Population Genetics Technologies Ltd.

10x Genomics, Inc.

Oxford Nanopore Technologies Limited

Genome Research Limited

Other

Agilent Technologies, Inc.

Agency for Science, Technology and Research

University of Rochester

Agency for Science, Technology and Research (a*star)

Personal Genome Diagnostics, Inc.

Population Genetics Technologies Litd.

University of Florida Research Foundation, Incorporated

Robert Osborne

Sydney Brenner

Gi Mikawa

Andrew Slatter

James Casbon

Andreas Claas

Esther Musgrave-Brown

Conrad Lichtenstein

Samuel Woodhouse

Barnaby Balmforth

Magdalena Stolarek-Januszkiewicz

Charles A Thornton

Thurman Wheeler

Maurice Scott Swanson

Krzysztof Sobczak

Jill Miller

Christopher Laumer

Federico Abascal

Stefanie Lensing

Inigo Martincorena

Krzysztof Sobezak

Maurice Swanson

Sam Woodhouse

Maurice S Swanson

Described herein, among other things, is a method of sequencing, comprising: concatenating a plurality of fragments of genomic DNA to produce concatenated DNA; sequencing the concatenated DNA to produce a plurality of sequence reads, wherein at least some of the sequence reads comprise: at least the sequence of the 3' and/or 5′ ends of a fragment that corresponds to the locus of interest and sequence of one or both of the fragments that flank the fragment in the concatenated DNA; and grouping the sequence reads that corresponds to the locus of interest using, for each of the grouped sequence reads: the 3′ and/or 5′ end sequences; and/or the flanking sequence.

Method of identifying sequence variants using concatenation

Disclosed is a hybridisation capture method based on the pyrophosphorolysis reaction. According to the present invention, there is provided a method for increasing the ratio of a first nucleic add sequence to second nucleic add sequence in a sample.

Nucleic acid enrichment and detection

Described herein is a method of sequencing a template that comprises a direct repeat, comprising: (a) in the same reaction, hybridizing a primer to a first site that is upstream of the first repeat sequence and hybridizing a primer to a second site that is upstream of the second repeat sequence, wherein the first and second sites are: (i) upstream of the first and second repeat sequences, respectively, and (ii) equidistant from the first and second repeat sequences; and (b) subjecting the hybridization product of (a) to a sequencing-by-synthesis sequencing reaction to produce a sequence read that comprises a combination of the first and second repeat sequences.

Method for sequencing a direct repeat

Described herein is a method of sequencing, comprising: splitting an asymmetrically tagged library into a plurality of subsamples, tagging the adaptor-ligated DNA in the sub-samples with sequence tags that identify the subsamples, optionally pooling the sub-samples, sequencing polynucleotides from each of the tagged sub-samples, or copies of the same, to produce sequence reads each comprising: i. a sub-sample identifier sequence and ii. the sequence of at least part of a fragment in the sample, wherein some of the sequence reads are derived from the top strand of a fragment in the sample and some of the sequence reads of are derived from the bottom strand of the same fragment.

Method for bidirectional sequencing

Among other things, a method for normalizing a sample is provided. In some embodiments, the method comprises: (a) reacting a sample with a limiting amount of a single-turnover sequence-specific endonuclease that recognizes a target sequence, thereby cleaving a portion of the nucleic acid molecules that comprise the target sequence and producing a normalized amount of a first cleavage product; and (b) isolating, transcribing or selectively amplifying the normalized amount of the first cleavage product. In this method, because a limiting amount of the endonuclease is used, the normalized amount of the first cleavage product is determined by the limiting amount of the first single-turnover sequence-specific endonuclease used in step (a).

Method for normalizing a nucleic acid sample

Described herein, among other things, is a method of sequencing, comprising: concatenating a plurality of fragments of genomic DNA to produce concatenated DNA; sequencing the concatenated DNA to produce a plurality of sequence reads, wherein at least some of the sequence reads comprise: at least the sequence of the 3' and/or 5&#x2032; ends of a fragment that corresponds to the locus of interest and sequence of one or both of the fragments that flank the fragment in the concatenated DNA; and grouping the sequence reads that corresponds to the locus of interest using, for each of the grouped sequence reads: the 3&#x2032; and/or 5&#x2032; end sequences; and/or the flanking sequence.

Described herein is a population of direct repeat molecules, where each molecule of the population contains a direct repeat composed of sequences that are amplified from the opposite strands of a double-stranded fragment of genomic DNA. Within each molecule, the first repeat (referred to as TOP) is amplified from the one strand of a double-stranded fragment of genomic DNA and the second repeat (referred to as BOT') is amplified from the other strand of the same fragment of double-stranded fragment of genomic DNA.

Duplex sequencing using direct repeat molecules

A method of evaluating a sequence variation in a sample is provided. In some embodiments, the method may involve: amplifying a nucleic acid product from an initial sample; fragmenting an amount of the nucleic acid product to produce fragments; attaching an adaptor to each end of the fragments to produce adaptor-tagged fragments; sampling no more than 10% of the tagged fragments and amplifying them; sequencing at least some of the copies of the fragments to produce a plurality of sequence reads; grouping sequence reads for copies of fragments that have the same fragmentation breakpoints; deriving a consensus sequence for each of the read groups; and aligning the consensus sequences with a reference sequence.

Method for evaluating minority variants in a sample

Aspects of the present invention include analyzing nucleic acids from single cells using methods that include using tagged polynucleotides containing multiplex identifier sequences.

Methods for analyzing nucleic acids

Methods for analyzing nucleic acids from single cells

Described herein is a method for adding a counter sequence to the individual polynucleotide molecules of an initial nucleic acid sample. After addition of the counter sequence, the sample may be amplified and the number of initial target molecules in the sample can be estimated by counting the number of counter sequences associated with the amplified target molecules.

Method for attaching a counter sequence to a nucleic acid sample

Providing herein, among other things, is a method for preparing a nucleic acid for sequencing. In some embodiments, the method comprises a) amplifying a nucleic acid template using a dNTP mix that contains 5-methyl dCTP, thereby producing product nucleic acid molecules that contains methylcytosines; b) digesting the product nucleic acid molecules with a methylation-dependent restriction endonuclease, thereby cleaving the product nucleic acid molecules at sites that are adjacent to at least some of the methylcytosine and producing fragments of the product nucleic acid molecules; and c) ligating double-stranded adaptors onto the ends of the fragments to produce adaptor-ligated products.

Method for fragmenting and ligating adapters onto a nucleic acid and kit for performing the same

Growing community of inventors

Great Chesterford, United Kingdom

Robert Osborne