Abstract: The invention relates to modified polymerase enzymes which exhibit improved incorporation of nucleotide analogues bearing substituents at the 3? position of the sugar moiety that are larger in size than the naturally occurring 3? hydroxyl group. Also described are methods of using the polymerases to incorporate nucleotides into polynucleotides, particularly in the context of DNA sequencing.
Type:
Application
Filed:
August 25, 2016
Publication date:
December 15, 2016
Applicant:
Illumina Cambridge Limited
Inventors:
Geoffrey Paul Smith, David Mark Dunstan Bailey, Raquel Maria Sanches-Kuiper, Harold Swerdlow, David James Earnshaw
Abstract: The present invention relates to a method for preparing a library of template polynucleotides and use thereof in methods of solid-phase nucleic acid amplification. More specifically, the invention relates to a method for preparing a library of template polynucleotides that have common sequences at their 5? ends and at their 3? ends.
Type:
Application
Filed:
June 3, 2016
Publication date:
December 8, 2016
Applicant:
ILLUMINA CAMBRIDGE LIMITED
Inventors:
Niall Anthony Gormley, Geoffrey Paul Smith, David Bentley, Roberto Rigatti, Shujun Luo
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.
Type:
Grant
Filed:
June 17, 2014
Date of Patent:
December 6, 2016
Assignee:
ILLUMINA CAMBRIDGE LIMITED
Inventors:
Helen Bignell, Louise Fraser, Niall Anthony Gormley
Abstract: The invention relates to methods of generating templates for a nucleic acid sequencing reaction which comprise: providing at least one double-stranded nucleic acid molecule, wherein both strands of the double-stranded nucleic acid molecule are attached to a solid support at the 5? end, cleaving one or both strands of the double-stranded nucleic acid molecule, and subjecting the cleaved strand(s) to denaturing conditions to remove the portion of the cleaved strand(s) not attached to the solid support, thereby generating a partially or substantially single-stranded template for a nucleic acid sequencing reaction.
Type:
Grant
Filed:
June 12, 2015
Date of Patent:
November 22, 2016
Assignee:
Illumina Cambridge Limited
Inventors:
Xiaohai Liu, John Milton, Geoffrey Paul Smith, Colin Lloyd Barnes, Isabelle Rasolonjatovo, Roberto Rigatti, Xiaolin Wu, Tobias William Barr Ost, Graham John Worsley, David James Earnshaw, Gerardo Turcatti, Anthony Romieu
Abstract: Methods for amplifying nucleic acids are provided. The methods can be used to minimize sequence specific bias caused by the preferential amplification of certain nucleic acid sequences. Methods are described which can lower the efficiency of AT rich templates relative to GC rich templates, thereby minimizing GC bias during amplification reactions with multiple templates of different sequence. The methods are suited to solid phase amplification, for example, utilizing flow cells.
Type:
Grant
Filed:
June 9, 2014
Date of Patent:
October 18, 2016
Assignee:
ILLUMINA CAMBRIDGE LIMITED
Inventors:
Roberto Rigatti, Jonathan Mark Boutell, Min-Jui Richard Shen
Abstract: The invention relates to modified polymerase enzymes which exhibit improved incorporation of nucleotide analogs bearing substituents at the 3? position of the sugar moiety that are larger in size than the naturally occurring 3? hydroxyl group. Also described are methods of using the polymerases to incorporate nucleotides into polynucleotides, particularly in the context of DNA sequencing.
Type:
Grant
Filed:
September 3, 2014
Date of Patent:
September 20, 2016
Assignee:
Illumina Cambridge Limited
Inventors:
Geoffrey Paul Smith, David Mark Dunstan Bailey, Raquel Maria Sanches-Kuiper, Harold Swerdlow, David James Earnshaw
Abstract: The invention provides a nucleotide or nucleoside having a base attached to a detectable label via a cleavable linker, characterized in that the cleavable linker contains a moiety selected from the group comprising: Formula (I) (wherein X is selected from the group comprising O, S, NH and NQ wherein Q is a C1-10 substituted or unsubstituted alkyl group, Y is selected from the group comprising O, S, NH and N(allyl), T is hydrogen or a C1-10 substituted or unsubstituted alkyl group and * indicates where the moiety is connected to the remainder of the nucleotide or nucleoside).
Type:
Grant
Filed:
August 7, 2015
Date of Patent:
August 9, 2016
Assignee:
Illumina Cambridge Limited
Inventors:
Xiaohai Liu, John Milton, Silke Ruediger
Abstract: The invention relates to an additive which can be added to buffers used in nucleotide detection processes and improved methods of nucleic acid sequencing using this additive. In particular the invention relates to use of the additive to improve the efficiency of fluorescence-based multiple cycle nucleic acid sequencing reactions.
Type:
Application
Filed:
February 22, 2016
Publication date:
July 21, 2016
Applicant:
Illumina Cambridge Limited
Inventors:
Milan Fedurco, Anthony Romieu, Gerardo Turcatti
Abstract: The invention provides modified nucleotide or nucleoside molecule comprising a purine or pyrimidine base and a ribose or deoxyribose sugar moiety having a removable 3?-OH blocking group covalently attached thereto, such that the 3? carbon atom has attached a group of the structure —O—Z wherein Z is any of —C(R?)2-O—R?, —C(R?)2-N(R?)2, —C(R?)2-N(H)R?, —C(R?)2-S—R? and —C(R?)2-F, wherein each R? is or is part of a removable protecting group; each R? is independently a hydrogen atom, an alkyl, substituted alkyl, arylalkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclic, acyl, cyano, alkoxy, aryloxy, heteroaryloxy or amido group, or a detectable label attached through a linking group; or (R?)2 represents an alkylidene group of formula ?C(R??)2 wherein each R?? may be the same or different and is selected from the group comprising hydrogen and halogen atoms and alkyl groups; and wherein said molecule may be reacted to yield an intermediate in which each R? is exchanged for H or, where Z is —C(R?)2-F, the F is ex
Type:
Grant
Filed:
August 7, 2015
Date of Patent:
July 12, 2016
Assignee:
Illumina Cambridge Limited
Inventors:
John Milton, Xiaolin Wu, Mark Smith, Joseph Brennan, Colin Barnes, Xiaohai Liu, Silke Ruediger
Abstract: The present invention relates to a method for preparing a library of template polynucleotides and use thereof in methods of solid-phase nucleic acid amplification. More specifically, the invention relates to a method for preparing a library of template polynucleotides that have common sequences at their 5? ends and at their 3? ends.
Type:
Grant
Filed:
September 10, 2013
Date of Patent:
June 28, 2016
Assignee:
Illumina Cambridge Limited
Inventors:
Niall Anthony Gormley, Geoffrey Paul Smith, David Bentley, Roberto Rigatti, Shujun Luo
Abstract: The present disclosure relates to new compounds and their use as fluorescent labels. The compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.
Type:
Application
Filed:
March 1, 2016
Publication date:
June 23, 2016
Applicant:
Illumina Cambridge Limited
Inventors:
Xiaohai Liu, Nikolai Nikolaevich Romanov
Abstract: The invention relates to methods for pairwise sequencing of a double-stranded polynucleotide template, which permit the sequential determination of nucleotide sequences in two distinct and separate regions on complementary strands of the double-stranded polynucleotide template. The two regions for sequence determination may or may not be complementary to each other.
Abstract: The invention relates to a method of preparing a library of template polynucleotides which reduces and/or prevents the formation of adaptor-dimers. The invention also relates to the use of a library of templates prepared using the method of the invention for solid-phase nucleic acid amplification. In particular, the invention relates to a method of preparing a library of template polynucleotides which have common sequences at their 5? ends and at their 3? ends which is substantially free of adaptor-dimers.
Type:
Grant
Filed:
July 30, 2007
Date of Patent:
May 3, 2016
Assignee:
Illumina Cambridge Limited
Inventors:
David James Earnshaw, Niall Anthony Gormley, Helen Rachel Bignell, Melanie Anne Smith
Abstract: Modified DNA polymerases have an affinity for DNA such that the polymerase has an ability to incorporate one or more nucleotides into a plurality of separate DNA templates in each reaction cycle. The polymerases are capable of forming an increased number of productive polymerase-DNA complexes in each reaction cycle. The modified polymerases may be used in a number of DNA sequencing applications, especially in the context of clustered arrays.
Type:
Application
Filed:
December 1, 2015
Publication date:
April 28, 2016
Applicant:
Illumina Cambridge Limited
Inventors:
Geoffrey Paul Smith, Roberto Rigatti, Tobias William Barr Ost, Shankar Balasubramanian, Raquel Maria Sanches-Kuiper
Abstract: The present disclosure relates to new compounds and their use as fluorescent labels. The compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.
Type:
Grant
Filed:
May 6, 2015
Date of Patent:
April 12, 2016
Assignee:
Illumina Cambridge Limited
Inventors:
Xiaohai Liu, Nikolai Nikolaevich Romanov