Abstract: The invention relates to methods of genotyping the differential representation of one or more target genomic DNA sequences in a genomic DNA sample relative to a reference genomic DNA sample. The method uses tagged primer extension in which a set of tag sequences correspond to the identity of the elected target DNA sequence. Primer extension products are PCR amplified using a common set of tag-specific primers, the downstream primers bearing distinguishable labels. Following separation by size and/or charge, the detection of distinguishable label in a product of the anticipated size determines the identity and representation of the target DNA sequence in the sample. The method is well-suited for the genotyping of multiple target DNA sequence differences in one series of reactions.

Abstract: The invention provides sampling methods that permit the quantitative analysis of nucleic acid amplification reactions. Quantitative information garnered during an amplification regimen permits the development of a detailed amplification profile that in turn permits the reliable determination of original template abundance. The methods disclosed are particularly useful for quantitative expression analysis of multiple genes or transcription units, both in the same amplification reaction and in multiple amplification reactions.

Abstract: The invention relates to methods of genotyping single nucleotide differences in a nucleic acid sample. More particularly, the invention provides methods of identifying the nucleotide at a polymorphic site or a group of polymorphic sites in a sample of genomic DNA. The method uses tagged primer extension in which a set of tag sequences correspond to the identity of the nucleotides at the polymorphic sites. Primer extension products are PCR amplified using a common set of tag-specific primers, the downstream primers bearing distinguishable labels. Following separation by size and/or charge, the detection of distinguishable label in a product of the anticipated size determines the identity of the nucleotide at the polymorphic site. The method is well-suited for the genotyping of multiple single-nucleotide differences in one series of reactions.

Abstract: An apparatus for expression profiling analysis, subjecting biological materials to polynucleotide extraction, amplification and analysis. The apparatus include an amplification device which permits the amplification of polynucleotides and an analysis device which quantifies the amount of the amplified polynucleotide products. The amplification device of the apparatus may further permit polynucleotide extraction to prepare the template for amplification, or sequence identification of a quantified polynucleotide product. A fraction collector may be included in the apparatus to collect a qualified polynucleotide product before its sequence is identified. The analysis device may further permit data generation, or alternatively, data can be generated by a separate data generation device provided with the apparatus. The devices within the apparatus are connected by connecting means which permit the transfer of a fluid or a signal for amplification and analysis.

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.

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.