10x Genomics, Inc.

Pacific Biosciences of California, Inc.

Pacific Biosciences for California, Inc.

Patrick Marks

Austin B Tomaney

Jon M Sorenson

Kenneth Mark Maxham

Michael Schnall-Levin

Kevin Travers

Stephen Wilson Turner

Benjamin A Flusberg

David J Holden

Devon Murphy

Kevin Hester

Sofia Kyriazopoulou-Panagiotopoulou

Jonas Korlach

Jeremiah Hanes

Cheryl Heiner

Dale R Webster

Andrey Kislyuk

Serge Saxonov

Mirna Jarosz

John Lyle

John S Eid

Jeffrey Wegener

Xinying Zheng

Lei Jia

Paul Ryvkin

Tyson A Clark

Igor D Vilfan

Jessica Michele Terry

Niranjan Srinivas

Chen-Shan Chin

Jessica Lee

David Jaffe

Kevin D Ness

Benjamin J Hindson

Christopher Hindson

John R Stuelpnagel

Robin A Emig

Donald M Gray

Tarjei Sigurd Mikkelsen

Zachary Bent

Alexander Y Wong

Malte Kühnemund

Neil Ira Weisenfeld

Vijay Kumar Sreenivasa Gopalan

Jeffrey Clark Mellen

Kevin J Wu

Preyas Shah

Mark Chaisson

Kristina Giorda

Joseph Puglisi

Nicolaus Lance Hepler

Jorge Iván Hernández Neuta

Nigel Delaney

David Alexander

Susan Tang

Aaron Klammer

William Haynes Heaton

Heather Ordonez

Patrice Mudivarti

Chaitanya Aluru

Methods and compositions for performing a rolling circle amplification (RCA) reaction using circularized template comprising identifier sequences are provided. Sequencing is performed on the RCA product using a polymerase to incorporate a plurality of cognate nucleotides into the sequencing primer or an extension product thereof to generate an extension product.

Compositions and methods for amplification and sequencing

The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address issues associated with the heterogeneity of analyte abundance (e.g., gene expression levels) and variations among reactions at different locations of a sample (e.g., amplification reaction starting earlier at one location than another location). In some aspects, a method disclosed herein provides a tighter distribution of signal spot size and intensity in a sample, as compared to methods that result in a wide and heterogeneous size and intensity distribution of signal spots.

Methods and compositions for synchronizing reactions in situ

Methods and compositions for analyzing a library comprising a plurality of amplicons comprising identifier sequences are provided, for example, a library of amplicons in a cell or tissue sample attached to a solid support. For example, amplicons are sequenced using a polymerase to incorporate a plurality of cognate nucleotides into the sequencing primer or an extension product thereof to generate a plurality of extension products.

Compositions and methods for gene expression library analysis

The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples.

Analysis of nucleic acid sequences

Methods for index hopping sequence read filtering are provided. Each read in a plurality of reads from a multiplexed reaction comprises an insert portion, and first (molecular identifier) and second (sample index) non-insert portions. For each of a plurality of hashes, a hash data structure is formed with a representation of each read. Each representation comprises a hash of the first non-insert portion of the corresponding read. Read pairs are identified in the hash data structures. Each pair includes a first and second read sharing a common hash value but differing index values. An entry is added into a heterogeneous data structure, for each such pair, that includes the first and second non-insert portions of the first and second reads of the pair. Reads with first non-insert portion values appearing more than a threshold number of times in the heterogeneous data structure are removed from the plurality of reads.

Systems and methods for index hopping filtering

The present disclosure provides methods and systems for producing full-length sequencing information of transcriptomes from single cells or from the bulk. Random ligation and circularization of barcoded or non-barcoded complementary deoxyribonucleic molecules can be used to provide a circular template for amplification and subsequent sequencing.

Transcriptome sequencing through random ligation

Systems and methods for analyzing first and second strings against a ground truth string are provided. A construct representing a plurality of components is obtained, each component for a different portion of the truth string. The construct comprises a plurality of measurement string sampling pools each having an identifier and a corresponding plurality of measurement samplings corresponding to one or two of the components. Each sampling has the identifier and a portion of the first or second string. Samplings are assigned to first, second or third classes when coding a portion of the first string, second string, or both the first and second string. First and second positions are tested for sequence events by calculating a plurality of sequence event models using assumptions on the components having samplings encompassing the first and second positions and class assignments. These assumptions are updated using the calculated models and the models are recalculated.

Systems and methods for identifying structural variants

A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity of a first type in a plurality of first entities of the first type and discrete attribute values for each first entity of a second type in a plurality of first entities of the second type for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters.

Systems and methods for visualizing a pattern in a dataset

Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.

Classification of nucleic acid templates

Described are computer-implemented methods, systems, and media for de novo phased diploid assembly of nucleic acid sequence data generated from a nucleic acid sample of an individual utilizing nucleic acid tags to preserve long-range sequence context for the individual such that a subset of short-read sequence data derived from a common starting sequence shares a common tag. The phased diploid assembly is achieved without alignment to a reference sequence derived from organisms other than the individual. The methods, systems, and media described are computer-resource efficient, allowing scale-up.

Systems, methods, and media for de novo assembly of whole genome sequence data

Systems and methods for determining structural variation and phasing using variant call data obtained from nucleic acid of a biological sample are provided. Sequence reads are obtained, each comprising a portion corresponding to a subset of the test nucleic acid and a portion encoding a barcode independent of the sequencing data. Bin information is obtained. Each bin represents a different portion of the sample nucleic acid. Each bin corresponds to a set of sequence reads in a plurality of sets of sequence reads formed from the sequence reads such that each sequence read in a respective set of sequence reads corresponds to a subset of the nucleic acid represented by the bin corresponding to the respective set. Binomial tests identify bin pairs having more sequence reads with the same barcode in common than expected by chance. Probabilistic models determine structural variation likelihood from the sequence reads of these bin pairs.

Systems and methods for determining structural variation and phasing using variant call data

The present invention is generally directed to a hierarchical genome assembly process for producing high-quality de novo genome assemblies. The method utilizes a single, long-insert, shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT&#xae;) DNA sequencing, and obviates the need for additional sample preparation and sequencing data sets required for previously described hybrid assembly strategies. Efficient de novo assembly from genomic DNA to a finished genome sequence is demonstrated for several microorganisms using as little as three SMRT&#xae; cells, and for bacterial artificial chromosomes (BACs) using sequencing data from just one SMRT&#xae; Cell. Part of this new assembly workflow is a new consensus algorithm which takes advantage of SMRT&#xae; sequencing primary quality values, to produce a highly accurate de novo genome sequence, exceeding 99.999% (QV 50) accuracy. The methods are typically performed on a computer and comprise an algorithm that constructs sequence alignment graphs from pairwise alignment of sequence reads to a common reference.

Hierarchical genome assembly method using single long insert library

Systems and methods for determining the integrity of test strings with respect to a ground truth string

Systems and methods for analyzing first and second strings against a ground truth string are provided. A construct representing a plurality of components is obtained, each component for a different portion of the truth string. The construct comprises a plurality of measurement string sampling pools each having an identifier and a corresponding plurality of measurement samplings corresponding to one or two of the components. Each sampling has the identifier and a portion of the first or second string. Samplings are assigned to first, second or third classes when coding a portion of the first string, second string, or both the first and second string. First and second positions are tested for events by calculating a plurality of event models using assumptions on the components having samplings encompassing the first and second positions and class assignments. These assumptions are updated using the calculated models and the models are recalculated.

Systems and methods for determining the integrity of test strings with respect to a reference genome

Identification of nucleic acid template-linked barcodes comprising nucleic acid modifications

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San Francisco, CA, United States of America

Patrick Marks