A composition for detecting SARS-CoV-2 is provided; moreover, a kit including the composition, the use of the kit, and a method for detecting SARS-CoV-2 are also provided.

Methods, systems, and apparatuses for efficiently amplifying and detecting certain nucleic acid sequences from a population. The selected population can be further characterised, for example by sequencing. A method involves combined solution phase and solid phase amplification.

Methods, systems, and apparatuses for efficiently amplifying and detecting certain nucleic acid sequences from a population. The selected population can be further characterised, for example by sequencing. A method involves combined solution phase and solid phase amplification.

Methods and compositions are described for multi-stage primer extension reactions such as multiplex polymerase chain reactions (PCR) and reverse transcriptase PCR. Primer extension stages are performed in a closed vessel without opening the vessel between stages. The multi-stage primer extension methods and compositions utilize earlier stage primers in an earlier stage and later stage primers in a later stage, wherein the later stage primers are blocked from extension during the earlier stage. The blocked primers of the present technology comprise photocleavable blocking groups and are substantially inactive until the blocking group is cleaved by exposure to ultraviolet light. The blocked primers can be activated by ultraviolet light without opening the vessel.

Methods and compositions are described for multi-stage primer extension reactions such as multiplex polymerase chain reactions (PCR) and reverse transcriptase PCR. Primer extension stages are performed in a closed vessel without opening the vessel between stages. The multi-stage primer extension methods and compositions utilize earlier stage primers in an earlier stage and later stage primers in a later stage, wherein the later stage primers are blocked from extension during the earlier stage. The blocked primers of the present technology comprise photocleavable blocking groups and are substantially inactive until the blocking group is cleaved by exposure to ultraviolet light. The blocked primers can be activated by ultraviolet light without opening the vessel.

A method for analysing insertion sites of an exogenous nucleotide sequence in a subject's genome, wherein the method comprises: (a) providing a sample from the subject comprising cell-free double-stranded DNA polynucleotides; (b) blunting the ends of the polynucleotides; (c) ligating an oligonucleotide to both ends of the polynucleotides; (d) amplifying polynucleotides comprising an insertion site; and (e) sequencing the product of step (d).

A method for analysing insertion sites of an exogenous nucleotide sequence in a subject's genome, wherein the method comprises: (a) providing a sample from the subject comprising cell-free double-stranded DNA polynucleotides; (b) blunting the ends of the polynucleotides; (c) ligating an oligonucleotide to both ends of the polynucleotides; (d) amplifying polynucleotides comprising an insertion site; and (e) sequencing the product of step (d).

The present invention relates to methods and devices for identifying and quantifying, including low abundance, nucleotide base mutations, insertions, deletions, translocations, splice variants, miRNA variants, alternative transcripts, alternative start sites, alternative coding sequences, alternative non-coding sequences, alternative splicings, exon insertions, exon deletions, intron insertions, or other rearrangement at the genome level and/or methylated nucleotide bases.

The present invention relates to methods and devices for identifying and quantifying, including low abundance, nucleotide base mutations, insertions, deletions, translocations, splice variants, miRNA variants, alternative transcripts, alternative start sites, alternative coding sequences, alternative non-coding sequences, alternative splicings, exon insertions, exon deletions, intron insertions, or other rearrangement at the genome level and/or methylated nucleotide bases.

Sets of experimentally validated gene specific primer pairs are provided. Embodiments of the sets include 10 or more gene specific primer pairs of forward and reverse primers. The forward and reverse primers of each primer pair include gene specific primers that are experimentally validated as suitable for use in a multiplex amplification assay. In some instances, each of the forward and reverse primers includes an anchor domain that includes a universal primer binding site. The sets find use in a variety of different applications, including high-throughput sequencing applications.