Biomarker signature method, and apparatus and kits therefor

Abstract

The present invention discloses methods, kits, and apparatus as well as reagents and compositions associated therewith for deriving an indicator for use in diagnosing the presence, absence or degree of at least one condition in a biological subject or in prognosing at least one condition in a biological subject. Also disclosed is a biomarker signature for use in diagnosing the presence, absence or degree of at least one condition in a biological subject or in prognosing at least one condition in a biological subject. The present invention further discloses methods, kits and apparatus, as well as reagents and compositions associated therewith, for identifying biomarkers for use in a biomarker signature.

1 - 30 . (canceled) 
     
     
         31 . Apparatus for differentiating between infection-negative systemic inflammatory response syndrome (inSIRS) and infection-positive systemic inflammatory response syndrome (ipSIRS) in a biological subject, the apparatus including at least one processing device that:
 a) obtains a sample taken from a biological subject showing a clinical sign of SIRS, the sample including polynucleotide expression products;   b) quantifies polynucleotide expression products within the sample to determine a first pair of biomarker values indicative of a concentration of first polynucleotide expression products of the PLA2G7 gene and PLAC8 gene;   c) determines a first test indicator indicative of a ratio of concentrations of the first polynucleotide expression products using the first pair of biomarker values;   d) compares the first test indicator to an indicator reference being indicative of inSIRS and to an indicator reference being indicative of ipSIRS; and,   e) determines a likelihood of the subject having inSIRS or ipSIRS in accordance with the results of the comparison.   
     
     
         32 . The apparatus of  claim 31 , wherein the polynucleotide expression products are quantified by: i) amplifying at least some polynucleotide expression products in the sample; and, ii) determining an amplification amount representing a degree of amplification required to obtain a defined level of each of the first polynucleotide expression products; and, b) determining the first test indicator by determining a difference between the corresponding amplification amounts. 
     
     
         33 . The apparatus of  claim 32 , wherein a respective amplification amount is at least one of: a cycle time; a number of cycles; a cycle threshold; an amplification time; and,
 relative to an amplification amount of another amplified product.   
     
     
         34 . The apparatus of  claim 31 , wherein the sample is a blood sample. 
     
     
         35 . The apparatus of  claim 31 , wherein the sample comprises leukocytes. 
     
     
         36 . The apparatus of  claim 31 , wherein the sample comprises peripheral blood mononuclear cells. 
     
     
         37 . The apparatus of  claim 31 , wherein the at least one processing device further:
 (i) quantifies polynucleotide expression products within the sample to determine a second pair of biomarker values indicative of a concentration of second polynucleotide expression products of the CEACAM4 gene and LAMP1 gene;   (ii) determines a second test indicator indicative of a ratio of concentrations of the second polynucleotide expression products using the second pair of biomarker values;   (iii) combines the first test indicator and the second test indicator to provide a combined test indicator;   (iv) compares the combined test indicator to an indicator reference being indicative of inSIRS and to an indicator reference being indicative of ipSIRS; and   (v) determines a likelihood of the subject having inSIRS or ipSIRS in accordance with the results of the comparison.   
     
     
         38 . The apparatus of  claim 37 , wherein the first test indicator and the second test indicator are combined using a combining function, the combining function being at least one of: a) an additive model; b) a linear model; c) a support vector machine; d) a neural network model; e) a random forest model; f) a regression model; g) a genetic algorithm; h) an annealing algorithm; i) a weighted sum; j) a nearest neighbor model; and, k) a probabilistic model. 
     
     
         39 . The apparatus of  claim 37 , wherein combination of the first test indicator and the second test indicator comprises addition of a first value representing the ratio of concentrations of the first polynucleotide expression products and a second value representing the ratio of concentrations of the second polynucleotide expression products. 
     
     
         40 . The apparatus of  claim 37 , wherein the polynucleotide expression products are quantified by: i) amplifying at least some polynucleotide expression products in the sample; and, ii) determining an amplification amount representing a degree of amplification required to obtain a defined level of each of the first and second polynucleotide expression products; and, b) determining a respective test indicator by determining a difference between the corresponding amplification amounts. 
     
     
         41 . The apparatus of  claim 37 , wherein the polynucleotide expression products are quantified by: i) amplifying at least some polynucleotide expression products in the sample; and, ii) determining an amplification amount representing a degree of amplification required to obtain a defined level of each of the first and second polynucleotide expression products; and, b) determining a respective test indicator by determining a difference between the corresponding amplification amounts, wherein a respective amplification amount is at least one of: a cycle time; a number of cycles; a cycle threshold; an amplification time; and, relative to an amplification amount of another amplified product. 
     
     
         42 . The apparatus of  claim 37 , wherein the sample is a blood sample. 
     
     
         43 . The apparatus of  claim 37 , wherein the sample comprises leukocytes. 
     
     
         44 . The apparatus of  claim 37 , wherein the sample comprises peripheral blood mononuclear cells. 
     
     
         45 . Apparatus for determining an indicator used in determining the likelihood of a biological subject having at least one medical condition, the apparatus including:
 a) a sampling device that obtains a sample taken from a biological subject, the sample including polynucleotide expression products;   b) a measuring device that quantifies polynucleotide expression products within the sample to determine a pair of biomarker values, the pair of biomarker values being selected from the group consisting of:
 i) a first pair of biomarker values indicative of a concentration of polynucleotide expression products of the PLA2G7 gene and PLAC8 gene; 
 ii) a second pair of biomarker values indicative of a concentration of polynucleotide expression products of the CEACAM4 gene and LAMP1 gene; 
   c) at least one processing device that:
 i) receives an indication of the pair of biomarker values from the measuring device; 
 ii) determines an indicator using a ratio of the concentration of the first and second polynucleotide expression products using the biomarker values; and, 
 iii) compares the indicator to at least one indicator reference; and, 
 iv) determines a likelihood of the subject having the at least one medical condition using the results of the comparison; and, 
 v) generates a representation of the indicator and the likelihood for display to a user. 
   
     
     
         46 . A method for differentiating between inSIRS and ipSIRS in a biological subject, the method including:
 a) obtaining a sample taken from a biological subject showing a clinical sign of SIRS, the sample including polynucleotide expression products;   b) in a measuring device:
 i) amplifying at least some polynucleotide expression products in the sample; 
 ii) determining an amplification amount representing a degree of amplification required to obtain a defined level of polynucleotide expression products including:
 (1) amplification amounts for a first pair of polynucleotide expression products of the PLA2G7 gene and PLAC8 gene; 
 (2) amplification amounts for a second pair of polynucleotide expression products of the CEACAM4 gene and LAMP1 gene; 
 
   c) in a processing system:
 i) retrieving the amplification amounts; 
 ii) determining an indicator by:
 (1) determining a first derived biomarker value indicative of a ratio of concentrations of the first pair of polynucleotide expression products by determining a difference between the amplification amounts for the first pair; 
 (2) determining a second derived biomarker value indicative of a ratio of concentrations of the second pair of polynucleotide expression products by determining a difference between the amplification amounts for the second pair; 
 (3) determining the indicator by adding the first and second derived biomarker values; 
 
 iii) retrieving previously determined first and second indicator references from a database, wherein the first and second indicator references are distributions of indicators determined for first and second groups of a reference population, the first and second group consisting of individuals diagnosed with inSIRS and ipSIRS respectively; 
 iv) comparing the indicator to the first and second indicator references; 
 v) using the results of the comparison to determine a probability of the subject being classified within the first or second group; 
 vi) generating a representation at least partially indicative of the indicator and the probability; and, 
 vii) providing the representation to a user to allow the user to assess the likelihood of a biological subject having at least one medical condition.