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 .- 17 . (canceled) 
     
     
         18 . A method comprising:
 partitioning data points associated with a signal between data points indicative of an amplification of a target nucleic acid in a sample and data points not indicative of the amplification of the target nucleic acid, wherein the data points include data pairs comprising an efficiency related value and a corresponding fractional cycle number; and   determining the presence of the target nucleic acid in the sample based on the data points.   
     
     
         19 . The method of  claim 18 , wherein the efficiency related value is a maximum ratio of sequential data points in the signal. 
     
     
         20 . The method of  claim 18 , wherein the efficiency value is the highest peak in a signal transform. 
     
     
         21 . The method of  claim 18 , wherein the efficiency value is the first peak above a threshold in a signal transform. 
     
     
         22 . The method of  claim 18  further comprising interpolating additional data points between the data points to define the efficiency related value and the fractional cycle number. 
     
     
         23 . The method of  claim 18  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. 
 
     
     
         24 . The method of  claim 18 , wherein the partitioning the data points based on amplification of the target nucleic acid is based on a threshold. 
     
     
         25 . The method of  claim 18  further comprising partitioning data points indicative of the amplification of the target nucleic acid between data points indicative of amplification inhibition and data points not indicative of amplification inhibition. 
     
     
         26 . The method of  claim 25 , wherein the partitioning the data points indicative of amplification inhibition is based on a multiple of a standard of deviation of the efficiency related values. 
     
     
         27 . The method of  claim 18  further comprising:
 determining a width of the signal at half of a maximum height of the signal; 
 comparing the width to a range of widths; 
 validating the amplification reaction if the width is within the range of widths; and 
 determining an abnormal assay if the width is not within the range of widths. 
 
     
     
         28 . A method comprising:
 partitioning data points associated with a signal indicative of an amplification of a target nucleic acid in a sample between data points indicative of amplification inhibition and data points not indicative of amplification inhibition, wherein the data points not indicative of amplification inhibition form quantifiable data points; and   determining the presence of the target nucleic acid in the sample based on the quantifiable data points.   
     
     
         29 . A system comprising:
 an interface to obtain a signal proportional to an amount of a target nucleic acid in a sample in contact with an amplification agent to induce an amplification reaction, the signal obtained during the amplification reaction; and   a processor to:
 determine efficiency related values based on the signal; 
 determine respective fractional cycle numbers of the efficiency related values; 
 partition data points comprising data sets of efficiency related values and corresponding fractional cycle numbers between data points indicative of the amplification reaction and data points not indicative of the amplification reaction; 
 determine the presence of the nucleic acid based on the data points; and 
 calculate a concentration of the target nucleic acid based on the fractional cycle numbers of the data points indicative of the amplification reaction where the presence of the target nucleic acid has been detected. 
   
     
     
         30 . The system of  claim 29 , wherein the efficiency related value is a maximum ratio of sequential data points in the signal. 
     
     
         31 . The system of  claim 29 , wherein the efficiency value is the highest peak in a signal transform. 
     
     
         32 . The system of  claim 29 , wherein the efficiency value is the first peak above a threshold in a signal transform. 
     
     
         33 . The system of  claim 29 , wherein the processor is to interpolate additional data points between the gathered data points to define the efficiency related value and the fractional cycle numbers. 
     
     
         34 . The system of  claim 29 , wherein the processor is to:
 determine a mean of a 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. 
     
     
         35 . The system of  claim 29 , wherein the processor is to partition the data points based on the amplification of the target nucleic acid based on a threshold. 
     
     
         36 . The system of  claim 29 , wherein the processor is to partition the data points indicative of the amplification of the target nucleic acid between data points indicative of amplification inhibition and data points not indicative of amplification inhibition. 
     
     
         37 . The system of  claim 36 , wherein the processor is to partition the data points indicative of the amplification inhibition based on a multiple of a standard of deviation of the efficiency related values. 
     
     
         38 . The system of  claim 29 , wherein the processor is to:
 determine a width of the signal at half of a maximum height of the signal;   compare the width to a range of widths;   validate the amplification reaction if the width is within the range of widths; and   determine an abnormal assay if the width is not within the range of widths.   
     
     
         39 . A tangible machine readable medium having instructions, which when read, cause a machine to at least:
 partition data points associated with a signal between data points indicative of an amplification of a target nucleic acid in a sample and data points not indicative of the amplification of the target nucleic acid, wherein the data points include data pairs comprising an efficiency related value and a corresponding fractional cycle number; and   determine the presence of the target nucleic acid in the sample based on the data points.   
     
     
         40 . The medium of  claim 39 , wherein the efficiency related value is a ratio of sequential data points in the signal. 
     
     
         41 . The medium of  claim 39 , wherein the efficiency value is the highest peak in a signal transform. 
     
     
         42 . The medium of  claim 39 , wherein the efficiency value is the first peak above a threshold in a signal transform. 
     
     
         43 . The medium of  claim 39 , wherein the instructions further cause the machine to interpolate additional data points between the gathered data points to define the efficiency related value and the fractional cycle numbers. 
     
     
         44 . The medium of  claim 39 , wherein the instructions further cause the machine 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.   
     
     
         45 . The medium of  claim 39 , wherein the instructions cause the machine to partition the data points based on the amplification of the target nucleic acid based on a threshold. 
     
     
         46 . The medium of  claim 39 , wherein the instructions cause the machine to partition the data points indicative of the amplification of the target nucleic acid between data points indicative of amplification inhibition and data points not indicative of amplification inhibition. 
     
     
         47 . The medium of  claim 46 , wherein the instructions cause the machine to partition the data points indicative of the amplification inhibition based on a multiple of a standard of deviation of the efficiency related values. 
     
     
         48 . The medium of  claim 39 , wherein the instructions further cause the machine to:
 determine a width of the signal at half of a maximum height of the signal;   compare the width to a range of widths;   validate the amplification reaction if the width is within the range of widths; and   determine an abnormal assay if the width is not within the range of widths.