Allison C Ryan

US Patent:

20110178719, Jul 21, 2011

Filed:

Aug 4, 2009

Appl. No.:

13/057350

Inventors:

Matthew Rabinowitz - Portola Valley CA, US
George Gemelos - San Jose CA, US
Milena Banjevic - New York NY, US
Allison Ryan - Redwood City CA, US
Joshua Sweetkind-Singer - San Jose CA, US

Assignee:

GENE SECURITY NETWORK, INC. - Redwood City CA

International Classification:

G06F 17/18
G06F 19/10

US Classification:

702 19

Abstract:

Disclosed herein is a system and method for making allele calls, and for determining the ploidy state, in one or a small set of cells, or where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed and the haplotypes are determined using expected similarities between the target genome and the knowledge of the genomes of genetically related individuals. In one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the genetic data from both parents, and possibly one or more sperm and/or sibling embryos. In another embodiment, the chromosome copy number can be determined using the same input data. In another embodiment, these determinations are made for embryo selection during IVF, for non-invasive prenatal diagnosis, or for making phenotypic predictions.

US Patent:

20110288780, Nov 24, 2011

Filed:

May 18, 2011

Appl. No.:

13/110685

Inventors:

Matthew Rabinowitz - San Francisco CA, US
George Gemelos - San Jose CA, US
Milena Banjevic - New York NY, US
Allison Ryan - Redwood City CA, US
Zachary Demko - Somerville MA, US
Matthew Hill - Menlo Park CA, US
Bernhard Zimmermann - San Mateo CA, US
Johan Baner - San Francisco CA, US

International Classification:

G06F 19/00
C07H 21/04

US Classification:

702 19, 536 235

Abstract:

Methods for non-invasive prenatal ploidy calling are disclosed herein. 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 are disclosed herein. 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.

US Patent:

20120122701, May 17, 2012

Filed:

Dec 22, 2011

Appl. No.:

13/335043

Inventors:

Allison Ryan - Redwood City CA, US
Styrmir Sigurjonsson - San Jose CA, US
Milena Banjevic - Los Altos Hill CA, US
George Gemelos - San Jose CA, US
Matthew Hill - Menlo Park CA, US
Johan Baner - San Francisco CA, US
Matthew Rabinowitz - San Francisco CA, US
Zachary Demko - Los Altos Hills CA, US

International Classification:

C12Q 1/68
G01N 33/53
G01N 21/64
C40B 20/00

US Classification:

506 2, 435 611, 436501

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.

US Patent:

20120185176, Jul 19, 2012

Filed:

Sep 30, 2010

Appl. No.:

13/499086

Inventors:

Matthew Rabinowitz - San Francisco CA, US
Allison Ryan - Redwood City CA, US
George Gemelos - San Jose CA, US
Milena Banjevic - Los Altos Hill CA, US
Zachary Demko - Los Altos Hills CA, US

International Classification:

G06F 19/00

US Classification:

702 19

Abstract:

Disclosed herein are methods for determining the copy number of a chromosome in a fetus in the context of non-invasive prenatal diagnosis. In an embodiment, the measured genetic data from a sample of genetic material that contains both fetal DNA and maternal DNA is analyzed, along with the genetic data from the biological parents of the fetus, and the copy number of the chromosome of interest is determined. In an embodiment, the maternal serum is measured using a single-nucleotide polymorphism (SNP) microarray, along with parental genomic data, and the determination of the chromosome copy number is used to make clinical decisions pertaining to the fetus.

US Patent:

20120270212, Oct 25, 2012

Filed:

Nov 18, 2011

Appl. No.:

13/300235

Inventors:

MATTHEW RABINOWITZ - SAN FRANCISCO CA, US
GEORGE GEMELOS - SAN JOSE CA, US
MILENA BANJEVIC - LOS ALTOS HILLS CA, US
ALLISON RYAN - REDWOOD CITY CA, US
ZACHARY DEMKO - LOS ALTOS HILLS CA, US
MATTHEW HILL - MENLO PARK CA, US
BERNHARD ZIMMERMANN - SAN MATEO CA, US
JOHAN BANER - SAN FRANCISCO CA, US

International Classification:

C12Q 1/68
G06F 19/20
G06F 19/24

US Classification:

435 611, 702 19, 435 612

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.

US Patent:

20130178373, Jul 11, 2013

Filed:

Mar 8, 2013

Appl. No.:

13/791397

Inventors:

Matthew Rabinowitz - San Francisco CA, US
George Gemelos - New York NY, US
Milena Banjevic - Los Altos Hills CA, US
Allison Ryan - Redwood City CA, US
Zachary Demko - Los Altos Hills CA, US
Matthew Hill - Menlo Park CA, US
Bernhard Zimmermann - San Mateo CA, US
Johan Baner - San Francisco CA, US

Assignee:

Natera, Inc. - San Carlos CA

International Classification:

C12Q 1/68

US Classification:

506 2, 435 611, 702 19

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.

US Patent:

20130225422, Aug 29, 2013

Filed:

Mar 18, 2013

Appl. No.:

13/846111

Inventors:

Matthew Rabinowitz - San Francisco CA, US
George Gemelos - New York NY, US
Milena Banjevic - Los Altos Hills CA, US
Allison Ryan - Redwood City CA, US
Joshua Sweetkind-Singer - San Jose CA, US

Assignee:

Natera, Inc. - San Carlos CA

International Classification:

G06F 19/18

US Classification:

506 2, 702 19, 435346, 435379, 435 611

Abstract:

Disclosed herein is a system and method for making allele calls, and for determining the ploidy state, in one or a small set of cells, or where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed and the haplotypes are determined using expected similarities between the target genome and the knowledge of the genomes of genetically related individuals. In one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the genetic data from both parents, and possibly one or more sperm and/or sibling embryos. In another embodiment, the chromosome copy number can be determined using the same input data. In another embodiment, these determinations are made for embryo selection during IVF, for non-invasive prenatal diagnosis, or for making phenotypic predictions.

US Patent:

20130261004, Oct 3, 2013

Filed:

Mar 18, 2013

Appl. No.:

13/846160

Inventors:

Allison Ryan - Redwood City CA, US
Styrmir Sigurjonsson - San Jose CA, US
Milena Banjevic - Los Altos Hills CA, US
George Gemelos - New York NY, US
Matthew Hill - Menlo Park CA, US
Johan Baner - San Francisco CA, US
Matthew Rabinowitz - San Francisco CA, US
Zachary Demko - Los Altos Hills CA, US

Assignee:

Natera, Inc. - San Carlos CA

International Classification:

C12Q 1/68

US Classification:

506 2, 435 611

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.