Artificial intelligence assisted precision medicine enhancements to standardized laboratory diagnostic testing
A system and method, the method comprising receiving a laboratory diagnostic testing result associated with a specimen of a subject, the steps of receiving a clinomic profile of the subject, identifying a cohort of similar subjects based at least in part on the clinomic profile of the subject, providing the diagnostic testing results, clinomic profile, and the cohort of similar subjects to a smart output module to generate a personalized, precision medicine based laboratory diagnostic testing result as a smart output and displaying the smart output to a user.
1 . A computer-implemented method for subject monitoring, the method comprising:
obtaining, by a computing system, an initial laboratory result, comprising a measurement of a first characteristic, from an examination of a specimen or an image associated with a subject, wherein at least one laboratory technology is used to determine the initial laboratory result;
obtaining, by the computing system, a first clinomic profile of the subject from a structured clinomic data repository;
comparing, by the computing system, the first clinomic profile with each clinomic profile in the structured clinomic data repository using a subject similarity metric that quantifies a degree to which each clinomic profile in the structured clinomic data repository is similar to the first clinomic profile, wherein the structured clinomic data repository comprises 1000 or more clinomic profiles representing 1000 or more subjects, thereby identifying a subset of clinomic profiles that are similar to the first clinomic profile;
identifying, by the computing system, a second characteristic common to the subset of clinomic profiles;
adjusting a threshold of interpretation, between at least one disease state and a normal state, of the measurement of the first characteristic in the initial laboratory result based on the second characteristic;
issuing, over a computer network, a structured report listing the initial laboratory result and the adjusted threshold of interpretation of the measurement of the first characteristic in the initial laboratory result;
originating, by the computing system, on the basis of the adjusted threshold of interpretation of the measurement of the first characteristic in the initial laboratory result, a request to perform an additional assay on the subject; and
obtaining, by the computing system, responsive to the request, a determination that the additional assay has been performed on the subject, thereby performing subject monitoring.
2 . The computer-implemented method of claim 1 , wherein the first clinomic profile comprises a gender of the subject.
3 . The computer-implemented method of claim 1 , wherein the first clinomic profile comprises a race of the subject.
4 . The computer-implemented method of claim 1 , wherein the first clinomic profile comprises molecular information of the subject.
5 . The computer-implemented method of claim 1 , wherein the first clinomic profile comprises genetic variant information of a specimen from the subject.
6 . The computer-implemented method of claim 1 , wherein the first clinomic profile comprises transcriptome information of a specimen from the subject.
7 . The computer-implemented method of claim 1 , wherein the first clinomic profile comprises genetic variant information and transcriptome information of at least one specimen from the subject.
8 . The computer-implemented method of claim 1 , wherein the first clinomic profile comprises at least one feature derived from an image associated with the subject.
9 . The computer-implemented method of claim 8 , wherein the image associated with the subject is an image of the subject.
10 . The computer-implemented method of claim 8 , wherein the image associated with the subject is an image of a specimen of the subject.
11 . The computer-implemented method of claim 1 , wherein the first clinomic profile comprises a prior result from an examination of a prior specimen associated with the subject.
12 . The computer-implemented method of claim 1 , wherein the obtaining, by the computer system, the first clinomic profile comprises:
a. receiving, by the computing system, a plurality of source records and a structured subject dataset for the subject;
b. extracting, by the computing system, a plurality of data elements from the plurality of source records; and
c. storing, by the computing system, the extracted data elements and the structured subject dataset in the clinomic data repository as the first clinomic profile.
13 . The computer-implemented method of claim 12 , wherein the plurality of source records comprises a structured genetic test report.
14 . The computer-implemented method of claim 13 , wherein the plurality of data elements comprises a genomic variant data element.
15 . The computer-implemented method of claim 12 , wherein the plurality of source records comprises a structured metabolomic test report.
16 . The computer-implemented method of claim 15 , wherein the plurality of data elements comprises a metabolomic data element.
17 . The computer-implemented method of claim 12 , wherein the plurality of source records comprises a structured transcriptome test report.
18 . The computer-implemented method of claim 17 , wherein the plurality of data elements comprises a transcriptome data element.
19 . The computer-implemented method of claim 18 , wherein the transcriptome data element comprises an expression level.
20 . The computer-implemented method of claim 18 , wherein the transcriptome data element comprises an over-expression determination.
21 . The computer-implemented method of claim 18 , wherein the transcriptome data element comprises an under-expression determination.
22 . The computer-implemented method of claim 1 , wherein the examination is a complete blood count.
23 . The computer-implemented method of claim 1 , wherein the examination is a red blood cell count.
24 . The computer-implemented method of claim 1 , wherein the examination is a hemoglobin count.
25 . The computer-implemented method of claim 1 , wherein the examination is a white blood cell count.
26 . The computer-implemented method of claim 1 , wherein the examination is a platelet count.
27 . The computer-implemented method of claim 1 , wherein the examination is a hemoglobin A1C examination and the first characteristic is A1C.
28 . The computer-implemented method of claim 27 , wherein the measurement of the first characteristic in the initial laboratory result is between 5.7 and 6.4 percent A1C.
29 . The computer-implemented method of claim 28 , wherein the adjusted threshold of interpretation of the measurement of the first characteristic is a single value that is less than 5.7 percent A1C, and wherein, when the measurement of the first characteristic in the initial laboratory result indicates that the hemoglobin A1C is below the single value, the subject is diagnosed as normal.
30 . The computer-implemented method of claim 28 , wherein the adjusted threshold of interpretation of the measurement of the first characteristic is above 6.4 percent A1C and wherein, when the of the measurement of the first characteristic in the initial laboratory result indicates that the hemoglobin A1C is above the threshold of interpretation, the subject is diagnosed as diabetic.
31 . The computer-implemented method of claim 27 , wherein
the measurement of the first characteristic in the initial laboratory result for the subject indicates the subject is normal, and
the adjusted threshold of interpretation of the measurement of the first characteristic in the initial laboratory result indicates the subject is prediabetic.
32 . The computer-implemented method of claim 31 , wherein the first clinomic profile comprises a genomic variant data element.
33 . The computer-implemented method of claim 27 , wherein
the measurement of the first characteristic in the initial laboratory result for the subject is normal, and
the adjusted threshold of interpretation of the measurement of the first characteristic in the initial laboratory result indicates the subject is diabetic.
34 . The computer-implemented method of claim 27 , wherein
the measurement of the first characteristic in the initial laboratory result for the subject indicates the subject is prediabetic, and
the adjusted threshold of interpretation of the measurement of the first characteristic in the initial laboratory result indicates the subject is normal.
35 . The computer-implemented method of claim 27 , wherein
the measurement of the first characteristic in the initial laboratory result for the subject indicates the subject is prediabetic, and
the adjusted threshold of interpretation of the measurement of the first characteristic in the initial laboratory result indicates the subject is diabetic.
36 . The computer-implemented method of claim 27 , wherein
the measurement of the first characteristic in the initial laboratory result for the subject indicates the subject is diabetic, and
the adjusted threshold of interpretation of the measurement of the first characteristic in the initial laboratory result indicates the subject is prediabetic.
37 . The computer-implemented method of claim 27 , wherein
the measurement of the first characteristic in the initial laboratory result for the subject indicates the subject is diabetic, and
the adjusted threshold of interpretation of the measurement of the first characteristic in the initial laboratory result indicates the subject is normal.
38 . The computer-implemented method of claim 27 , wherein the first characteristic is A1C and the threshold of interpretation of the measurement of the first characteristic in the initial laboratory result is adjusted to less than 5.7 percent A1C for “normal”, between 5.7 and 6.4 percent A1C for “prediabetes”, or 6.5 percent A1C or above for “diabetes”.
39 . The computer-implemented method of claim 1 , wherein the adjusting the threshold of interpretation of the measurement of the first characteristic of the initial laboratory result comprises increasing a quantity of the threshold of interpretation of the measurement of the first characteristic of the initial laboratory result.
40 . The computer-implemented method of claim 1 , wherein the adjusting the threshold of interpretation of the measurement of the first characteristic of the initial laboratory result comprises decreasing a quantity of the threshold of interpretation of the measurement of the first characteristic of the initial laboratory result.
41 . The computer-implemented method of claim 1 , wherein the threshold of interpretation of the measurement of the first characteristic of the initial laboratory result comprises increasing a percentage value of the threshold of interpretation of the measurement of the first characteristic of the initial laboratory result.
42 . The computer-implemented method of claim 1 , wherein the threshold of interpretation of the measurement of the first characteristic of the initial laboratory result comprises decreasing a percentage value of the threshold of interpretation of the measurement of the first characteristic of the initial laboratory result.
43 . The computer-implemented method of claim 1 , wherein the threshold of interpretation of the measurement of the first characteristic of the initial laboratory result is a detected/not detected threshold.
44 . The computer-implemented method of claim 1 , wherein the adjusted threshold of interpretation of the measurement of the first characteristic of the initial laboratory result reflects a diagnosis related to cancer for the subject.
45 . The computer-implemented method of claim 1 , wherein the adjusted threshold of interpretation of the measurement of the first characteristic of the initial laboratory result reflects a diagnosis related to infectious disease for the subject.
46 . The computer-implemented method of claim 1 , wherein the adjusted threshold of interpretation of the measurement of the first characteristic of the initial laboratory result reflects a diagnosis related to diabetes for the subject.
47 . The computer-implemented method of claim 1 , wherein the adjusted threshold of interpretation of the measurement of the first characteristic of the initial laboratory result reflects a diagnosis related to depression for the subject.
48 . The computer-implemented method of claim 1 , wherein the adjusted threshold of interpretation of the measurement of the first characteristic of the initial laboratory result reflects a diagnosis related to cholesterol level for the subject.
49 . The computer-implemented method of claim 1 , wherein the adjusted threshold of interpretation of the measurement of the first characteristic of the initial laboratory result reflects a diagnosis related to a cardiac condition for the subject.
50 . The computer-implemented method of claim 1 , wherein the adjusted threshold of interpretation of the measurement of the first characteristic of the initial laboratory result reflects a diagnosis related to an immune condition for the subject.
51 . The computer-implemented method of claim 1 , wherein the initial laboratory result is from the examination of the specimen and wherein the specimen is a blood specimen.
52 . The computer-implemented method of claim 1 , wherein the initial laboratory result is from the examination of the specimen and wherein the specimen is a tissue specimen.
53 . The computer-implemented method of claim 1 , wherein the initial laboratory result is from the examination of the specimen and wherein the specimen is a spinal fluid specimen.
54 . The computer-implemented method of claim 1 , wherein the initial laboratory result is from the examination of the specimen and wherein the specimen is a bone marrow specimen.
55 . The computer-implemented method of claim 1 , wherein the initial laboratory result is from the examination of the specimen and wherein the specimen is a solid tumor specimen.
56 . The computer-implemented method of claim 1 , wherein the initial laboratory result is from the examination of the specimen and wherein the specimen is circulating tumor DNA.
57 . The computer-implemented method of claim 1 , wherein the initial laboratory result is from the examination of the specimen and wherein the specimen is cell-free DNA.
58 . The computer-implemented method of claim 1 , wherein the initial laboratory result is from the examination of the specimen and wherein the specimen is plasma.
59 . The computer-implemented method of claim 1 , wherein the initial laboratory result is from the examination of the specimen and wherein the specimen is buffy coat.
60 . The computer-implemented method of claim 1 , wherein the initial laboratory result is from the image and wherein the image is a pathology image.
61 . The computer-implemented method of claim 1 , wherein the initial laboratory result is from the image and wherein the image is a radiology image.
62 . The computer-implemented method of claim 1 , wherein the initial laboratory result is from the image and wherein the image is a CT image.
63 . The computer-implemented method of claim 1 , the method further comprising entering, using the computer system, the adjusted threshold of interpretation of the measurement of the first characteristic of the initial laboratory result into an electronic health record associated with the subject.
64 . The computer-implemented method of claim 1 , wherein the issuing communicates the structured report to a health care professional across a computer network.
65 . The computer-implemented method of claim 1 , wherein the issuing communicates the structured report to a group of expert clinicians across a computer network.
66 . The computer-implemented method of claim 1 , wherein the structured report further comprises a diagnosis of the subject.
67 . The computer-implemented method of claim 1 , wherein the structured report further comprises a treatment for the subject.
68 . The computer-implemented method of claim 1 , wherein the structured report further comprises a representation of the subset of clinomic profiles.
69 . The computer-implemented method of claim 1 , wherein the structured report further comprises a gene-drug interaction associated with genetic variant information of the subject.
70 . The computer-implemented method of claim 67 , wherein the structured report further comprises a gene-drug interaction associated with genetic variant information of the specimen from the subject.
71 . The computer-implemented method of claim 1 , wherein the structured clinomic data repository comprises 100,000 or more clinomic profiles representing 100,000 or more subjects.
72 . The computer-implemented method of claim 1 , wherein the structured clinomic data repository comprises 1×10 6 or more clinomic profiles representing 1×10 6 or more subjects.
73 . The computer-implemented method of claim 1 , wherein
the issuing comprises issuing the structured report to the subject or a medical practitioner associated with the subject over a computer network,
the structured report identifies a treatment or therapy for a condition afflicting the subject, and
the method further comprises receiving confirmation, over the computer network that the subject has taken the treatment or therapy for the condition responsive to the structured report.
74 . The computer-implemented method of claim 73 , wherein the condition is cancer.
75 . The computer-implemented method of claim 1 , the method further comprising using an anonymizer module to anonymize each clinomic profile in the plurality of clinomic profiles.
76 . The computer-implemented method of claim 1 , the method further comprising radially displaying, through an interactive software interface, each respective clinomic profile in the subset of clinomic profiles with respect to the first clinomic profile as a function of a value of the subject similarity metric between the respective clinomic profile and the first clinomic profile.
77 . The computer-implemented method of claim 76 , the method further comprising obtaining, through the interactive software interface, selection of one or more clinomic profiles to retain in the subset of clinomic profiles.
78 . The computer-implemented method of claim 1 , wherein the additional assay is a blood test.
79 . The computer-implemented method of claim 1 , wherein the additional assay is an imaging test.
80 . The computer-implemented method of claim 1 , wherein the additional assay is an accelerated screening test.
81 . The computer-implemented method of claim 80 , wherein the accelerated screening test is a cholesterol test, a blood glucose test, a blood count test, a prothrombin time blood test, a metabolic panel blood test, a lipid panel blood test, or a liver panel blood test.
82 . A computer-implemented method for subject monitoring, the method comprising:
obtaining, by a computing system, an initial laboratory result, comprising a measurement of a first characteristic, from an examination of a specimen or an image associated with a subject, wherein at least one laboratory technology is used to determine the initial laboratory result;
obtaining, by the computing system, a first clinomic profile of the subject from a structured clinomic data repository;
comparing, by the computing system, the first clinomic profile with each clinomic profile in the structured clinomic data repository using a subject similarity metric that quantifies a degree to which each clinomic profile in the structured clinomic data repository is similar to the first clinomic profile, wherein the structured clinomic data repository comprises 1000 or more clinomic profiles representing 1000 or more subjects, thereby identifying a subset of clinomic profiles that are similar to the first clinomic profile;
identifying, by the computing system, a second characteristic common to the subset of clinomic profiles;
adjusting a threshold of interpretation, between at least one disease state and a normal state, of the measurement of the first characteristic in the initial laboratory result based on the second characteristic;
issuing a structured report listing the initial laboratory result and the adjusted threshold of interpretation of the measurement of the first characteristic in the initial laboratory result;
originating, by the computing system, on the basis of the adjusted threshold of interpretation of the measurement of the first characteristic in the initial laboratory result, a request to perform an additional assay on the subject; and
obtaining, by the computing system, responsive to the request, a determination that the additional assay has been performed on the subject, thereby performing subject monitoring.