公开(公告)号：US11939634B2

公开(公告)日：2024-03-26

申请号：US17018966

申请日：2020-09-11

Applicant: Natera, Inc.

Inventor： Joshua Babiarz ,  Tudor Pompiliu Constantin ,  Lane A. Eubank ,  George Gemelos ,  Matthew Micah Hill ,  Huseyin Eser Kirkizlar ,  Matthew Rabinowitz ,  Onur Sakarya ,  Styrmir Sigurjonsson ,  Bernhard Zimmermann

IPC: C12Q1/68 ,  C12Q1/6809 ,  C12Q1/6811 ,  C12Q1/6844 ,  C12Q1/6848 ,  C12Q1/6851 ,  C12Q1/6855 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q1/6883

CPC classification number: C12Q1/6883 ,  C12Q1/6809 ,  C12Q1/6811 ,  C12Q1/6844 ,  C12Q1/6848 ,  C12Q1/6851 ,  C12Q1/6855 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q2600/156 ,  C12Q1/6848 ,  C12Q2527/107 ,  C12Q2537/143 ,  C12Q1/6809 ,  C12Q2527/107 ,  C12Q2537/143 ,  C12Q1/6851 ,  C12Q2531/113 ,  C12Q2535/122 ,  C12Q2537/143 ,  C12Q2563/159

Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

公开(公告)号：US11530454B2

公开(公告)日：2022-12-20

申请号：US17738354

申请日：2022-05-06

Applicant: Natera, Inc.

Inventor： Joshua Babiarz ,  Tudor Pompiliu Constantin ,  Lane A. Eubank ,  George Gemelos ,  Matthew Micah Hill ,  Huseyin Eser Kirkizlar ,  Matthew Rabinowitz ,  Onur Sakarya ,  Styrmir Sigurjonsson ,  Bernhard Zimmermann

IPC: C12Q1/6886 ,  G06N20/00 ,  G16B15/00 ,  G16B25/00 ,  G16B40/00 ,  C12Q1/6869 ,  G16B40/20 ,  G16B20/10 ,  G16B20/00 ,  G16B20/20 ,  G16Z99/00 ,  G16H50/20 ,  G06N7/00 ,  G16H10/40 ,  G16B25/20

Abstract: The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.

公开(公告)号：US11525159B2

公开(公告)日：2022-12-13

申请号：US17165592

申请日：2021-02-02

Applicant: Natera, Inc.

Inventor： Solomon Moshkevich ,  Bernhard Zimmermann ,  Tudor Pompiliu Constantin ,  Huseyin Eser Kirkizlar ,  Allison Ryan ,  Styrmir Sigurjonsson ,  Felipe Acosta Archila ,  Ryan Swenerton

IPC: C12Q1/68 ,  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：US11482300B2

公开(公告)日：2022-10-25

申请号：US17494745

申请日：2021-10-05

Applicant: Natera, Inc.

Inventor： Matthew Rabinowitz ,  George Gemelos ,  Milena Banjevic ,  Allison Ryan ,  Zachary Demko ,  Matthew Hill ,  Bernhard Zimmermann ,  Johan Baner ,  Styrmir Sigurjonsson

IPC: C12Q1/68 ,  G16B20/00 ,  G16B20/20 ,  G16B20/40 ,  G16B20/10 ,  C12Q1/6806 ,  C12Q1/6827 ,  C12Q1/686 ,  C12Q1/6862 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q1/6883 ,  G16B40/00

Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. 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：US11479812B2

公开(公告)日：2022-10-25

申请号：US15573800

申请日：2016-05-10

Applicant: Natera, Inc.

Inventor： Huseyin Eser Kirkizlar ,  Raheleh Salari ,  Styrmir Sigurjonsson ,  Bernhard Zimmermann ,  Allison Ryan ,  Naresh Vankayalapati

IPC: C07H21/04 ,  C12Q1/6858 ,  G16B20/00 ,  C12Q1/6869 ,  G16B20/10 ,  G16H10/40 ,  C12Q1/6886

Abstract: The invention provides improved methods, compositions, and kits for detecting ploidy of chromosome regions, e.g. for detecting cancer or a chromosomal abnormality in a gestating fetus. The methods can utilize a set of more than 200 SNPs that are found within haploblocks and can include analyzing a series of target chromosomal regions related to cancer or a chromosomal abnormality in a gestating fetus. Finally the method may use knowledge about chromosome crossover locations or a best fit algorithm for the analysis. The compositions may comprise more than 200 primers located within haplotype blocks known to show CNV.

公开(公告)号：US11450408B2

公开(公告)日：2022-09-20

申请号：US17494745

申请日：2021-10-05

Applicant: Natera, Inc.

Inventor： Matthew Rabinowitz ,  George Gemelos ,  Milena Banjevic ,  Allison Ryan ,  Zachary Demko ,  Matthew Hill ,  Bernhard Zimmermann ,  Johan Baner ,  Styrmir Sigurjonsson

IPC: C12Q1/68 ,  G16B20/00 ,  G16B20/20 ,  G16B20/40 ,  G16B20/10 ,  C12Q1/6806 ,  C12Q1/6827 ,  C12Q1/686 ,  C12Q1/6862 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q1/6883 ,  G16B40/00

Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. 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：US11447820B2

公开(公告)日：2022-09-20

申请号：US15573800

申请日：2016-05-10

Applicant: Natera, Inc.

Inventor： Huseyin Eser Kirkizlar ,  Raheleh Salari ,  Styrmir Sigurjonsson ,  Bernhard Zimmermann ,  Allison Ryan ,  Naresh Vankayalapati

IPC: C07H21/04 ,  C12Q1/6858 ,  G16B20/00 ,  C12Q1/6869 ,  G16B20/10 ,  G16H10/40 ,  C12Q1/6886

Abstract: The invention provides improved methods, compositions, and kits for detecting ploidy of chromosome regions, e.g. for detecting cancer or a chromosomal abnormality in a gestating fetus. The methods can utilize a set of more than 200 SNPs that are found within haploblocks and can include analyzing a series of target chromosomal regions related to cancer or a chromosomal abnormality in a gestating fetus. Finally the method may use knowledge about chromosome crossover locations or a best fit algorithm for the analysis. The compositions may comprise more than 200 primers located within haplotype blocks known to show CNV.

公开(公告)号：US11312996B2

公开(公告)日：2022-04-26

申请号：US16747833

申请日：2020-01-21

Applicant: Natera, Inc.

Inventor： Joshua Babiarz ,  Tudor Pompiliu Constantin ,  Lane A. Eubank ,  George Gemelos ,  Matthew Micah Hill ,  Huseyin Eser Kirkizlar ,  Matthew Rabinowitz ,  Onur Sakarya ,  Styrmir Sigurjonsson ,  Bernhard Zimmermann

IPC: C12Q1/68 ,  C12Q1/6883 ,  C12Q1/6811 ,  C12Q1/6848 ,  C12Q1/6855 ,  C12Q1/6874

Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

公开(公告)号：US11198905B2

公开(公告)日：2021-12-14

申请号：US16795973

申请日：2020-02-20

Applicant: Natera, Inc.

Inventor： Matthew Rabinowitz ,  George Gemelos ,  Milena Banjevic ,  Allison Ryan ,  Zachary Demko ,  Matthew Hill ,  Bernhard Zimmermann ,  Johan Baner ,  Styrmir Sigurjonsson

IPC: C12Q1/68 ,  G01N33/48 ,  C12P19/34 ,  C12Q1/6869 ,  G16B20/00 ,  C12Q1/6827 ,  C12Q1/6862 ,  C12Q1/686 ,  G16B20/10 ,  G16B20/20 ,  G16B20/40 ,  C12Q1/6883 ,  C12Q1/6806 ,  C12Q1/6874 ,  G16B40/00

Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. 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：US11085085B2

公开(公告)日：2021-08-10

申请号：US16014961

申请日：2018-06-21

Applicant: Natera, Inc.

Inventor： Joshua Babiarz ,  Tudor Pompiliu Constantin ,  Lane A. Eubank ,  George Gemelos ,  Matthew Micah Hill ,  Huseyin Eser Kirkizlar ,  Matthew Rabinowitz ,  Onur Sakarya ,  Styrmir Sigurjonsson ,  Bernhard Zimmermann

IPC: C12Q1/6886 ,  C12Q1/6869 ,  G06N20/00 ,  G16B15/00 ,  G16B25/00 ,  G16B40/00 ,  G16B40/20 ,  G16B20/10 ,  G16B20/00 ,  G16B20/20 ,  G16H50/20 ,  G06N7/00 ,  G16H10/40 ,  G06F19/00 ,  G16B25/20

Abstract: The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.