公开(公告)号：US20250137044A1

公开(公告)日：2025-05-01

申请号：US18677483

申请日：2024-05-29

Applicant: GUARDANT HEALTH, INC.

Inventor： Andrew KENNEDY ,  Oscar WESTESSON ,  Yupeng HE ,  Matthew SCHULTZ

IPC: C12Q1/6851 ,  C12Q1/682 ,  C12Q1/6827 ,  C12Q1/6832 ,  C12Q1/6855 ,  C12Q1/6858 ,  C12Q1/6881 ,  C12Q1/6883 ,  C40B70/00 ,  G16B20/00 ,  G16B25/10

Abstract: In an aspect, a method for evaluating the partitioning of nucleic acid molecules in a sample of polynucleotides based on epigenetic state, comprising: (a) adding a set of epigenetic-control nucleic acid molecules to the nucleic acid molecules in the sample of polynucleotides, whereby producing a spiked-in sample; (b) partitioning nucleic acid molecules of the spiked-in sample into plurality of partitioned sets; (c) enriching a subset of molecules from the plurality of partitioned sets to generate enriched molecules, wherein the enriched molecules comprises a group of epigenetic-control nucleic acid molecules and a group of nucleic acid molecules from the sample of polynucleotides; (d) sequencing the enriched molecules to produce sequencing reads; (e) analyzing the sequencing reads to generate one or more epigenetic partition scores of the epigenetic-control nucleic acid molecules; and (f) comparing the one or more epigenetic partition scores with one or more epigenetic partition cut-offs.

公开(公告)号：US20200248272A1

公开(公告)日：2020-08-06

申请号：US16778572

申请日：2020-01-31

Applicant: GUARDANT HEALTH, INC.

Inventor： Andrew KENNEDY ,  Ariel JAIMOVICH ,  Matthew SCHULTZ ,  William J. GREENLEAF

IPC: C12Q1/6886

Abstract: Disclosed herein are compositions and methods for isolating DNA, such as cell-free DNA (cfDNA). In some embodiments, the cell-free DNA is from a subject having or suspected of having cancer and/or the cell-free DNA comprises DNA produced by a tumor. In some embodiments, the DNA isolated by the method is captured using a sequence-variable target region set and an epigenetic target region set, wherein the sequence-variable target region set is captured with a greater capture yield than the epigenetic target region set. In some embodiments, captured cfDNA of the sequence-variable target region set is sequenced to a greater depth of sequencing than captured cfDNA of the epigenetic target region set.

公开(公告)号：US20230323474A1

公开(公告)日：2023-10-12

申请号：US18314056

申请日：2023-05-08

Applicant: GUARDANT HEALTH, INC.

Inventor： Andrew KENNEDY ,  Ariel JAIMOVICH ,  Matthew SCHULTZ ,  William J. GREENLEAF

IPC: C12Q1/6886

CPC classification number: C12Q1/6886 ,  C12Q2600/154 ,  G01N2800/50

Abstract: Disclosed herein are compositions and methods for isolating DNA, such as cell-free DNA (cfDNA). In some embodiments, the cell-free DNA is from a subject having or suspected of having cancer and/or the cell-free DNA comprises DNA produced by a tumor. In some embodiments, the DNA isolated by the method is captured using a sequence-variable target region set and an epigenetic target region set, wherein the sequence-variable target region set is captured with a greater capture yield than the epigenetic target region set. In some embodiments, captured cfDNA of the sequence-variable target region set is sequenced to a greater depth of sequencing than captured cfDNA of the epigenetic target region set.

公开(公告)号：US20190390253A1

公开(公告)日：2019-12-26

申请号：US16450918

申请日：2019-06-24

Applicant: Guardant Health, Inc.

Inventor： Andrew KENNEDY ,  Stefanie Ann Ward MORTIMER ,  Helmy ELTOUKHY ,  AmirAli TALASAZ ,  Diana ABDUEVA ,  Matthew SCHULTZ

IPC: C12Q1/6806 ,  C12Q1/6886 ,  C12Q1/6874 ,  C12N15/10

Abstract: The disclosure provides methods for processing nucleic acid populations containing different forms (e.g., RNA and DNA, single-stranded or double-stranded) and/or extents of modification (e.g., cytosine methylation, association with proteins). These methods accommodate multiple forms and/or modifications of nucleic acid in a sample, such that sequence information can be obtained for multiple forms. The methods also preserve the identity of multiple forms or modified states through processing and analysis, such that analysis of sequence can be combined with epigenetic analysis.