Allison W Ryan

US Patent:

20190256908, Aug 22, 2019

Filed:

Apr 30, 2019

Appl. No.:

16/399991

Inventors:

- San Carlos CA, US
George Gemelos - New York NY, US
Milena Banjevic - Los Altos Hills CA, US
Allison Ryan - Redwood City CA, US
Zachary Demko - San Francisco 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 1/6869
C12Q 1/6862
C12Q 1/6806
G16B 20/00
C12Q 1/6827
C12Q 1/6874
C12Q 1/6883

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.

US Patent:

20150072872, Mar 12, 2015

Filed:

Nov 18, 2014

Appl. No.:

14/546321

Inventors:

- San Carlos 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 - Redwood City CA, US
Bernhard Zimmermann - San Mateo CA, US
Johan Baner - Stockholm CA, US

International Classification:

C12Q 1/68
G06F 19/00
G06F 19/18

US Classification:

506 2, 506 9, 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 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.

US Patent:

20150051087, Feb 19, 2015

Filed:

Nov 4, 2014

Appl. No.:

14/532666

Inventors:

- San Carlos 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

International Classification:

C12Q 1/68

US Classification:

506 2

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:

20140336060, Nov 13, 2014

Filed:

Jul 29, 2014

Appl. No.:

14/446232

Inventors:

- San Carlos 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 - Redwood City CA, US
Bernhard Zimmermann - San Mateo CA, US
Johan Baner - Stockholm, SE

International Classification:

C12Q 1/68
G06F 19/22

US Classification:

506 2

Abstract:

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.

US Patent:

20140162269, Jun 12, 2014

Filed:

Feb 12, 2014

Appl. No.:

14/179399

Inventors:

- San Carlos 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 - Redwood City CA, US
Bernhard Zimmerman - San Mateo CA, US
Johan Baner - Stockholm, SE

Assignee:

Natera, Inc. - San Carlos CA

International Classification:

C12Q 1/68

US Classification:

435 611

Abstract:

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.

US Patent:

20140100134, Apr 10, 2014

Filed:

Dec 9, 2013

Appl. No.:

14/100928

Inventors:

- San Carlos 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 Hill CA, US
Matthew Hill - Redwood City CA, US
Bernhard Zimmermann - San Mateo CA, US
Johan Baner - Stockholm, SE

Assignee:

Natera, Inc. - San Carlos CA

International Classification:

G06F 19/12

US Classification:

506 9, 435 611, 702 20, 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 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.