公开(公告)号：US20240132960A1

公开(公告)日：2024-04-25

申请号：US18279006

申请日：2022-02-24

Applicant: Natera, Inc.

Inventor： Zachary DEMKO ,  Ebad AHMED ,  Ryan SWENERTON ,  Paul VAN HUMMELEN

IPC: C12Q1/6883 ,  C12Q1/6869

CPC classification number: C12Q1/6883 ,  C12Q1/6869 ,  C12Q2600/156

Abstract: The present disclosure provides methods of amplifying and sequencing DNA, comprising: extracting cell-free DNA from a blood, plasma, serum or urine sample of a transplant recipient who has received transplantation of one or more organs including simultaneous or sequential transplantation of multiple organs, wherein the extracted cell-free DNA comprises donor-derived cell-free DNA and recipient-derived cell-free DNA; performing targeted amplification at 200-50,000 target loci in a single reaction volume using 200-50,000 primer pairs, wherein the target loci comprise polymorphic loci and non-polymorphic loci; sequencing the amplification products by high-throughput sequencing to obtain a sequencing reads and quantifying the amount of donor-derived cell-free DNA and the amount of total cell-free DNA based on the sequencing reads; and determining whether the amount of donor-derived cell-free DNA or a function thereof exceeds a cutoff threshold indicating transplant rejection or graft injury.

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.

公开(公告)号：US20230203573A1

公开(公告)日：2023-06-29

申请号：US17925693

申请日：2021-05-27

Applicant: Natera, Inc.

Inventor： Ryan SWENERTON ,  Bernhard ZIMMERMANN ,  Ebad AHMED ,  Nathan LIANG ,  Allison RYAN ,  Fei LU ,  Paul VAN HUMMELEN

IPC: C12Q1/6851 ,  C12Q1/686 ,  C12Q1/6876

CPC classification number: C12Q1/6851 ,  C12Q1/686 ,  C12Q1/6876 ,  C12Q2600/158

Abstract: The present disclosure provides methods for quantifying the amount of total cell-free DNA in a biological sample, comprising: isolating cell-free DNA from the biological sample, wherein a first Tracer DNA composition is added before or after isolation of the cell-free DNA; performing targeted amplification at 100 or more different target loci in a single reaction volume using 100 or more different primer pairs; sequencing the amplification products by high-throughput sequencing to generate sequencing reads; and quantifying the amount of total cell-free DNA using sequencing reads derived from the first Tracer DNA composition.

公开(公告)号：US20210222240A1

公开(公告)日：2021-07-22

申请号：US17214485

申请日：2021-03-26

Applicant: Natera, Inc.

Inventor： Solomon MOSHKEVICH ,  Bernhard ZIMMERMANN ,  Tudor Pompiliu CONSTANTIN ,  Huseyin Eser KIRKIZLAR ,  Allison RYAN ,  Styrmir SIGURJONSSON ,  Felipe ACOSTA ARCHILA ,  Ryan SWENERTON

IPC: C12Q1/6869 ,  C12Q1/6876 ,  C12Q1/6851

Abstract: The present disclosure provides methods for determining the status of an allograft within a transplant recipient from genotypic data measured from a mixed sample of DNA comprising DNA from both the transplant recipient and from the donor. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.

公开(公告)号：US20180155776A1

公开(公告)日：2018-06-07

申请号：US15716331

申请日：2017-09-26

Applicant: Natera, Inc.

Inventor： Bernhard ZIMMERMANN ,  Ryan SWENERTON ,  Matthew RABINOWITZ ,  Styrmir SIGURJONSSON ,  George GEMELOS ,  Apratim GANGULY ,  Himanshu SETHI

IPC: C12Q1/68

Abstract: The present disclosure provides methods and compositions for sequencing nucleic acid molecules and identifying individual sample nucleic acid molecules using Molecular Index Tags (MITs). Furthermore, reaction mixtures, kits, and adapter libraries are provided.

公开(公告)号：US20180155775A1

公开(公告)日：2018-06-07

申请号：US15716058

申请日：2017-09-26

Applicant: Natera, Inc.

Inventor： Bernhard ZIMMERMANN ,  Ryan SWENERTON ,  Matthew RABINOWITZ ,  Styrmir SIGURJONSSON ,  George GEMELOS ,  Apratim GANGULY ,  Himanshu SETHI

IPC: C12Q1/68

Abstract: The present disclosure provides methods and compositions for sequencing nucleic acid molecules and identifying individual sample nucleic acid molecules using Molecular Index Tags (MITs). Furthermore, reaction mixtures, kits, and adapter libraries are provided.

公开(公告)号：US20230287497A1

公开(公告)日：2023-09-14

申请号：US17252068

申请日：2019-07-03

Applicant: Natera, Inc.

Inventor： Solomon MOSHKEVICH ,  Bernhard ZIMMERMANN ,  Tudor Pompiliu CONSTANTIN ,  Huseyin Eser KIRKIZLAR ,  Allison RYAN ,  Styrmir SIGURJONSSON ,  Felipe ACOSTA ARCHILA ,  Ryan SWENERTON

IPC: C12Q1/6883

CPC classification number: C12Q1/6883 ,  C12Q2600/156

Abstract: The present disclosure provides methods for determining the status of an allograft within a transplant recipient from genotypic data measured from a mixed sample of DNA comprising DNA from both the transplant recipient and from the donor. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.

公开(公告)号：US20220154249A1

公开(公告)日：2022-05-19

申请号：US17600789

申请日：2020-04-14

Applicant: Natera, Inc.

Inventor： Bernhard ZIMMERMANN ,  Ryan SWENERTON ,  Fei LU ,  James STRAY ,  Jason TONG

IPC: C12Q1/6806 ,  C12Q1/686

Abstract: Provided herein are improved methods of determining the sequences of cell-free DNA (cfDNA). The methods in certain embodiments are used for the analysis of circulating DNA in serum samples, such as circulating fetal DNA, circulating donor derived DNA, or circulating tumor DNA. In certain embodiments, the methods include selectively enriching trinucleosomal, dinucleosomal, mononucleosomal or sub-mononucleosomal DNA from the isolated cfDNA.

公开(公告)号：US20210071246A1

公开(公告)日：2021-03-11

申请号：US16959949

申请日：2019-01-11

Applicant: Natera, Inc.

Inventor： Bernhard ZIMMERMANN ,  Ryan SWENERTON ,  Scott DASHNER ,  Fei LU ,  Himanshu SETHI

IPC: C12Q1/6853 ,  C12Q1/6858

Abstract: Disclosed here is a composition comprising a primer that is (a) a loopable primer comprising a target-specific section, an adaptor section, and a stem-forming section, wherein the stem-forming section is hybridizable to a portion of the target-specific section to form a stem structure, or (b) a split primer comprising a first target-specific section, a second target-specific section, and an adaptor section positioned between the first target-specific section and the second target-specific section, or (c) a split-loopable primer comprising a first target-specific section, a second target-specific section, a stem-forming section positioned between the first target-specific section and the second target-specific section, and an adaptor section, or comprising a first adaptor section, a second adaptor section, a stem-forming section positioned between the first adaptor section and the second adaptor section, and a target-specific section. Also disclosed is a method for amplifying a target locus of interest from a template DNA, comprising at least two pre-amplification cycles using the loopable primer, the split primer and/or the split-loopable primer, wherein each amplification cycle comprises annealing the primer to the template DNA or pre-amplification product thereof and elongating the annealed primer. Further disclosed is a kit for amplifying a target locus of interest, comprising the loopable primer, the split primer, and/or the split-loopable primer.

公开(公告)号：US20180155779A1

公开(公告)日：2018-06-07

申请号：US15372279

申请日：2016-12-07

Applicant: Natera, Inc.

Inventor： Bernhard ZIMMERMANN ,  Ryan SWENERTON ,  Matthew RABINOWITZ ,  Styrmir SIGURJONSSON ,  George GEMELOS ,  Apratim GANGULY ,  Himanshu SETHI

IPC: C12Q1/68

CPC classification number: C12Q1/6869 ,  C12Q1/6806 ,  C12Q2525/179 ,  C12Q2535/122 ,  C12Q2563/179 ,  C12Q2537/16

Abstract: The present disclosure provides methods and compositions for sequencing nucleic acid molecules and identifying individual sample nucleic acid molecules using Molecular Index Tags (MITs). Furthermore, reaction mixtures, kits, and adapter libraries are provided.