公开(公告)号：US11939636B2

公开(公告)日：2024-03-26

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

CPC classification number: C12Q1/6886 ,  C12Q2600/112 ,  C12Q2600/156 ,  C12Q2600/158

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：US11946044B2

公开(公告)日：2024-04-02

申请号：US17389199

申请日：2021-07-29

Applicant: GUARDANT HEALTH, INC.

Inventor： Ariel Jaimovich ,  Sven Jeffrey Duenwald ,  Peter Vilem Grauman ,  Yupeng He ,  Charbel Said Eid ,  Haley Dara Axelrod

IPC: C12N15/10 ,  C12Q1/6886

CPC classification number: C12N15/1065 ,  C12Q1/6886 ,  C12Q2600/154 ,  C12Q2600/156

Abstract: Disclosed herein are methods for isolating DNA, such as cell-free DNA (cfDNA) or DNA from a tissue sample, e.g., in which the DNA is partitioned into hypermethylated and hypomethylated partitions. After differential tagging of the partitions, portions of the hypomethylated partition are pooled with the hypermethylated partition or pooled separately. Epigenetic and sequence-variable target regions are captured from the pool comprising DNA from the hypermethylated and hypomethylated partitions, and sequence-variable target regions are captured from the pool comprising DNA from the hypomethylated partition. This approach can reduce costs and/or bandwidth by limiting sequencing of epigenetic target regions from the hypomethylated partition, which may be less informative than other DNA.