Abstract: The present disclosure provides systems and methods for sequencing nucleic acid molecules using tunneling labels. A sequence of a nucleic acid molecule may be identified with high accuracy using a chip comprising sensors, wherein each individual sensor may comprise at least two electrodes separated by a gap. The electrodes may be configured to generate at least one electrical signal upon binding of a tunneling label associated with a nucleotide. Epigenetic information can also be determined at the same time as a nucleic acid sequence.

Abstract: The disclosed embodiments concern methods, apparatus, systems and computer program products for determining the presence or absence of repeat expansions of interest, including repeat expansions of repeat sequences that are medically significant. Some embodiments provide methods for identifying and calling medically relevant repeat expansions using anchored reads. An anchored read is a paired end read that is unaligned to a repeat sequence under consideration, but it is paired with an anchor read that is aligned to or near the repeat sequence. Some embodiments use both anchor and anchored reads to determine the presence or absence of the repeat expansions. System, apparatus, and computer program products are also provided for determining repeat expansion implementing the methods disclosed.

Abstract: The present invention provides methods for creating an array of features on a surface based on content transferred from a plurality of beads to the surface. Nucleic acid content can be transferred using a method including the steps of (a) providing a surface having one or more primer oligonucleotides attached to the surface; (b) providing a pool of beads, wherein beads in the pool have a plurality of templates attached thereto, the plurality comprising multiple copies of a single nucleic acid template sequence; (c) arraying the beads onto the surface by hybridizing the templates to the primer oligonucleotides; and (d) extending the primers to produce copies of the templates attached to the surface.

Abstract: Methods and compositions are disclosed relating to the localization of nucleic acids to arrays such as silane-free arrays, and of sequencing the nucleic acids localized thereby.

Abstract: Cyanine dyes with improved fluorescence intensity and photostability.

Abstract: The invention relates to methods for indexing samples during the sequencing of polynucleotide templates, resulting in the attachment of tags specific to the source of each nucleic acid sample such that after a sequencing run, both the source and sequence of each polynucleotide can be determined. Thus, the present invention pertains to analysis of complex genomes (e.g., human genomes), as well as multiplexing less complex genomes, such as those of bacteria, viruses, mitochondria, and the like.

Abstract: The invention relates to a method of preparing template constructs for solid-phase nucleic acid amplification and to use of the templates in methods of solid-phase nucleic acid amplification. The method involves carrying out two ligation reactions: (a) a ligation reaction in which the first end of one or more target polynucleotide molecules are ligated to surface-bound adaptor polynucleotide molecules, and (b) a ligation reaction in which solution-phase adaptor polynucleotide molecules are ligated to the second end of said target polynucleotide molecules, in order to produce one or more template constructs attached to a solid support.

Abstract: The invention relates to methods for indexing samples during the sequencing of polynucleotide templates, resulting in the attachment of tags specific to the source of each nucleic acid sample such that after a sequencing run, both the source and sequence of each polynucleotide can be determined. Thus, the present invention pertains to analysis of complex genomes (e.g., human genomes), as well as multiplexing less complex genomes, such as those of bacteria, viruses, mitochondria, and the like.

Abstract: The invention relates to methods for pairwise sequencing of a double-stranded polynucleotide template, which methods result in the sequential determination of nucleotide sequences in two distinct and separate regions of the polynucleotide template. Using the methods of the invention it is possible to obtain two linked or paired reads of sequence information from each double-stranded template on a clustered array, rather than just a single sequencing read from one strand of the template.

Abstract: A nucleic acid molecule can be annealed to an appropriate immobilised primer. The primer can then be extended and the molecule and the primer can be separated from one another. The extended primer can then be annealed to another immobilised primer and the other primer can be extended. Both extended primers can then be separated from one another and can be used to provide further extended primers. The process can be repeated to provide amplified, immobilised nucleic acid molecules. These can be used for many different purposes, including sequencing, screening, diagnosis, in situ nucleic acid synthesis, monitoring gene expression, nucleic acid fingerprinting, etc.

Abstract: Methods for isothermal amplification of nucleic acid by means of a solid support are disclosed. These methods are useful for applications needing high throughput, in particular nucleic acid sequencing.