Method for Determining Coronary Artery Disease Risk

Abstract

Markers and methods useful for assessing coronary artery disease in a subject are provided, along with kits for measuring their expression. Also provided are predictive models, based on the markers, as well as computer systems, and software embodiments of the models for scoring and optionally classifying samples.

1 . A method for determining coronary artery disease risk in a subject, comprising:
 performing at least one nucleotide-based assay on a sample from the subject to generate a dataset comprising data representing mRNA expression levels corresponding to each gene in at least one term, wherein the at least one term comprises term 1, term 2, term 3, term 4, term 5, term 6, or term 7;   wherein term 1 comprises gene 1, gene 2, and gene 3, wherein gene 1 is AF161365, wherein gene 2 is HNRPF or ACBD5, and wherein gene 3 is TFCP2 or DDX18;   wherein term 2 comprises gene 4, gene 5, and gene 6, wherein gene 4 is AF289562 or CD248, wherein gene 5 is HNRPF or ACBD5, and wherein gene 6 is TFCP2 or DDX18;   wherein term 3 comprises gene 7, gene 8, gene 9, and gene 10 wherein gene 7 is CD79B or CD19, wherein gene 8 is SPIB or BLK, wherein gene 9 is CD3D or LCK, and wherein gene 10 is TMC8 or CCT2;   wherein term 4 comprises gene 11, gene 12, gene 13, and gene 14, wherein gene 11 is S100A12 or MMP9, wherein gene 12 is CLEC4E or ALOX5AP,   wherein gene 13 is S100A8 or NAMPT, and wherein gene 14 is RPL28 or SSRP1;   wherein term 5 comprises gene 15, gene 16, gene 17, gene 18, and gene 19, wherein gene 15 is S100A12 or MMP9, wherein gene 16 is CLEC4E or ALOX5AP, wherein gene 17 is S100A8 or NAMPT, wherein gene 18 is AQP9 or GLT1D1, and wherein gene 19 is NCF4 or NCF2;   wherein term 6 comprises gene 20, gene 21, gene 22, gene 23, gene 24, gene 25, and gene 26, wherein gene 20 is CASP5 or H3F3B, wherein gene 21 is IL18RAP or TXN, wherein gene 22 is TNFAIP6 or PLAUR, wherein gene 23 is IL8RB or BCL2A1, wherein gene 24 is TNFRSF10C or PTAFR, wherein gene 25 is KCNE3 or LAMP2, and wherein gene 26 is TLR4 or TYROBP; and   wherein term 7 comprises gene 27, gene 28, gene 29, and gene 30, wherein gene 27 is SLAMF7 or CX3CR1, wherein gene 28 is KLRC4 or CD8A, wherein gene 29 is CD3D or LCK, and wherein gene 30 is TMC8 or CCT2;   obtaining data representing age of the subject and data representing gender of the subject; and   generating, by a computer processor, a score indicative of coronary artery disease (CAD) risk by mathematically combining the data representing the mRNA expression levels, the data representing the age of the subject, and the data representing the gender of the subject, wherein a higher score relative to a control subject having less than 50% stenosis in all major vessels indicates an increased likelihood that the subject has CAD or a lower score relative to a control subject having greater than or equal to 50% stenosis in at least one major coronary vessel indicates a decreased likelihood that the subject has CAD.   
     
     
         2 . The method of  claim 1 , wherein the dataset comprises data representing mRNA expression levels corresponding to each gene in term 1, term 2, term 3, term 4, term 5, term 6, and term 7. 
     
     
         3 . The method of  claim 1 , further comprising classifying the sample according to the score. 
     
     
         4 . The method of  claim 1 , further comprising rating CAD risk using the score. 
     
     
         5 . The method of  claim 1 , wherein the sample comprises RNA extracted from peripheral blood cells. 
     
     
         6 . The method of  claim 1 , wherein the subject has stable chest pain, the subject has typical angina or atypical angina or an anginal equivalent, the subject has no previous diagnosis of MI, the subject has not had a revascularization procedure, the subject does not have diabetes, the subject does not have a systemic autoimmune or infectious condition, and/or the subject is not currently taking a steroid, an immunosuppressive agent, or a chemotherapeutic agent. 
     
     
         7 . The method of  claim 1 , wherein CAD is obstructive CAD. 
     
     
         8 . The method of  claim 1 , wherein the method performance is characterized by an area under the curve (AUC) ranging from 0.68 to 0.70, 0.70 to 0.79, 0.80 to 0.89, or 0.90 to 0.99. 
     
     
         9 . A method for determining coronary artery disease risk in a subject, comprising:
 performing at least one nucleotide-based assay on a sample from the subject to generate a dataset comprising data representing mRNA expression levels corresponding to at least two genes comprising AF161365, HNRPF, ACBD5, TFCP2, DDX18, AF289562, CD248, CD79B, CD19, SPIB, BLK, CD3D, LCK, TMC8, CCT2, S100A12, MMP9, CLEC4E, ALOX5AP, S100A8, NAMPT, RPL28, SSRP1, AQP9, GLT1D1, NCF4, NCF2, CASP5, H3F3B, IL18RAP, TXN, TNFAIP6, PLAUR, IL8RB, BCL2A1, TNFRSF10C, PTAFR, KCNE3, LAMP2, TLR4, TYROBP, SLAMF7, CX3CR1, KLRC4, and CD8A;   obtaining data representing age of the subject and data representing gender of the subject; and   generating, by a computer processor, a score indicative of CAD risk by mathematically combining the data representing the mRNA expression levels, the data representing the age of the subject, and the data representing the gender of the subject, wherein a higher score relative to a control subject having less than 50% stenosis in all major vessels indicates an increased likelihood that the subject has CAD or a lower score relative to a control subject having greater than or equal to 50% stenosis in at least one major coronary vessel indicates a decreased likelihood that the subject has CAD.   
     
     
         10 . The method of  claim 9 , further comprising classifying the sample according to the score. 
     
     
         11 . The method of  claim 9 , further comprising rating CAD risk using the score. 
     
     
         12 . The method of  claim 9 , wherein the method performance is characterized by an area under the curve (AUC) ranging from 0.68 to 0.70, 0.70 to 0.79, 0.80 to 0.89, or 0.90 to 0.99. 
     
     
         13 . The method of  claim 9 , wherein the subject has stable chest pain, the subject has typical angina or atypical angina or an anginal equivalent, the subject has no previous diagnosis of myocardial infarction (MI), the subject has not had a revascularization procedure, the subject does not have diabetes, the subject does not have a systemic autoimmune or infectious condition, and/or the subject is not currently taking a steroid, an immunosuppressive agent, or a chemotherapeutic agent. 
     
     
         14 . The method of  claim 9 , wherein CAD is obstructive CAD. 
     
     
         15 . A method for generating a dataset comprising data representing mRNA expression levels for a subject that has CAD or is suspected of having CAD, comprising:
 obtaining a sample from the subject, wherein the subject has CAD or is suspected of having CAD;   performing at least one nucleotide-based assay on the sample to generate a dataset comprising data representing mRNA expression levels corresponding to each gene in at least one term, wherein the at least one term comprises term 1, term 2, term 3, term 4, term 5, term 6, or term 7;
 wherein term 1 comprises gene 1, gene 2, and gene 3, wherein gene 1 is AF161365, wherein gene 2 is HNRPF or ACBD5, and wherein gene 3 is TFCP2 or DDX18; 
 wherein term 2 comprises gene 4, gene 5, and gene 6, wherein gene 4 is AF289562 or CD248, wherein gene 5 is HNRPF or ACBD5, and wherein gene 6 is TFCP2 or DDX18; 
 wherein term 3 comprises gene 7, gene 8, gene 9, and gene 10 wherein gene 7 is CD79B or CD19, wherein gene 8 is SPIB or BLK, wherein gene 9 is CD3D or LCK, and wherein gene 10 is TMC8 or CCT2; 
 wherein term 4 comprises gene 11, gene 12, gene 13, and gene 14, wherein gene 11 is S100A12 or MMP9, wherein gene 12 is CLEC4E or ALOX5AP, wherein gene 13 is S100A8 or NAMPT, and wherein gene 14 is RPL28 or SSRP1; 
 wherein term 5 comprises gene 15, gene 16, gene 17, gene 18, and gene 19, wherein gene 15 is S100A12 or MMP9, wherein gene 16 is CLEC4E or ALOX5AP, wherein gene 17 is S100A8 or NAMPT, wherein gene 18 is AQP9 or GLT1D1, and wherein gene 19 is NCF4 or NCF2; 
 wherein term 6 comprises gene 20, gene 21, gene 22, gene 23, gene 24, gene 25, and gene 26, wherein gene 20 is CASP5 or H3F3B, wherein gene 21 is IL18RAP or TXN, wherein gene 22 is TNFAIP6 or PLAUR, wherein gene 23 is IL8RB or BCL2A1, wherein gene 24 is TNFRSF10C or PTAFR, wherein gene 25 is KCNE3 or LAMP2, and wherein gene 26 is TLR4 or TYROBP; and 
 wherein term 7 comprises gene 27, gene 28, gene 29, and gene 30, wherein gene 27 is SLAMF7 or CX3CR1, wherein gene 28 is KLRC4 or CD8A, wherein gene 29 is CD3D or LCK, and wherein gene 30 is TMC8 or CCT2. 
   
     
     
         16 . The method of  claim 15 , wherein the dataset comprises data representing mRNA expression levels corresponding to each gene in term 1, term 2, term 3, term 4, term 5, term 6, and term 7. 
     
     
         17 . The method of  claim 15 , wherein the sample comprises RNA extracted from peripheral blood cells. 
     
     
         18 . The method of  claim 15 , wherein the subject has stable chest pain, the subject has typical angina or atypical angina or an anginal equivalent, the subject has no previous diagnosis of MI, the subject has not had a revascularization procedure, the subject does not have diabetes, the subject does not have a systemic autoimmune or infectious condition, and/or the subject is not currently taking a steroid, an immunosuppressive agent, or a chemotherapeutic agent. 
     
     
         19 . The method of  claim 15 , wherein CAD is obstructive CAD. 
     
     
         20 . The method of  claim 15 , wherein the at least one nucleotide-based assay comprises a DNA assay, a microarray, a hybridization-based assay, a polymerase chain reaction (PCR), RT-PCR, a Southern blot, or a Northern blot.