Systems and methods for detecting the presence of a biological status using clustering

Abstract

A method for determining the presence of a biological entity. The method may include entering into a digital computer, at least a plurality of first input values associated with a first genetic element, a plurality of second input values associated with a second genetic element, and a plurality of third input values associated with a third genetic element associated with a plurality of samples. The method also includes determining a threshold value associated with the third genetic element, separating the samples using the threshold value into a first set of samples and a second set of samples, clustering the first set of samples in a feature space defined by the first genetic element and the second genetic element, defining a first boundary space using the first set of samples, and defining a second boundary space using the second set of samples.

1 . A method comprising:
 entering into a digital computer, at least a plurality of first input values associated with a first genetic element, a plurality of second input values associated with a second genetic element, and a plurality of third input values associated with a third genetic element associated with a plurality of known samples, wherein each known sample includes a first input value in the plurality of first input values, a second input value in the plurality of second input values, and a third input value in the plurality of third input values;   determining a threshold value associated with the third genetic element;   separating the known samples using the threshold value into a first set of known samples and a second set of known samples;   clustering the first set of known samples in a feature space defined by the first genetic element and the second genetic element;   defining a first boundary space using the first set of known samples, wherein the first boundary space differentiates a biological status from other biological statuses; and   defining a second boundary space using the second set of known samples, wherein the second boundary space differentiates the biological status from other biological statuses.   
     
     
         2 . The method of  claim 1  wherein the first genetic element comprises mecA, and the second genetic element comprises a  Staphylococcus aureus -specific target gene sequence, and wherein the biological status comprises an MRSA status. 
     
     
         3 . The method of  claim 1  wherein the first boundary space and the second boundary space are defined by first and second ellipses, respectively. 
     
     
         4 . The method of  claim 1  wherein the first, second and third values are Ct values. 
     
     
         5 . The method of  claim 1  further comprising, prior to entering:
 subjecting the known samples to conditions that will expose nucleic acids in the known samples; and 
 amplifying and detecting the presence and amounts of at least the first genetic element, the second genetic element and the third genetic element. 
 
     
     
         6 . A computer readable medium comprising code executable by a processor, for implementing a method comprising.
 entering into a digital computer, at least a plurality of first input values associated with a first genetic element, a plurality of second input values associated with a second genetic element, and a plurality of third input values associated with a third genetic element associated with a plurality of known samples, wherein each known sample includes a first input value in the plurality of first input values, a second input value in the plurality of second input values, and a third input value in the plurality of third input values;   determining a threshold value associated with the third genetic element;   separating the known samples using the threshold value into a first set of known samples and a second set of known samples;   clustering the first set of known samples in a feature space defined by the first genetic element and the second genetic element;   defining a first boundary space using the first set of known samples, wherein the first boundary space differentiates a biological status from other biological statuses; and   defining a second boundary space using the second set of known samples, wherein the second boundary space differentiates the biological status from other biological statuses.   
     
     
         7 . A digital computer comprising the computer readable medium of  claim 7 , and a processor coupled to the computer readable medium. 
     
     
         8 . A system comprising a measuring module coupled to the digital computer of  claim 7 . 
     
     
         9 . A method for using an analytical model created according to the method of  claim 1  wherein the method for using the analytical model comprises:
 entering a first input value, second input value, and third input value associated with an unknown sample into the digital computer or other digital computer, wherein the first input value, the second input value and the third input value is associated with the first, second, and third genetic elements in the unknown sample; and 
 classifying the unknown sample as being associated with the biological status using the first boundary space or the second boundary space using the digital computer or other digital computer. 
 
     
     
         10 . The method of  claim 9  wherein the biological status comprises a MRSA status. 
     
     
         11 .- 16 . (canceled) 
     
     
         17 . A computer readable medium comprising code executable by a processor, for implementing a method comprising:
 entering, into a digital computer, at least a plurality of first input values associated with a first genetic element, a plurality of second input values associated with a second genetic element, and a plurality of third input values associated with a third genetic element;   creating one or more intermediate values using at least the plurality of first input values and at least the second input values associated with a second genetic element using the digital computer; and   creating a boundary space for the biological status using the one or more intermediate values and the plurality of third input values using the digital computer,   wherein the boundary space differentiates the biological status from other biological statuses.   
     
     
         18 . A digital computer comprising the computer readable medium of claim  11 , and a processor coupled to the computer readable medium. 
     
     
         19 . A system comprising a measuring module coupled to the digital computer of  claim 18 . 
     
     
         20 .- 66 . (canceled)