公开(公告)号：US20210355536A1

公开(公告)日：2021-11-18

申请号：US17377802

申请日：2021-07-16

Applicant: Natera, Inc.

Inventor： Matthew RABINOWITZ ,  George GEMELOS ,  Milena BANJEVIC ,  Allison RYAN ,  Zachary DEMKO ,  Matthew HILL ,  Bernhard ZIMMERMANN ,  Johan BANER ,  Styrmir SIGURJONSSON

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

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：US20210324463A1

公开(公告)日：2021-10-21

申请号：US17320540

申请日：2021-05-14

Applicant: Natera, Inc.

Inventor： Matthew RABINOWITZ ,  Matthew HILL ,  Bernhard ZIMMERMANN ,  Johan BANER ,  George GEMELOS ,  Milena BANJEVIC ,  Allison RYAN ,  Styrmir SIGURJONSSON ,  Zachary DEMKO

IPC: C12Q1/6869 ,  G16B10/00 ,  C12Q1/6876 ,  C12Q1/6844

Abstract: Methods for non-invasive prenatal paternity testing are disclosed herein. The method uses genetic measurements made on plasma taken from a pregnant mother, along with genetic measurements of the alleged father, and genetic measurements of the mother, to determine whether or not the alleged father is the biological father of the fetus. This is accomplished by way of an informatics based method that can compare the genetic fingerprint of the fetal DNA found in maternal plasma to the genetic fingerprint of the alleged father.

公开(公告)号：US20210198743A1

公开(公告)日：2021-07-01

申请号：US17196722

申请日：2021-03-09

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: C12Q1/6883 ,  C12Q1/6811 ,  C12Q1/6848 ,  C12Q1/6809 ,  C12Q1/6851 ,  C12Q1/6844 ,  C12Q1/6869 ,  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：US20200157629A1

公开(公告)日：2020-05-21

申请号：US16777700

申请日：2020-01-30

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: C12Q1/6883 ,  C12Q1/6811 ,  C12Q1/6848 ,  C12Q1/6809 ,  C12Q1/6851 ,  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：US20190316200A1

公开(公告)日：2019-10-17

申请号：US16411446

申请日：2019-05-14

Applicant: Natera, Inc.

Inventor： Matthew RABINOWITZ ,  Milena BANJEVIC ,  Zachary DEMKO ,  David JOHNSON

IPC: C12Q1/6883 ,  G16B20/00 ,  C12Q1/6827 ,  G16B30/00 ,  G16B25/00 ,  C12Q1/6876 ,  G16B40/00

Abstract: A system and method for determining the genetic data for one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available, are disclosed. Genetic data for the target individual is acquired and amplified using known methods, and poorly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related subjects. In accordance with one embodiment of the invention, incomplete genetic data is acquired from embryonic cells, fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals.

公开(公告)号：US20190300950A1

公开(公告)日：2019-10-03

申请号：US16412043

申请日：2019-05-14

Applicant: Natera, Inc.

Inventor： Matthew RABINOWITZ ,  George GEMELOS ,  Milena BANJEVIC ,  Allison RYAN ,  Zachary DEMKO ,  Matthew HILL ,  Bernhard ZIMMERMANN ,  Johan BANER

IPC: C12Q1/6869 ,  C12Q1/6883 ,  C12Q1/6806 ,  C12Q1/686 ,  G16B20/00 ,  C12Q1/6827 ,  C12Q1/6862 ,  C12Q1/6874

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：US20190264288A1

公开(公告)日：2019-08-29

申请号：US16411507

申请日：2019-05-14

Applicant: Natera, Inc.

Inventor： Matthew RABINOWITZ ,  Milena BANJEVIC ,  Zachary DEMKO ,  David JOHNSON

IPC: C12Q1/6883 ,  G16B20/00 ,  C12Q1/6827 ,  G16B30/00 ,  G16B25/00 ,  C12Q1/6876 ,  G16B40/00

Abstract: A system and method for determining the genetic data for one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available, are disclosed. Genetic data for the target individual is acquired and amplified using known methods, and poorly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related subjects. In accordance with one embodiment of the invention, incomplete genetic data is acquired from embryonic cells, fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals.

公开(公告)号：US20190264280A1

公开(公告)日：2019-08-29

申请号：US16283188

申请日：2019-02-22

Applicant: Natera, Inc.

Inventor： Matthew RABINOWITZ ,  Milena BANJEVIC ,  Zachary DEMKO ,  David JOHNSON ,  Dusan KIJACIC ,  Dimitri PETROV ,  Joshua SWEETKIND-SINGER ,  Jing XU

IPC: C12Q1/6876 ,  G06N7/00 ,  G16B20/00 ,  C12Q1/6855 ,  G16B40/00 ,  C12Q1/6883 ,  C12Q1/6851 ,  C12Q1/6848

Abstract: Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.

公开(公告)号：US20190256909A1

公开(公告)日：2019-08-22

申请号：US16401535

申请日：2019-05-02

Applicant: Natera, Inc.

Inventor： Matthew RABINOWITZ ,  George GEMELOS ,  Milena BANJEVIC ,  Allison RYAN ,  Zachary DEMKO ,  Matthew HILL ,  Bernhard ZIMMERMANN ,  Johan BANER

IPC: C12Q1/6869 ,  C12Q1/6862 ,  C12Q1/6806 ,  G16B20/00 ,  C12Q1/6827 ,  C12Q1/6874 ,  C12Q1/6883

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：US20190211406A1

公开(公告)日：2019-07-11

申请号：US16359917

申请日：2019-03-20

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 ,  G16B40/00 ,  G16B25/00 ,  G16B15/00 ,  G06N20/00 ,  G06N7/00 ,  G16H50/20 ,  G16H10/40 ,  C12Q1/6869

CPC classification number: C12Q1/6886 ,  C12Q1/6869 ,  C12Q2539/10 ,  C12Q2600/156 ,  C12Q2600/158 ,  C12Q2600/16 ,  C12Q2600/172 ,  G06F19/00 ,  G06N7/005 ,  G06N20/00 ,  G16B15/00 ,  G16B25/00 ,  G16B40/00 ,  G16H10/40 ,  G16H50/20

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.