Classifications

• • 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
  • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
  • G01N33/6893—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids related to diseases not provided for elsewhere
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N30/00—Investigating or analysing materials by separation into components using adsorption, absorption or similar phenomena or using ion-exchange, e.g. chromatography or field flow fractionation
  • G01N30/02—Column chromatography
  • G01N30/62—Detectors specially adapted therefor
  • G01N30/72—Mass spectrometers
  • G01N30/7233—Mass spectrometers interfaced to liquid or supercritical fluid chromatograph
• • 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
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/5308—Immunoassay; Biospecific binding assay; Materials therefor for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites
• • 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
  • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
  • G01N33/689—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids related to pregnancy or the gonads
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N30/00—Investigating or analysing materials by separation into components using adsorption, absorption or similar phenomena or using ion-exchange, e.g. chromatography or field flow fractionation
  • G01N30/02—Column chromatography
  • G01N30/88—Integrated analysis systems specially adapted therefor, not covered by a single one of the groups G01N30/04 - G01N30/86
  • G01N2030/8809—Integrated analysis systems specially adapted therefor, not covered by a single one of the groups G01N30/04 - G01N30/86 analysis specially adapted for the sample
  • G01N2030/8813—Integrated analysis systems specially adapted therefor, not covered by a single one of the groups G01N30/04 - G01N30/86 analysis specially adapted for the sample biological materials
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2800/00—Detection or diagnosis of diseases
  • G01N2800/04—Endocrine or metabolic disorders
  • G01N2800/042—Disorders of carbohydrate metabolism, e.g. diabetes, glucose metabolism
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2800/00—Detection or diagnosis of diseases
  • G01N2800/36—Gynecology or obstetrics
  • G01N2800/368—Pregnancy complicated by disease or abnormalities of pregnancy, e.g. preeclampsia, preterm labour

Definitions

• GDM gestational diabetes mellitus
• GDM screening has evolved from targeting gravidas with risk factors (Wilkerson 1957; Carr 1998) to universal surveillance with the 1 -h 50-g oral glucose challenge test (GCT) (Hoet 1954; Moyer 2014; O’Sullivan et al.1973; Wilkerson 1957; Carr 1998; ACOG).
• GCT 1 -h 50-g oral glucose challenge test
• the diagnosis is commonly established by the beginning of the third trimester of pregnancy (0.75 term ) with oral glucose tolerance test (GTT).
• the GCT and GTT have remained central components of prenatal care for more than 50 years, although the specific protocol and diagnostic criteria remain controversial (Carpenter & Coustan 1982; World Health Organization 1998; ADA 2017; IADPSG 2010; Carr 1998).
• This strategy has major disadvantages for the patient, including the discomfort of venipuncture, inconvenience, time commitment, and late pregnancy diagnosis.
• Accurate identification in the first trimester of gravidas who will develop GDM would enable therapeutic interventions to normalize maternal metabolic milieu throughout the second and third trimesters.
• Earlier control of maternal glycemia has the potential to optimize maternal and perinatal outcomes and reduce the offspring risk of type 2 DM and other disorders (McCabe & Pemg, 2017; Brink 2016).
• a method of screening for susceptibility to diabetes in a subject comprises measuring the amount of a plurality of metabolic markers present in a test sample obtained from the subject; comparing the amount of the metabolic markers present in the test sample to reference levels of the markers; and identifying a subject as susceptible to diabetes when the amount of each of the measured markers present in the test sample is increased or decreased relative to the reference levels.
• provided is a method of detecting diabetes in a subject.
• the method comprises measuring the amount of a plurality of metabolic markers present in a test sample obtained from the subject; comparing the amount of the metabolic markers present in the test sample to reference levels of the markers; and identifying a subject as having diabetes when the amount of each of the measured markers present in the test sample is increased or decreased relative to the reference levels. Also provided is a method of treating diabetes in a subject. In some embodiments, the method comprises measuring the amount of a plurality of metabolic markers present in a test sample obtained from the subject; comparing the amount of the metabolic markers present in the test sample to reference levels of the markers; and treating the subject for diabetes when the amount of each of the measured markers present in the test sample is increased or decreased relative to the reference levels.
• the metabolic marker is dihydroorotate and one or more of: argininate, phenol glucuronide, 7,8-dihydroneopterin, nicotinate ribonucleoside, saccharopine; and lanthionine.
• the marker is a combination of a decrease in dihydroorotate, and an increase in argininate, 7,8- dihydroneopterin, and saccharopine.
• the marker is a combination of an increase in dihydroorotate, phenol glucuronide, and nicotinate ribonucleoside.
• the marker is a combination of an increase in dihydroorotate, phenol glucuronide, nicotinate ribonucleoside, and a decrease in lanthionine.
• the plurality of metabolic markers comprises each of dihydroorotate, argininate, phenol glucuronide, 7,8-dihydroneopterin, nicotinate ribonucleoside, saccharopine; and lanthionine.
• the identifying of a subject as having diabetes is determined according to the classification tree depicted in Figure 2.
• the reference levels are determined with respect to the values shown in the classification tree of Figure 2.
• the plurality of metabolic markers comprises each of dihydroorotate, phenol glucuronide, nicotinate ribonucleoside, and saccharopine. In some embodiments, the plurality of metabolic markers comprises an increase in dihydroorotate, phenol glucuronide, and saccharopine; and a decrease in nicotinate ribonucleoside.
• the identifying of a subject as having diabetes is determined according to the classification tree depicted in Figure 4. In some embodiments, the reference levels are determined with respect to the values shown in the classification tree of Figure 4.
• the metabolic markers further include one or more additional markers selected from the group consisting of: dopamine, octanoylcarnitine (c8), 3- methylglutarate/2-methylglutarate, and/or isocitric lactone; and wherein an increase in the additional marker is indicative of diabetes.
• additional markers selected from the group consisting of: dopamine, octanoylcarnitine (c8), 3- methylglutarate/2-methylglutarate, and/or isocitric lactone; and wherein an increase in the additional marker is indicative of diabetes.
• the plurality of metabolic markers comprises 3-hydroxybutyrate, 1 , 5-anhydroglucitol, homocamosine, and 3- hydroxydodecanedioate.
• the marker is a combination of a decrease in 1 , 5-anhydroglucitol and/or homocamosine, and an increase in 3-hydroxybutyrate, and/or 3-hydroxydodecanedioate.
• the plurality of metabolic markers comprises each of 3-hydroxybutyrate, 1, 5-anhydroglucitol, homocamosine, and 3- hydroxydodecanedioate.
• the identifying of a subject as having diabetes is determined according to the classification tree depicted in Figure 3.
• the reference levels are determined with respect to the values shown in the classification tree of Figure 3.
• the treating comprises dietary modification including supplements, administration of an oral hypoglycemia agent, or insulin therapy.
• the treating comprises diet, exercise, and glycemia surveillance (e.g., frequent testing of blood glucose levels, up to daily monitoring).
• the measuring comprises chromatography or spectrometry.
• the chromatography is gas or liquid chromatography.
• the spectrometry is mass spectrometry.
• the subject is 6-40 weeks pregnant. In some embodiments, the subject is 6-24 weeks pregnant. In some embodiments, the subject is 6-20 weeks pregnant. In some embodiments, the subject is 20- 40 weeks pregnant. In some embodiments, the subject is postpartum. In some embodiments, the subject is not pregnant.
• the diabetes is diabetes mellitus.
• test sample is urine.
• the metabolic marker is osmolality normalized.
• a classification tree will provide the final algorithm for determining when the markers are increased or decreased for separating diabetes vs normal.
• Also described herein is a non-transitory computer-readable medium embodying at least one program that, when executed by a computing device comprising at least one processor, causes the computing device to perform a method described herein.
• at least one program contains algorithms, instructions or codes for causing at least one processor to perform the method.
• Non-transitory computer-readable storage medium storing computer-readable algorithms, instructions or codes that, when executed by a computing device comprising at least one processor, cause or instruct the at least one processor to perform the method described herein, or steps within the method.
• the system comprises: a sample receiver for receiving a sample provided by an individual; a digital processing device comprising an operating system configured to perform executable instructions and a memory; and a computer program including instructions executable by the digital processing device to provide a treatment to a healthcare provider based on the sample.
• the computer program comprises: (i) a metabolite analysis module configured to determine a metabolite level in the sample for at least one metabolite comprising dihydroorotate and one or more of: argininate, phenol glucuronide, 7,8- dihydroneopterin, nicotinate ribonucleoside, saccharopine; and lanthionine, and, any of the metabolites listed in Table 2; (ii) a detection and/or treatment determination module configured to determine the status and/or treatment based on the metabolic marker level; and (iii) a display module configured to provide the status and/or treatment to the healthcare provider.
• a metabolite analysis module configured to determine a metabolite level in the sample for at least one metabolite comprising dihydroorotate and one or more of: argininate, phenol glucuronide, 7,8- dihydroneopterin, nicotinate ribonucleoside, saccharopine; and lanthi
• FIG. 1 Consensus metabolite selection. This flow chart depicts the selection process of candidate metabolites that distinguished GDM from CON by random-forest prediction accuracy, random forest GINI worsening, or gradient-boost model.
• Candidate metabolites for the final model included nine derived from the consensus of all three criteria plus an additional two with very high ranking by random forest.
• FIG. 2 Final Classification tree model. This shows the classification tree analysis of the seven metabolites with the best separation of GDM versus CON.
• the green color indicates a node where the majority and the prediction is control.
• the gold color indicates a node where the majority and prediction is GDM.
• the number displayed at each node represents the metabolite level scaled to the respective median and referenced to osmolality in the original scale, illustrates a classification tree that can guide implementation of one embodiment of the method using osmolality normalized urine metabolite measurements from a subject to determine diabetic status.
• Disclosed herein is a method for the detection of a metabolic profile of maternal urine that accurately predicts the development of gestational diabetes. This method eliminates the patient burden of the glucose tolerance test and identifies those who will develop gestational diabetes as early as the first trimester. Thus, the implementation of therapeutic interventions can begin in early pregnancy, thereby improving maternal, fetal, and newborn outcomes and reducing the risk of obesity and diabetes mellitus in adolescence and adulthood.
• a “control” or “reference” sample means a sample that is representative of normal measures of the respective marker, such as would be obtained from normal, healthy control subjects, or a baseline amount of marker to be used for comparison. Typically, a baseline will be a measurement taken from the same subject or patient. The sample can be an actual sample used for testing, or a reference level or range, based on known normal measurements of the corresponding marker. Markers described herein are referred to, interchangeably, as “metabolites” and as “metabolic markers”.
• a “significant difference” means a difference that can be detected in a manner that is considered reliable by one skilled in the art, such as a statistically significant difference, or a difference that is of sufficient magnitude that, under the circumstances, can be detected with a reasonable level of reliability.
• an increase or decrease of 10% relative to a reference sample is a significant difference.
• an increase or decrease of 20%, 30%, 40%, or 50% relative to the reference sample is considered a significant difference.
• an increase of two-fold relative to a reference sample is considered significant.
• the term “subject” includes any human or non-human animal.
• the term “non-human animal” includes all vertebrates, e.g., mammals and non-mammals, such as non-human primates, horses, sheep, dogs, cows, pigs, chickens, and other veterinary subjects.
• the subject is a human.
• predictive accuracy means the proportion of the observations or subjects that are correctly predicted by the model (random forest, boosting or other model). For example, the proportion of GDM observations that are predicted to be GDM and the proportion of control observations that are predicted to be controls.
• a random subset of the data and a random subset of the variables (metabolites) are selected and a classification tree is created to predict the (GDM or control) outcome.
• the data NOT selected to make the tree is called the “out of bag” (OOB) part of the sample for this tree.
• OOB out of bag
• This process is repeated many times (typically 500 times or more) to create many trees.
• the final prediction of GBM or control is obtained by a “vote” across all trees. Accuracy is evaluated across the OOB samples.
• boosted (logistic) regression means, for a binary outcome and the simplest form of boosting (ie LogitBoost), all observations are initially given a the same weight of 1/n.
• a two branch tree (tree “stump”), also called a “weak learner”, is generated by splitting on the value of the variable (metabolite) that best distinguishes GDM from control (variable with highest accuracy). The observations are then re-weighted, where observations incorrectly classified by the weak leaner are given higher weight than those correctly classified by the first weak learner. Once the observations are re-weighed, a second weak learner is generated which may use a different variable or the same variable and gives better predictions for the observations with higher weight.
• the invention provides methods for screening, detection, and treatment of diabetes, including diabetes mellitus and gestational diabetes mellitus (GDM).
• GDM gestational diabetes mellitus
• described is a method of screening for susceptibility to diabetes in a subject.
• the method comprises measuring the amount of a plurality of metabolic markers present in a test sample obtained from the subject; comparing the amount of the metabolic markers present in the test sample to reference levels of the markers; and identifying a subject as susceptible to diabetes when the amount of each of the measured markers present in the test sample is increased or decreased relative to the reference levels.
• provided is a method of detecting diabetes in a subject.
• the method comprises measuring the amount of a plurality of metabolic markers present in a test sample obtained from the subject; comparing the amount of the metabolic markers present in the test sample to reference levels of the markers; and identifying a subject as having diabetes when the amount of each of the measured markers present in the test sample is increased or decreased relative to the reference levels. Also provided is a method of treating diabetes in a subject. In some embodiments, the method comprises measuring the amount of a plurality of metabolic markers present in a test sample obtained from the subject; comparing the amount of the metabolic markers present in the test sample to reference levels of the markers; and treating the subject for diabetes when the amount of each of the measured markers present in the test sample is increased or decreased relative to the reference levels.
• the metabolic marker is dihydroorotate and one or more of: argininate, phenol glucuronide, 7,8-dihydroneopterin, nicotinate ribonucleoside, saccharopine; and lanthionine.
• the marker is a combination of a decrease in dihydroorotate, and an increase in argininate, 7,8- dihydroneopterin, and saccharopine.
• the marker is a combination of an increase in dihydroorotate, phenol glucuronide, and nicotinate ribonucleoside.
• the marker is a combination of an increase in dihydroorotate, phenol glucuronide, nicotinate ribonucleoside, and a decrease in lanthionine.
• the plurality of metabolic markers comprises each of dihydroorotate, argininate, phenol glucuronide, 7,8-dihydroneopterin, nicotinate ribonucleoside, saccharopine; and lanthionine.
• the identifying of a subject as having diabetes is determined according to the classification tree depicted in Figure 2. In some embodiments, the reference levels are those shown in the classification tree of Figure 2.
• the metabolic markers further include one or more additional markers selected from the group consisting of: dopamine, octanoylcamitine (c8), 3-methylglutarate/2-methylglutarate, and/or isocitric lactone; and wherein an increase in the additional marker is indicative of diabetes.
• additional markers selected from the group consisting of: dopamine, octanoylcamitine (c8), 3-methylglutarate/2-methylglutarate, and/or isocitric lactone; and wherein an increase in the additional marker is indicative of diabetes.
• the sample is assayed for argininate. If the measured level of argininate is greater than the reference level of 0.79, the sample is assayed for 7,8-dihydroneopterin. If the measured level of 7,8-dihydroneopterin is greater than the reference level of 0.45, the sample is assayed for saccharopine. If the measured level of saccharopine is greater than the reference level of 1.2, the subject is identified as a subject in need of treatment for diabetes mellitus. Further examples of this progression of the analysis are described below.
• the plurality of metabolic markers comprises each of dihydroorotate, phenol glucuronide, nicotinate ribonucleoside, and saccharopine. In some embodiments, the plurality of metabolic markers comprises an increase in dihydroorotate, phenol glucuronide, and saccharopine; and a decrease in nicotinate ribonucleoside.
• the identifying of a subject as having diabetes is determined according to the classification tree depicted in Figure 4 (see Example 4 below). In some embodiments, the reference levels are those shown in the classification tree of Figure 4.
• the plurality of metabolic markers comprises 3-hydroxybutyrate, 1 , 5-anhydroglucitol, homocamosine, and 3- hydroxydodecanedioate.
• the marker is a combination of a decrease in 1 , 5-anhydroglucitol and/or homocamosine, and an increase in 3-hydroxybutyrate, and/or 3-hydroxydodecanedioate.
• the plurality of metabolic markers comprises each of 3-hydroxybutyrate, 1, 5-anhydroglucitol, homocamosine, and 3- hydroxydodecanedioate.
• the identifying of a subject as having diabetes is determined according to the classification tree depicted in Figure 3.
• the reference levels are those shown in the classification tree of Figure 3.
• the treating comprises glycemia surveillance (frequent, up to daily measurement of maternal glucose levels), dietary alterations, antioxidant supplements, exercise, and/or the administration of an oral hypoglycemia agent or insulin therapy.
• Dietary antioxidants can bolster maternal/fetal mitochondrial function, which can ameliorate the metabolic milieu and potentially reduce the need for hypoglycemic agents.
• Such intervention in the first-trimester can reduce fetal and maternal morbidity and lower the risk of significant medical disorders in adult offspring.
• the measuring comprises chromatography or spectrometry.
• the chromatography is gas or liquid chromatography.
• the spectrometry is mass spectrometry.
• the subject is 6-40 weeks pregnant. In some embodiments, the subject is 6-24 weeks pregnant. In some embodiments, the subject is 6-20 weeks pregnant. In some embodiments, the subject is 20- 40 weeks pregnant. In some embodiments, the subject is postpartum.
• the diabetes is diabetes mellitus.
• test sample is urine.
• the metabolic marker is osmolality normalized.
• a classification tree of metabolites identified by multivariate methods will provide the algorithm for determining when the markers are increased or decreased.
• a sample of urine obtained from a subject is assayed for the levels of the seven metabolic markers identified in Figure 2 (top seven metabolites of Table 2). Typically the subject is between 6 and 20 weeks pregnant. In some embodiments, the subject is greater than 20 weeks pregnant.
• the measured amounts are normalized to urine osmolality.
• the analysis begins with the first level shown in the classification tree depicted in Figure 2, dihydroorotate. If the level of dihydroorotate is below the reference level for dihydroorotate (e.g., 0.24 osmolality normalized units), the analysis moves to argininate, following the left side of the classification tree.
• argininate is below the reference level for this marker, then the subject does not have gestational diabetes mellitus. If argininate is above the reference level, then the analysis moves to 7,8-dihydroneopterin. If 7,8-dihydroneopterin is below its reference level (e.g., 0.45), then the subject does not have GDM. If 7,8-dihydroneopterin is above its reference level, then the analysis moves to saccharopine. Sacchoropine below its reference level (1.2), combined with argininate at or above 0.98, is indicative of a subject who does not have GDM.
• Saccharopine above its reference level is indicative of GDM.
• dihydroorotate is above the reference level (0.24), then the analysis moves to phenol glucuronide. If phenol glucuronide is below its reference level (e.g., 0.22), the subject does not have GDM. If phenol glucuronide is above its reference level, then the analysis moves to nicotinate ribonucleoside. If nicotinate ribonucleoside is below its reference level (0.75), and lanthionine is at or above its reference level (0.71), the subject does not have GDM.
• nicotinate ribonucleoside is below its reference level and lanthionine is below its reference level, the subject has GDM. If nicotinate ribonucleoside is above its reference level, but dihydroorotate is below 1.5, the subject does not have GDM. If nicotinate ribonucleoside is above its reference level and dihydroorotate is above 1.5, then the subject has GDM.
• sample include, but are not limited to, blood, plasma or serum, saliva, urine, cerebral spinal fluid, milk, cervical secretions, semen, tissue, cell cultures, and other bodily fluids or tissue specimens.
• sample is urine.
• Methods of measuring metabolites include, but are not limited to, nuclear magnetic resonance (NMR) spectroscopy, high performance liquid chromatography (HPLC), gas chromatography, thin layer chromatography, electrochemical analysis, mass spectroscopy, refractive index spectroscopy, ultra-violet spectroscopy, fluorescent analysis, radiochemical analysis, near-infrared spectroscopy, gas chromatography, and light scattering analysis.
• NMR nuclear magnetic resonance
• HPLC high performance liquid chromatography
• gas chromatography thin layer chromatography
• electrochemical analysis mass spectroscopy
• refractive index spectroscopy refractive index spectroscopy
• ultra-violet spectroscopy fluorescent analysis
• radiochemical analysis radiochemical analysis
• near-infrared spectroscopy gas chromatography
• light scattering analysis e.g., XPSI and light scattering analysis.
• kits comprising a set of reagents suitable for use in the methods described herein, and optionally, one or more suitable containers containing reagents of the invention.
• Reagents include molecules that specifically bind and/or amplify and/or detect one or more markers of the invention. Such molecules can be provided in the form of a microarray or other article of manufacture for use in an assay described herein.
• Kits of the invention optionally comprise an assay standard or a set of assay standards, either separately or together with other reagents.
• An assay standard can serve as a normal control by providing a reference level of normal expression for a given marker that is representative of a healthy individual.
• the invention provides a device suitable for use in the methods described herein.
• a device is capable of detecting and measuring one or more metabolic markers of the invention.
• the device optionally comprises a processor programmed to perform an analysis of the measurements of metabolic markers according to the methods described herein.
• the analysis includes implementation of the classification tree depicted in Figure 2.
• the analysis includes implementation of the classification tree depicted in Figure 3.
• the analysis includes implementation of the classification tree depicted in Figure 4.
• computer implemented systems for use in methods herein, such as methods of screening, methods of detecting, methods of treatment, methods of metabolic profiling, and methods of recommending a treatment.
• computer implemented systems herein comprise: (a) a sample receiver for receiving a sample provided by an individual; (b) a digital processing device comprising an operating system configured to perform executable instructions and a memory; and (c) a computer program including instructions executable by the digital processing device to provide a treatment to a healthcare provider based on the sample.
• the computer program comprises: (i) a metabolite analysis module configured to determine a metabolite level in the sample for at least one metabolite comprising argininate, phenol glucuronide, 7,8-dihydroneopterin, nicotinate ribonucleoside, saccharopine; and lanthionine, and, any combination of the metabolites listed in Table 2; (ii) a treatment determination module configured to determine the treatment based on the metabolite expression level relative to a reference level; and (iii) a display module configured to provide the result and/or treatment to the healthcare provider.
• a metabolite analysis module configured to determine a metabolite level in the sample for at least one metabolite comprising argininate, phenol glucuronide, 7,8-dihydroneopterin, nicotinate ribonucleoside, saccharopine; and lanthionine, and, any combination of the metabolites listed in Table 2
• the invention provides a non-transitory computer-readable medium encoded with computer-executable instructions for performing the methods described herein.
• the invention provides a non-transitory computer-readable medium embodying at least one program that, when executed by a computing device comprising at least one processor, causes the computing device to perform one or more of the methods described herein.
• the at least one program contains algorithms, instructions or codes for causing the at least one processor to perform the method(s).
• the invention provides a non-transitory computer-readable storage medium storing computer- readable algorithms, instructions or codes that, when executed by a computing device comprising at least one processor, cause or instruct the at least one processor to perform a method described herein.
• the computer programs/algorithms for performing the present method can be implemented with, e.g., a general-purpose processor, a digital signal processor (DSP), an application-specific integrated circuit (ASIC), a field-programmable gate array (FPGA), or other programmable logic device, discrete gate or transistor logic, discrete hardware components, or any combination thereof designed to perform the functions and steps described herein.
• DSP digital signal processor
• ASIC application-specific integrated circuit
• FPGA field-programmable gate array
• a general-purpose processor can be a microprocessor, but alternatively the processor can be any conventional processor, controller, microcontroller or state machine.
• a processor can also be implemented as a combination of computing devices, e.g., a combination of a DSP and a microprocessor, a plurality of microprocessors, one or more microprocessors in conjunction with a DSP core, or any other such configuration.
• a software module can reside in, e.g., RAM memory, flash memory, ROM memory, EPROM memory, EEPROM memory, registers, a hard drive, a solid-state drive, a removable disk or disc, a CD-ROM, or any other form of storage medium known in the art.
• An exemplary storage medium is coupled to the processor such that the processor can read information from, and write information to, the storage medium.
• the storage medium can be integral to the processor.
• the processor and the storage medium can reside in, e.g., an ASIC, which in turn can reside in, e.g., a user terminal. In the alternative, the processor and the storage medium can reside as discrete components in, e.g., a user terminal.
• the functions for carrying out the method described herein can be implemented in hardware, software, firmware or any combination thereof. If implemented in software, the functions can be stored on or transmitted over a computer-readable medium as instructions or codes.
• Computer-readable media include without limitation computer storage media and communication media, including any medium that facilitates transfer of a computer program/algorithm from one place to another.
• a storage medium can be any available medium that can be accessed by a general-purpose or special-purpose computer or processor.
• computer-readable media can comprise RAM, ROM, EEPROM, CD-ROM or other optical disc storage, magnetic disk storage or other magnetic storage devices, or any other medium that can be used to carry or store a computer program/algorithm in the form of instructions/codes and/or data structures and that can be accessed by a general-purpose or special-purpose computer or processor.
• any connection is deemed a computer-readable medium.
• the software is transmitted from a website, a server or other remote source using a coaxial cable, fiber optic cable, twisted pair, digital subscriber line (DSL), or a wireless technology such as infrared, radio wave or microwave
• the coaxial cable, fiber optic cable, twisted pair, DSL, or wireless technology such as infrared, radio wave or microwave are computer-readable media.
• Discs and disks include without limitation compact disc (CD), laser disc, optical disc, digital versatile disc (DVD), blu-ray disc, hard disk and floppy disk, where discs normally reproduce data optically using a laser, while disks normally reproduce data magnetically. Combinations of the above are also included within the scope of computer-readable media.
• the methods described herein can be automated. Accordingly, in some embodiments the method is implemented with a computer system (e.g., a server, a desktop computer, a laptop, a tablet or a smartphone) comprising at least one processor.
• the computer system can be configured or provided with algorithms, instructions or codes for performing the method which are executable by the at least one processor.
• the computer system can generate a report containing information on any or all aspects relating to the method, including results of the analysis of the biological sample from the subject.
• the disclosure further provides a non-transitory computer-readable medium encoded with computer-executable instructions for performing the present method..
• Example embodiment 1 is a method of screening for susceptibility to diabetes in a subject, the method comprising: (a) measuring the amount of a plurality of metabolic markers present in a test sample obtained from the subject; (b) comparing the amount of the metabolic markers present in the test sample to reference levels of the markers; (c) identifying a subject as susceptible to diabetes when the amount of each of the measured markers present in the test sample is increased or decreased relative to the reference levels; wherein the plurality of metabolic markers comprises dihydroorotate and one or more of: argininate, phenol glucuronide, 7,8-dihydroneopterin, nicotinate ribonucleoside, saccharopine; and lanthionine.
• Embodiment 2 is a method of detecting diabetes in a subject, the method comprising: (a) measuring the amount of a plurality of metabolic markers present in a test sample obtained from the subject; (b) comparing the amount of the metabolic markers present in the test sample to reference levels of the markers; (c) identifying a subject as having diabetes when the amount of each of the measured markers present in the test sample is increased or decreased relative to the reference levels; wherein the metabolic markers comprise dihydroorotate and one or more of: argininate, phenol glucuronide, 7,8-dihydroneopterin, nicotinate ribonucleoside, saccharopine; and lanthionine.
• Embodiment 3 is a method of treating diabetes in a subject, the method comprising: (a) measuring the amount of a plurality of metabolic markers present in a test sample obtained from the subject; (b) comparing the amount of the metabolic markers present in the test sample to reference levels of the markers; (c) treating the subject for diabetes when the amount of each of the measured markers present in the test sample is increased or decreased relative to the reference levels; wherein the metabolic markers comprise dihydroorotate and one or more of: argininate, phenol glucuronide, 7,8-dihydroneopterin, nicotinate ribonucleoside, saccharopine; and lanthionine.
• Embodiment 4 The method of any of the preceding embodiments, wherein the marker is a combination of a decrease in dihydroorotate, and an increase in argininate, 7,8- dihydroneopterin, and saccharopine.
• Embodiment 5 The method of any of the preceding embodiments, wherein the marker is a combination of an increase in dihydroorotate, phenol glucuronide, and nicotinate ribonucleoside.
• Embodiment 6 The method of any of the preceding embodiments, wherein the marker is a combination of an increase in dihydroorotate, phenol glucuronide, nicotinate ribonucleoside, and a decrease in lanthionine.
• Embodiment 7 The method of embodiment 4, wherein the plurality of metabolic markers comprises each of dihydroorotate, argininate, phenol glucuronide, 7,8- dihydroneopterin, nicotinate ribonucleoside, saccharopine; and lanthionine.
• Embodiment 8 The method any of the preceding embodiments, wherein the identifying of a subject as having diabetes is determined according to the classification tree depicted in Figure 2.
• Embodiment 9 The method of embodiment 8, wherein the reference levels are those shown in the classification tree of Figure 2.
• Embodiment 10 The method of any of embodiments 4 to 9, wherein the metabolic markers further include one or more additional markers selected from the group consisting of: dopamine, octanoylcamitine (c8), 3-methylglutarate/2-methylglutarate, and/or isocitric lactone; and wherein an increase in the additional marker is indicative of diabetes.
• Embodiment 11 The method of embodiment 3, wherein the treating comprises dietary modification, administration of an oral hypoglycemia agent, or insulin therapy.
• Embodiment 12 The method of any of the preceding embodiments, wherein the measuring comprises chromatography or spectrometry.
• Embodiment 13 The method of embodiment 12, wherein the chromatography is gas or liquid chromatography.
• Embodiment 14 The method of embodiment 12, wherein the spectrometry is mass spectrometry.
• Embodiment 15 The method of any one of embodiments 1 to 14, wherein the subject is 6-40 weeks pregnant.
• Embodiment 16 The method of any one of embodiments 1 to 14, wherein the subject is postpartum.
• Embodiment 17 The method of any of the preceding embodiments wherein the diabetes is diabetes mellitus.
• Embodiment 18 The method of any of the preceding embodiments wherein test sample is urine.
• Embodiment 19 The method of embodiment 18, wherein the metabolic marker is osmolality normalized.
• Embodiment 20 The method of any of the preceding embodiments, wherein multivariate statistical analysis and/or a mathematical method is used to determine when the markers are increased or decreased.
• Embodiment 21 is a method of screening for susceptibility to diabetes in a subject, the method comprising: (a) measuring the amount of a plurality of metabolic markers present in a test sample obtained from the subject; (b) comparing the amount of the metabolic markers present in the test sample to reference levels of the markers; (c) identifying a subject as susceptible to diabetes when the amount of each of the measured markers present in the test sample is increased or decreased relative to the reference levels; wherein the plurality of metabolic markers comprises 3-hydroxybutyrate, 1, 5-anhydroglucitol, homocarosine, and 3-hydroxydodecanedioate.
• Embodiment 22 is a method of detecting diabetes in a subject, the method comprising: (a) measuring the amount of a plurality of metabolic markers present in a test sample obtained from the subject; (b) comparing the amount of the metabolic markers present in the test sample to reference levels of the markers; (c) identifying a subject as having diabetes when the amount of each of the measured markers present in the test sample is increased or decreased relative to the reference levels; wherein the metabolic markers comprise 3-hydroxybutyrate, 1 , 5-anhydroglucitol, homocarnosine, and 3- hydroxydodecanedioate.
• Embodiment 23 is a method of treating diabetes in a subject, the method comprising: (a) measuring the amount of a plurality of metabolic markers present in a test sample obtained from the subject; (b) comparing the amount of the metabolic markers present in the test sample to reference levels of the markers; (c) treating the subject for diabetes when the amount of each of the measured markers present in the test sample is increased or decreased relative to the reference levels; wherein the plurality of metabolic markers comprises 3-hydroxybutyrate, 1, 5-anhydroglucitol, homocarosine, and 3- hydroxydodecanedioate.
• Embodiment 24 The method of any of embodiments 21 to 23, wherein the marker is a combination of a decrease in 1, 5-anhydroglucitol and/or homocarnosine, and an increase in 3-hydroxybutyrate, and/or 3-hydroxydodecanedioate.
• Embodiment 25 The method of embodiment 24, wherein the plurality of metabolic markers comprises each of 3-hydroxybutyrate, 1 , 5-anhydroglucitol, homocarnosine, and 3- hydroxydodecanedioate.
• Embodiment 26 The method any of the preceding embodiments, wherein the identifying of a subject as having diabetes is determined according to the classification tree depicted in Figure 3.
• Embodiment 27 The method of embodiment 26, wherein the reference levels are those shown in the classification tree of Figure 3.
• Embodiment 28 The method of embodiment 23, wherein the treating comprises dietary modification, administration of an oral hypoglycemia agent, or insulin therapy.
• Embodiment 29 The method of any of embodiments 21 to 28, wherein the measuring comprises chromatography or spectrometry.
• Embodiment 30 The method of embodiment 29, wherein the chromatography is gas or liquid chromatography.
• Embodiment 31 The method of embodiment 29, wherein the spectrometry is mass spectrometry.
• Embodiment 32 The method of embodiment 21 , wherein the subject is 6-40 weeks pregnant.
• Embodiment 33 The method of embodiment 21 , wherein the subject is postpartum.
• Embodiment 34 The method of any of embodiments 21 to 33, wherein the diabetes is diabetes mellitus.
• Embodiment 35 The method of any of embodiments 21 to 34, wherein test sample is urine.
• Embodiment 36 The method of embodiment 35, wherein the metabolic marker is osmolality normalized.
• Embodiment 37 The method of any of embodiments 21 to 36, wherein multivariate statistical analysis and/or a mathematical method is used to determine when the markers are increased or decreased.
• Embodiment 38 is a non-transitory computer-readable medium embodying at least one program that, when executed by a computing device comprising at least one processor, causes the computing device to perform the method of any one of embodiments 1-37.
• Embodiment 39 The medium of embodiment 38, wherein the at least one program contains algorithms, instructions or codes for causing the at least one processor to perform the method.
• Embodiment 40 is a non-transitory computer-readable storage medium storing computer-readable algorithms, instructions or codes that, when executed by a computing device comprising at least one processor, cause or instruct the at least one processor to perform the method of any one of embodiments 1-39.
• Example 1 Early Pregnancy Metabolites Predict Gestational Diabetes Mellitus
• This Example demonstrates that a maternal metabolic profile as early as the first prenatal visit can accurately identify GDM.
• Advanced analytical methods were used to generate a urinary metabolite model that accurately predicted gestational diabetes (GDM) in early pregnancy.
• GDM gestational diabetes
• a model comprising seven eariy-pregnancy urinary metabolites predicted GDM with high accuracy (96.7%). The accuracy of the model was independent of maternal age, body mass index, and time of urine collection.
• This Example reports the first proof of the concept that an algorithm utilizing a metabolic profile in early pregnancy can accurately identify GDM.
• a major pregnancy adaptation is insulin resistance, which emerges by 14 weeks' gestation (0.37 term) and rises up to two-fold by late pregnancy.
• This gestational diabetes (GDM) increases the short-term morbidity risk for the mother (preeclampsia, cesarean delivery) and fetus (macrosomia, birth trauma).
• GDM gestational diabetes
• glucose challenge/tolerance tests have been the diagnostic standard for GDM, usually performed in late pregnancy.
• a further rationale for treating GDM in early pregnancy is the growing evidence that gestational diabetes via adverse intrauterine programming predisposes the fetus in later life to obesity, type 2 diabetes, and cardiovascular disease.
• 5,6,7,8,9,10,11,12,13,14,15 Normalizing the maternal metabolic milieu in early pregnancy may diminish the oxidative stress and inflammation that putatively impair insulin sensitivity and pancreatic ⁇ -cell function, which predispose the mother and child to disabling medical disorders.
• 5,6,7 With an accuracy ⁇ 80%, first-trimester biomarkers have lacked sufficient sensitivity and specificity for GDM diagnosis.
• a nested, observational case-control study determined the metabolic profile of urine from normal singleton gravidas [control (CON)] versus those who developed GDM by glucose challenge (GCT)/tolerance tests (GTT). 3
• the GTC results were considered diagnostic for plasma glucose levels ⁇ 200 mg/dl, or a little lower for some patients with risk factors.
• Fasting glucose level of >95 mg/dl (for GCT intolerant) or a first-trimester HbAic ( ⁇ 5.7%) were also used to identify GDM.
• GDM were paired to CON subjects by age, pre- pregnancy body mass index (BMI), and gestational age at urine collection.
• Urine samples were analyzed for 951 diverse, low-molecular weight ( ⁇ 1000) biochemicals by ultra-performance liquid chromatography/mass spectrometry-tandem mass spectroscopy (UPLC-MS/MS) with positive ion mode electrospray ionization, UPLC-MS/MS with negative ion mode electrospray ionization, and gas chromatography/mass spectrometry. 21
• the platform identified metabolites by comparison to mass spectra from purified standards. The total process variability was 10%. Quality control samples provided process control. Peak areas for each metabolite were scaled to the median value and osmolality to adjust for fluid intake. [0100] Bivariate Analysis.
• the p values for comparing continuous variables that follow the normal distribution were computed with t tests.
• the p values for non-time dependent continuous variables that did not follow the normal distribution on any scale were computed using the Wilcoxon rank sum test.
• the p values for comparing categorical variables such as race/ethnicity were computed using the exact permutation chi-square test or Fisher's exact test. Means ⁇ SB were reported. Differences were significant at p ⁇ 0.05.
• Table 3 Predictive accuracy in early pregnancy for GDM according to the classification tree level.
• this panel predicted GDM with a ROC area of 0.8485, a sensitivity of 78%, specificity of 75%, and accuracy of 76.5%.
• PAPP-A, glycine, arginine, isovalerylcamitine, and maternal risk factors had a ROC area of 0.83.
• Another metabolomics study reported ROC areas ranging from 0.641 to 0.858 for single urinary metabolites of tryptophan or purines. 19
• the classification tree selected a subset of seven metabolites for identifying GDM.
• the algorithm high predictive accuracy (96.7%) was substantially greater than that previously reported for one or more first-trimester biochemicals, even with the addition of maternal risk factors. 18,17,18
• the present study indicates that a urinary metabolic phenotype in early pregnancy can accurately identify GDM subsequently diagnosed in early or late pregnancy, enabling randomized, innovative interventions (including dietary enhancement of mitochondrial function 29 ) targeting short- and long-term perinatal morbidity.
• a validation metabolomics study would further support the high diagnostic accuracy of this promising model, which could replace the GCT and GTT. Validation will also allow urinary measurements to be restricted to model metabolites, reducing cost. This achievement will enable longitudinal studies on whether regulating the maternal metabolic milieu from early pregnancy will diminish GDM prevalence, perinatal morbidity, and the long-term risks of obesity, type 2 diabetes, and cardiovascular disease.
• random forest predictive accuracy random forest GINI worsening, and gradient boost model were used for multivariate analysis.
• This consensus analysis bolstered confidence in the identifying true positives albeit at the likely expense of increasing false negatives.
• Example 3 Gestational Diabetics Have Perturbed Energy Metabolism in Early Pregnancy [0166] Gestational diabetics (GD) have impaired insulin sensitivity prior to conception.
• the objective of this Example was to determine whether maternal urinary metabolites in early pregnancy reveal altered metabolic pathways.
• Results The case and control groups had similar mean maternal age [GD: 32 ⁇ 0.7 (SE); NG: 32 ⁇ 0.6 years], prepregnancy body mass index (GM: 31.5 ⁇ 1.0; NG 30.0
• GD 11.7 ⁇ 0.4; NG: 12.0 ⁇ 0.4 weeks
• Multivariate criteria identified 26 compounds simultaneously distinguishing GD vs control.
• Changes in microbiome- derived metabolites (n 7) included cognates of bile acids (3), lysine (2), and phenylalanine
• GD exhibit in early pregnancy perturbations in metabolic pathways that are consistent with increased oxidative stress, disrupted energy metabolism, and insulin resistance.
• Example 4 Urinary Metabolites Identified in Early Pregnancy Also Predict GDM in Late Pregnancy Urine (>20 weeks’ gestation)
• the classification table shown in Table 6 indicates the GDM sensitivity of 84.5%; the NG specificity was 87%, and the nominal accuracy was 86%.
• the area under the curve (AUC) was 0.0.879.

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