Abstract: Provided herein are methods and compositions for performing PCR with primers with blocked 3?-ends that are unblocked when these primers anneal to the template. The multiplexed PCR can be used as real-time qPCR, for end-point detection or as enrichment method for next generation sequencing (NGS). Also described herein are methods and compositions to improve sensitivity of mutation-specific PCR when targeting closely-spaced mutations.

Abstract: Provided herein are compositions, materials, methods and kits for immobilizing a template polynucleotide in a first orientation, and immobilizing a complementary sequence of the template polynucleotide in an orientation that is flipped compared to the orientation of the template polynucleotide. Provided herein are adaptive oligonucleotides that can be used in various nucleic acid manipulations to generate immobilized complement polynucleotides that are flipped in orientation compared to the orientation of the immobilized template polynucleotides.

Abstract: Provided are methods and compositions for detecting the presence or amount of one or more target nucleic acids in a sample. Methods of the present invention include linking universal nucleic acid segments into a single molecule in a linking reaction dependent on a target nucleic acid of interest. A variety of universal segment linking strategies are provided, including preamplification by polymerase chain reaction, ligation-based strategies, reverse transcription and linear polymerase extension. Linking the universal segments into a single molecule generates a tagged target nucleic acid which is detected in a manner dependent on an intramolecular interaction between one universal segment and a second portion of the tagged target nucleic acid. In certain embodiments, the intramolecular interaction includes the formation of a hairpin having a stem between a universal segment at one end of the tagged target nucleic acid and a second universal segment at the opposite end of the tagged target nucleic acid.

Abstract: A method and kit for detecting a target nucleic acid in a sample is described. The sample to be analyzed may include a primer which hybridizes to at least a portion of the target nucleic acid, a probe having a first region which hybridizes to at least a portion of the target nucleic acid and a second region having a detectable label, a polymerase which extends the hybridized primer and an enzyme comprising exonuclease activity that can cleave the hybridized hybridization probe to thereby generate a labeled probe fragment. At least one portion of the hybridization probe hybridizes to another portion of the hybridization probe to thereby form a folded structure. The method can involve melting the sample, reducing the temperature of the sample to allow primer and probe to each hybridize to at least a portion of single stranded target nucleic acid in the sample, elongating the primer and releasing the labeled probe fragment.

Abstract: The present teachings provide methods for reverse transcribing, and detecting, a plurality of small nucleic acids such as micro RNAs, from the same reaction mixture as a plurality of messenger RNAs. High levels of multiplexing are provided by the use of a plurality of zip-coded stem-loop reverse transcription primers, along with an oligo-dT-promoter-containing reverse transcription primer, in the same reverse transcription reaction mixture. The resulting products can be amplified in an in vitro transcription reaction, and detected on a solid support such as an array. The present teachings also provide compositions, kits, and devices for performing and detecting the reverse transcription reactions described herein.

Abstract: The present invention relates to methods and kits for detecting the presence or absence of (or quantitating) target nucleic acid sequences using ligation and amplification. The invention also relates to methods, reagents, and kits that employ addressable portions and labeled probes.

Abstract: The present teachings generally relate to methods, kits, and compositions for detecting target polynucleotide sequences. The teachings also relate to ligation and amplification reactions that generate self-complementary polynucleotide products. In some embodiments, ligation reactions are performed with probes that result in the formation a self-complementary ligation product. Ligation of a hairpin linker to the self-complementary ligation product can form a loop ligation product. In some embodiments, the loop ligation product can be amplified with rolling circle amplification. Detection of a loop ligation product can serve to determine the identity of a target polynucleotide.

Abstract: The teachings relate to methods and kits for detecting whether target nucleic acid sequences are present and/or quantitating target nucleic acid sequences.

Abstract: The present teachings generally relate to methods, kits, and compositions for detecting target polynucleotide sequences. The teachings also relate to ligation and amplification reactions that generate self-complementary polynucleotide products. In some embodiments, ligation reactions are performed with probes that result in the formation a self-complementary ligation product. Ligation of a hairpin linker to the self-complementary ligation product can form a loop ligation product. In some embodiments, the loop ligation product can be amplified with rolling circle amplification. Detection of a loop ligation product can serve to determine the identity of a target polynucleotide.

Abstract: Libraries of assays and methods of compiling the libraries are provided. The assays can identify Single Nucleotide Polymorphisms (SNPs). Methods of validating SNPs are provided. Methods of constructing linkage disequilibrium maps using sets or subsets of SNPs are also provided.

Abstract: The invention relates generally to the field of nucleic acid sequence analysis. In certain embodiments, the analysis is genotyping. In certain embodiments, the analysis involves detecting single nucleotide polymorphisms (SNPs). The invention also relates to methods, kits, and computer software for nucleic acid analysis.

Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the secreted peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the secreted peptides, and methods of identifying modulators of the secreted peptides.

Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the secreted peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the secreted peptides, and methods of identifying modulators of the secreted peptides.

Abstract: The invention relates generally to the field of nucleic acid sequence analysis. In certain embodiments, the analysis is genotyping. In certain embodiments, the analysis involves detecting single nucleotide polymorphisms (SNPs). The invention also relates to methods, kits, and computer software for nucleic acid analysis.

Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the secreted peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the secreted peptides, and methods of identifying modulators of the secreted peptides.

Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the secreted peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the secreted peptides, and methods of identifying modulators of the secreted peptides.