Karius, Inc.

Pacific Biosciences of California, Inc.

Igor D Vilfan

Timothy A Blauwkamp

Rene Sit

Fred C Christians

Michael Kertesz

Michael Rosen

Stephen Wilson Turner

Shivkumar Venkatasubrahmanyam

Jonas Korlach

Jeremiah Hanes

Kevin Travers

Cheryl Heiner

John Lyle

Jeffrey Wegener

Benjamin A Flusberg

Patrick Marks

Jon M Sorenson

Lei Jia

Austin B Tomaney

Tyson A Clark

Dale R Webster

Khai Luong

Yu-Chih Tsai

Andrey Kislyuk

Jessica Lee

Scott Alexander Smith

Damek Spacek

Joseph Puglisi

David K Hong

Trupti Kawli

Scott Smith

Liza Huijse

Sivan Bercovici

Lily Blair

Peter J Eugster

Michael J Rosen

Provided herein are direct-to-library methods, systems, and compositions.

Direct-to-library methods, systems, and compositions

This disclosure provides methods and compositions that are useful for enriching a particular population of nucleic acids (a 'population of interest') within a complex mixture of nucleic acids. The population of interest may make up a minor portion of a complex mixture of nucleic acids. The methods and compositions provided herein are useful for detecting, predicting, diagnosing, or monitoring a disease or disorder, particularly a disease or disorder caused by a foreign microbe or pathogen.

Compositions and methods for enriching populations of nucleic acids

The disclosure provides methods, compositions, systems, and kits for the concurrent detection and analysis of different structural and chemical forms of nucleic acids in a sample.

Sample preparation methods, systems and compositions

This disclosure provides methods for determining relative abundance of one or more non-host species in a sample from a host. Also provided are methods involving addition of known concentrations of synthetic nucleic acids to a sample and performing sequencing assays to identify non-host species such as pathogens. Also provided are methods of tracking samples, tracking reagents, and tracking diversity loss in sequencing assays.

Synthetic nucleic acid spike-ins

This disclosure provides methods, compositions and kits for determining if nucleic acids detected in a sample such as a clinical sample are derived from contaminant pathogens or clinically-relevant pathogens.

Sample series to differentiate target nucleic acids from contaminant nucleic acids

Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations.

Compositions and methods for enrichment of nucleic acids

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.

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

The present invention provides methods and compositions useful for supplying high throughput nucleic acid sequencing systems with templates. The methods circumvent the need for costly, labor-intensive cloning and cell culture methods and can be scaled to accommodate template production for a variety of sequencing applications, e.g., sequencing individuals' genomes, sequencing subpopulations of transcripts from a gene of interest, and/or gene expression profiling. Particularly preferred embodiments of the methods vastly improve the preparation of cDNA from mRNA samples, e.g., by randomizing errors introduced during the process, thereby allowing these errors to be readily distinguished from true variants present in the mRNA samples.

Methods and compositions for nucleic acid sample preparation

Methods for identifying nucleic acid modifications

Growing community of inventors

East Palo Alto, CA, United States of America

Igor D Vilfan