Leland Stanford Junior University

Karius, Inc.

Michael Kertesz

Stephen R Quake

Fred C Christians

Hannah Valantine

Igor D Vilfan

Timothy A Blauwkamp

Kiran Kaur Khush

Lance Martin

Mark Alec Kowarsky

Iwijn De Vlaminck

Michael Rosen

Rene Sit

Shivkumar Venkatasubrahmanyam

Dmitry Pushkarev

Ayelet Voskoboynik

Scott Alexander Smith

Scott Smith

Iwijn De Vlaminick

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

Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

Cell-free nucleic acids for the analysis of the human microbiome and components thereof

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

Cell-free nucleic acids for the analysis of the human microbiome associated with respiratory infection

Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with a therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

The invention generally relates to methods for obtaining a sequence, such as a consensus sequence or a haplotype sequence. In certain embodiments, methods of the invention involve determining an amount of amplifiable nucleic acid present in a sample, partitioning the nucleic acid based upon results of the determining step such that each partitioned portion includes, on average, a subset of unique sequences, sequencing the nucleic acid to obtain sequence reads, and assembling a consensus sequence from the reads.

Methods for obtaining a sequence

Growing community of inventors

Menlo Park, CA, United States of America

Michael Kertesz