公开(公告)号：US20240336973A1

公开(公告)日：2024-10-10

申请号：US18294066

申请日：2022-07-29

申请人： Natera, Inc.

发明人： Georgina GOLDRING ,  Wendy DiNONNO ,  Wenbo XU ,  Samantha LEONARD ,  Jeffrey MELTZER

IPC分类号： C12Q1/6886 ,  C12Q1/6806 ,  C12Q1/6858 ,  C12Q1/6869 ,  G16B20/10 ,  G16B20/20

CPC分类号： C12Q1/6886 ,  C12Q1/6806 ,  C12Q1/6858 ,  C12Q1/6869 ,  G16B20/10 ,  G16B20/20 ,  C12Q2600/156

摘要： The invention provides methods for preparing a preparation of amplified DNA derived from a biological sample of a pregnant woman useful for identifying neoplasm in a pregnant woman, comprising: (a) isolating cell-free DNA from a biological sample of a pregnant woman comprising a mixture of fetal cell-free DNA and maternal cell-free DNA; (b) preparing a preparation of amplified DNA by performing targeted multiplex amplification on the isolated cell-free DNA to amplify at least 100 polymorphic loci; (c) analyzing the preparation of amplified DNA by sequencing the amplified DNA to obtain sequence reads of the at least 100 polymorphic loci and using the sequence reads to identify copy number variations (CNVs) in fetal and maternal chromosomes or chromosomal segments of interest, and identifying neoplasm in the pregnant woman by the presence of two or more of CNVs in the maternal chromosomes or chromosomal segments of interest.

公开(公告)号：US20240327919A1

公开(公告)日：2024-10-03

申请号：US18747138

申请日：2024-06-18

申请人： Natera, Inc.

发明人： MATTHEW RABINOWITZ ,  Matthew Micah HILL ,  Bernhard ZIMMERMANN ,  Johan BANER ,  George GEMELOS ,  Milena Eser BANJEVIC ,  Allison RYAN ,  Styrmir SIGURJONSSON ,  Zachary DEMKO

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

CPC分类号： C12Q1/6883 ,  C12Q1/6809 ,  C12Q1/6811 ,  C12Q1/6844 ,  C12Q1/6848 ,  C12Q1/6851 ,  C12Q1/6855 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q2600/156

摘要： 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：US20240318252A1

公开(公告)日：2024-09-26

申请号：US18733659

申请日：2024-06-04

申请人： Natera, Inc.

发明人： Matthew RABINOWITZ ,  Matthew Micah HILL ,  Bernhard A. ZIMMERMANN ,  Johan BANER ,  George GEMELOS ,  Milena BANJEVIC ,  Allison RYAN ,  Styrmir SIGURJONSSON ,  Zachary DEMKO

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

CPC分类号： C12Q1/6883 ,  C12Q1/6809 ,  C12Q1/6811 ,  C12Q1/6844 ,  C12Q1/6848 ,  C12Q1/6851 ,  C12Q1/6855 ,  C12Q1/6869 ,  C12Q1/6874 ,  C12Q2600/156

摘要： 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：US20240309472A1

公开(公告)日：2024-09-19

申请号：US18282390

申请日：2022-03-16

申请人： Natera, Inc.

发明人： Phil GAUTHIER ,  Hossein TABRIZIANI ,  Paul VAN HUMMELEN ,  Jessica TANG

IPC分类号： C12Q1/70 ,  C12Q1/6851 ,  C12Q1/6883

CPC分类号： C12Q1/701 ,  C12Q1/6851 ,  C12Q1/6883 ,  C12Q2600/118 ,  C12Q2600/156

摘要： The present disclosure provides methods for preparation and analysis of biological samples of transplant recipients for determination of transplant rejection, comprising: (a) measuring the amount of Torque teno virus (TTV) in a blood, plasma, serum, or urine sample of a transplant recipient; (b) measuring the amount of donor-derived cell-free DNA in a blood, plasma, serum, or urine sample of the transplant recipient; and (c) determining whether the amount of donor-derived cell-free DNA or a function thereof exceeds a cutoff threshold indicating transplant rejection and whether the transplant recipient has an increased or decreased amount of TTV indicating decreased or increased immune response, respectively.

公开(公告)号：US20240301495A1

公开(公告)日：2024-09-12

申请号：US18632703

申请日：2024-04-11

申请人： Natera, Inc.

发明人： MATTHEW RABINOWITZ ,  Milena BANJEVIC ,  Zachary DEMKO ,  David JOHNSON ,  Dusan KIJACIC ,  Dimitri PETROV ,  Joshua SWEETKIND-SINGER ,  Jing XU

IPC分类号： C12Q1/6883 ,  C12Q1/6806 ,  C12Q1/6827 ,  C12Q1/6855 ,  C12Q1/6869 ,  C12Q1/6876 ,  C12Q1/6886 ,  G16B20/00 ,  G16B25/00 ,  G16B30/00 ,  G16B40/00

CPC分类号： C12Q1/6883 ,  C12Q1/6806 ,  C12Q1/6827 ,  C12Q1/6855 ,  C12Q1/6869 ,  C12Q1/6876 ,  C12Q1/6886 ,  G16B20/00 ,  G16B25/00 ,  G16B30/00 ,  G16B40/00 ,  C12Q2537/149 ,  C12Q2545/114 ,  C12Q2600/118 ,  C12Q2600/156 ,  C12Q2600/158

摘要： 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：US20240287610A1

公开(公告)日：2024-08-29

申请号：US18633282

申请日：2024-04-11

申请人： Natara, Inc.

发明人： MATTHEW RABINOWITZ ,  Milena Banjevic ,  Zachary Demko ,  David Johnson ,  Dusan Kijacic ,  Dimitri Petrov ,  Joshua Sweetkind-Singer ,  Jing Xu

IPC分类号： C12Q1/6883 ,  C12Q1/6827 ,  C12Q1/6855 ,  C12Q1/686 ,  C12Q1/6869 ,  C12Q1/6876 ,  G16B20/00 ,  G16B25/00 ,  G16B30/00 ,  G16B40/00

CPC分类号： C12Q1/6883 ,  C12Q1/6827 ,  C12Q1/6855 ,  C12Q1/686 ,  C12Q1/6869 ,  C12Q1/6876 ,  G16B20/00 ,  G16B25/00 ,  G16B30/00 ,  G16B40/00 ,  C12Q2600/118 ,  C12Q2600/156 ,  C12Q2600/158

摘要： 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：US20240132957A1

公开(公告)日：2024-04-25

申请号：US18376355

申请日：2023-10-02

申请人： Natera, Inc.

发明人： Aoy Tomita MITCHELL ,  Karl STAMM

IPC分类号： C12Q1/6876 ,  C12Q1/686

CPC分类号： C12Q1/6876 ,  C12Q1/686 ,  C12Q2600/158

摘要： Provided herein are methods for determining levels of cell lysis in samples, particularly sampled in which amounts of non-self cell-free DNA may be determined.

公开(公告)号：US20230343411A1

公开(公告)日：2023-10-26

申请号：US18220183

申请日：2023-07-10

申请人： Natera, Inc.

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

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

CPC分类号： G16B20/00 ,  C12Q1/6827 ,  C12Q1/6862 ,  C12Q1/686 ,  G16B20/10 ,  G16B20/20 ,  G16B20/40 ,  C12Q1/6883 ,  C12Q1/6869 ,  C12Q1/6806 ,  C12Q1/6874 ,  G16B40/00

摘要： 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：US11746376B2

公开(公告)日：2023-09-05

申请号：US16796748

申请日：2020-02-20

申请人： Natera, Inc.

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

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

CPC分类号： C12Q1/6869 ,  C12Q1/6844 ,  C12Q1/6876 ,  G16B10/00 ,  C12Q2600/156

摘要： 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：US20230203573A1

公开(公告)日：2023-06-29

申请号：US17925693

申请日：2021-05-27

申请人： Natera, Inc.

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

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

CPC分类号： C12Q1/6851 ,  C12Q1/686 ,  C12Q1/6876 ,  C12Q2600/158

摘要： 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.