Grail, Inc.

Illumina Corporation

Illumina France Sarl

Arash Jamshidi

Samuel S Gross

Oliver Claude Venn

Seyedmehdi Shojaee

Tarun Kumar Khurana

John Beausang

Hamed Amini

Robert C Kain

Min-Jui Richard Shen

Yir-Shyuan Wu

Alex Aravanis

Anton Valouev

Helmy A Eltoukhy

Sebastian Bohm

Richard P Rava

M Shane Bowen

Joerg Bredno

Steven Mark Barnard

Dietrich A Dehlinger

Kenneth M Kuhn

Alexander P Fields

H John Kim

Jeffrey S Fisher

Jian Gong

Yan-you Lin

Sarah Stuart

Jian-Bing Fan

Maria Candelaria Rogert Bacigalupo

Poorya Sabounchi

Onur Sakarya

Cyril Delattre

Bala Murali Venkatesan

Arnaud Rival

Gordon M Cann

AmirAli Talasaz

Matthew H Larson

Eric Hans Vermaas

M Cyrus Maher

Srinka Ghosh

Nick Eattock

Fiona Kaper

Yan-You Lin

Jennifer Olivia Foley

Farnaz Absalan

Foad Mashayekhi

Qinwen Liu

Jan Schellenberger

Rongsu Qi

George Sakaldasis

Neeraj Salathia

Wenying Pan

Rick Klausner

Nicholas Eattock

Majid Babazadeh

John F Beausang

Described herein are methods of preparing dual-indexed nucleic acid libraries for methylation profiling using bisulfite conversion sequencing. In various embodiments, the methods use a two-step indexing process to tag bisulfite-treated DNA with unique molecular identifiers (UMIs).

Methods of preparing dual-indexed DNA libraries for bisulfite conversion sequencing

The present description provides a cancer assay panel for targeted detection of cancer-specific methylation patterns. Further provided herein includes methods of designing, making, and using the cancer assay panel for diagnosis of cancer.

Methylation markers and targeted methylation probe panel

The present description provides a cancer assay panel for targeted detection of cancer-specific methylation patterns. Further provided herein are methods of designing, making, and using the cancer assay panel for the diagnosis of cancer.

A method and system for determining one or more sources of a cell free deoxyribonucleic acid (cfDNA) test sample from a test subject. The cfDNA test sample contains a plurality of deoxyribonucleic acid (DNA) molecules with numerous CpG sites that may be methylated or unmethylated. A trained deconvolution model comprises a plurality of methylation parameters, including a methylation level at each CpG site for each source, and a function relating a sample vector as input and a source of origin prediction as output. The method generates a test sample vector comprising a site methylation metric relating to DNA molecules from the test sample that are methylated at that CpG site. The method inputs the test sample vector into the trained deconvolution model to generate a source of origin prediction indicating a predicted DNA molecule contribution of each source.

Source of origin deconvolution based on methylation fragments in cell-free DNA samples

In accordance with embodiments herein a method for capturing cells of interest in a digital microfluidic system is provided, comprising utilizing a droplet actuator to transport a sample droplet to a microwell device. The microwell device includes a substrate having a plurality of microwells that open onto a droplet operations surface of the microwell device. The sample droplet includes cells of interest that enter the microwells. The method introduces capture beads to the microwells, and the capture elements are immobilized on the capture beads. The method utilizes the droplet actuator to transport a cell lysis reagent droplet to the microwell device. Portions of the cell lysis reagent droplet enter the microwells and, during an incubation period, cause the cells of interest to release analyte that is captured by the capture elements on the capture beads.

Digital microfluidic system for single-cell isolation and characterization of analytes

Provided herein are methods of enriching mutated cell free nucleic acids for detection and diagnosis of cancer. Also provided are methods using a CRISPR-Cas system to target and deplete unwanted more abundant cell free nucleic acid sequences thereby enriching for less abundant sequences.

Enrichment of mutated cell free nucleic acids for cancer detection

Aspects of the invention include methods for preparing sequencing libraries, performing sequencing procedures that can correct for process-related errors, and identifying rare variants that are or may be indicative of cancer.

Library preparation and use thereof for sequencing based error correction and/or variant identification

Methods for measuring subpopulations of ribonucleic acid (RNA) molecules are provided. In some embodiments, methods of generating a sequencing library from a plurality of RNA molecules in a test sample obtained from a subject are provided, as well as methods for analyzing the sequencing library to detect, e.g., the presence or absence of a disease.

Methods for detecting disease using analysis of RNA

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Menlo Park, CA, United States of America

Arash Jamshidi