A method for performing multiple digital PCR assays within multiple channels of a microfluidic chip to identify DNA sequence variations in each of a plurality of patient samples to diagnose a disease status, a disease risk or to predict a therapeutic drug response for each patient, said method comprising: A. for each patient sample, providing a flow of genomic DNA sample within one of the channels; B. introducing an assay-specific reagent solution to the flow of genomic DNA sample to form a test mixture; C. performing a PCR procedure on the test mixture within the channel; D. performing a thermal melt procedure on the test mixture after performing the PCR procedure; E. collecting data on the thermal melt procedure; F. performing an analysis of the collected thermal melt data with a controller programmed to ascertain the presence or absence of a DNA sequence variation of interest within the test mixture G. converting the results of the analyzing step with the controller to a digital signal by designating a result indicating the presence of the DNA sequence variation of interest as 1 and designating a result indicating the absence of the DNA sequence variation of interest as 0, or vice versa; H. performing an analysis of the outcome of step G with the controller for each of the patient samples to determine whether the outcome is ambiguous, such that if the controller determines that the outcome is ambiguous, the controller causes the repeating of steps B through G at least once with the same assay-specific reagent solution used in step B to improve the confidence in the determination of the presence or absence of the DNA sequence variation of interest; I. performing an analysis of the outcome of step G with the controller for each of the patient samples to determine whether the outcome is ambiguous, such that if the controller determines that the outcome is not ambiguous, the controller causes the repeating of steps B through H at least one time with a different assay-specific reagent solution adapted to identify a different DNA sequence variation relevant to the diagnosis or prediction; and J. performing a statistical analysis on the results of steps B through I to derive a diagnosis or a prediction and a level of confidence in the diagnosis or prediction. A. for each patient sample, providing a flow of genomic DNA sample within one of the channels; B. introducing an assay-specific reagent solution to the flow of genomic DNA sample to form a test mixture; C. performing a PCR procedure on the test mixture within the channel; D. performing a thermal melt procedure on the test mixture after performing the PCR procedure; E. collecting data on the thermal melt procedure; F. performing an analysis of the collected thermal melt data with a controller programmed to ascertain the presence or absence of a DNA sequence variation of interest within the test mixture G. converting the results of the analyzing step with the controller to a digital signal by designating a result indicating the presence of the DNA sequence variation of interest as 1 and designating a result indicating the absence of the DNA sequence variation of interest as 0, or vice versa; H. performing an analysis of the outcome of step G with the controller for each of the patient samples to determine whether the outcome is ambiguous, such that if the controller determines that the outcome is ambiguous, the controller causes the repeating of steps B through G at least once with the same assay-specific reagent solution used in step B to improve the confidence in the determination of the presence or absence of the DNA sequence variation of interest; I. performing an analysis of the outcome of step G with the controller for each of the patient samples to determine whether the outcome is ambiguous, such that if the controller determines that the outcome is not ambiguous, the controller causes the repeating of steps B through H at least one time with a different assay-specific reagent solution adapted to identify a different DNA sequence variation relevant to the diagnosis or prediction; and J. performing a statistical analysis on the results of steps B through I to derive a diagnosis or a prediction and a level of confidence in the diagnosis or prediction.