Abstract: A system for specifying user-defined assay parameters of a user-defined assay protocol for processing a sample includes a first graphical user interface for defining an analyte extraction parameter for an extraction process to extract a targeted analyte from the sample, a second graphical user interface for defining a target parameter specifying one or more channels of a multi-channel signal detector for detecting the targeted analyte, a third graphical user interface for defining parameters of a thermal profile specifying thermal conditions to which a reaction mixture is to be exposed to amplify the targeted analyte, and system-defined assay protocols pre-programmed into storage media and performed in accordance with system-defined assay parameters that are not changeable by a user and wherein at least one of the system-defined assay parameters is combined with the user-defined assay parameters to form the user-defined assay protocol.

Abstract: Performing multiple nucleic acid amplification assays in an automated analyzer comprises loading the analyzer with a sample-containing receptacles, producing a purified form of a first sample to isolate a first analyte, producing a purified form of a second sample to isolate a second analyte, forming first and second amplification reaction mixtures with the purified first and second samples, the first mixture containing first amplification oligomers for amplifying a first region of the first analyte and the second mixture containing second amplification oligomers for amplifying a second region of the second analyte, exposing the second mixture to thermal conditions for amplifying the second region, exposing the first mixture to thermal conditions for amplifying the first region, determining the presence or absence of the second analyte in the second mixture, and determining the presence or absence of the first analyte in the first mixture.

Abstract: A system comprising an analyzer for performing nucleic acid amplification assays includes a controller configured to send instructions to purify a first sample by immobilizing a first analyte, purify a second sample by immobilizing a second analyte, form a first reaction mixture by combining a dissolved second reagent with the purified second sample, wherein a second solvent for dissolving the second reagent contains second amplification oligomers for amplifying the second analyte and the second reagent contains a polymerase but does not contain amplification oligomers for amplifying the second analyte, and form a second reaction mixture by combining a dissolved first reagent with the purified first sample, wherein the first reagent contains a polymerase and first amplification oligomers for amplifying the first analyte and a first solvent for dissolving the first reagent does not contain an amplification oligomer or a polymerase for amplifying the first analyte.

Abstract: Analyzing samples using an automated analyzer comprises retaining a first container containing a first solvent lacking an amplification oligomer at a first location of the analyzer, retaining a second container having a different structure than the first container and supporting solvent-containing vials at a second location of the analyzer, the solvent in each vial including an amplification oligomer, combining a first non-liquid reagent including at least one amplification oligomer with the first solvent and a first sample to form a first reaction mixture, combining a second non-liquid reagent lacking an amplification oligomer with the solvent included in a vial of the second container and a second sample to form a second reaction mixture, performing first and second amplification reactions with the first and second reaction mixtures, and determining the presence or absence of one or more analytes in the first and second reaction mixtures.

Abstract: A computer-implemented method for determining the amount of an analyte in a sample comprises associating a nucleic acid amplification assay defined at least partly by user-defined assay parameters to the sample. The assay is performed by dissolving a unit-dose reagent with a solvent, wherein the solvent includes one or more amplification oligomers adapted to amplify a region of the analyte and the reagent does not include an amplification oligomer for performing the assay. A reaction mixture, including the dissolved reagent and the sample, is exposed to a temperature condition and measurements of fluorescence indicative of an amount of amplification products formed during the exposing are collected. The measurements are assessed with a computer using data analysis parameters provided by the user to compute results indicative of the amount of the analyte in the sample.

Abstract: A method of determining whether one or more forms of a nucleic acid analyte are present in a sample. The method includes dissolving an amplification reagent with a first solvent, where the amplification reagent contains oligonucleotides sufficient to amplify and detect a first region of a first form of the analyte, where the first solvent contains one or more oligonucleotides which, in combination with the oligonucleotides of the amplification reagent, are sufficient to amplify and detect a second region of a second form of the analyte, where the one or more oligonucleotides of the first solvent are insufficient to amplify and detect the first or second form of the analyte, and where the first and second regions each comprise a different nucleotide base sequence.

Abstract: An automated system for performing nucleic acid amplification assays on samples provided to the system, where the system includes data input components configured to enable input specifying one or more user-defined assay parameters; data storage media storing a first set of assay parameters, the first set of assay parameters consisting of system-defined parameters, and a second set of assay parameters, the second set of assay parameters including the one or more user-defined parameters; and command input components configured to enable input specifying (i) that a first nucleic acid amplification assay be performed on a first sample in accordance with the first set of assay parameters, and (ii) that a second nucleic acid amplification assay be performed on a second sample in accordance with the second set of assay parameters.

Abstract: A method of performing a lab developed test for detecting a nucleic acid analyte on an automated analyzer. The method includes a first step of using a computer to select, define or modify one or more user-defined parameters of a protocol for performing the lab developed test on the analyzer, where each user-defined parameter of the protocol defines a step to be performed by the analyzer during the lab developed test. The method further includes a second step of performing the lab developed test with the protocol of the first step, where the analyzer stores one or more system-defined parameters for performing the lab developed test, the one or more system-defined parameters being installed on the analyzer prior to performing first step.

Abstract: Systems and methods for performing a plurality of nucleic acid amplification assays in an automated analyzer. A first nucleic acid amplification assay of the plurality is performed in accordance with a first set of assay parameters which consist of system-defined parameters. And a second nucleic acid amplification assay of the plurality is performed in accordance with a second set of assay parameters which includes one or more user-defined parameters.

Abstract: A system, method and computer readable medium enabling a user to specify user-defined assay parameters of an assay protocol for processing a sample and causing a computer-controlled analyzer to perform an assay in accordance with the assay protocol.