. [Modes for carrying out the invention]

[0012] The following describes in detail, with reference to the drawings, an embodiment of a method for analyzing gene mutations and an apparatus for analyzing gene mutations.

[0013] (First embodiment) A method for analyzing gene mutations according to the first embodiment includes the steps of obtaining first gene mutation information identified by a ctDNA test of a subject, second gene mutation information output by analyzing an image of a first target site in the subject, and third gene mutation information output by analyzing an image of a second target site different from the first target site in the subject, and determining whether a tumor-specific gene mutation included in the first gene mutation information is related to a gene mutation in the first target site included in the second gene mutation information, or a gene mutation in the second target site included in the third gene mutation information. This method may be an in vitro method, a diagnostic aid, or the like.

[0014] The method for analyzing gene mutations according to the first embodiment includes the steps of obtaining gene mutation information identified by a ctDNA test of the subject, gene mutation information output by analyzing an image of a first target area in the subject, and gene mutation information output by analyzing an image of a second target area in the subject that is different from the first target area.

[0015] In the method for analyzing gene mutations according to the first embodiment, the "ctDNA test" is not particularly limited as long as it is a test capable of detecting tumor-specific gene mutations in ctDNA (e.g., point mutations, indel mutations, HBV integration, etc.), and can be performed according to known methods, for example, by PCR-based hotspot mutation detection methods, capture sequencing, etc.

[0016] The gene mutation information identified by the "ctDNA test" in the method for analyzing gene mutations according to the first embodiment includes information on tumor-specific gene mutations possessed by the subject of the "ctDNA test". The format of the output of such information is not particularly limited, and may be, for example, a record in which the presence or absence of tumor-specific gene mutations is determined for each specific region (e.g., a gene locus) of the subject's genome.

[0017] The method for obtaining the result of "ctDNA test" in the method for analyzing gene mutations according to the first embodiment is not particularly limited. The person who conducts the method may obtain the test result by himself / herself, or if there is an external institution capable of appropriately performing the "ctDNA test", the test may be委托 to the institution to obtain the test result. Also, if there is a previously obtained test result, it may be referred to and used.

[0018] The measurement sample used in the "ctDNA test" in the method for analyzing gene mutations according to the first embodiment is not particularly limited as long as it contains ctDNA, but is preferably one that can be obtained from the subject with minimal invasion. Such measurement samples specifically include blood, urine, cerebrospinal fluid, saliva, semen, bile, pleural effusion, ascites, feces, vaginal fluid, etc., and preferably blood.

[0019] The "subject" in the method for analyzing gene mutations according to the first embodiment is not particularly limited as long as it has multiple tumors. For example, mammals such as humans, primates including chimpanzees, pet animals such as dogs and cats, livestock animals such as cows, horses, sheep, and goats, and rodents such as mice and rats can be mentioned. The "subject" in the method for analyzing gene mutations according to the first embodiment is preferably a human.

[0020] The "image" in the method for analyzing gene mutations according to the first embodiment is not particularly limited. For example, radiographic images, magnetic resonance images, ultrasonic images, etc. can be mentioned, and preferably radiographic images. The method for taking this image is not particularly limited. For example, an operator such as a doctor (e.g., a radiologist, etc.) or a diagnostic radiographer may operate a device capable of taking the image to take the image.

[0021] In the method for analyzing gene mutations according to the first embodiment, the "image" may be analyzed by dividing it into a plurality of regions. For example, the "image" may be divided by a grid (mesh) having a predetermined shape and scale. The grid may, for example, correspond one-to-one to pixels, or a plurality of pixels may be included in the grid.

[0022] When the "image" in the method for analyzing gene mutations according to the first embodiment is a planar image, the grid is, for example, square. The grid may have a shape other than square. The grid may have a shape surrounded by straight lines such as a rectangle or a regular polygon other than square. When the "image" in the method for analyzing gene mutations according to the first embodiment is a three-dimensional image, the grid is, for example, a cube, but may also be a rectangular parallelepiped other than a cube, or may have other shapes.

[0023] In the method for analyzing gene mutations according to the first embodiment, the method for analyzing the image of the imaging target site is not particularly limited. For example, it can be performed by calculating image feature amounts. In this case, the image feature amounts may be calculated for each single image, or may be calculated for each of a plurality of regions. The image feature amounts are not particularly limited as long as they can determine whether the imaging target site has gene mutations. For example, they may be various image feature amounts handled in radiogenomics (radiology genomics: a science that systematically handles a large amount of information related to genes).

[0024] In the method for analyzing gene mutations according to the first embodiment, the gene mutation information output by analyzing the image of the imaging target site includes information capable of determining the presence or absence of gene mutations in the imaging target site. The format of this output is not particularly limited. For example, for each specific region (e.g., gene locus, etc.) of the genome of the subject, it may be described whether there is a gene mutation, or it may be described the class classification of gene mutations, or it may be described the estimated probability of gene mutations, or it may be described by combining these.

[0025] The method for calculating the estimated probability of this gene mutation is not particularly limited and can be calculated according to known methods. For example, it can be calculated by further probability calibration of the results output by an appropriate radiogenomics model.

[0026] In the method for analyzing gene mutations according to the first embodiment, the image of a first target site is analyzed, and the image of a second target site different from the first target site is analyzed. Here, "different" includes not only cases where the organ that is the first target site and the organ that is the second target site are not the same organ, but also cases where, even if the organ that is the first target site and the organ that is the second target site are the same organ, the gene mutation information output by analyzing the image of the first target site and the gene mutation information output by analyzing the image of the second target site different from the first target site are not the same.

[0027] The "target site for imaging" in the method for analyzing gene mutations according to the first embodiment is not particularly limited as long as it is a site where a tumor is present or has been present in the past. Such tumors may be primary or metastatic. Examples of such tumors include carcinomas (malignant epithelial tumors), sarcomas (malignant non-epithelial tumors), and specifically include lung cancer, colorectal cancer, breast cancer, prostate cancer, liver cancer, brain cancer, kidney cancer, ovarian cancer, stomach cancer, skin cancer, bone cancer, gastric cancer, breast cancer, pancreatic cancer, glioma, glioblastoma, hepatocellular carcinoma, papillary renal carcinoma, head and neck squamous cell carcinoma, melanoma, and the like.

[0028] The method for analyzing gene mutations according to the first embodiment includes a step of determining whether a tumor-specific gene mutation included in the gene mutation information identified by ctDNA testing is related to a gene mutation in a first target site or a gene mutation in a second target site. This determination may be made, for example, by determining that if a gene mutation is determined to be present by ctDNA testing and the same gene mutation is also determined to be present in the first target site or the second target site, the tumor present in the target site where the same gene mutation was determined to be present is found to have that gene mutation, and the tumor present in the target site where the same gene mutation was not determined to be absent is found to have no such gene mutation.

[0029] The method for analyzing gene mutations according to the first embodiment may further include a step of correcting information regarding the presence or absence of gene mutations in the target area, which is included in at least one of the gene mutation information output by analyzing an image of a first target area and the gene mutation information output by analyzing an image of a second target area different from the first target area.

[0030] Correction of information regarding the presence or absence of gene mutations in the target area may include optimization of the gene mutation information output based on a pre-set threshold used to determine the presence or absence of gene mutations. Such optimization can be performed, for example, by correcting a judgment result that indicates a mutation is present to one that indicates no mutation when the estimated probability of the outputted gene mutation is smaller than a predetermined threshold.

[0031] Furthermore, the correction of information regarding the presence or absence of gene mutations in the target area may include the optimization of the threshold. Such optimization can be performed, for example, by determining the optimal threshold based on values ​​calculated using image data with / without gene mutations, separate from the training data, for a trained radiogenomics model. Also, for example, for gene mutations where all of the judgment results for the presence or absence of gene mutations output by each radiogenomics model indicate no mutation, it is possible to use the estimated probability of the gene mutation output by other radiogenomics models as the threshold.

[0032] Furthermore, if the analysis of images of the target area includes the calculation of image features, the correction of information regarding the presence or absence of gene mutations in the target area may include the optimization of gene mutation information output based on correction coefficients. Such optimization can be performed, for example, by determining the optimal correction coefficient for a trained radiogenomics model based on values ​​calculated using image data with / without gene mutations, separate from the training data.

[0033] The method for analyzing gene mutations according to the first embodiment includes a step of determining whether a tumor-specific gene mutation included in the gene mutation information identified by ctDNA testing is related to a gene mutation in a first target site or a gene mutation in a second target site. If, in this step, it is determined that neither the gene mutation in the first target site nor the gene mutation in the second target site is related to the tumor-specific gene mutation, the method for analyzing gene mutations according to the first embodiment may include a step of indicating that the tumor-specific gene mutation is located in a new site that is neither the first target site nor the second target site.

[0034] The method for analyzing gene mutations according to the first embodiment makes it possible to identify gene mutations specific to the site where a tumor is located. If drug therapy is performed on the tumor and the identified gene mutation changes from present to absent, it is possible to predict that the drug will have a therapeutic effect on the tumor. Therefore, the method for analyzing gene mutations according to the first embodiment may further include the step of determining that if it is determined that the tumor-specific gene mutation is present in any target imaging site at a first determination time, and if it is determined that the tumor-specific gene mutation is not present in the target imaging site at a second determination time after any time has elapsed from the first measurement time, then it is determined that the drug applied to the subject up to the second determination time has a therapeutic effect on the disease associated with the tumor-specific gene mutation.

[0035] Examples of such drugs include molecularly targeted drugs and cancer immune checkpoint inhibitors.

[0036] Figure 1 is a diagram showing an example of a flow chart of a method for analyzing gene mutations according to the first embodiment. The method for analyzing gene mutations shown in Figure 1 includes the steps of (1) obtaining ctDNA test results from a patient with multiple tumors, (2) obtaining a tumor image at one site and running a radiogenomics model, (3) obtaining a tumor image at another site and running a radiogenomics model, and (4) determining tumor-specific gene mutations. Step (1) may then include a step of obtaining first gene mutation information including tumor-specific gene mutations. Step (2) may then include a step of obtaining second gene mutation information including gene mutations at the aforementioned site. Step (3) may then include a step of obtaining third gene mutation information including gene mutations at another site. The determination in step (4) may include a step of confirming whether the tumor-specific gene mutations included in the first gene mutation information are related to the gene mutations at the first target site included in the second gene mutation information, or to the gene mutations at the second target site included in the third gene mutation information.

[0037] (Second embodiment) The apparatus for analyzing gene mutations according to the second embodiment includes an acquisition unit that acquires first gene mutation information identified by a ctDNA test of a subject, second gene mutation information output by analyzing an image of a first target site in the subject, and third gene mutation information output by analyzing an image of a second target site in the subject that is different from the first target site, and a determination unit that determines whether a tumor-specific gene mutation included in the first gene mutation information is related to a gene mutation in the first target site included in the second gene mutation information, or a gene mutation in the second target site included in the third gene mutation information.

[0038] The meanings and references of the terms used to describe the second embodiment are the same as those used to describe the first embodiment.

[0039] According to at least one embodiment described above, it is possible to analyze tumor-specific gene mutations in a subject with multiple tumors based on gene mutation information identified by ctDNA testing.

[0040] While several embodiments have been described, these embodiments are presented as examples only and are not intended to limit the scope of the invention. These embodiments can be implemented in a variety of other forms, and various omissions, substitutions, modifications, and combinations of embodiments are possible without departing from the spirit of the invention. These embodiments and their variations are included in the scope and spirit of the invention, as well as in the claims and their equivalents.

[0041] The present invention will be specifically described based on the following examples, but the present invention is not limited to these examples.

[0042] Determination of tumor-specific gene mutations in patients with multiple tumors. We obtained ctDNA test results from patients with lung cancer and pancreatic cancer from publicly available databases.

[0043] Based on the acquired ctDNA test results, images were taken of organs where tumors were predicted to be present, and the presence or absence of gene mutations in the tumors was determined using a radiogenomics model following these steps: Image features (Radiomics features, etc.) were calculated from the training image data. A radiogenomics model that classifies the presence or absence of gene mutations in tumors was trained using these image features as input. Subsequently, image features (Radiomics features, etc.) were calculated from the validation image data. These image features were input into the trained radiogenomics model to classify the presence or absence of gene mutations in tumors.

[0044] The results of the determination of the presence or absence of gene mutations using radiogenomics models were corrected using the following procedure. First, if the estimated probability of a gene mutation output by each radiogenomics model (lung cancer, pancreatic cancer) was smaller than a predetermined threshold, the output determination result was reversed. As the threshold, a value determined using image data with / without gene mutations, separate from the training data, was used for the trained radiogenomics model. For gene mutations where all the determination results for the presence or absence of gene mutations output by each radiogenomics model were "no mutation," the estimated probability of the gene mutation output by the other radiogenomics model was used as the threshold, and if it was larger than the predetermined threshold, the output determination result was reversed.

[0045] Furthermore, using image data with / without gene mutation labels, separate from the training data, the correction coefficient α for the estimated gene mutation output by the radiogenomics model was optimized. The determination of whether or not a gene mutation was present was determined by the relationship between the output estimated gene mutation probability × correction coefficient and a threshold. The results are shown in Table 1 below. In the gene mutation column of the table, "Genetic mutation present" is indicated as "1" and "Genetic mutation absent" as "0".

[0046] [Table 1] *1: The numbers in parentheses represent the estimated probabilities that were output. *2: If the estimated probability is greater than or equal to the threshold, it is set to 1; otherwise, it is set to 0.

[0047] Determination of the presence or absence of undetected tumor gene mutations in patients with tumors. For gene mutations that were determined to be present by ctDNA (true value), but for which all results from each modified radiogenomics model indicated no gene mutation, we considered the possibility that ctDNA originating from an undiscovered tumor was detected. Therefore, we conducted a screening for the presence or absence of gene mutations using radiogenomics models to determine the presence or absence of gene mutations in undiscovered tumors.

[0048] Determining the therapeutic effect of drugs on patients with tumors. Based on the obtained ctDNA test results and the results of each radiogenomics model indicating the presence or absence of gene mutations, the therapeutic effect of the drug on patients with tumors was determined by determining that the treatment was effective if no tumor growth was observed after treatment.

[0049] Based on the embodiments disclosed herein and in the drawings, it is possible to analyze tumor-specific gene mutations in subjects with multiple tumors based on gene mutation information identified by ctDNA testing.

Claims

1. A step of obtaining first gene mutation information identified by ctDNA testing of the subject, second gene mutation information output by analyzing images of a first target area in the subject, and third gene mutation information output by analyzing images of a second target area in the subject that is different from the first target area, and A step of determining whether a tumor-specific gene mutation included in the first gene mutation information is related to a gene mutation in the first target site for imaging included in the second gene mutation information, or a gene mutation in the second target site for imaging included in the third gene mutation information. A method for analyzing gene mutations, comprising [the specified elements].

2. The method according to claim 1, further comprising the step of modifying information regarding the presence or absence of gene mutations in the target area, which is included in at least one of the second gene mutation information and the third gene mutation information.

3. The method according to claim 1, wherein if the determination step determines that neither the gene mutation in the first target site for imaging nor the gene mutation in the second target site for imaging is related to the tumor-specific gene mutation, the method further includes the step of indicating that the tumor-specific gene mutation is located in a new site that is neither the first target site nor the second target site for imaging.

4. The method according to claim 1 or 3, further comprising the step of determining that, if it is determined that the tumor-specific gene mutation is present in any target area at a first determination time, and if it is determined that the tumor-specific gene mutation is not present in the target area at a second determination time after any time has elapsed from the first measurement time, then determining that the drug applied to the subject up to the second determination time has a therapeutic effect on the disease associated with the tumor-specific gene mutation.

5. An acquisition unit that acquires first gene mutation information identified by ctDNA testing of the subject, second gene mutation information output by analyzing images of a first target area on the subject, and third gene mutation information output by analyzing images of a second target area on the subject that is different from the first target area. A determination unit that determines whether a tumor-specific gene mutation included in the first gene mutation information is related to a gene mutation in the first target imaging site included in the second gene mutation information, or a gene mutation in the second target imaging site included in the third gene mutation information, A device equipped with a mechanism for analyzing gene mutations.

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