Abstract: The invention provides compositions, methods and systems for dynamic transcription profiling of two or more samples. The method of the invention comprises the uses of sample-specific primers for cDNA synthesis and for subsequent amplification of the synthesized cDNAs. The levels of abundance of genes are compared between samples for the identification of differentially expressed genes.

Abstract: Described are novel quantification methods and systems that permit, within the context of multiplex PCR, the quantification of all targets within a single reaction tube. The methods employ quantitation algorithms applied to the amplification profiles of internal calibration controls or standards utilizing a plurality of nucleic acid templates that are amplified within the same reaction tube as the nucleic acid target(s) interrogated.

Abstract: The invention allows for the quantitative detection of a plurality of pathogens in a single sample. The method includes the amplification of a sample with a plurality of pathogen-specific primer pairs to generate amplicons of distinct sizes from each of the pathogen specific primer pairs. The method further includes the use of a plurality of competitor polynucleotide targets that correspond to each of the pathogen-specific primer pairs. The competitor polynucleotides are added to the reaction mixture at a known concentration to allow for the quantitation of the amount of pathogen in the sample. The method can be used for monitoring pathogen infection in an individual, preferably an immunocompromised individual.

Abstract: The invention provides sampling methods that permit the quantitative analysis of nucleic acid amplification reactions. The methods disclosed permit quantitative expression analysis of multiple genes or transcription units, both in the same amplification reaction and in multiple amplification reactions. In one aspect, the methods disclosed include, briefly, dispensing or withdrawing an aliquot from a reaction mixture at plural stages of an amplification regimen, separating and detecting nucleic acids in the aliquot, determining the quantity of a plurality of separated nucleic acid species in the aliquot, and for each separated nucleic acid species from each stage, correlating the quantity of the species with the stage at which the aliquot comprising the species was dispensed, thereby generating a profile of the amplification.

Abstract: Described herein are approaches to the measurement of gene expression for chosen genes in a biological sample. The methods permit the quantitation of target nucleic acids, e.g., DNAs or RNAs in a nucleic acid sample, both singly and in a multiplex format that permits the determination of levels (e.g., expression levels or copy numbers) for two or more target nucleic acids in a single reaction.

Abstract: The invention allows for the quantitative detection of a plurality of pathogens in a single sample. The method includes the amplification of a sample with a plurality of pathogen-specific primer pairs to generate amplicons of distinct sizes from each of the pathogen specific primer pairs. The method further includes the use of a plurality of competitor polynucleotide targets that correspond to each of the pathogen-specific primer pairs. The competitor polynucleotides are added to the reaction mixture at a known concentration to allow for the quantitation of the amount of pathogen in the sample. The method can be used for monitoring pathogen infection in an individual, preferably an immunocompromised individual.

Abstract: Described herein are approaches to the detection and quantitation of short RNAs in a biological sample. The methods permit the detection and quantitation of individual species of short RNA in a nucleic acid sample, both singly and in a multiplex format that permits the determination of expression levels for two or more target short RNAs in a single reaction.

Abstract: Described herein are compositions and methods for enriching a nucleic acid sample for target sequence(s). The compositions comprise an oligonucleotide attached to a solid support, directly or indirectly, wherein the oligonucleotide does not serve as a primer for a polymerase enzyme.

Abstract: The invention relates to methods of monitoring the amplification of one or more nucleic acid sequences of interest. More particularly, the invention relates to methods of monitoring the amplification of sequences of interest in real time. The methods disclosed herein provide methods for monitoring the amplification of one sequence or two or more sequences from a single sample, as well as methods for monitoring the amplification of one or more than one sequence from two or more samples. The monitoring methods of the invention permit improved determination of the abundance of one or more target nucleic acids, especially target RNA species, in one or more original samples.