454 Life science Inc.

Branford, Connecticut, United States

454 Life science Inc.

Branford, Connecticut, United States
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Patent
454 LIFE science CORPORATION | Date: 2013-08-19

An embodiment of a method for sequencing a species of nucleic acid template using pH inert reference sensors is described that comprises the steps of: introducing a nucleotide species to an array of wells where a plurality of the wells comprise a species of nucleic acid template and a plurality of the wells comprise a plurality of functional groups with a high pH buffering characteristic, and in at least a first well a polymerase species incorporates the nucleotide species into a plurality of strands complementary to the species of nucleic acid template disposed in the first well and results in a release of a plurality of hydrogen ions; detecting a signal in the first well that is responsive to the hydrogen ions and one or more noise sources; detecting a signal in a second well comprising the functional groups with the high pH buffering characteristic that is responsive to the one or more noise sources; and subtracting the second well signal from the first well signal to generate a corrected signal associated with the detected hydrogen ions.


Patent
454 LIFE science CORPORATION | Date: 2013-02-12

A method for sequencing a nucleic acid is described that comprises the steps of: coupling an adaptor to at least one end of a template nucleic acid molecule; circularizing the adaptor coupled nucleic acid molecule; amplifying the adaptor coupled nucleic acid molecule to form a linear amplified concatamer molecule comprising a plurality of copies of the template nucleic acid molecule; compacting the linear amplified concatamer molecule with a branched polyelectrolyte species to form a branched polyelectrolyte compacted amplified concatamer molecule; and sequencing the branched polyelectrolyte compacted amplified concatamer molecule to produce a sequence composition of the template nucleic acid molecule.


Patent
454 LIFE science CORPORATION | Date: 2014-10-20

Disclosed are methods for nucleic acid amplification wherein nucleic acid templates, beads, and amplification reaction solution are emulsified and the nucleic acid templates are amplified to provide clonal copies of the nucleic acid templates attached to the beads. Also disclosed are kits and apparatuses for performing the methods of the invention.


An embodiment of a method and of a system for correcting an error associated with phasic synchrony of sequence data generated from a population of substantially identical copies of a template molecule.


Patent
454 Life science Corporation | Date: 2013-03-13

An embodiment of a method for generating a flow order that minimizes the accumulation of phasic synchrony error in sequence data is described that comprises the steps of: (a) generating a plurality of sequential orderings of nucleotides species comprising a k-base length, wherein the sequential orderings define a sequence of introduction of nucleotide species into a sequencing by synthesis reaction environment; (b) simulating acquisition of sequence data from one or more reference genomes using the sequential orderings, wherein the sequence data comprises an accumulation of phasic synchrony error; and (c) selecting one or more of the sequential orderings using a read length parameter and an extension rate parameter.


Patent
454 Life science Corporation | Date: 2014-08-22

An embodiment of a method for generating a population of amplified concatamer products is described that comprises amplifying a template nucleic acid molecule using a first nucleic acid primer immobilized on a bead substrate and a second nucleic acid primer in solution to generate a population of substantially identical copies of the template nucleic acid molecule immobilized on the bead substrate; and amplifying the population of substantially identical copies of the template nucleic acid molecule using a concatamer primer that comprises a first region complementary to an end region of the population of substantially identical copies of the template nucleic acid molecule and a second region to generate a population of immobilized concatamer products of the substantially identical copies of the template nucleic acid molecule.


Patent
454 Life science Corporation | Date: 2014-08-25

An embodiment of a device for automatically executing a process of generating an emulsion containing nucleic acids, amplifying the nucleic acids in the emulsion, breaking the emulsion, and separating and purifying said amplified nucleic acids, is described that comprises an emulsion generation unit for sealing beads to which nucleic acids are bound in a water-in-oil type emulsion; a nucleic acid amplification unit provided with a reaction vessel for amplifying said nucleic acids and a heating and cooling part for heating and cooling the reaction vessel; an emulsion breaking unit for breaking the emulsion after nucleic acid amplification; and a nucleic acid purification unit for recovering said amplified nucleic acids from said emulsion breaking unit.


Patent
454 LIFE science CORPORATION | Date: 2013-09-25

Disclosed are methods for nucleic acid amplification wherein nucleic acid templates, beads, and amplification reaction solution are emulsified and the nucleic acid templates are amplified to provide clonal copies of the nucleic acid templates attached to the beads. Also disclosed are kits and apparatuses for performing the methods of the invention.


Patent
454 Life science Corporation | Date: 2016-06-23

Disclosed are methods for nucleic acid amplification wherein nucleic acid templates, beads, and amplification reaction solution are emulsified and the nucleic acid templates are amplified to provide clonal copies of the nucleic acid templates attached to the beads. Also disclosed are kits and apparatuses for performing the methods of the invention.


Patent
454 Life science Corporation and Ibm | Date: 2013-04-29

A nanopore device includes a multi-layer structure comprising a surface defining an aperture extending through the multi-layer structure, wherein at least the surface comprising a minimal diameter comprises a monosilane functionalized silicon dioxide having a silicon-oxygen-silicon bond, the monosilane functionalized silicon dioxide having the following structure: wherein n is an integer from 1 to 12; R_(2 )and R_(3 )are each independently a methyl group, an ethyl group, a propyl group, an isopropyl group, a butyl group, or a tert-butyl group; and R_(4 )is a chloride, a carboxylic acid group, an amine group, an amide group, a thiol group, an alcohol group, an acyl chloride group, an acyl bromide group, an acyl iodide group, an alkene group, an alkyne group, or a polyether group. Also disclosed are methods for making, wetting, and operating the nanopore device.

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