Patents Assigned to NATERA, INC.
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Patent number: 11707701Abstract: Provided herein are materials and methods relating to cell-free DNA. In particular, the technology relates to methods and materials for the preparation and handling of blood samples for future use in applications involving cell-free DNA.Type: GrantFiled: April 3, 2020Date of Patent: July 25, 2023Assignee: Natera, Inc.Inventor: Aoy Tomita Mitchell
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Publication number: 20230212693Abstract: 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.Type: ApplicationFiled: March 13, 2023Publication date: July 6, 2023Applicant: Natera, Inc.Inventors: Matthew RABINOWITZ, Milena BANJEVIC, Zachary DEMKO, David JOHNSON, Dusan KIJACIC, Dimitri PETROV, Joshua SWEETKIND-SINGER, Jing XU
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Publication number: 20230203573Abstract: 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.Type: ApplicationFiled: May 27, 2021Publication date: June 29, 2023Applicant: Natera, Inc.Inventors: Ryan SWENERTON, Bernhard ZIMMERMANN, Ebad AHMED, Nathan LIANG, Allison RYAN, Fei LU, Paul VAN HUMMELEN
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Publication number: 20230193387Abstract: 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.Type: ApplicationFiled: June 9, 2022Publication date: June 22, 2023Applicant: Natera, Inc.Inventors: Matthew RABINOWITZ, Milena BANJEVIC, Zachary DEMKO, David JOHNSON, Dusan KIJACIC, Dimitri PETROV, Joshua SWEETKIND-SINGER, Jing XU
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Publication number: 20230060579Abstract: Disclosed here is a method for detecting genome rearrangement in a biological sample, comprising: obtaining a contact matrix plotted from proximity ligation sequencing data of at least one chromosome; identifying an abnormal contact pattern in the contact matrix compared to the contact matrix of a reference genome; comparing the abnormal contact pattern in the contact matrix to one or more known patterns associated with genomic rearrangement to identify a type of genomic rearrangement causing the abnormal contact pattern.Type: ApplicationFiled: October 31, 2022Publication date: March 2, 2023Applicant: Natera, Inc.Inventor: Axel BETHKE
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Patent number: 11591649Abstract: 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.Type: GrantFiled: February 20, 2020Date of Patent: February 28, 2023Assignee: Natera, Inc.Inventors: Matthew Rabinowitz, Matthew Hill, Bernhard Zimmermann, Johan Baner, George Gemelos, Milena Banjevic, Allison Ryan, Styrmir Sigurjonsson, Zachary Demko
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Publication number: 20230054494Abstract: 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.Type: ApplicationFiled: September 15, 2022Publication date: February 23, 2023Applicant: Natera, Inc.Inventors: Matthew RABINOWITZ, George GEMELOS, Milena BANJEVIC, Allison RYAN, Zachary DEMKO, Matthew HILL, Bernhard ZIMMERMANN, Johan BANER
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Publication number: 20230053752Abstract: 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.Type: ApplicationFiled: July 19, 2022Publication date: February 23, 2023Applicant: Natera, Inc.Inventors: Matthew RABINOWITZ, Matthew Micah HILL, Bernhard ZIMMERMANN, Johan BANER, George GEMELOS, Milena BANJEVIC, Allison RYAN, Styrmir SIGURJONSSON, Zachary DEMKO
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Publication number: 20230042405Abstract: 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.Type: ApplicationFiled: October 4, 2022Publication date: February 9, 2023Applicant: Natera, Inc.Inventors: Joshua BABIARZ, Tudor Pompiliu CONSTANTIN, Lane A. EUBANK, George GEMELOS, Matthew Micah HILL, Huseyin Eser KIRKIZLAR, Matthew RABINOWITZ, Onur SAKARYA, Styrmir SIGURJONSSON, Bernhard ZIMMERMANN
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Publication number: 20220411875Abstract: 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.Type: ApplicationFiled: July 19, 2022Publication date: December 29, 2022Applicant: Natera, Inc.Inventors: Matthew RABINOWITZ, Matthew Micah HILL, Bernhard ZIMMERMANN, Johan BANER, George GEMELOS, Milena BANJEVIC, Allison RYAN, Styrmir SIGURJONSSON, Zachary DEMKO
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Publication number: 20220403461Abstract: 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.Type: ApplicationFiled: June 21, 2022Publication date: December 22, 2022Applicant: Natera, Inc.Inventors: Huseyin Eser KIRKIZLAR, Raheleh SALARI, Styrmir SIGURJONSSON, Bernhard ZIMMERMANN, Allison RYAN, Naresh VANKAYALAPATI
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Patent number: 11530442Abstract: 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.Type: GrantFiled: May 21, 2019Date of Patent: December 20, 2022Assignee: Natera, Inc.Inventors: Bernhard Zimmermann, Ryan Swenerton, Matthew Rabinowitz, Styrmir Sigurjonsson, George Gemelos, Apratim Ganguly, Himanshu Sethi
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Patent number: 11530454Abstract: 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.Type: GrantFiled: May 6, 2022Date of Patent: December 20, 2022Assignee: Natera, Inc.Inventors: Joshua Babiarz, Tudor Pompiliu Constantin, Lane A. Eubank, George Gemelos, Matthew Micah Hill, Huseyin Eser Kirkizlar, Matthew Rabinowitz, Onur Sakarya, Styrmir Sigurjonsson, Bernhard Zimmermann
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Patent number: 11525162Abstract: 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.Type: GrantFiled: March 25, 2020Date of Patent: December 13, 2022Assignee: Natera, Inc.Inventors: Matthew Rabinowitz, Matthew Micah Hill, Bernhard Zimmermann, Johan Baner, George Gemelos, Milena Banjevic, Allison Ryan, Styrmir Sigurjonsson, Zachary Demko
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Patent number: 11525159Abstract: 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.Type: GrantFiled: February 2, 2021Date of Patent: December 13, 2022Assignee: Natera, Inc.Inventors: Solomon Moshkevich, Bernhard Zimmermann, Tudor Pompiliu Constantin, Huseyin Eser Kirkizlar, Allison Ryan, Styrmir Sigurjonsson, Felipe Acosta Archila, Ryan Swenerton
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Patent number: 11519035Abstract: 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.Type: GrantFiled: July 21, 2020Date of Patent: December 6, 2022Assignee: Natera, Inc.Inventors: Matthew Rabinowitz, Matthew Micah Hill, Bernhard Zimmermann, Johan Baner, George Gemelos, Milena Banjevic, Allison Ryan, Styrmir Sigurjonsson, Zachary Demko
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Patent number: 11519028Abstract: 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.Type: GrantFiled: October 5, 2021Date of Patent: December 6, 2022Assignee: Natera, Inc.Inventors: Bernhard Zimmermann, Ryan Swenerton, Matthew Rabinowitz, Styrmir Sigurjonsson, George Gemelos, Apratim Ganguly, Himanshu Sethi
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Publication number: 20220356530Abstract: The invention provides methods for determining the growth rate of ctDNA, comprising (a) sequencing nucleic acids isolated from a biological sample of a cancer patient to identify patient-specific cancer mutations; (b) quantify the amount of ctDNA in a first liquid biopsy sample collected from the cancer patient by performing a multiplex amplification reaction to amplify target loci from cfDNA isolated from the first liquid biopsy sample, wherein each target locus spans at least one patient-specific cancer mutation, and sequencing the amplified target loci to identify the patient-specific cancer mutations and quantify the amount of ctDNA in the first liquid biopsy sample; (c) quantify the amount of ctDNA in a second liquid biopsy sample collected from the cancer patient by performing a multiplex amplification reaction to amplify target loci from cfDNA isolated from the second liquid biopsy sample, wherein each target locus spans at least one patient-specific cancer mutation, and sequencing the amplified targetType: ApplicationFiled: April 20, 2022Publication date: November 10, 2022Applicant: Natera, Inc.Inventors: Shruti SHARMA, Bernhard ZIMMERMANN, Himanshu SETHI, Alexey ALESHIN, Svetlana SHCHEGROVA
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Publication number: 20220356526Abstract: 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.Type: ApplicationFiled: June 16, 2022Publication date: November 10, 2022Applicant: Natera, Inc.Inventors: Joshua BABIARZ, Tudor Pompiliu CONSTANTIN, Lane A. EUBANK, George GEMELOS, Matthew Micah HILL, Huseyin Eser KIRKIZLAR, Matthew RABINOWITZ, Onur SAKARYA, Styrmir SIGURJONSSON, Bernhard ZIMMERMANN
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Patent number: 11486008Abstract: 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.Type: GrantFiled: June 21, 2018Date of Patent: November 1, 2022Assignee: Natera, Inc.Inventors: Joshua Babiarz, Tudor Pompiliu Constantin, Lane A. Eubank, George Gemelos, Matthew Micah Hill, Huseyin Eser Kirkizlar, Matthew Rabinowitz, Onur Sakarya, Styrmir Sigurjonsson, Bernhard Zimmermann