The present invention relates to a method of detecting specific nucleic acid sequences and a device for performing the method therein. The specific nucleic acid may be prepared from a subject-specimen or from an environmental specimen and the method is performed in isothermal conditions.

The present invention relates to a method of detecting specific nucleic acid sequences and a device for performing the method therein. The specific nucleic acid may be prepared from a subject-specimen or from an environmental specimen and the method is performed in isothermal conditions.

Provided herein are methods for generating circular nucleic acid molecules and circular nucleic acid libraries. The methods can be used to generate clonal populations of target nucleic acid molecules for downstream applications such as sequencing. Nucleic acid sequence methods, systems and kits are also provided for sequencing circular nucleic acid molecules.

Provided herein are methods for generating circular nucleic acid molecules and circular nucleic acid libraries. The methods can be used to generate clonal populations of target nucleic acid molecules for downstream applications such as sequencing. Nucleic acid sequence methods, systems and kits are also provided for sequencing circular nucleic acid molecules.

The present invention belongs to the fields of biomedical technology and molecular diagnosis. Disclosed is a high-throughput detection method for a rare mutation of a gene, comprising: designing specific probes; connecting Y-shaped universal linkers to a test DNA subjected to fragmentation processing, and performing amplification and enrichment of a target site by universal sequence combination of the specific probes and the linkers; performing genomic sequence alignment on sequences to be sequenced; sorting and analyzing said sequences at the same starting and ending positions, and filtering sequencing errors; and after the data filtering, the sequencing depth count of a reference allele of the target site being a, and the sequencing depth count of other alleles being b, and thus the actual mutation ratio of the site being b/(a+b). This technique can perform, by DNA fragmentation, universal linker connection, multiplex PCR amplification of specific primers and linker sequence primers, and high-throughput high-depth sequencing, enrichment and parallel sequencing on a plurality of sites to be tested.

The present invention belongs to the fields of biomedical technology and molecular diagnosis. Disclosed is a high-throughput detection method for a rare mutation of a gene, comprising: designing specific probes; connecting Y-shaped universal linkers to a test DNA subjected to fragmentation processing, and performing amplification and enrichment of a target site by universal sequence combination of the specific probes and the linkers; performing genomic sequence alignment on sequences to be sequenced; sorting and analyzing said sequences at the same starting and ending positions, and filtering sequencing errors; and after the data filtering, the sequencing depth count of a reference allele of the target site being a, and the sequencing depth count of other alleles being b, and thus the actual mutation ratio of the site being b/(a+b). This technique can perform, by DNA fragmentation, universal linker connection, multiplex PCR amplification of specific primers and linker sequence primers, and high-throughput high-depth sequencing, enrichment and parallel sequencing on a plurality of sites to be tested.

Methods and compositions for determining the proximity of two barcoding oligonucleotides (e.g., in a single partition or adjacent on a tissue section) using a determination of the presence of a 9 bp sequence resulting from tagmentation in different nucleic acid fragments linked to different barcoding oligonucleotides is provided.

In an example method, a series of time-based clustering images is generated for a plurality of library fragments from a genome sample. Each time-based clustering image in the series is sequentially generated. To generate each time-based clustering image in the series: i) a respective sample is introduced to a flow cell, the respective sample including contiguity preserved library fragments of the plurality of library fragments, wherein the contiguity preserved library fragments are attached to a solid support or are attached to each other; ii) the contiguity preserved library fragments are released from the solid support or from each other; iii) the contiguity preserved library fragments are amplified to generate a plurality of respective template strands; iv) the respective template strands are stained; and v) the respective template strands are imaged.

In an example method, a series of time-based clustering images is generated for a plurality of library fragments from a genome sample. Each time-based clustering image in the series is sequentially generated. To generate each time-based clustering image in the series: i) a respective sample is introduced to a flow cell, the respective sample including contiguity preserved library fragments of the plurality of library fragments, wherein the contiguity preserved library fragments are attached to a solid support or are attached to each other; ii) the contiguity preserved library fragments are released from the solid support or from each other; iii) the contiguity preserved library fragments are amplified to generate a plurality of respective template strands; iv) the respective template strands are stained; and v) the respective template strands are imaged.

Provided herein are oligomers, compositions, kits, and methods for capturing target polynucleotides, e.g., for downstream applications such as amplification, library preparation, or sequencing. In some embodiments, a capture oligomer is provided or used that comprises a capture sequence that is annealed to a complement that prevents capture until the complement is displaced in a target-polynucleotide dependent manner. In some embodiments, an amount of target polynucleotide is captured that is less than or equal to a predetermined amount.