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：US20240002946A1

公开(公告)日：2024-01-04

申请号：US18050855

申请日：2022-10-28

Applicant: GUARDANT HEALTH, INC.

Inventor： Ariel JAIMOVICH ,  Yupeng HE ,  Oscar WESTESSON ,  William J. GREENLEAF

IPC: C12Q1/6886 ,  C12Q1/6827 ,  C12Q1/6869

CPC classification number: C12Q1/6886 ,  C12Q1/6869 ,  C12Q1/6827

Abstract: In an aspect, a method for detecting the presence or absence of cancer in a subject comprises: (a) obtaining samples from the subject from different time points, wherein a first sample obtained at first time point is a polynucleotide sample from a tumor tissue specimen and a second sample obtained at second time point is a cell-free polynucleotide sample from a blood sample; (b) processing polynucleotides from each of the samples, comprising: i) tagging at least a portion of the polynucleotides, thereby generating tagged parent polynucleotides; ii) amplifying at least a portion of the tagged parent polynucleotides to generate progeny polynucleotides; iii) enriching at least a portion of the progeny polynucleotides for target genomic regions; thereby generating enriched polynucleotides; and iv) sequencing at least a portion of the enriched polynucleotides to generate sequencing reads; and (c) analyzing genomic regions for at least one epigenetic feature from the sequencing reads.

公开(公告)号：US20210407623A1

公开(公告)日：2021-12-30

申请号：US17219338

申请日：2021-03-31

Applicant: GUARDANT HEALTH, INC.

Inventor： Oscar WESTESSON ,  Yupeng He ,  William J. GREENLEAF ,  Ariel JAIMOVICH ,  AmirAli TALASAZ

IPC: G16B30/10 ,  G16B30/00 ,  G16B20/20

Abstract: The application is directed to systems and processes to determine an estimate for tumor fraction of a sample. In various examples, amounts of methylation of nucleic acids can be determined based on a strength of binding by the nucleic acids to methyl binding domain (MBD). The nucleic acids can be partitioned according to the strength of binding to MBD. Additionally, a number of cytosine-guanine regions for the nucleic acids can be determined. Amounts of methylation of classification regions of the nucleic acids can be determined based on the partition information associated with the nucleic acids and the number of cytosine-guanine regions of the nucleic acids. The classification regions can have differing amounts of methylation in tumor cells and non-tumor cells. The estimate for tumor fraction of the sample can be determined according to the amounts of methylation of the classification regions.

公开(公告)号：US20210214803A1

公开(公告)日：2021-07-15

申请号：US17153742

申请日：2021-01-20

Applicant: GUARDANT HEALTH, INC.

Inventor： Ariel JAIMOVICH ,  Yupeng HE ,  Oscar WESTESSON ,  William J. GREENLEAF

IPC: C12Q1/6886 ,  C12Q1/6869 ,  C12Q1/6827

Abstract: In an aspect, a method for detecting the presence or absence of cancer in a subject comprises: (a) obtaining samples from the subject from different time points, wherein a first sample obtained at first time point is a polynucleotide sample from a tumor tissue specimen and a second sample obtained at second time point is a cell-free polynucleotide sample from a blood sample; (b) processing polynucleotides from each of the samples, comprising: i) tagging at least a portion of the polynucleotides, thereby generating tagged parent polynucleotides; ii) amplifying at least a portion of the tagged parent polynucleotides to generate progeny polynucleotides; iii) enriching at least a portion of the progeny polynucleotides for target genomic regions; thereby generating enriched polynucleotides; and iv) sequencing at least a portion of the enriched polynucleotides to generate sequencing reads; and (c) analyzing genomic regions for at least one epigenetic feature from the sequencing reads.

公开(公告)号：US20210017605A1

公开(公告)日：2021-01-21

申请号：US16889659

申请日：2020-06-01

Applicant: GUARDANT HEALTH, INC.

Inventor： Ariel JAIMOVICH ,  Yupeng HE ,  Oscar WESTESSON ,  William J. GREENLEAF

IPC: C12Q1/6886

Abstract: In an aspect, a method for detecting the presence or absence of cancer in a subject comprises: (a) obtaining samples from the subject from different time points, wherein a first sample obtained at first time point is a polynucleotide sample from a tumor tissue specimen and a second sample obtained at second time point is a cell-free polynucleotide sample from a blood sample; (b) processing polynucleotides from each of the samples, comprising: i) tagging at least a portion of the polynucleotides, thereby generating tagged parent polynucleotides; ii) amplifying at least a portion of the tagged parent polynucleotides to generate progeny polynucleotides; iii) enriching at least a portion of the progeny polynucleotides for target genomic regions; thereby generating enriched polynucleotides; and iv) sequencing at least a portion of the enriched polynucleotides to generate sequencing reads; and (c) analyzing genomic regions for at least one epigenetic feature from the sequencing reads.