Illumina Cambridge Limited

Illumina Corporation

Massachusetts Institute of Technology

Niall Anthony Gormley

Roberto Rigatti

Jonathan Mark Boutell

Geoffrey Paul Smith

Louise Fraser

Helen Rachel Bignell

David Bentley

Shujun Luo

Colin Lloyd Barnes

Jason Richard Betley

Tobias William Barr Ost

Vincent Peter Smith

Eric Hans Vermaas

Andreas Gnirke

Andrew Slatter

Graham John Worsley

Harris Nusbaum

David Jaffe

Esther Musgrave-Brown

Paula Kokko-Gonzales

Melanie Anne Smith

Susan C Verity

Frank J Steemers

Allen E Eckhardt

Natalie Morrell

Rosamond Jackson

Avgousta Ioannou

Kevin L Gunderson

M Shane Bowen

Molly Min He

Mostafa Ronaghi

Min-Jui Richard Shen

Jeffrey S Fisher

Maria Candelaria Rogert Bacigalupo

Amirali Kia

Igor Yu Goryshin

Lewis J Kraft

Kay Klausing

Rigo Pantoja

Gerardo Turcatti

David James Earnshaw

Dmitry K Pokholok

Fan Zhang

John Moore

Wouter Meuleman

Kevin Hall

Gareth Jenkins

Dirk Evers

Jacqueline Weir

Steven J Norberg

Helen Bignell

Epameinondas Fritzilas

Vincent Smith

Igor Goryshin

Geoffery Smith

Matthew Hims

John Stephen West

Gerado Turcatti

The present disclosure relates to methods, compositions, and kits for generating a library of tagged nucleic acid fragments without using PCR amplification, including methods and compositions for fragmenting and tagging nucleic acids (e.g., DNA) using transposome complexes immobilized on solid support.

Complex surface-bound transposome complexes

A method of generating an asymmetric closed-ended double stranded nucleic acid template from a double stranded nucleic acid template having free 5' and 3′ ends by use of hairpin or dumbbell adaptors, and sequencing therefrom.

Methods for generating, and sequencing from, asymmetric adaptors on the ends of polynucleotide templates comprising hairpin loops

The invention relates to a method of preparing and using a library of template polynucleotides suitable for use as templates in solid-phase nucleic acid amplification and sequencing reactions to determine the methylation status of the cytosine bases in the library. In particular, the invention relates to a method of preparing and analysing a library of template polynucleotides suitable for methylation analysis.

Preparation of templates for methylation analysis

Provided herein is a method for sequencing a polynucleotide molecules. The method includes the steps of providing a plurality of polynucleotide molecules attached to a surface, wherein a first portion of each polynucleotide molecule is attached to a first location of the surface and a second portion of each polynucleotide molecule is attached to a second location of the surface, the relative proximity of the first and second locations being correlated with the probability that the first and second portions are paired, separating the first and second portions of the polynucleotide molecules on the surface, determining the sequences of the first and second portions of the polynucleotide molecules and comparing the relative proximities and the sequences to determine which first and second portions are paired and to determine the sequence of the target polynucleotide molecules.

Methods for sequencing polynucleotides

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.

Method of preparing libraries of template polynucleotides

Presented are methods and compositions for using immobilized transposase and a transposon end for generating an immobilized library of 5′-tagged double-stranded target DNA on a surface. The methods are useful for generating 5′- and 3′-tagged DNA fragments for use in a variety of processes, including massively parallel DNA sequencing.

Sample preparation on a solid support

Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.

Contiguity preserving transposition

Provided herein is a method of using transposition to improve methods of sequencing RNA molecules. Provided herein is a method of tagging nucleic acid duplexes, such as DNA:RNA duplexes or DNA:DNA duplexes. The method includes the steps of providing a transposase and a transposon composition, providing one or more nucleic acid duplexes immobilized on a support, and contacting the transposase and transposon composition with the one or more nucleic acid duplexes under conditions wherein the one or more nucleic acid duplexes and transposon composition undergo a transposition reaction to produce one or more tagged nucleic acid duplexes, wherein the transposon composition comprises a double stranded nucleic acid molecule comprising a transferred strand and a non-transferred strand.

Methods of nucleic acid sequencing

Provided is a method, including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments. Also provided is a method including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments.

Separating polynucleotide fragments

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.

Methods for indexing samples and sequencing multiple polynucleotide templates

Presented herein are methods and compositions surface-based tagmentation. In particular embodiments, methods of preparing an immobilized library of fragmented and tagged DNA molecules on a solid surface are presented. In particular embodiments, the solid surface comprises immobilized transposomes in a dried format, suitable for reconstitution upon contact with liquid, such as a liquid sample.

Surface-based tagmentation

Embodiments provided herein relate to methods and compositions for next generation sequencing. Some embodiments include the preparation of a template library from a target nucleic acid in contact with a surface, and sequencing the library on the surface.

Methods and compositions for preparing sequencing libraries

Growing community of inventors

Nr Saffron Walden, United Kingdom

Niall Anthony Gormley