Methods, compositions, reaction mixtures, kits, and/or systems for producing a complementary sequence to a region in a target polynucleotide in a sample are provided. In some aspects, the methods, compositions, reaction mixtures, kits, and/or systems comprise subjecting the sample to a nucleic acid amplification reaction in a reaction mixture under conditions to yield the complete sequence to the region of the target polynucleotide. In some aspects, the complementary sequence produced is amplified.

Method of identifying a cognate nucleotide (i.e., the “next correct nucleotide”) for a primed template nucleic acid molecule. In some embodiments, an ordered or random array of primed target nucleic acids characterized by different cognate nucleotides can be evaluated using a single imaging step to identify different cognate nucleotides for a collection of different primed template nucleic acid molecules. An optional incorporation step can follow the identifying step. A polymerase different from the ones used in the binding and examination steps can be used to incorporate a nucleotide, such as a reversible terminator nucleotide, preliminary to identification of the next cognate nucleotide.

Method of identifying a cognate nucleotide (i.e., the “next correct nucleotide”) for a primed template nucleic acid molecule. In some embodiments, an ordered or random array of primed target nucleic acids characterized by different cognate nucleotides can be evaluated using a single imaging step to identify different cognate nucleotides for a collection of different primed template nucleic acid molecules. An optional incorporation step can follow the identifying step. A polymerase different from the ones used in the binding and examination steps can be used to incorporate a nucleotide, such as a reversible terminator nucleotide, preliminary to identification of the next cognate nucleotide.

Provided is a method for detecting the chemical modification of a target RNA site X, comprising the steps as follows: (1) acquiring an RNA sample and selecting in the RNA sample a target RNA segment comprising the target RNA site X; (2) SELECT; (3) PCR amplification; (4) comprising the PCR cycle threshold value with a reference PCR cycle threshold value, or comparing the PCR amplification product quantity with a reference PCR amplification product quantity, so as to determine whether there is a target chemical modification in the target RNA site X. Further provided are a method for identifying a substrate target site of RNA modification enzyme or RNA demodification enzyme and a method for quantifying an RNA modification rate in a transcript.

Provided is a method for detecting the chemical modification of a target RNA site X, comprising the steps as follows: (1) acquiring an RNA sample and selecting in the RNA sample a target RNA segment comprising the target RNA site X; (2) SELECT; (3) PCR amplification; (4) comprising the PCR cycle threshold value with a reference PCR cycle threshold value, or comparing the PCR amplification product quantity with a reference PCR amplification product quantity, so as to determine whether there is a target chemical modification in the target RNA site X. Further provided are a method for identifying a substrate target site of RNA modification enzyme or RNA demodification enzyme and a method for quantifying an RNA modification rate in a transcript.

The present disclosure relates generally to methods for targeted hybrid capture of rearranged T cell receptors. More particularly, some embodiments relate to a method for direct and quantitative, error-corrected counting of genomic sequences for determining immune response gene repertoires.

The present disclosure relates generally to methods for targeted hybrid capture of rearranged T cell receptors. More particularly, some embodiments relate to a method for direct and quantitative, error-corrected counting of genomic sequences for determining immune response gene repertoires.

The present invention relates generally to an improved method of amplifying a nucleic acid region of interest and to primers for use therein. More particularly, the present invention is directed to an improved method of amplifying a nucleic acid region which has resulted from the recombination of two or more immunoglobulin or T cell receptor gene segments and primers for use therein. The method of the present invention is based on the determination that performing the amplification step using primers which exhibit a high Tm and/or using a high annealing temperature enables higher levels of sensitivity than has previously been achievable in the context of prior art methods of amplifying rearranged immunological or T cell receptor genes. Still further improvements in sensitivity are achievable where the subject primer hybridises to at least two N regions of the recombined gene. The provision of a highly sensitive yet simple means of detecting specific immunological and T cell receptor nucleic acid recombination events is useful in a range of applications including, but not limited to, the diagnosis and/or monitoring of clonal lymphoid cell populations or disease conditions which are characterised by specific V/D/J recombination events (such as detecting minimal residual disease in leukaemias) or the analysis or identification of immunological or T cell receptor gene regions of interest.

The present invention relates generally to an improved method of amplifying a nucleic acid region of interest and to primers for use therein. More particularly, the present invention is directed to an improved method of amplifying a nucleic acid region which has resulted from the recombination of two or more immunoglobulin or T cell receptor gene segments and primers for use therein. The method of the present invention is based on the determination that performing the amplification step using primers which exhibit a high Tm and/or using a high annealing temperature enables higher levels of sensitivity than has previously been achievable in the context of prior art methods of amplifying rearranged immunological or T cell receptor genes. Still further improvements in sensitivity are achievable where the subject primer hybridises to at least two N regions of the recombined gene. The provision of a highly sensitive yet simple means of detecting specific immunological and T cell receptor nucleic acid recombination events is useful in a range of applications including, but not limited to, the diagnosis and/or monitoring of clonal lymphoid cell populations or disease conditions which are characterised by specific V/D/J recombination events (such as detecting minimal residual disease in leukaemias) or the analysis or identification of immunological or T cell receptor gene regions of interest.

The present invention provides methods for enriching a target complementary DNA (cDNA), comprising: (a) providing a plurality of cDNAs, each comprising a first universal sequence at an end, and wherein the plurality of cDNAs comprises the target cDNA; (b) amplifying the target cDNA with a universal forward primer complementary to the first universal sequence and a gene specific reverse primer, and wherein a second universal sequence is added to an end of the cDNA opposite the first universal sequence, by a nucleic acid amplification reaction, by ligation, or by a primer extension reaction; and (c) amplifying the amplicons or extension products using the universal forward primer and a universal reverse primer complementary to the second universal sequence. In one embodiment, the universal forward primer, the gene specific reverse primer and the second universal reverse primer are provided in the same reaction mixture such that the amplifying is a single step.