Methods and systems to analyze reactions using an information system

Abstract

Disclosed are example methods and systems to determine the quantity of an analyte initially present in a chemical and or biological reaction. Also disclosed are computer implemented methods and systems to automate portions of the analysis comprising mathematical or graphical analysis of an amplification reaction.

1 . A method for determining a presence of a target nucleic acid in a sample, the method comprising:
 accessing, using a processor, data associated with a signal related to an amplification of the target nucleic acid in the sample, the data including a data pair comprising an efficiency related value and a corresponding amplification interval;   performing a comparison of the data pair to criteria data, the criteria data including a first set indicative of amplification of the target nucleic acid and a second set not indicative of amplification of the target nucleic acid; and   determining, using the processor, the presence of the target nucleic acid in the sample based on the comparison, wherein if the data pair falls within the first set, the sample is determined to contain the target nucleic acid.   
     
     
         2 . The method of  claim 1 , wherein the amplification interval is one of an increment of time or a cycle number. 
     
     
         3 . The method of  claim 1 , wherein the amplification interval is a fractional cycle number and further comprising interpolating additional data between the data to define the efficiency related value and the fractional cycle number. 
     
     
         4 . The method of  claim 1 , wherein the amplification interval is a threshold cycle number. 
     
     
         5 . The method of  claim 1 , wherein the amplification interval is an increment of time and the amplification is an isothermal amplification. 
     
     
         6 . The method of  claim 1 , wherein the criterion data is one of a criterion curve or a region partitioned between data pairs indicative of amplification of the target nucleic acid and data pairs not indicative of amplification of the target nucleic acid. 
     
     
         7 . The method of  claim 6 , further comprising:
 identifying, based on the criterion curve, a first region indicative of a presence of the target nucleic acid, a second region indicative of absence of the target nucleic acid, and a third region indicative of an inhibited presence of the target nucleic acid, the third region statistically offset from the first region; and   performing a comparison of the data pair to the first region, the second region, and the third region; and   determining the presence of the target nucleic acid in the sample based on the comparison.   
     
     
         8 . The method of  claim 1 , further comprising:
 determining a mean of data points associated with multiple signals;   establishing a confidence corridor within a range around the mean; and   using only data points within the confidence corridor to determine the presence of the target nucleic acid.   
     
     
         9 . The method of  claim 1 , wherein the amplification interval is a fractional cycle number and further comprising determining the fractional cycle number by:
 accessing, using the processor, a data curve representative of the amplification;   identifying a peak in the curve; and   determining the fractional cycle number based on a location of the peak in the curve, wherein the location of the peak is measured based on one of a time or a cycle number from an initiation of the amplification.   
     
     
         10 . The method of  claim 9 , wherein the efficiency related value is a maximum value of the peak. 
     
     
         11 . The method of  claim 1 , wherein the criteria data includes a third set different from the first set and the second set, and wherein if the data pair falls within the third set, the sample is deemed subject to error. 
     
     
         12 . A system comprising:
 an interface to obtain data associated with a signal related to amplification of a target nucleic acid in a sample, the data including a data pair comprising an efficiency related value and a corresponding amplification interval; and   a processor to:
 perform a comparison of the data pair to criteria data, the criteria data including a first set indicative of amplification of the target nucleic acid and a second set not indicative of amplification of the target nucleic acid; and 
 determine a presence of the target nucleic acid in the sample based on the comparison, wherein if the data pair falls within the first set, the sample is determined to contain the target nucleic acid. 
   
     
     
         13 . The system of  claim 12 , wherein the amplification interval is one of an increment of time or a cycle number. 
     
     
         14 . The system of  claim 12 , wherein the amplification interval is a fractional cycle number and wherein the processor is to interpolate additional data points between the data points to define the efficiency related value and the fractional cycle number. 
     
     
         15 . The system of  claim 12 , wherein the amplification interval is a threshold cycle number. 
     
     
         16 . The system of  claim 12 , wherein the amplification interval is an increment of time and the amplification is an isothermal amplification. 
     
     
         17 . The system of  claim 12 , wherein the criterion data is one of a criterion curve or a region partitioned between data pairs indicative of amplification of the target nucleic acid and data pairs not indicative of amplification of the target nucleic acid. 
     
     
         18 . The system of  claim 17 , wherein the processor is to:
 identify, based on the criterion curve, a first region indicative of a presence of the target nucleic acid, a second region indicative of absence of the target nucleic acid, and a third region indicative of an inhibited presence of the target nucleic acid, the third region statistically offset from the first region; and   perform a comparison of the data pair to the first region, the second region, and the third region; and   determine the presence of the target nucleic acid in the sample based on the comparison.   
     
     
         19 . The system of  claim 12 , wherein the processor is to:
 determine a mean of data points associated with multiple signals;   establish a confidence corridor within a range around the mean; and   use only data points within the confidence corridor to determine the presence of the target nucleic acid.   
     
     
         20 . The system of  claim 12 , wherein the amplification interval is a fractional cycle number and wherein the processor is to:
 identify a peak in a data curve representative of the amplification; and   determine the fractional cycle number based on a location of the peak in the curve, wherein the location of the peak is measured based on one of a time or a cycle number from an initiation of the amplification.   
     
     
         21 . The system of  claim 20 , wherein the efficiency related value is a maximum value of the peak. 
     
     
         22 . The system of  claim 12 , wherein the criteria data includes a third set different from the first set and the second set, and wherein if the data pair falls within the third set, the processor is to deem the sample subject to error. 
     
     
         23 . A tangible machine readable medium having instructions, which when read, cause a machine to at least:
 access data associated with a signal related to an amplification of a target nucleic acid in a sample, the data including a data pair comprising an efficiency related value and a corresponding amplification interval;   perform a comparison of the data pair to criteria data, the criteria data including a first set indicative of amplification of the target nucleic acid and a second set not indicative of amplification of the target nucleic acid; and   determine the presence of the target nucleic acid in the sample based on the comparison, wherein if the data pair falls within the first set, the sample is determined to contain the target nucleic acid.