Illumina Corporation

Personalis, Inc.

Jason Harris

Mark R Pratt

Ming Chu Li

Dale Buermann

Stanley S Hong

John West

Richard Chen

Mark Wang

Bryan Crane

John A Moon

Matthew William Hage

Mark J Nibbe

Stephen Tanner

Mark T Reed

Erik Lewis Williamson

Drew R Verkade

Jason Bryant

Patrick Leung

Frederick G Erie

Alexander Kindwall

Andrew James Carson

Alexander P Kindwall

Eric Williamson

Nicholas Phillips

Frederick Erie

The disclosure provides methods for estimating tumor purity from tumor samples without use of matched-normal controls. A set of genomic regions are identified based on a nucleic acid sequence data that is aligned to a reference genome. Each genomic region of the set of genomic regions includes one or more nucleotide-sequence variants relative to a corresponding genomic region of the reference genome. A B-allele frequency distribution for the biological sample is determined based on a B-allele frequency determined for each genomic region of the set of genomic regions. The B-allele frequency distribution is processed using a trained machine-learning model to estimate a metric identifying tumor purity in the biological sample.

Estimating tumor purity from single samples

A computer-implemented method for processing and/or analyzing nucleic acid sequencing data comprises receiving a first data input and a second data input. The first data input comprises untargeted sequencing data generated from a first nucleic acid sample obtained from a subject. The second data input comprises target-specific sequencing data generated from a second nucleic acid sample obtained from the subject. Next, with the aid of a computer processor, the first data input and the second data input are combined to produce a combined data set. Next, an output derived from the combined data set is generated. The output is indicative of the presence or absence of one or more polymorphisms of the first nucleic acid sample and/or the second nucleic acid sample.

Methods and systems for genomic analysis

A detection apparatus having a read head including a plurality of microfluorometers positioned to simultaneously acquire a plurality of the wide-field images in a common plane; and (b) a translation stage configured to move the read head along a substrate that is in the common plane. The substrate can be a flow cell that is included in a cartridge, the cartridge also including a housing for (i) a sample reservoir; (ii) a fluidic line between the sample reservoir and the flow cell; (iii) several reagent reservoirs in fluid communication with the flow cell, (iv) at least one valve configured to mediate fluid communication between the reservoirs and the flow cell; and (v) at least one pressure source configured to move liquids from the reservoirs to the flow cell. The detection apparatus and cartridge can be used together or independent of each other.

Integrated optoelectronic read head and fluidic cartridge useful for nucleic acid sequencing

The present techniques provides methods for use in conjunction with an article of manufacture having a plurality of sample sites of an array and to identify sample sites based on image data. The array may be divided into a series of domains with each domain having patterns of sample sites. Neighboring domains may be oriented at different angles such that each domain does not have the same pattern orientation.

Sample site location identification on arrays having rotated patterns

An article of manufacture having a plurality of sites in domains of regular patterns. Neighboring domains are oriented at different angles to improve the identification of the sites.

Array domains having rotated patterns

A fluidic device holder configured to orient a fluidic device. The device holder includes a support structure configured to receive a fluidic device. The support structure includes a base surface that faces in a direction along the Z-axis and is configured to have the fluidic device positioned thereon. The device holder also includes a plurality of reference surfaces facing in respective directions along an XY-plane. The device holder also includes an alignment assembly having an actuator and a movable locator arm that is operatively coupled to the actuator. The locator arm has an engagement end. The actuator moves the locator arm between retracted and biased positions to move the engagement end away from and toward the reference surfaces. The locator arm is configured to hold the fluidic device against the reference surfaces when the locator arm is in the biased position.

Systems, methods, and apparatuses to image a sample for biological or chemical analysis

Growing community of inventors

San Ramon, CA, United States of America

Jason Harris