The present disclosure relates to a method of target enrichment and amplification of selective target regions of genomes or nucleic acid samples and further analysis by systems such as NGS. The disclosure provides methods and kits that can be used in numerous downstream procedures including DNA sequencing. The disclosed methods can be utilized to sequence the target nucleic acid sequences such as to detect the presence of genetic variations for biological assays, assessment of disease, to count copies of target regions, and to allow such target enrichment prior to sequencing.

Provided are methods and systems for detecting formation of nucleotide-specific ternary complexes comprising a DNA polymerase, a nucleic acid, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide without requiring chemical incorporation of the nucleotide into the primer. These results can even be achieved in procedures employing unlabeled, native nucleotides.

Provided are methods and systems for detecting formation of nucleotide-specific ternary complexes comprising a DNA polymerase, a nucleic acid, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide without requiring chemical incorporation of the nucleotide into the primer. These results can even be achieved in procedures employing unlabeled, native nucleotides.

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.

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.

A nucleic acid isothermal amplification method is based on a polymerase spiral reaction using only one pair of primers. The method employs a self-spiraling amplification method, and has a high amplification efficiency.

A nucleic acid isothermal amplification method is based on a polymerase spiral reaction using only one pair of primers. The method employs a self-spiraling amplification method, and has a high amplification efficiency.

The present invention relates to detecting aberrant expression of genes which may be associated with a disease or disorder using haplotype phasing. In particular, the invention relates to a method of obtaining an indication of dysregulation between the expression levels of at least two alleles of a gene in a target eukaryotic cell. The method comprises the steps of for a plurality of genes from one or more target eukaryotic cells, (a) obtaining pre-mRNAs of at least two alleles of the same gene; and (b) determining the ratios (Ri,j) between amounts of the pre-mRNAs of one or more pairs of alleles (i,j) of the same gene.

The present invention relates to detecting aberrant expression of genes which may be associated with a disease or disorder using haplotype phasing. In particular, the invention relates to a method of obtaining an indication of dysregulation between the expression levels of at least two alleles of a gene in a target eukaryotic cell. The method comprises the steps of for a plurality of genes from one or more target eukaryotic cells, (a) obtaining pre-mRNAs of at least two alleles of the same gene; and (b) determining the ratios (Ri,j) between amounts of the pre-mRNAs of one or more pairs of alleles (i,j) of the same gene.

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.