WO2011072177A2 - Dosage de biomarqueurs pour le diagnostic et le classement des maladies cardiovasculaires - Google Patents

Dosage de biomarqueurs pour le diagnostic et le classement des maladies cardiovasculaires Download PDF

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WO2011072177A2
WO2011072177A2 PCT/US2010/059781 US2010059781W WO2011072177A2 WO 2011072177 A2 WO2011072177 A2 WO 2011072177A2 US 2010059781 W US2010059781 W US 2010059781W WO 2011072177 A2 WO2011072177 A2 WO 2011072177A2
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classification
mir
biological sample
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human
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WO2011072177A3 (fr
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Doug Harrington
Evangelos Hytopoulos
Bruce Phelps
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Aviir, Inc.
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Priority to JP2012543298A priority Critical patent/JP2013513387A/ja
Priority to AU2010328019A priority patent/AU2010328019A1/en
Priority to CA2783536A priority patent/CA2783536A1/fr
Priority to CN2010800635211A priority patent/CN102762743A/zh
Priority to EP10791032A priority patent/EP2510116A2/fr
Publication of WO2011072177A2 publication Critical patent/WO2011072177A2/fr
Publication of WO2011072177A3 publication Critical patent/WO2011072177A3/fr

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Definitions

  • Atherosclerotic cardiovascular disease is the primary cause of morbidity and mortality worldwide. Almost 60% of myocardial infarctions (Mis) occur in people with 0 or 1 risk factor. That is, the majority of people that experience a cardiac event are in the low- intermediate or intermediate risk categories as assessed by current methods.
  • a combination of genetic and environmental factors is responsible for the initiation and progression of the disease.
  • Atherosclerosis is often asymptomatic and goes undetected by current diagnostic methods.
  • the first symptom of atherosclerotic cardiovascular disease is heart attack or sudden cardiac death.
  • a method for assessing the cardiovascular health of a human comprising: a) obtaining a biological sample from a human; b) determining levels of at least 2 miRNA markers selected from miRNAs listed in Table 20 in the biological sample; c) obtaining a dataset comprised of the levels of each miRNA marker; d) inputting the data into an analytical classification process that uses the data to classify the biological sample, wherein the classification is selected from the group consisting of an atherosclerotic cardiovascular disease classification, a healthy classification, a medication exposure classification, a no medication exposure classification; and e) determining a treatment regimen for the human based on the classification in step (d); wherein the cardiovascular health of the human is assessed.
  • a method for assessing the cardiovascular health of a human comprising: a) obtaining a biological sample from a human; b) determining levels of at least 3 protein markers selected from the group consisting of IL-16, sFas, Fas ligand, MCP- 3, HGF, CTACK, EOTAXIN, adiponectin, IL-18, TIMP.4, TIMP.1 , CRP, VEGF, and EGF in the biological sample; c) obtaining a dataset comprised of the levels of each protein marker; d) inputting the data into an analytical classification process that uses the data to classify the biological sample, wherein the classification is selected from the group consisting of an atherosclerotic cardiovascular disease classification, a healthy classification, a medication exposure classification, a no medication exposure classification; and e) determining a treatment regimen for the human based on the classification in step (d); wherein the cardiovascular health of the human is assessed.
  • a method for assessing the cardiovascular health of a human to determine the need for or effectiveness of a treatment regimen comprising: obtaining a biological sample from a human; determining levels of at least 2 miRNA markers selected from miRNAs listed in Table 20 in the biological sample; determining levels of at least 3 protein biomarker selected from the group consisting of IL-16, sFas, Fas ligand, MCP-3, HGF, CTACK, EOTAXIN, adiponectin, IL-18, TIMP.4, TIMP.1 , CRP, VEGF, and EGF in the biological sample; obtaining a dataset comprised of the individual levels of the miRNA markers and the protein biomarkers; inputting the data into an analytical classification process that uses the data to classify the biological sample, wherein the classification is selected from the group consisting of an atherosclerotic cardiovascular disease classification, a healthy classification, a medication exposure classification, a no medication exposure classification; and classifying the biological sample according to the output of the classification process and determining a treatment
  • a kit for assessing the cardiovascular health of a human to determine the need for or effectiveness of a treatment regimen comprises: an assay for determining levels of at least two miRNA markers selected from the miRNAs listed in Table 20 in the biological sample and/or for determining the levels of at least 3 protein markers selected from the group consisting of IL-16, sFas, Fas ligand, MCP-3, HGF, CTACK, EOTAXIN, adiponectin, IL-18, TIMP.4, TIMP.1 , CRP, VEGF, and EGF in the biological sample; instructions for (1) obtaining a dataset comprised of the levels of each miRNA and/or protein marker, (2) inputting the data into an analytical classification process that uses the data to classify the biological sample, wherein the classification is selected from the group consisting of an atherosclerotic cardiovascular disease classification, a healthy classification, a medication exposure classification, a no medication exposure classification; (3) and determining a treatment regimen for the human based
  • methods for assessing the risk of a cardiovascular event of a human comprising: a) obtaining a biological sample from a human; b) determining levels of three or more protein biomarkers selected from the group consisting of IL-16, sFas, Fas ligand, MCP-3, HGF, CTACK, EOTAXIN, adiponectin, IL-18, TIMP.4, TIMP.1 , CRP, VEGF, and EGF and/or 2 or more of the miRNAs in Table 20 in the sample; c) obtaining a dataset comprised of the levels of each protein and/or miRNA biomarkers; d) inputting the data into a risk prediction analysis process to determine the risk of a cardiovascular event based on the dataset; and e) determining a treatment regimen for the human based on the predicted risk of a cardiovascular event in step (d); wherein the risk of a cardiovascular event of the human is assessed.
  • Figure 1 is a graph depicting the expected classification performance for a set of 52 samples (26 cases and 26 controls) based on a logistic regression approach.
  • the expected AUC and corresponding 95% confidence interval was obtained from 500 simulations of classifying sets of 52 either individual or pooled samples.
  • Open circles on error bars represent the expected value and the confidence interval using pooled samples (5 samples in each pool), with a biomarker concentration or score value assumed to follow a log-normal distribution.
  • Open circles on solid error bars represent expected value and confidence interval using individual samples from the same distribution.
  • Solid black dots represent the theoretical result.
  • the x-axis represent differences in the mean for the case and control biomarker or score distribution.
  • Figure 2 is a graph depicting the expected classification performance for a set of 52 samples (26 cases and 26 controls) based on a logistic regression approach.
  • the expected AUC and corresponding 95% confidence interval was obtained from 500 simulations of classifying sets of 52 either individual or pooled samples.
  • Open circles on dashed error bars represent the expected value and the confidence interval using pooled samples (5 samples in each pool), with a biomarker concentration or score value assumed to follow a normal distribution.
  • Open circles on solid error bars represent expected value and confidence interval using individual samples from the same distribution.
  • Solid black dots represent the theoretical result.
  • the x-axis represents differences in the mean for the case and control biomarker or score distribution.
  • Figure 3 is a graph of the AUC values distribution for the classification of pooled samples based on based on models selecting covariates from a set of 44 miR species.
  • the calculation of the AUC values is based on obtaining 100 prevalidated classification score vectors through fitting penalized logistic regression models (with L1 penalty) to the data.
  • the x-axis represents the AUC and the y-axis represents the frequency. As shown, the average AUC is 0.68.
  • Figure 4 is a graph of the AUC values distribution for the classification of individual samples based on models selecting covariates from a set of 44 miR species. The calculation of the AUC values is based on obtaining 100 prevalidated classification score vectors through fitting penalized logistic regression models (with L1 penalty) to the data. As shown, the average AUC is 0.78.
  • Figure 6 is a graph showing distribution of the correlations between miR and protein, including the highest negative correlation and highest positive correlation indicated by the vertical lines.
  • Figure 7 is a graph showing the distribution of the correlations between the miRs alone.
  • Figure 8 is a graph showing the AUC distribution based on prevalidated score (500 repeats) calculated based on protein biomarker data alone.
  • Figure 9 is a graph showing the univariate hazard ratio for the protein biomarkers normalized to the mean and standard deviation of the controls.
  • Figure 10 is a graph showing the adjusted hazard ratio (HR) for protein biomarkers. Adjustment was based on traditional risk factors (TRFs): age, gender, systolic blood pressure (BP), diastolic BP, cholesterol, high density lipoprotein (HDL), hypertension, use of hypertension drug, hyperlipidemia, diabetes, and smoking status.
  • TRFs traditional risk factors
  • Figures 11 A and B are graphs showing the markers with the highest time-dependent AUC and corresponding values for up to 5 years of follow-up.
  • the AUC for sFas, NT.proBNP, MIG, IL.16, MIG, and ANG2 are shown in Fig. 11A and FasLigand, SCD40L, adiponectin, MCP.3, leptin and rantes are shown in Fig. 11 B.
  • Figure 12 is a graph of the absolute value and standard error of the drop- in-deviance as a function of the number of terms in a Cox proportional Hazard regression modeL The optimum number of markers to be included in a model is selected using the 1 -standard error rule.
  • Figures 13 A and B are graphs showing the kernel density estimate of the linear predictor obtained from 4 Cox PH models on the Marshfield sample set for controls and cases, respectively.
  • Figures 14 A and B are graphs showing the kernel density estimate of linear predictor obtained from 4 Cox PH models on the MESA sample set for controls and cases, respectively.
  • the disclosure provides methods, assays and kits for assessing the cardiovascular health of a human, and particularly, to predict, diagnose, and monitor atherosclerotic cardiovascular disease (ASCVD) in a human.
  • the disclosed methods, assays and kits identify circulating micro ribonucleic acid (miRNA) biomarkers and/or protein biomarkers for assessing the cardiovascular health of a human.
  • miRNA micro ribonucleic acid
  • circulating miRNA and/or protein biomarkers are identified for assessing the cardiovascular health of a human.
  • the disclosure provides a method for assessing the cardiovascular health of a human to determine the need for, or effectiveness of, a treatment regimen comprising: obtaining a biological sample from a human; determining levels of at least 2 miRNA markers selected from the group consisting of the list in Table 20 in the biological sample; obtaining a dataset comprised of the levels of each miRNA marker; inputting the data into an analytical classification process that uses the data to classify the biological sample, wherein the classification is selected from the group consisting of an atherosclerotic cardiovascular disease classification, a healthy classification, a medication exposure classification, a no medication exposure classification; and classifying the biological sample according to the output of the classification process and determining a treatment regimen for the human based on the classification.
  • a method for assessing the cardiovascular health of a human to determine the need for, or effectiveness of, a treatment regimen comprising: obtaining a biological sample from a human; determining levels of at least 3 protein biomarkers selected from the group consisting of IL-16, sFas, Fas ligand, MCP-3, HGF, CTACK, EOTAXIN, adiponectin, IL-18, TIMP.4, TIMP.1 , CRP, VEGF, and EGF in the biological sample; obtaining a dataset comprised of the levels of each protein marker; inputting the data into an analytical classification process that uses the data to classify the biological sample, wherein the classification is selected from the group consisting of an atherosclerotic cardiovascular disease classification, a healthy classification, a medication exposure classification, a no medication exposure classification; and classifying the biological sample according to the output of the classification process and determining a treatment regimen for the human based on the classification.
  • a method for assessing the cardiovascular health of a human.
  • the assessment can be used to determine the need for or effectiveness of a treatment regimen.
  • the method comprises: obtaining a biological sample from a human; determining levels of at least two miRNA markers selected from the miRNAs listed in Table 20 in the biological sample; determining levels of at least three protein biomarker selected from the group consisting of IL-16, sFas, Fas ligand, MCP-3, HGF, CTACK, EOTAXIN, adiponectin, IL-18, TIMP.4, TIMP.1 , CRP, VEGF, and EGF in the biological sample; obtaining a dataset comprised of the levels of the indivdual miRNA markers and the protein biomarkers; inputting the data into an analytical classification process that uses the data to classify the biological sample, wherein the classification is selected from the group consisting of an atherosclerotic cardiovascular disease classification, a healthy classification, a medication exposure classification, a no
  • the data is input into a risk prediction analysis process to predict the risk of a cardiovascular event based on the dataset; and a treatment regimen can be determined for the human based on the predicted risk of a cardiovascular event.
  • the risk of a cardiovascular even can be predicted for about 1 year, about 2 years, about 3 years, about 4 years, about 5 years or more from the date on which the sample is obtained and/or analyzed.
  • the predicted cardiovascular event as described below, can be development of atherosclerotic disease, a Ml, etc.
  • Atherosclerotic disease is also known as atherosclerosis, arteriosclerosis, atheromatous vascular disease, arterial occlusive disease, or cardiovascular disease, and is characterized by plaque accumulation on vessel walls and vascular inflammation.
  • Vascular inflammation is a hallmark of active atherosclerotic disease, unstable plaque, or vulnerable plaque.
  • the plaque consists of accumulated intracellular and extracellular lipids, smooth muscle cells, connective tissue, inflammatory cells, and glycosaminoglycans. Certain plaques also contain calcium. Unstable or active or vulnerable plaques are enriched with inflammatory cells.
  • the present disclosure includes methods for generating a result useful in diagnosing and monitoring atherosclerotic disease by obtaining a dataset associated with a sample, where the dataset at least includes quantitative data about miRNA markers alone or in combination with protein biomarkers which have been identified as predictive of atherosclerotic disease, and inputting the dataset into an analytic process that uses the dataset to generate a result useful in diagnosing and monitoring atherosclerotic disease.
  • This quantitative data can include DNA, RNA, protein expression levels, and a combination thereof.
  • Ml myocardial infarction
  • stroke stroke
  • heart failure a common complication
  • Ml myocardial infarction
  • an acute thrombus often associated with plaque rupture, occludes the artery that supplies the damaged area. Plaque rupture occurs generally in arteries previously partially obstructed by an atherosclerotic plaque enriched in inflammatory cells.
  • the present disclosure identifies profiles of biomarkers of inflammation that can be used for diagnosis and classification of atherosclerotic cardiovascular disease as well as prediction of the risk of a cardiovascular event (e.g., Ml) within a specific period of time from blood draw for a given individual.
  • the miRNA and protein biomarkers assayed in the present disclosure are those identified using a learning algorithm as being capable of distinguishing between different atherosclerotic classifications, e.g., diagnosis, staging, prognosis, monitoring, therapeutic response, and prediction of pseudo-coronary calcium score.
  • Other data useful for making atherosclerotic classifications such as clinical indicia (e.g., traditional risk factors) may also be a part of a dataset used to generate a result useful for atherosclerotic classification.
  • Datasets containing quantitative data for the various miRNA and protein biomarkers markers disclosed herein, alone or in combination, , and quantitative data for other dataset components can be input into an analytical process and used to generate a result.
  • the analytic process may be any type of learning algorithm with defined parameters, or in other words, a predictive model.
  • Predictive models can be developed for a variety of atherosclerotic classifications or risk prediction by applying learning algorithms to the appropriate type of reference or control data.
  • the result of the analytical process/predictive model can be used by an appropriate individual to take the appropriate course of action. For example, if the classification is "healthy" or "atherosclerotic cardiovascular disease", then a result can be used to determine the appropriate clinical course of treatment for an individual.
  • MicroRNA also referred to herein as miRNA, pRNA, mi-R
  • miRNA is a form of single-stranded RNA molecule of about 17-27 nucleotides in length, which regulates gene expression. miRNAs are encoded by genes from whose DNA they are transcribed but miRNAs are not translated into protein (i.e. they are non-coding RNAs); instead each primary transcript (a pri-miRNA) is processed into a short stem- loop structure called a pre-miRNA and finally into a functional miRNA.
  • miRNA markers associated with inflammation and useful for assessing the cardiovascular health of a human include, but are not limited to, one or more of miR-26a, miR-16, miR-222, miR-10b, miR-93, miR-192, miR-15a, miR-125-a.5p, miR-130a, miR-92a, miR-378, miR-20a, miR-20b, miR-107, miR-186, hsa.let.7f, miR-19a, miR-150, miR-106b, miR-30c, and let 7b.
  • the miRNA markers include one or more of miR-26a, miR-16, miR-222, miR-10b, miR- 93, miR-192, miR-15a, miR-125-a.5p, miR-130a, miR-92a, miR-378, and let 7b.
  • the miRNAs listed in Table 20 are useful in assessing cardiovascular health of a human.
  • Protein biomarkers associated with inflammation and useful for assessing the cardiovascular health of a human include, but are not limited to, one or more of RANTES, TIMP1 , MCP-1 , MCP-2, MCP-3, MCP-4, eotaxin, IP-10, -CSF, IL-3, TNFa, Ang-2, IL-5, IL-7, IGF-1 , sVCAM, slCAM-1 , E-selectin, P-selection, interleukin-6, interleukin-18, creatine kinase, LDL, oxLDL, LDL particle size, Lipoprotein(a), troponin I, troponin T, LPPLA2, CRP, HDL, triglycerides, insulin, BNP, fractalkine, osteopontin, osteoprotegerin, oncostatin-M, Myeloperoxidase, ADMA, PAI-1 (plasminogen activator inhibitor), SAA (circulating amyloid A), t-
  • the protein biomarkers include one or more of IL-16, sFas, Fas ligand, MCP-3, HGF, CTACK, EOTAXIN, adiponectin, IL-18, TIMP.4, TIMP.1 , CRP, VEGF, and EGF.
  • the disclosure further includes biomarker variants that are about 90%, about 95%, or about 97% identical to the exemplified sequences.
  • Variants, as used herein, include polymorphisms, splice variants, mutations, and the like.
  • Protein biomarkers can be detected in a variety of ways. For example, in vivo imaging may be utilized to detect the presence of atherosclerosis-associated proteins in heart tissue. Such methods may utilize, for example, labeled antibodies or ligands specific for such proteins.
  • a detectably-labeled moiety e.g., an antibody, ligand, etc., which is specific for the polypeptide is administered to an individual (e.g., by injection), and labeled cells are located using standard imaging techniques, including, but not limited to, magnetic resonance imaging, computed tomography scanning, and the like. Detection may utilize one, or a cocktail of, imaging reagents.
  • Additional markers can be selected from one or more clinical indicia, including but not limited to, age, gender, LDL concentration, HDL concentration, triglyceride concentration, blood pressure, body mass index, CRP concentration, coronary calcium score, waist circumference, tobacco smoking status, previous history of cardiovascular disease, family history of cardiovascular disease, heart rate, fasting insulin concentration, fasting glucose concentration, diabetes status, and use of high blood pressure medication.
  • clinical indicia including but not limited to, age, gender, LDL concentration, HDL concentration, triglyceride concentration, blood pressure, body mass index, CRP concentration, coronary calcium score, waist circumference, tobacco smoking status, previous history of cardiovascular disease, family history of cardiovascular disease, heart rate, fasting insulin concentration, fasting glucose concentration, diabetes status, and use of high blood pressure medication.
  • Additional clinical indicia useful for making atherosclerotic classifications can be identified using learning algorithms known in the art, such as linear discriminant analysis, support vector machine classification, recursive feature elimination, prediction analysis of microarray, logistic regression, CART, FlexTree, LART, random forest, MART, and/or survival analysis regression, which are known to those of skill in the art and are further described herein.
  • learning algorithms known in the art, such as linear discriminant analysis, support vector machine classification, recursive feature elimination, prediction analysis of microarray, logistic regression, CART, FlexTree, LART, random forest, MART, and/or survival analysis regression, which are known to those of skill in the art and are further described herein.
  • the analytical classification disclosed herein can comprise the use of a predictive model.
  • the predictive model further comprises a quality metric of at least about .68 or higher for classification.
  • the quality metric is at least about .70 or higher for classification.
  • the quality metric is selected from area under the curve (AUC), hazard ratio (HR), relative risk (RR), reclassification, positive predictive value (PPV), negative predictive value (NPV), accuracy, sensitivity and specificity, Net reclassification Index, Clinical Net reclassification Index.
  • AUC area under the curve
  • HR hazard ratio
  • RR relative risk
  • reclassification positive predictive value
  • NPV negative predictive value
  • accuracy sensitivity and specificity
  • Net reclassification Index can be used as described herein.
  • various terms can be selected to provide a quality metric.
  • Quantitative data is obtained for each component of the dataset and input into an analytic process with previously defined parameters (the predictive model) and then used to generate a result.
  • the data may be obtained via any technique that results in an individual receiving data associated with a sample.
  • an individual may obtain the dataset by generating the dataset himself by methods known to those in the art.
  • the dataset may be obtained by receiving a dataset or one or more data values from another individual or entity.
  • a laboratory professional may generate certain data values while another individual, such as a medical professional, may input all or part of the dataset into an analytic process to generate the result.
  • the expression pattern in blood, serum, etc. of the protein markers provided herein is obtained.
  • the quantitative data associated with the protein markers of interest can be any data that allows generation of a result useful for atherosclerotic classification, including measurement of DNA or RNA levels associated with the markers but is typically protein expression patterns. Protein levels can be measured via any method known to those of skill in the art that generates a quantitative measurement either individually or via high-throughput methods as part of an expression profile.
  • a blood-derived patient sample e.g., blood, plasma, serum, etc. may be applied to a specific binding agent or panel of specific binding agents to determine the presence and quantity of the protein markers of interest.
  • Blood samples, or samples derived from blood, e.g. plasma, serum, etc. are assayed for the presence of expression levels of the miRNA markers alone or in combination with protein markers of interest.
  • a blood sample is drawn, and a derivative product, such as plasma or serum, is tested.
  • the sample can be derived from other bodily fluids such as saliva, urine, semen, milk or sweat.
  • Samples can further be derived from tissue, such as from a blood vessel, such as an artery, vein, capillary and the like.
  • tissue such as from a blood vessel, such as an artery, vein, capillary and the like.
  • miRNA and protein biomarkers when both miRNA and protein biomarkers are assayed, they can be derived from the same or different samples. That is, for example, an miRNA biomarker can be assayed in a blood derived sample and a protein biomarker can be assayed in a tissue sample.
  • the quantitative data associated with the miRNA and protein markers of interest typically takes the form of an expression profile.
  • Expression profiles constitute a set of relative or absolute expression values for a number of miRNA or protein products corresponding to the plurality of markers evaluated.
  • expression profiles containing expression patterns at least about 2, 3, 4, 5, 6, 7 or more markers are produced.
  • the expression pattern for each differentially expressed component member of the expression profile may provide a particular specificity and sensitivity with respect to predictive value, e.g., for diagnosis, prognosis, monitoring treatment, etc.
  • Numerous methods for obtaining expression data are known, and any one or more of these techniques, singly or in combination, are suitable for determining expression patterns and profiles in the context of the present disclosure.
  • nucleic acid molecules preferably in isolated form.
  • a nucleic acid molecule is to be "isolated” when the nucleic acid molecule is substantially separated from contaminant nucleic acid molecules encoding other polypeptides.
  • nucleic acid is defined as coding and noncoding RNA or DNA. Nucleic acids that are complementary to, that is, hybridize to, and remain stably bound to the molecules under appropriate stringency conditions are included within the scope of this disclosure.
  • sequences exhibit at least 50%, 60%, 70% or 75%, preferably at least about 80-90%, more preferably at least about 92-94%, and even more preferably at least about 95%, 98%, 99% or more nucleotide sequence identity with the RNAs disclosed herein, and include insertions, deletions, wobble bases, substitutions and the like. Further contemplated are sequences sharing at least about 50%, 60%, 70% or 75%, preferably at least about 80-90%, more preferably at least about 92-94%, and most preferably at least about 95%, 98%, 99% or more identity with the protein biomarker sequences disclosed herein
  • genomic DNA e.g., genomic DNA, cDNA, RNA (mRNA, pri-miRNA, pre-miRNA, miRNA, hairpin precursor RNA, RNP, etc.) molecules, as well as nucleic acids based on alternative backbones or including alternative bases, whether derived from natural sources or synthesized.
  • RNA mRNA, pri-miRNA, pre-miRNA, miRNA, hairpin precursor RNA, RNP, etc.
  • nucleic acids based on alternative backbones or including alternative bases, whether derived from natural sources or synthesized.
  • BLAST Basic Local Alignment Search Tool
  • the approach used by the BLAST program is to first consider similar segments, with and without gaps, between a query sequence and a database sequence, then to evaluate the statistical significance of all matches that are identified and finally to summarize only those matches which satisfy a preselected threshold of significance.
  • the search parameters for histogram, descriptions, alignments, expect i.e., the statistical significance threshold for reporting matches against database sequences
  • cutoff i.e., the statistical significance threshold for reporting matches against database sequences
  • cutoff i.e., the statistical significance threshold for reporting matches against database sequences
  • cutoff matrix and filter (low complexity) are at the default settings.
  • the default scoring matrix used by blastp, blastx, tblastn, and tblastx is the BLOSUM62 matrix, recommended for query sequences over 85 nucleotides or amino acids in length.
  • the scoring matrix is set by the ratios of M (i.e., the reward score for a pair of matching residues) to N (i.e., the penalty score for mismatching residues), wherein the default values for M and N are 5 and -4, respectively.
  • M i.e., the reward score for a pair of matching residues
  • N i.e., the penalty score for mismatching residues
  • "Stringent conditions" are those that (1) employ low ionic strength and high temperature for washing, for example, 0.015 M NaCl/0.0015 M sodium citrate/0.1 % SDS at 50°C, or (2) employ during hybridization a denaturing agent such as formamide, for example, 50% (vol/vol) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM NaCl, 75 mM sodium citrate at 42°C.
  • a denaturing agent such as formamide, for example, 50% (vol/vol) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM NaCl, 75 mM sodium citrate at 42°C.
  • a fragment of a nucleic acid molecule refers to a small portion of the coding or non-coding sequence.
  • the size of the fragment will be determined by the intended use. For example, if the fragment is chosen so as to encode an active portion of the protein, the fragment will need to be large enough to encode the functional region(s) of the protein. For instance, fragments which encode peptides corresponding to predicted antigenic regions may be prepared. If the fragment is to be used as a nucleic acid probe or PCR primer, then the fragment length is chosen so as to obtain a relatively small number of false positives during probing/priming.
  • Protein expression patterns can be evaluated by any method known to those of skill in the art which provides a quantitative measure and is suitable for evaluation of multiple markers extracted from samples such as one or more of the following methods: ELISA sandwich assays, flow cytometry, mass spectrometric detection, calorimetric assays, binding to a protein array (e.g., antibody array), or fluorescent activated cell sorting (FACS).
  • ELISA sandwich assays e.g., flow cytometry, mass spectrometric detection, calorimetric assays, binding to a protein array (e.g., antibody array), or fluorescent activated cell sorting (FACS).
  • FACS fluorescent activated cell sorting
  • an approach involves the use of labeled affinity reagents (e.g., antibodies, small molecules, etc.) that recognize epitopes of one or more protein products in an ELISA, antibody-labelled fluorescent bead array, antibody array, or FACS screen.
  • labeled affinity reagents e.g., antibodies, small molecules, etc.
  • Methods for producing and evaluating antibodies are well known in the art.
  • a number of suitable high throughput formats exist for evaluating expression patterns and profiles of the disclosed biomarkers.
  • the term high throughput refers to a format that performs at least about 100 assays, or at least about 500 assays, or at least about 1000 assays, or at least about 5000 assays, or at least about 10,000 assays, or more per day.
  • the number of samples or the number of markers assayed can be considered.
  • microtiter plates are determined by the methods and equipment, e.g., robotic handling and loading systems, used for sample preparation and analysis.
  • exemplary systems include, e.g., xMAP® technology from Luminex (Austin, TX), the SECTOR® Imager with MULTI-ARRAY® and MULTI-SPOT® technologies from Meso Scale Discovery (Gaithersburg, MD), the ORCATM system from Beckman-Coulter, Inc. (Fullerton, Calif.) and the ZYMATETM systems from Zymark Corporation (Hopkinton, MA), miRCURY LNATM microRNA Arrays (Exiqon, Woburn, MA).
  • a variety of solid phase arrays can favorably be employed to determine expression patterns in the context of the disclosed methods, assays and kits.
  • Exemplary formats include membrane or filter arrays (e.g., nitrocellulose, nylon), pin arrays, and bead arrays (e.g., in a liquid "slurry").
  • probes corresponding to nucleic acid or protein reagents that specifically interact with (e.g., hybridize to or bind to) an expression product corresponding to a member of the candidate library are immobilized, for example by direct or indirect cross-linking, to the solid support.
  • any solid support capable of withstanding the reagents and conditions necessary for performing the particular expression assay can be utilized.
  • functionalized glass silicon, silicon dioxide, modified silicon, any of a variety of polymers, such as (poly)tetrafluoroethylene, (poly)vinylidenedifluoride, polystyrene, polycarbonate, or combinations thereof can all serve as the substrate for a solid phase array.
  • polymers such as (poly)tetrafluoroethylene, (poly)vinylidenedifluoride, polystyrene, polycarbonate, or combinations thereof can all serve as the substrate for a solid phase array.
  • the array is a "chip" composed, e.g., of one of the above-specified materials.
  • Polynucleotide probes e.g., RNA or DNA, such as cDNA, synthetic oligonucleotides, and the like, or binding proteins such as antibodies or antigen-binding fragments or derivatives thereof, that specifically interact with expression products of individual components of the candidate library are affixed to the chip in a logically ordered manner, i.e., in an array.
  • any molecule with a specific affinity for either the sense or anti-sense sequence of the marker nucleotide sequence can be fixed to the array surface without loss of specific affinity for the marker and can be obtained and produced for array production, for example, proteins that specifically recognize the specific nucleic acid sequence of the marker, ribozymes, peptide nucleic acids (PNA), or other chemicals or molecules with specific affinity.
  • proteins that specifically recognize the specific nucleic acid sequence of the marker ribozymes, peptide nucleic acids (PNA), or other chemicals or molecules with specific affinity.
  • PNA peptide nucleic acids
  • Microarray expression may be detected by scanning the microarray with a variety of laser or CCD-based scanners, and extracting features with numerous software packages, for example, IMAGENETM (Biodiscovery), Feature Extraction Software (Agilent), SCANLYZETM (Stanford Univ., Stanford, CA.), GENEPIXTM (Axon Instruments).
  • High-throughput protein systems include commercially available systems from Ciphergen Biosystems, Inc. (Fremont, Calif.) such as PROTEIN CHIPTM arrays, and FASTQUANTTM human chemokine protein microspot array (S&S Bioscences Inc., Keene, N.H., US).
  • the quantitative data thus obtained about the miRNA, protein markers and other dataset components is subjected to an analytic process with parameters previously determined using a learning algorithm, i.e., inputted into a predictive model.
  • the parameters of the analytic process may be those disclosed herein or those derived using the guidelines described herein.
  • Learning algorithms such as linear discriminant analysis, recursive feature elimination, a prediction analysis of microarray, logistic regression, CART, FlexTree, LART, random forest, MART, or another machine learning algorithm are applied to the appropriate reference or training data to determine the parameters for analytical processes suitable for a variety of atherosclerotic classifications.
  • the analytic process used to generate a result may be any type of process capable of providing a result useful for classifying a sample, for example, comparison of the obtained dataset with a reference dataset, a linear algorithm, a quadratic algorithm, a decision tree algorithm, or a voting algorithm.
  • Various analytic processes for obtaining a result useful for making an atherosclerotic classification are described herein, however, one of skill in the art will readily understand that any suitable type of analytic process is within the scope of this disclosure.
  • the data in each dataset is collected by measuring the values for each marker, usually in duplicate or triplicate or in multiple replicates.
  • the data may be manipulated, for example, raw data may be transformed using standard curves, and the average of replicate measurements used to calculate the average and standard deviation for each patient. These values may be transformed before being used in the models, e.g. log-transformed, Box-Cox transformed, etc. This data can then be input into the analytical process with defined parameters.
  • the analytic process may set a threshold for determining the probability that a sample belongs to a given class.
  • the probability preferably is at least 50%, or at least 60% or at least 70% or at least 80%, at least 90%, or higher.
  • the analytic process determines whether a comparison between an obtained dataset and a reference dataset yields a statistically significant difference. If so, then the sample from which the dataset was obtained is classified as not belonging to the reference dataset class. Conversely, if such a comparison is not statistically significantly different from the reference dataset, then the sample from which the dataset was obtained is classified as belonging to the reference dataset class.
  • the analytical process will be in the form of a model generated by a statistical analytical method such as those described below.
  • Examples of such analytical processes may include a linear algorithm, a quadratic algorithm, a polynomial algorithm, a decision tree algorithm, a voting algorithm.
  • a linear algorithm may have the form: where R is the useful result obtained.
  • C 0 is a constant that may be zero.
  • C , and x are the constants and the value of the applicable biomarker or clinical indicia, respectively, and N is the total number of markers.
  • a quadratic algorithm may have the form: where R is the useful result obtained.
  • C 0 is a constant that may be zero.
  • C, and x j are the constants and the value of the applicable biomarker or clinical indicia, respectively, and N is the total number of markers.
  • a polynomial algorithm is a more generalized form of a linear or quadratic algorithm that may have the form:
  • C 0 is a constant that may be zero.
  • C , and x are the constants and the value of the applicable biomarker or clinical indicia, respectively; y, is the power to which Xj is raised and N is the total number of markers.
  • an appropriate reference or training dataset can be used to determine the parameters of the analytical process to be used for classification, i.e., develop a predictive model.
  • the reference or training dataset to be used will depend on the desired atherosclerotic classification to be determined.
  • the dataset may include data from two, three, four or more classes.
  • a supervised learning algorithm to determine the parameters for an analytic process used to diagnose atherosclerosis
  • a dataset comprising control and diseased samples is used as a training set.
  • the training set may include data for each of the various stages of cardiovascular disease.
  • Biomarkers whose corresponding features values are capable of discriminating ' between, e.g., healthy and atherosclerotic, are identified herein.
  • the identity of these markers and their corresponding features can be used to develop an analytical process, or plurality of analytical processes, that discriminate between classes of patients.
  • the examples below illustrate how data analysis algorithms can be used to construct a number of such analytical processes.
  • Each of the data analysis algorithms described in the examples use features (e.g., expression values) of a subset of the markers identified herein across a training population that includes healthy and atherosclerotic patients.
  • the analytical process can be used to classify a test subject into one of the two or more phenotypic classes (e.g. a healthy or atherosclerotic patient) and/or predict survival/time-to-event. This is accomplished by applying one or more analytical processes to one or more marker profile(s) obtained from the test subject.
  • phenotypic classes e.g. a healthy or atherosclerotic patient
  • marker profile(s) obtained from the test subject.
  • Such analytical processes therefore, have enormous value as diagnostic indicators.
  • the disclosed methods, assays and kits provide, in one aspect, for the evaluation of one or more marker profile(s) from a test subject to marker profiles obtained from a training population.
  • each marker profile obtained from subjects in the training population, as well as the test subject comprises a feature for each of a plurality of different markers.
  • this comparison is accomplished by (i) developing an analytical process using the marker profiles from the training population and (ii) applying the analytical process to the marker profile from the test subject.
  • the analytical process applied in some embodiments of the methods disclosed herein is used to determine whether a test subject has atherosclerosis.
  • the methods disclosed herein determine whether or not a subject will experience a Ml, and/or can predict time-to-event (e.g. Ml and/or survival).
  • the subject when the results of the application of an analytical process indicate that the subject will likely experience a Ml, the subject is diagnosed/classified as a "Ml" subject. Alternately, if, for example, the results of the analytical process indicate that a subject will likely develop atherosclerosis, the subject is diagnosed as an "atherosclerotic" subject. If the results of an application of an analytical process indicate that the subject will not develop atherosclerosis, the subject is diagnosed as a healthy subject.
  • the result in the above-described binary decision situation has four possible outcomes: (i) truly atherosclerotic, where the analytical process indicates that the subject will develop atherosclerosis and the subject does in fact develop atherosclerosis during the definite time period (true positive, TP); (ii) falsely atherosclerotic, where the analytical process indicates that the subject will develop atherosclerosis and the subject, in fact, does not develop atherosclerosis during the definite time period (false positive, FP); (iii) truly healthy, where the analytical process indicates that the subject will not develop atherosclerosis and the subject, in fact, does not develop atherosclerosis during the definite time period (true negative, TN); or (iv) falsely healthy, where the analytical process indicates that the subject will not develop atherosclerosis and the subject, in fact, does develop atherosclerosis during the definite time period (false negative, FN).
  • a number of quantitative criteria can be used to communicate the performance of the comparisons made between a test marker profile and reference marker profiles (e.g., the application of an analytical process to the marker profile from a test subject). These include positive predicted value (PPV), negative predicted value (NPV), specificity, sensitivity, accuracy, and certainty.
  • PPV positive predicted value
  • NPV negative predicted value
  • ROC receiver operator curves
  • PPV TP/(TP+FP)
  • NPV TN/(TN+FN)
  • specificity TN/(TN+FP)
  • sensitivity TP/(TP+FN)
  • the population comprises subjects whose samples and phenotypic data (e.g., feature values of markers and an indication of whether or not the subject developed atherosclerosis) was used to construct or refine an analytical process.
  • phenotypic data e.g., feature values of markers and an indication of whether or not the subject developed atherosclerosis
  • the population comprises subjects that were not used to construct the analytical process.
  • a population is referred to herein as a validation population.
  • the population represented by N is either exclusively a training population or exclusively a validation population, as opposed to a mixture of the two population types. It will be appreciated that scores such as accuracy will be higher (closer to unity) when they are based on a training population as opposed to a validation population.
  • N is more than 1 , more than 5, more than 10, more than 20, between 10 and 100, more than 100, or less than 1000 subjects.
  • An analytical process (or other forms of comparison) can have at least about 99% certainty, or even more, in some embodiments, against a training population or a validation population.
  • the certainty is at least about 97%, at least about 95%, at least about 90%, at least about 85%, at least about 80%, at least about 75%, at least about 70%, at least about 65%, or at least about 60% against a training population or a validation population.
  • the useful degree of certainty may vary, depending on the particular method.
  • the sensitivity and/or specificity is at least about 97%, at least about 95%, at least about 90%, at least about 85%, at least about 80%, at least about 75%, or at least about 70% against a training population or a validation population.
  • such analytical processes are used to predict the development of atherosclerosis with the stated accuracy.
  • such analytical processes are used to diagnoses atherosclerosis with the stated accuracy.
  • such analytical processes are used to determine a stage of atherosclerosis with the stated accuracy.
  • the number of features that may be used by an analytical process to classify a test subject with adequate certainty is 2 or more. In some embodiments, it is 3 or more, 4 or more, 10 or more, or between 10 and 200. Depending on the degree of certainty sought, however, the number of features used in an analytical process can be more or less, but in all cases is at least 2. In one embodiment, the number of features that may be used by an analytical process to classify a test subject is optimized to allow a classification of a test subject with high certainty.
  • the proportional hazards assumption is the assumption that covariates multiply hazard.
  • a treatment with a drug may, say, halve a subject's hazard at any given time t, while the baseline hazard may vary.
  • the covariate is not restricted to binary predictors; in the case of a continuous covariate x, the hazard responds logarithmically; each unit increase in x results in proportional scaling of the hazard.
  • the baseline hazard is "integrated out", or heuristically removed from consideration, and the remaining partial likelihood is maximized.
  • the effect of covariates estimated by any proportional hazards model can thus be reported as hazard ratios.
  • the Cox model assumes that if the proportional hazards assumption holds, it is possible to estimate the effect parameters without consideration of the hazard function.
  • comparison of a test subject's marker profile to a marker profile(s) obtained from a training population is performed, and comprises applying an analytical process.
  • the analytical process is constructed using a data analysis algorithm, such as a computer pattern recognition algorithm.
  • Other suitable data analysis algorithms for constructing analytical process include, but are not limited to, logistic regression or a nonparametric algorithm that detects differences in the distribution of feature values (e.g., a Wilcoxon Signed Rank Test (unadjusted and adjusted)).
  • the analytical process can be based upon 2, 3, 4, 5, 10, 20 or more features, corresponding to measured observables from 1 , 2, 3, 4, 5, 10, 20 or more markers. In one embodiment, the analytical process is based on hundreds of features or more.
  • each marker profile from a training population can comprise at least 3 features, where the features are predictors in a classification tree algorithm.
  • the analytical process predicts membership within a population (or class) with an accuracy of at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 97%, at least about 98%, at least about 99%, or about 100%.
  • a data analysis algorithm of the disclosure comprises Classification and Regression Tree (CART), Multiple Additive Regression Tree (MART), Prediction Analysis for Microarrays (PAM), or Random Forest analysis.
  • CART Classification and Regression Tree
  • MART Multiple Additive Regression Tree
  • PAM Prediction Analysis for Microarrays
  • Random Forest analysis Such algorithms classify complex spectra from biological materials, such as a blood sample, to distinguish subjects as normal or as possessing biomarker levels characteristic of a particular disease state.
  • a data analysis algorithm of the disclosure comprises ANOVA and nonparametric equivalents, linear discriminant analysis, logistic regression analysis, nearest neighbor classifier analysis, neural networks, principal component analysis, quadratic discriminant analysis, regression classifiers and support vector machines. While such algorithms may be used to construct an analytical process and/or increase the speed and efficiency of the application of the analytical process and to avoid investigator bias, one of ordinary skill in the art will realize that computer-based algorithms are not required to carry out the methods of the present disclosure.
  • Analytical processes can be used to evaluate biomarker profiles, regardless of the method that was used to generate the marker profile.
  • suitable analytical processes can be used to evaluate marker profiles generated using gas chromatography, spectra obtained by static time-of-flight secondary ion mass spectrometry (TOF-SIMS), distinguishing between bacterial strains with high certainty (79-89% correct classification rates) by analysis of MALDI-TOF-MS spectra, use of MALDI-TOF-MS and liquid chromatography-electrospray ionization mass spectrometry (LC/ESI-MS) to classify profiles of biomarkers in complex biological samples.
  • TOF-SIMS static time-of-flight secondary ion mass spectrometry
  • LC/ESI-MS liquid chromatography-electrospray ionization mass spectrometry
  • One approach to developing an analytical process using expression levels of markers disclosed herein is the nearest centroid classifier.
  • Such a technique computes, for each class (e.g., healthy and atherosclerotic), a centroid given by the average expression levels of the markers in the class, and then assigns new samples to the class whose centroid is nearest.
  • This approach is similar to k- means clustering except clusters are replaced by known classes. This algorithm can be sensitive to noise when a large number of markers are used.
  • One enhancement to the technique uses shrinkage: for each marker, differences between class centroids are set to zero if they are deemed likely to be due to chance. This approach is implemented in the Prediction Analysis of Microarray, or PAM. Shrinkage is controlled by a threshold below which differences are considered noise.
  • MART Multiple additive regression trees
  • an analytical process used to classify subjects is built using regression.
  • the analytical process can be characterized as a regression classifier, preferably a logistic regression classifier.
  • a regression classifier includes a coefficient for each of the markers (e.g., the expression level for each such marker) used to construct the classifier.
  • the coefficients for the regression classifier are computed using, for example, a maximum likelihood approach.
  • the features for the biomarkers e.g., RT-PCR, microarray data
  • molecular marker data from only two trait subgroups is used (e.g., healthy patients and atherosclerotic patients) and the dependent variable is absence or presence of a particular trait in the subjects for which marker data is available.
  • the training population comprises a plurality of trait subgroups (e.g., three or more trait subgroups, four or more specific trait subgroups, etc.). These multiple trait subgroups can correspond to discrete stages in the phenotypic progression from healthy, to mild atherosclerosis, to medium atherosclerosis, etc. in a training population.
  • a generalization of the logistic regression model that handles multi-category responses can be used to develop a decision that discriminates between the various trait subgroups found in the training population. For example, measured data for selected molecular markers can be applied to any of the multi-category logit models in order to develop a classifier capable of discriminating between any of a plurality of trait subgroups represented in a training population.
  • the analytical process is based on a regression model, preferably a logistic regression model.
  • a regression model includes a coefficient for each of the markers in a selected set of markers disclosed herein.
  • the coefficients for the regression model are computed using, for example, a maximum likelihood approach.
  • molecular marker data from the two groups e.g., healthy and diseased
  • the dependent variable is the status of the patient corresponding to the marker characteristic data.
  • Some embodiments of the disclosed methods, assays and kits provide generalizations of the logistic regression model that handle multi-category (polychotomous) responses. Such embodiments can be used to discriminate an organism into one or three or more classifications. Such regression models use multicategory logit models that simultaneously refer to all pairs of categories, and describe the odds of response in one category instead of another. Once the model specifies logits for a certain (J-1) pairs of categories, the rest are redundant.
  • LDA Linear discriminant analysis
  • LDA seeks the linear combination of variables that maximizes the ratio of between-group variance and within-group variance by using the grouping information. Implicitly, the linear weights used by LDA depend on how the expression of a marker across the training set separates in the two groups (e.g., a group that has atherosclerosis and a group that does not have atherosclerosis) and how this expression correlates with the expression of other markers.
  • LDA is applied to the data matrix of the N members in the training sample by K genes in a combination of genes described in the present disclosure. Then, the linear discriminant of each member of the training population is plotted. Ideally, those members of the training population representing a first subgroup (e.g.
  • Quadratic discriminant analysis takes the same input parameters and returns the same results as LDA.
  • QDA uses quadratic equations, rather than linear equations, to produce results.
  • LDA and QDA are roughly interchangeable (though there are differences related to the number of subjects required), and which to use is a matter of preference and/or availability of software to support the analysis.
  • Logistic regression takes the same input parameters and returns the same results as LDA and QDA.
  • One type of analytical process that can be constructed using the expression level of the markers identified herein is a decision tree.
  • the "data analysis algorithm” is any technique that can build the analytical process
  • the final “decision tree” is the analytical process.
  • An analytical process is constructed using a training population and specific data analysis algorithms. Tree-based methods partition the feature space into a set of rectangles, and then fit a model (like a constant) in each one.
  • the training population data includes the features (e.g., expression values, or some other observable) for the markers across a training set population.
  • One specific algorithm that can be used to construct an analytical process is a classification and regression tree (CART).
  • Other specific decision tree algorithms include, but are not limited to, ID3, C4.5, MART, and Random Forests. All such algorithms are known in the art.
  • decision trees are used to classify patients using expression data for a selected set of markers.
  • Decision tree algorithms belong to the class of supervised learning algorithms.
  • the aim of a decision tree is to induce an analytical process (a tree) from real-world example data. This tree can be used to classify unseen examples which have not been used to derive the decision tree.
  • a decision tree is derived from training data.
  • An example contains values for the different attributes and what class the example belongs.
  • the training data is expression data for a combination of markers described herein across the training population.
  • the l-value shows how much information is needed in order to be able to describe the outcome of a classification for the specific dataset used. Supposing that the dataset contains p positive (e.g. has atherosclerosis) and n negative (e.g. healthy) examples (e.g. individuals), the information contained in a correct answer is:
  • log2 is the logarithm using base two.
  • v is the number of unique attribute values for attribute A in a certain dataset
  • i is a certain attribute value
  • p is the number of examples for attribute A where the classification is positive (e.g. atherosclerotic)
  • n is the number of examples for attribute A where the classification is negative (e.g. healthy).
  • the information gain of a specific attribute A is calculated as the difference between the information content for the classes and the remainder of attribute A:
  • the information gain is used to evaluate how important the different attributes are for the classification (how well they split up the examples), and the attribute with the highest information.
  • the expression data for a selected set of markers across a training population is standardized to have mean zero and unit variance.
  • the members of the training population are randomly divided into a training set and a test set. For example, in one embodiment, two thirds of the members of the training population are placed in the training set and one third of the members of the training population are placed in the test set.
  • the expression values for a select combination of markers described herein is used to construct the analytical process. Then, the ability for the analytical process to correctly classify members in the test set is determined.
  • this computation is performed several times for a given combination of markers.
  • the members of the training population are randomly assigned to the training set and the test set. Then, the quality of the combination of molecular markers is taken as the average of each such iteration of the analytical process computation.
  • multivariate decision trees can be implemented as an analytical process. In such multivariate decision trees, some or all of the decisions actually comprise a linear combination of expression levels for a plurality of markers. Such a linear combination can be trained using known techniques such as gradient descent on a classification or by the use of a sum- squared-error criterion.
  • xiand x ⁇ refer to two different features for two different markers from among the markers disclosed herein.
  • xiand x ⁇ refer to two different features for two different markers from among the markers disclosed herein.
  • the values of features Xi and x 2 are obtained from the measurements obtained from the unclassified subject. These values are then inserted into the equation. If a value of less than 500 is computed, then a first branch in the decision tree is taken. Otherwise, a second branch in the decision tree is taken.
  • MARS multivariate adaptive regression splines
  • the expression values for a selected set of markers are used to cluster a training set. For example, consider the case in which ten markers are used. Each member m of the training population will have expression values for each of the ten markers. Such values from a member m in the training population define the vector:
  • Xi m is the expression level of the i th marker in subject m. If there are m organisms in the training set, selection of i markers will define m vectors. Note that the methods disclosed herein do not require that each the expression value of every single marker used in the vectors be represented in every single vector m. In other words, data from a subject in which one of the i th marker is not found can still be used for clustering. In such instances, the missing expression value is assigned either a "zero" or some other normalized value. In some embodiments, prior to clustering, the expression values are normalized to have a mean value of zero and unit variance.
  • Those members of the training population that exhibit similar expression patterns across the training group will tend to cluster together.
  • a particular combination of markers is considered to be a good classifier in this aspect of the methods disclosed herein when the vectors cluster into the trait groups found in the training population. For instance, if the training population includes healthy patients and atherosclerotic patients, a clustering classifier will cluster the population into two groups, with each group uniquely representing either healthy patients and atherosclerotic patients.
  • the clustering problem is described as one of finding natural groupings in a dataset.
  • two issues are addressed.
  • a way to measure similarity (or dissimilarity) between two samples is determined. This metric (similarity measure) is used to ensure that the samples in one cluster are more like one another than they are to samples in other clusters.
  • a mechanism for partitioning the data into clusters using the similarity measure is determined.
  • One way to begin a clustering investigation is to define a distance function and to compute the matrix of distances between all pairs of samples in a dataset. If distance is a good measure of similarity, then the distance between samples in the same cluster will be significantly less than the distance between samples in different clusters.
  • clustering does not require the use of a distance metric.
  • a nonmetric similarity function s(x, x') can be used to compare two vectors x and x'.
  • s(x, x') is a symmetric function whose value is large when x and x' are somehow "similar.”
  • clustering requires a criterion function that measures the clustering quality of any partition of the data. Partitions of the data set that extremize the criterion function are used to cluster the data.
  • Particular exemplary clustering techniques that can be used with the methods disclosed herein include, but are not limited to, hierarchical clustering (agglomerative clustering using nearest-neighbor algorithm, farthest-neighbor algorithm, the average linkage algorithm, the centroid algorithm, or the sum-of-squares algorithm), k-means clustering, fuzzy k-means clustering algorithm, and Jarvis-Patrick clustering.
  • PCA Principal components
  • PCA can also be used to create an analytical process as disclosed herein.
  • vectors for a selected set of markers can be constructed in the same manner described for clustering.
  • the set of vectors, where each vector represents the expression values for the select markers from a particular member of the training population can be considered a matrix.
  • this matrix is represented in a Free-Wilson method of qualitative binary description of monomers, and distributed in a maximally compressed space using PCA so that the first principal component (PC) captures the largest amount of variance information possible, the second principal component (PC) captures the second largest amount of all variance information, and so forth until all variance information in the matrix has been accounted for.
  • each of the vectors (where each vector represents a member of the training population) is plotted.
  • Many different types of plots are possible.
  • a one-dimensional plot is made.
  • the value for the first principal component from each of the members of the training population is plotted.
  • the expectation is that members of a first group (e.g. healthy patients) will cluster in one range of first principal component values and members of a second group (e.g., patients with atherosclerosis) will cluster in a second range of first principal component values (one of skill in the art would appreciate that the distribution of the marker values need to exhibit no elongation in any of the variables for this to be effective).
  • the training population comprises two groups: healthy patients and patients with atherosclerosis.
  • the first principal component is computed using the marker expression values for the selected markers across the entire training population data set. Then, each member of the training set is plotted as a function of the value for the first principal component.
  • those members of the training population in which the first principal component is positive are the healthy patients and those members of the training population in which the first principal component is negative are atherosclerotic patients.
  • the members of the training population are plotted against more than one principal component.
  • the members of the training population are plotted on a two-dimensional plot in which the first dimension is the first principal component and the second dimension is the second principal component.
  • the expectation is that members of each subgroup represented in the training population will cluster into discrete groups. For example, a first cluster of members in the two-dimensional plot will represent subjects with mild atherosclerosis, a second cluster of members in the two-dimensional plot will represent subjects with moderate atherosclerosis, and so forth.
  • the members of the training population are plotted against more than two principal components and a determination is made as to whether the members of the training population are clustering into groups that each uniquely represents a subgroup found in the training population.
  • principal component analysis is performed by using the R mva package (a statistical analysis language), which is known to those of skill in the art.
  • Nearest neighbor classifiers are memory-based and require no model to be fit. Given a query point x 0 , the k training points ⁇ (r) , r k closest in distance to xo are identified and then the point x 0 is classified using the k nearest neighbors. Ties can be broken at random. In some embodiments, Euclidean distance in feature space is used to determine distance as:
  • the members of the training population are randomly assigned to the training set and the test set. Then, the quality of the combination of markers is taken as the average of each such iteration of the nearest neighbor computation.
  • the nearest neighbor rule can be refined to deal with issues of unequal class priors, differential misclassification costs, and feature selection. Many of these refinements involve some form of weighted voting for the neighbors.
  • Bagging, boosting, the random subspace method, and additive trees are data analysis algorithms known as combining techniques that can be used to improve weak analytical processes. These techniques are designed for, and usually applied to, decision trees, such as the decision trees described above. In addition, such techniques can also be useful in analytical processes developed using other types of data analysis algorithms such as linear discriminant analysis.
  • a 1 ,a 2 ,....,a m are computed by the boosting algorithm and their purpose is to weigh the contribution of each respective G m (x). Their effect is to give higher influence to the more accurate classifiers in the sequence.
  • the current classifier G m (x) is induced on the weighted observations at line 2a.
  • the resulting weighted error rate is computed at line 2b.
  • Line 2c calculates the weight a m given to G m (x) in producing the final classifier G m (line 3).
  • the individual weights of each of the observations are updated for the next iteration at line 2d.
  • Observations misclassified by G m (x) have their weights scaled by a factor exp( ⁇ m ), increasing their relative influence for inducing the next classifier G m +l(x) in the sequence.
  • boosting or adaptive boosting methods are used.
  • feature preselection is performed using a technique such as the nonparametric scoring method.
  • Feature preselection is a form of dimensionality reduction in which the markers that discriminate between classifications the best are selected for use in the classifier.
  • the LogitBoost procedure is used rather than the boosting procedure.
  • the boosting and other classification methods are used in the disclosed methods.
  • classifiers are constructed in random subspaces of the data feature space. These classifiers are usually combined by simple majority voting in the final decision rule (i.e., analytical process).
  • the statistical techniques described herein are merely examples of the types of algorithms and models that can be used to identify a preferred group of markers to include in a dataset and to generate an analytical process that can be used to generate a result using the dataset. Further, combinations of the techniques described above and elsewhere can be used either for the same task or each for a different task. Some combinations, such as the use of the combination of decision trees and boosting, have been described. However, many other combinations are possible. By way of example, other statistical techniques in the art such as Projection Pursuit and Weighted Voting can be used to identify a preferred group of markers to include in a dataset and to generate an analytical process that can be used to generate a result using the dataset.
  • An optimum number of dataset components to be evaluated in an analytical process can be determined.
  • one of skill in the art may select a subset of markers, i.e. at least 3, at least 4, at least 5, at least 6, up to the complete set of markers, to define the analytical process.
  • a subset of markers will be chosen that provides for the needs of the quantitative sample analysis, e.g. availability of reagents, convenience of quantitation, etc., while maintaining a highly accurate predictive model.
  • the selection of a number of informative markers for building classification models requires the definition of a performance metric and a user- defined threshold for producing a model with useful predictive ability based on this metric.
  • the performance metric may be the AUC, the sensitivity and/or specificity of the prediction as well as the overall accuracy of the prediction model.
  • a desired quality threshold is a predictive model that will classify a sample with an accuracy of at least about 0.7, at least about 0.75, at least about 0.8, at least about 0.85, at least about 0.9, at least about 0.95, or higher.
  • a desired quality threshold may refer to a predictive model that will classify a sample with an AUC of at least about 0.7, at least about 0.75, at least about 0.8, at least about 0.85, at least about 0.9, or higher.
  • the relative sensitivity and specificity of a predictive model can be "tuned" to favor either the selectivity metric or the sensitivity metric, where the two metrics have an inverse relationship.
  • the limits in a model as described above can be adjusted to provide a selected sensitivity or specificity level, depending on the particular requirements of the test being performed.
  • One or both of sensitivity and specificity may be at least about at least about 0.7, at least about 0.75, at least about 0.8, at least about 0.85, at least about 0.9, or higher.
  • Various methods are used in a training model.
  • the selection of a subset of markers may be via a forward selection or a backward selection of a marker subset.
  • the number of markers to be selected is that which will optimize the performance of a model without the use of all the markers.
  • One way to define the optimum number of terms is to choose the number of terms that produce a model with desired predictive ability (e.g. an AUC>0.75, or equivalent measures of sensitivity/specificity) that lies no more than one standard error from the maximum value obtained for this metric using any combination and number of terms used for the given algorithm.
  • the result can be any type of information useful for making an atherosclerotic classification, e.g. a classification, a continuous variable, or a vector.
  • a classification e.g. a classification, a continuous variable, or a vector.
  • the value of a continuous variable or vector may be used to determine the likelihood that a sample is associated with a particular classification.
  • Atherosclerotic classification refer to any type of information or the generation of any type of information associated with an atherosclerotic condition, for example, diagnosis, staging, assessing extent of atherosclerotic progression, prognosis, monitoring, therapeutic response to treatments, screening to identify compounds that act via similar mechanisms as known atherosclerotic treatments, prediction of pseudo-coronary calcium score, stable (i.e., angina) vs. unstable (i.e., myocardial infarction), identifying complications of atherosclerotic disease, etc.
  • the result is used for diagnosis or detection of the occurrence of an atherosclerosis, particularly where such atherosclerosis is indicative of a propensity for myocardial infarction, heart failure, etc.
  • a reference or training set containing "healthy” and “atherosclerotic” samples is used to develop a predictive model.
  • a dataset, preferably containing protein expression levels of markers indicative of the atherosclerosis, is then inputted into the predictive model in order to generate a result.
  • the result may classify the sample as either "healthy” or "atherosclerotic".
  • the result is a continuous variable providing information useful for classifying the sample, e.g., where a high value indicates a high probability of being an "atherosclerotic" sample and a low value indicates a low probability of being a "healthy” sample.
  • the result is used for atherosclerosis staging.
  • a reference or training dataset containing samples from individuals with disease at different stages is used to develop a predictive model.
  • the model may be a simple comparison of an individual dataset against one or more datasets obtained from disease samples of known stage or a more complex multivariate classification model.
  • inputting a dataset into the model will generate a result classifying the sample from which the dataset is generated as being at a specified cardiovascular disease stage. Similar methods may be used to provide atherosclerosis prognosis, except that the reference or training set will include data obtained from individuals who develop disease and those who fail to develop disease at a later time.
  • the result is used to determine response to atherosclerotic disease treatments.
  • the reference or training dataset and the predictive model is the same as that used to diagnose atherosclerosis (samples of from individuals with disease and those without).
  • the dataset is composed of individuals with known disease which have been administered a particular treatment and it is determined whether the samples trend toward or lie within a normal, healthy classification versus an atherosclerotic disease classification.
  • Treatment as used herein can include, without limitation, a follow-up checkup in 3, 6, or 12 months; pharmacologic intervention such as beta-blocker, calcium channel blocker, aspirin, cholesterol lowering agents, etc; and/or further testing to determine the existence or degree of cardiovascular condition/disease. In certain instances, no immediate treatment will be required.
  • the result is used for drug screening, i.e., identifying compounds that act via similar mechanisms as known atherosclerotic drug treatments
  • a reference or training set containing individuals treated with a known atherosclerotic drug treatment and those not treated with the particular treatment can be used develop a predictive model.
  • a dataset from individuals treated with a compound with an unknown mechanism is input into the model. If the result indicates that the sample can be classified as coming from a subject dosed with a known atherosclerotic drug treatment, then the new compound is likely to act via the same mechanism.
  • the result is used to determine a "pseudo- coronary calcium score," which is a quantitative measure that correlates to coronary calcium score (CCS).
  • CCS is a clinical cardiovascular disease screening technique which measures overall atherosclerotic plaque burden.
  • imaging techniques can be used to quantitate the calcium area and density of atherosclerotic plaques.
  • CCS is a function of the x-ray attenuation coefficient and the area of calcium deposits.
  • a score of 0 is considered to indicate no atherosclerotic plaque burden, >0 to 10 to indicate minimal evidence of plaque burden, 11 to 100 to indicate at least mild evidence of plaque burden, 101 to 400 to indicate at least moderate evidence of plaque burden, and over 400 as being extensive evidence of plaque burden.
  • CCS used in conjunction with traditional risk factors improves predictive ability for complications of cardiovascular disease.
  • the CCS is also capable of acting as an independent predictor of cardiovascular disease complications.
  • a reference or training set containing individuals with high and low coronary calcium scores can be used to develop a model for predicting the pseudo- coronary calcium score of an individual. This predicted pseudo-coronary calcium score is useful for diagnosing and monitoring atherosclerosis. In some embodiments, the pseudo-coronary calcium score is used in conjunction with other known cardiovascular diagnosis and monitoring methods, such as actual coronary calcium score derived from imaging techniques to diagnose and monitor cardiovascular disease.
  • reagents and kits thereof for practicing one or more of the above-described methods.
  • the subject reagents and kits thereof may vary greatly.
  • Reagents of interest include reagents specifically designed for use in production of the above described expression profiles of circulating miRNA markers, protein biomarkers, or a combination of miRNA and protein markers associated with atherosclerotic conditions.
  • a kit for assessing the cardiovascular health of a human to determine the need for or effectiveness of a treatment regimen comprises: an assay for determining levels of at least two miRNA markers selected from the the miRNAs in Table 20 in the biological sample; instructions for obtaining a dataset comprised of the levels of each miRNA marker, inputting the data into an analytical classification process that uses the data to classify the biological sample, wherein the classification is selected from the group consisting of an atherosclerotic cardiovascular disease classification, a healthy classification, a medication exposure classification, a no medication exposure classification; and classifying the biological sample according to the output of the classification process and determining a treatment regimen for the human based on the classification.
  • the kit further comprises an assay for determining levels of at least three protein biomarker selected from the group consisting IL-16, sFas, Fas ligand, MCP-3, HGF, CTACK, EOTAXIN, adiponectin, IL- 18, TIMP.4, TIMP.1 , CRP, VEGF, and EGF in the biological sample; and instructions for obtaining a dataset comprised of the indivdual levels of the protein markers, inputting the data of the miRNA and protein markers into an analytical classification process that uses the data to classify the biological sample, wherein the classification is selected from the group consisting of an atherosclerotic cardiovascular disease classification, a healthy classification, a medication exposure classification, a no medication exposure classification; and classifying the biological sample according to the output of the classification process and determining a treatment regimen for the human based on the classification.
  • the classification is selected from the group consisting of an atherosclerotic cardiovascular disease classification, a healthy classification, a medication exposure classification, a no medication exposure classification
  • One type of such reagent is an array or kit of antibodies that bind to a marker set of interest.
  • array or kit compositions of interest include or consist of reagents for quantitation of at least 2, at least 3, at least 4, at least 5 or more miRNA markers alone or in combination with protein markers.
  • the reagent can be for quantitation of at least 1 , at least 2, at least 3, at least 4, at least 5 miRNA markers selected from the miRNAs listed in Table 1 and preferably, the miRNAs listed in Table 20.
  • the reagent can be for quantitation of at least 1 , at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9 or at least 10 protein biomarkers selected from TABLE 2
  • the protein biomarkers are selected from IL-16, sFas, Fas ligand, MCP-3, HGF, CTACK, EOTAXIN, adiponectin, IL-18, TIMP.4, TIMP.1 , CRP, VEGF, and EGF.
  • the subject kits will further include instructions for practicing the subject methods. These instructions may be present in the subject kits in a variety of forms, one or more of which may be present in the kit.
  • One form in which these instructions may be present is as printed information on a suitable medium or substrate, e.g., a piece or pieces of paper on which the information is printed, in the packaging of the kit, in a package insert, etc.
  • Yet another means would be a computer readable medium, e.g., diskette, CD, etc., on which the information has been recorded.
  • Yet another means that may be present is a website address which may be used via the internet to access the information at a removed site. Any convenient means may be present in the kits.
  • the methods assays and kits disclosed herein can be used to detect a biomarker in a pooled sample. This method is particularly useful when only a small amount of multiple samples are available (for example, archived clinical sample sets) and/or to create useful datasets relevant to a disease or control population.
  • equal amounts for example, about 10 ⁇ _, about 15 pl_, about 20 ⁇ _, about 30 ⁇ _, about 40 ⁇ _, about 50 ⁇ , or more
  • a sample can be obtained from multiple (about 2, 5, 10, 15, 20, 30, 50, 100 or more) individuals.
  • the individuals can be matched by various indicia.
  • the indicia can include age, gender, history of disease, time to event, etc.
  • the equal amounts of sample obtained from each individual can be pooled and analyzed for the presence of one or more biomarkers.
  • the results can be used to create a reference set, make predictions, determine biomarkers associated with a given condition, etc by using the prediction and classifying models described herein.
  • this method can be used to detect DNA, RNA (mRNA, miRNA, hairpin precursor RNA, RNP), proteins, and the like, associated with a variety of diseases and conditions.
  • monitoring refers to the use of results generated from datasets to provide useful information about an individual or an individual's health or disease status.
  • Monitoring can include, for example, determination of prognosis, risk-stratification, selection of drug therapy, assessment of ongoing drug therapy, determination of effectiveness of treatment, prediction of outcomes, determination of response to therapy, diagnosis of a disease or disease complication, following of progression of a disease or providing any information relating to a patient's health status over time, selecting patients most likely to benefit from experimental therapies with known molecular mechanisms of action, selecting patients most likely to benefit from approved drugs with known molecular mechanisms where that mechanism may be important in a small subset of a disease for which the medication may not have a label, screening a patient population to help decide on a more invasive/expensive test, for example, a cascade of tests from a non-invasive blood test to a more invasive option such as biopsy, or testing to assess side effects of drugs used to treat another indication.
  • Quantitative data refers to data associated with any dataset components (e.g., miRNA markers, protein markers, clinical indicia, metabolic measures, or genetic assays) that can be assigned a numerical value.
  • Quantitative data can be a measure of the DNA, RNA, or protein level of a marker and expressed in units of measurement such as molar concentration, concentration by weight, etc.
  • quantitative data for that marker can be protein expression levels measured using methods known to those of skill in the art and expressed in mM or mg/dL concentration units.
  • mammal as used herein includes both humans and non- humans and include but is not limited to humans, non-human primates, canines, felines, murines, bovines, equines, and porcines.
  • percent "identity" in the context of two or more nucleic acid or polypeptide sequences refer to two or more sequences or subsequences that have a specified percentage of nucleotides or amino acid residues that are the same, when compared and aligned for maximum correspondence, as measured using one of the sequence comparison algorithms described below (e.g., BLASTP and BLASTN or other algorithms available to persons of skill) or by visual inspection.
  • sequence comparison algorithms e.g., BLASTP and BLASTN or other algorithms available to persons of skill
  • the percent “identity” can exist over a region of the sequence being compared, e.g., over a functional domain, or, alternatively, exist over the full length of the two sequences to be compared.
  • the "effectiveness" of a treatment regimen is determined.
  • a treatment regimen is considered effective based on an improvement, amelioration, reduction of risk, or slowing of progression of a condition or disease. Such a determination is readily made by one of skill in the art.
  • the performance of the test in terms of AUC depends on the distribution of measured values (for individual markers) or of that of the score, which at the time of the experimental design was unknown.
  • a number of simulations were performed using different assumed distributions for the variables and number of samples in a pool.
  • the assumed distributions used were: a) normal, b) chisq and c) log-normal. For each distribution and number of samples in a pool the appropriate number of "controls" was randomly selected and the corresponding number of cases was selected from a distribution with known shift in the mean, in order to represent differences between the populations.
  • each pooled sample is created by averaging the values of M samples. The process was repeated 500 times and a distribution of expected AUCs was estimated for a given number of pooled samples and population distance.
  • the QIAGEN RNEASY ® Mini spin column was transferred to a new collection tube and centrifuge at 15,000 x g for 2 min at room temperature.
  • the QIAGEN RNEASY ® Mini spin column was transferred to a new microcentrifuge tube and the lid was uncapped for 1 min to dry.
  • RNA was eluted by adding 50 ⁇ _ of RNase-free water to the membrane of the QIAGEN RNEASY® mini spin column and incubated for 1 min before centrifugation at 15,000 x g for 1 min at room temperature. RNA was stored in -70°C freezer until shipment on dry ice. Thirty-eight miRNAs were selected for analysis (Table 3).
  • RNA sample was reverse transcribed (RT) into cDNA in three independent RT reactions and run as singlicate real-time PCR or qPCR reaction.
  • RT reverse transcribed
  • Each 384 well plate contained reactions for all the samples for 2 miRNA assays. Negative controls were included in the experiment: No template control (RNA replaced with water) in RT step, and a No enzyme control in the RT step (pooled RNA as template). All assays passed this quality control step in that the no template control and no enzyme control were negative.
  • the amplification curves were analyzed using the LIGHTCYCLER ® software (Roche, Indianapolis, IN) both for determination of Cp (crossing point, i.e., the point where the measured signal crosses above a predesignated threshold value, indicating a measurable concentration of the target sequence) (by 2 nd derivative method) and for melting curve analysis.
  • PCR efficiency was also assessed by analysis of the PCR amplification curve with the LIN REG ® software (Open Source Software) The performance of five housekeeping miRNAs (miR-16, miR-93, miR-103, miR-192 & miR-451) was used to evaluate the quality of the RNA extracted from the supplied serum samples.
  • AUC was calculated using a prevalidated score.
  • the prevalidation is very similar to a cross-validation approach, where the association of a "score" with a given outcome is based on values that for a given subject have been predicted from a model that was fit without using the specific subject in the training set.
  • prevalidated scores were calculated based on two approaches: a) k-fold cross-validation and b) leave- one-out cross validation.
  • the prevalidation iteration has been repeated N times (where N is usually equal to 100-1000). The complete sequence of the analysis is as follows:
  • Figure 3 presents the distribution of AUC values obtained using a penalized logistic regression model (L1 penalty - lasso) with 100 repeats of the prevalidation score calculation.
  • Table 4 presents the top miRNAs selected during the process of model selection and fitting using penalized logistic regression (L1 penalty-lasso), and 10-fold cross-validation for prevalidated score calculation. The maximum number of times that a marker can be selected in this run is 1000 (100 repeats of score prevalidation x 10-fold cross validation during each repeat).
  • Table 5 presents the count of biomarkers selected using the leave-one- out (LOOV) cross-validation in combination with an L1 penalized logistic regression approach.
  • the two methods provide highly overlapping sets of biomarkers, selected at approximately the same order. The difference in the counts is due to the number of samples in the set. The corresponding AUC is 0.66.
  • Example 2 The same methodlogy described in Example 1 was utilized for analysis of this data set. Using a penalized logistic regression with a leave-one-out crossvalidation produced an AUC equal to 0.778. The number of times individual miRNAs were selected in the models used in the prevalidated score calculation is shown in Table 7 (50 models total since there were 50 samples). The average model size was ⁇ 8 terms (top 8 miRNAs are indicated by " * "). The expected value is higher than the corresponding value obtained for the pooled data.
  • Table 8 provides the miRNAs selected when an L1 penalized logistic regression approach with 4-fold cross validation was applied to 50 individual samples. Again, considerable overlap in the markers and order is observed between the two methods.
  • Figure 4 presents the distribution of AUC values obtained from this analysis.
  • Models were developed that included protein only data (from the Marshfield cohort utilized in Examples 1 and 2). A total of 47 unique protein biomarkers (Table 9) were analyzed. Serum samples were collected and kept frozen at -80 °C, then thawed immediately prior to use. Each sample was analyzed in duplicate using two distinct detection technologies: xMAP ® technology from Luminex (Austin, TX) and the SECTOR ® Imager with MULTI-SPOT ® technology from Meso Scale Discovery (MSD, Gaithersburg, MD).
  • the Luminex xMAP technology utilizes analyte-specific antibodies that are pre-coated onto color-coded microparticles. Microparticles, standards and samples are pipetted into wells and the immobilized antibodies bind the analytes of interest. After an appropriate incubation period, the particles are re-suspended in wash buffer multiple times to remove any unbound substances. A biotinylated antibody cocktail specific to the analytes of interest is added to each well. Following a second incubation period and a wash to remove any unbound biotinylated antibody, streptavidin-phycoerythrin conjugate (Streptavidin-PE), which binds to the biotinylated detection antibodies, is added to each well.
  • streptavidin-PE streptavidin-phycoerythrin conjugate
  • a final wash removes unbound Streptavidin-PE and the microparticles are resuspended in buffer and read using the Luminex analyzer.
  • the analyzer uses a flow cell to direct the microparticles through a multi-laser detection system.
  • One laser is microparticle-specific and determines which analyte is being detected.
  • the other laser determines the magnitude of the phycoerythrin-derived signal, which is in direct proportion to the amount of analyte bound.
  • Curves are constructed using the signals generated by the standards and protein biomarker concentrations of the samples are read off each curve. Sensitivity (Limit of Detection, LOD) and precision (intra- and inter- assay %CV) of the 47 Luminex protein biomarker assays is shown in Table 10.
  • the MSD technology utilizes specialized 96-well microtiterplates constructed with a carbon surface on the bottom of each plate. Antibodies specific for each protein biomarker are spotted in spatial arrays on the bottom of each well of the microtiterplate. Standards and samples are pipetted into the wells of the precoated plates and the immobilized antibodies bind the analytes of interest. After an appropriate incubation period, the plates are washed multiple times to remove any unbound substances. A cocktail of analyte-specific secondary antibodies labeled with a SULFO-TAGTM is added to each well. Following a second incubation period, the plates are again washed multiple times to remove any unbound materials and a specialized Read Buffer is added to each well.
  • the plates are then placed into the SECTOR ® Imager where an electric current is applied to the carbon electrode on the bottom of the microtiterplate.
  • the SULFO-TAGTM labels bound to the specific secondary antibodies at each spot emit light upon this electrochemical stimulation, which is detected using a sensitive CCD camera.
  • Curves are constructed using the signals generated by the standards and protein biomarker concentrations of the samples are read off each curve. Sensitivity (Limit of Detection, LOD) and precision (intra- and inter- assay %CV) of the 10 MSD protein biomarker assays is shown in Table 12.
  • Models were developed that included both protein and miRNAs data (from Examples 1 and 2).
  • the protein data across 47 biomarkers (from Example 3) were obtained using two distinct detection technologies: Luminex (Luminex Corp, Austin, TX) and Mesoscale Discovery System. Since the protein and miRNAs data were combined, the number of candidate explanatory variables exceeds the number of samples. In this situation, the use of the unpenalized methods is not appropriate, thus models were built and performance was evaluated using the penalized logistic regression with LOOV or k-fold cross-validation for the* calculation of the prevalidated score as described above.
  • Figure 5 provides the AUC distribution for models based on both miRNAs and proteins.
  • the levels of the miRNA describe the risk of an event (here Ml) occurring over time.
  • Univariate and multivariate classification and survival analyses of 112 candidate miRNA markers were performed. Classification results were obtained based on the methodologies described in Examples 2 and 3. Survival analysis was performed using a Cox proportional hazard regression approach.
  • the response variables for the later analysis included the time when an event took place or the time to the end of the study and an index indicating if the time corresponds to an event or the end of the study (censoring). For the 52 samples described in Example 2, the time of event or end of follow-up time was known.
  • the indicator variable for an event was set to 1 and for the 26 subjects without an event within the duration of the study the indicator variable was set to 0.
  • Explanatory variables included in the analysis were: a) the protein levels alone, b) the miRNA levels alone and c) either the miRNA and/or protein levels.
  • Model fitting was accomplished using both penalized and unpenalized versions of the Cox proportional hazard model.
  • the L1- penalty (Lasso) was used whenever the penalized version of the model was applied.
  • variable selection for each model was performed using the same approaches described in Example 1 , i.e., using a) the Bayesian information criterion with forward selection for the unpenalized version, of the models and b) a cross-validation based selection of the optimum penalty for the penalized approach.
  • the calculation of a prevalidated score obtained in a manner similar to the one described in Example 1 was employed.
  • Table 16 shows the results for the univariate classification analysis. The markers in this table have been ordered by the predicted AUC.
  • Table 18 shows the selection frequency of miRNAs in multivariate classification models. Multiple logistic regression models were built during the prevalidation process on training sets obtained through a LOOV approach, providing a score for the left-out-sample. The model size was determined by the use of the Bayesian Information Criterion. The average classification performance was based on the vector of prevalidated calssification scores and was equal to 0.7.
  • Table 18 shows the results from the univariate survival analysis. Again, the markers in this table have been ordered by the predicted AUC. Top selected markers were almost identical to those obtained from the classification analysis and overall performance, as measured by time-dependent AUC, was comparable to that obtained from the classification approach.
  • RNA extracts previously obtained from the fifty-two serum samples from Example 2 were screened for the presence of 720 miRNA target sequences shown in Table 1 , using Exiqon's mercury LIMATM Universal RT microRNA PCR array technology platform, currently updated to miRBASE 13. .
  • a number of analyses were combined to provide an overall significance of each miRNA biomarker. Univariate classification and survival analyses provided AUC values for each individual miRNA target which were used to rank each target in order of significance. Multivariate analysis was also conducted to generate 47 multivariate models. miRNA targets were ranked by the number of models for which they were selected. A t-test analysis (1 -tailed) was also conducted comparing Cp values measured for each miRNA target in the case and control populations. Lastly, a quartile analysis was conducted for the data set. For each miRNA target, all samples (combined case and control populations) were ranked according to Cp value (low to high). The ranked population was then divided into four quartiles, each containing 25% of the total population. The number of case and control subjects in each quartile was then recorded. If greater than 65% or less than 35% of the total number of 26 cases were ranked in the "low" quartile, then that miRNA target was considered significant.
  • the available data included 59 (47 unique) protein biomarkers measured for each individual and 107 clinical characteristics including demographic (age, gender, race, diabetes status, family history of Ml, smoking, etc.) and laboratory measurements (total cholesterol, HDL, LDL, etc.) and medication use (statin, antihypertensive medication, hypoglycemic medication, etc.).
  • Multivariate analysis development of prognostic score for Ml and/or UA.
  • the development of a prognostic score was based on the inclusion of TRFs as well as protein biomarkers. Given the known association of age, gender, diabetes, and family history with cardiovascular events, these four parameters were included in the model. The inclusion of these 4 parameters was confirmed by running a number of forward marker selection algorithms. All of the algorithms selected the four variables in the final multivariate algorithms. The determination of the optimum model size was based on the use of the following criteria: (a) Akaike information criterion, (b) Bayesian information criterion, (c) Drop-in-deviance criterion.
  • the first 2 are known in-sample error estimators and the third utilizes a cross-validation loop to estimate the goodness-of-fit.
  • the model size was selected for the model that best fit the data, avoiding overfitting.
  • a characteristic drop-in-deviance curve for model selection (a plot of the absolute value of the quantity) is shown in Figure 12.
  • the size of the model was selected based on using the 1 standard error rule, i.e., the maximum of the curve was identified and then a line was drawn from the 1 standard error point below the maximum.
  • the optimum number of protein biomarkers was selected as the smallest number that its corresponding average absolute deviance value exceeded the aforementioned line.
  • That number corresponded to 7 protein biomarkers, i.e., the optimum risk score was therefore composed of 4 TRFs and 7 protein biomarkers (Figure 12). All three methods selected between 5 and 7 biomarkers as the optimum number of biomarkers in the model. The smaller set of biomarkers was always a subset of the larger set. Table 21 shows the frequency and ranking of the selected biomarkers after age, gender, diabetes, and family history of Ml have been inserted into the model. These counts and rankings were obtained from the different models that were built during the cross-validation process; one model is built for every training fold, the size of which is selected by one of the model selection methods mentioned above. The cross-validation process was repeated in order to average over the variability introduced by the membership assignment of each subject.
  • Table 21 shows the frequency selection, average, minimum and maximum rank of each biomarker over 4 repeats of a 5-fold prevalidation (a form of cross-validation) process.
  • the 4 TRFs were included in each of the models.
  • the equation measures the improvement for the cases and controls separately in terms of a percent and combines the results into a single number.
  • a positive percentile for the cases and a negative for the controls represents improvement in performance introduced by the disclosed model.
  • the risk category is defined by establishing appropriate thresholds for the risk scores predicted by the existing and disclosed models.
  • the CNRI is defined in the same way but applies to a subset of the population that can gain from an improved method of identifying the true risk within the group. For cardiovascular disease, application of the NRI metric in the intermediate risk population, as defined by the Franimgham score for example, satisfies this criterion. The calculated value represents the CNRI performance for the intermediate risk category.
  • the intermediate risk category as calculated by the Framingham score for 10 year risk, has been defined as those individuals with risk score between 10% and 20%.
  • the results presented here are based on the following cutoffs for defining the intermediate risk category: ⁇ 3.5%, >7.5%. The use of these lower cutoffs is justified because: a) the disclosed model focuses on a time horizon of 5 years, and b) the event rate in the current population is lower than the one observed when the Framingham score was developed.
  • the reclassification comparison required the calculation of an absolute risk, from each model, for a given subject.
  • the calculation of an absolute risk for each individual using a Cox Proportional Hazard (Cox PH) model required the calculation of the relative risk for this individual based on their characteristics and the estimation of a baseline hazard.
  • the Cox PH model is designed to predict the relative risk but does not require specification of the hazard function.
  • To produce absolute risk estimates from a Cox PH model we needed the absolute risk for any individual, or for an "average" individual; then using the risk estimates relative to this individual or the average, the absolute risk for any individual was computed. The average is a hypothetical individual with the population average value for each predictor.
  • Tables 22, 23, and 24 present the NRI and CNRI expected performance of the.pre-validated models containing biomarkers against three alternative models: 1.) the Framingham risk score ("FRS"); 2.) a model fitted on the Marshfield data using 4 TRFs ("4-TRF”; age, gender, diabetes, and family history of Ml) as covariates; and 3.) an alternate model fitted on the Marshfield data using 9 TRFs ("9- TRF"; age, gender, diabetes, family history of Ml, smoking, total cholesterol, HDL, hypertension medication, and systolic pressure) as covariates.
  • FRS Framingham risk score
  • Table 22 shows the expected reclassification performance of the disclosed model score against the calibrated FRS score based on pre-validation (Marshfield data set).
  • Tables 23 and 24 show the expected reclassification score against the 4-TRF and 9-TRF model scores, respectively, based on pre-validation (Marshfield data set).
  • the external validation step was conducted by testing the disclosed protein model on the MESA sample set as a demonstration of the disclosed protein model's transportability.
  • 824 samples 222 cases and 602 controls were assayed using the panel of protein biomarkers described in Example 7 (IL-16, eotaxin, fas ligand, CTACK, MCP-3, HGF, and sFas).
  • the Marshfield-trained model was used to predict a score for each subject of the MESA sample with marker selection and model fitting performed on the Marshfield population without any knowledge or input from the MESA results.
  • Tables 25 and 26 present the comparison between the disclosed model vs. the 3 other models in terms of NRI and CNRI presented earlier, as well comparison against the Reynolds score [Ridker PM, Buring JE, Rifai N, et al. Development and validation of improved algorithms for the assessment of global cardiovascular risk in women: the Reynolds Risk Score JAMA 2007;297:611-619].
  • the comparisons were consistent with the predicted performance from the Marshfield set.
  • the disclosed model provided better clinical net reclassification over any other transported model presented here.
  • the method using the average of the scores for estimating the baseline survivor function also provided a better balance in reclassification between cases and controls, when compared to the method using the individual estimates.
  • the CNRI is based on a baseline range of risk of 3.5-10% of the reference model. Subjects with missing biomarker data have been excluded from the comparison.
  • the CNRI is based on a baseline range of risk of 3.5-7.5% of the reference model. Subjects with missing biomarker data have been excluded from the comparison.
  • miRNAs can be measured in a human fluid, such as blood, and used to predict future cardiovascular events in a subject.
  • the prognostic power of a hybrid miRNA/protein biomarker set is determined by building a hybrid prognostic model with covariates selected from the miRNA set presented in Table 28 and the disclosed protein biomarker model (see Examples 7-9) as single score, using a case-cohort study design.
  • the TRFs and protein predictors are treated in terms of a single calculated score (single variable), unless univariate association of the miRNA biomarkers is stronger than that observed for the protein biomarkers or TRFs.

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Abstract

Les méthodes, dosages et nécessaires de la présente invention permettent l'identification de biomarqueurs, en particulier de biomarqueurs protéiques et/ou de type ARNmi, à des fins d'évaluation de la santé cardiovasculaire d'un être humain. Dans certains modes de réalisation, méthodes, dosages et nécessaires, des biomarqueurs circulants protéiques et/ou de type ARNmi sont identifiés afin d'évaluer la santé cardiovasculaire d'un être humain.
PCT/US2010/059781 2009-12-09 2010-12-09 Dosage de biomarqueurs pour le diagnostic et le classement des maladies cardiovasculaires WO2011072177A2 (fr)

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