Patents by Inventor Allison Ryan
Allison Ryan has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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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: 11482300Abstract: 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: GrantFiled: October 5, 2021Date of Patent: October 25, 2022Assignee: NATERA, INC.Inventors: Matthew Rabinowitz, George Gemelos, Milena Banjevic, Allison Ryan, Zachary Demko, Matthew Hill, Bernhard Zimmermann, Johan Baner, Styrmir Sigurjonsson
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Patent number: 11479812Abstract: 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: GrantFiled: May 10, 2016Date of Patent: October 25, 2022Assignee: Natera, Inc.Inventors: Huseyin Eser Kirkizlar, Raheleh Salari, Styrmir Sigurjonsson, Bernhard Zimmermann, Allison Ryan, Naresh Vankayalapati
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Patent number: 11459615Abstract: 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: October 4, 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: 11447820Abstract: 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: GrantFiled: May 10, 2016Date of Patent: September 20, 2022Assignee: Natera, Inc.Inventors: Huseyin Eser Kirkizlar, Raheleh Salari, Styrmir Sigurjonsson, Bernhard Zimmermann, Allison Ryan, Naresh Vankayalapati
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Patent number: 11450408Abstract: 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: GrantFiled: October 5, 2021Date of Patent: September 20, 2022Assignee: NATERA, INC.Inventors: Matthew Rabinowitz, George Gemelos, Milena Banjevic, Allison Ryan, Zachary Demko, Matthew Hill, Bernhard Zimmermann, Johan Baner, Styrmir Sigurjonsson
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Patent number: 11408031Abstract: 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: June 19, 2018Date of Patent: August 9, 2022Assignee: Natera, Inc.Inventors: Allison Ryan, Styrmir Sigurjonsson, Milena Banjevic, George Gemelos, Matthew Hill, Johan Baner, Matthew Rabinowitz, Zachary Demko, Bernhard Zimmerman
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Patent number: 11345960Abstract: 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: June 19, 2018Date of Patent: May 31, 2022Assignee: Natera, Inc.Inventors: Allison Ryan, Styrmir Sigurjonsson, Milena Banjevic, George Gemelos, Matthew Hill, Johan Baner, Matthew Rabinowitz, Zachary Demko, Bernhard Zimmerman
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Patent number: 11345962Abstract: 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: May 31, 2022Assignee: 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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Patent number: 11339429Abstract: 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: GrantFiled: May 14, 2019Date of Patent: May 24, 2022Assignee: Natera, Inc.Inventors: Matthew Rabinowitz, George Gemelos, Milena Banjevic, Allison Ryan, Zachary Demko, Matthew Hill, Bernhard Zimmermann, Johan Baner, Styrmir Sigurjonsson
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Patent number: 11332793Abstract: 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: January 30, 2020Date of Patent: May 17, 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: 11332785Abstract: 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: GrantFiled: May 14, 2019Date of Patent: May 17, 2022Assignee: Natera, Inc.Inventors: Matthew Rabinowitz, George Gemelos, Milena Banjevic, Allison Ryan, Zachary Demko, Matthew Hill, Bernhard Zimmermann, Johan Baner, Styrmir Sigurjonsson
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Patent number: 11326208Abstract: 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: May 14, 2021Date of Patent: May 10, 2022Assignee: 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: 20220139495Abstract: 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: January 11, 2022Publication date: May 5, 2022Applicant: Natera, Inc.Inventors: Matthew RABINOWITZ, George GEMELOS, Milena BANJEVIC, Allison RYAN, Zachary DEMKO, Matthew HILL, Bernhard ZIMMERMANN, Johan BANER, Styrmir SIGURJONSSON
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Patent number: 11322224Abstract: 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: GrantFiled: November 4, 2014Date of Patent: May 3, 2022Assignee: Natera, Inc.Inventors: Matthew Rabinowitz, George Gemelos, Milena Banjevic, Allison Ryan, Zachary Demko, Matthew Hill, Bernhard Zimmermann, Johan Baner
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Patent number: 11306357Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a sample of DNA from the mother of the fetus and from the fetus, and from genotypic data from the mother and optionally also from the father. The ploidy state is determined by using a joint distribution model to create a set 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. In an embodiment, the mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias.Type: GrantFiled: February 12, 2014Date of Patent: April 19, 2022Assignee: Natera, Inc.Inventors: Matthew Rabinowitz, George Gemelos, Milena Banjevic, Allison Ryan, Zachary Demko, Matthew Hill, Bernhard Zimmerman, Johan Baner
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Publication number: 20220098667Abstract: 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: December 8, 2021Publication date: March 31, 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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Patent number: 11286530Abstract: 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 9, 2021Date of Patent: March 29, 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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Publication number: 20220073979Abstract: 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: November 18, 2021Publication date: March 10, 2022Applicant: 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: 20220073978Abstract: 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: November 18, 2021Publication date: March 10, 2022Applicant: Natera, Inc.Inventors: Matthew RABINOWITZ, George GEMELOS, Milena BANJEVIC, Allison RYAN, Zachary DEMKO, Matthew HILL, Bernhard ZIMMERMANN, Johan BANER