公开(公告)号：US20220056509A1

公开(公告)日：2022-02-24

申请号：US17461298

申请日：2021-08-30

Applicant: Natera, Inc.

Inventor： Bernhard ZIMMERMANN ,  Raheleh SALARI ,  Ryan SWENERTON ,  Hsin-Ta WU ,  Himanshu SETHI

IPC: C12Q1/6827 ,  C12Q1/6886

Abstract: The invention provides methods for detecting single nucleotide variants in breast cancer, bladder cancer, or colorectal cancer. Additional methods and compositions, such as reaction mixtures and solid supports comprising clonal populations of nucleic acids, are provided. For example, provided here is a method for monitoring and detection of early relapse or metastasis of breast cancer, bladder cancer, or colorectal cancer, comprising generating a set of amplicons by performing a multiplex amplification reaction on nucleic acids isolated from a sample of blood or urine or a fraction thereof from a patient who has been treated for a breast cancer, bladder cancer, or colorectal cancer, wherein each amplicon of the set of amplicons spans at least one single nucleotide variant locus of a set of patient-specific single nucleotide variant loci associated with the breast cancer, bladder cancer, or colorectal cancer; and determining the sequence of at least a segment of each amplicon of the set of amplicons that comprises a patient-specific single nucleotide variant locus, wherein detection of one or more patient-specific single nucleotide variants is indicative of early relapse or metastasis of breast cancer, bladder cancer, or colorectal cancer.

公开(公告)号：US20250109441A1

公开(公告)日：2025-04-03

申请号：US18726359

申请日：2023-01-04

Applicant: Natera, Inc.

Inventor： Ekaterina KALASHNIKOVA ,  Hsin-Ta WU ,  Samay MEHTA ,  Raheleh SALARI ,  Bernhard ZIMMERMANN ,  Paul R. BILLINGS ,  Alexey ALESHIN

IPC: C12Q1/6886

Abstract: The invention provides methods for preparing a preparation of amplified DNA derived from a biological sample of a patient who has been diagnosed with cancer useful for determining relapse or metastasis of cancer, comprising (a) sequencing DNA isolated from hematopoiesis cells in a blood or bone marrow sample of the patient or a fraction thereof to determine the presence or absence of one or more clonal hematopoiesis of indeterminate potential (CHIP) mutations; (b) sequencing (i) DNA isolated from a tumor biopsy sample of the patient or (ii) cell-free DNA isolated from the blood or bone marrow sample or a fraction thereof, to identify a plurality of patient-specific somatic mutations associated with the cancer; (c) preparing a preparation of amplified DNA by performing targeted multiplex amplification on cell-free DNA isolated from a longitudinally collected biological sample of the patient or a fraction thereof to amply a plurality of target loci to obtain amplified DNA, wherein each of the target loci spans a patient-specific somatic mutation identified in step (b) and does not span any CHIP mutation identified in step (a), wherein the biological sample is a blood, urine, or bone marrow sample; and (d) analyzing the preparation of amplified DNA by sequencing the amplified DNA to determine the presence or absence of the patient-specific somatic mutations, wherein the presence of two or more patient-specific somatic mutations associated with the cancer and the presence of one or more CHIP mutations are indicative of relapse or metastasis of the cancer.

公开(公告)号：US20190316184A1

公开(公告)日：2019-10-17

申请号：US16382520

申请日：2019-04-12

Applicant: Natera, Inc.

Inventor： Bernhard ZIMMERMANN ,  Raheleh SALARI ,  Ryan SWENERTON ,  Hsin-Ta WU ,  Himanshu SETHI

IPC: C12Q1/6827 ,  G16H50/30 ,  C12Q1/6886

Abstract: The invention provides methods for detecting single nucleotide variants in breast cancer, bladder cancer, or colorectal cancer. Additional methods and compositions, such as reaction mixtures and solid supports comprising clonal populations of nucleic acids, are provided. For example, provided here is a method for monitoring and detection of early relapse or metastasis of breast cancer, bladder cancer, or colorectal cancer, comprising generating a set of amplicons by performing a multiplex amplification reaction on nucleic acids isolated from a sample of blood or urine or a fraction thereof from a patient who has been treated for a breast cancer, bladder cancer, or colorectal cancer, wherein each amplicon of the set of amplicons spans at least one single nucleotide variant locus of a set of patient-specific single nucleotide variant loci associated with the breast cancer, bladder cancer, or colorectal cancer; and determining the sequence of at least a segment of each amplicon of the set of amplicons that comprises a patient-specific single nucleotide variant locus, wherein detection of one or more patient-specific single nucleotide variants is indicative of early relapse or metastasis of breast cancer, bladder cancer, or colorectal cancer.