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Johan Baner Phones & Addresses

  • Palo Alto, CA
  • San Francisco, CA
  • South Ozone Park, NY

Publications

Us Patents

Methods For Non-Invasive Prenatal Ploidy Calling

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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.

Methods For Non-Invasive Prenatal Paternity Testing

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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.

Methods For Non-Invasive Prenatal Ploidy Calling

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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.

Methods For Non-Invasive Prenatal Ploidy Calling

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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.

Informatics Enhanced Analysis Of Fetal Samples Subject To Maternal Contamination

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US Patent:
20130196862, Aug 1, 2013
Filed:
Feb 28, 2013
Appl. No.:
13/780022
Inventors:
Johan Baner - San Francisco CA, US
George Gemelos - San Jose CA, US
Mathew M. Hill - Menlo Park CA, US
Assignee:
NATERA, INC. - SAN CARLOS CA
International Classification:
C12Q 1/68
US Classification:
506 2
Abstract:
The invention provides methods for chromosome copy number calling on genetic samples, such as fetal samples subject to contamination from maternal DNA. The present disclosure provides methods for determining the ploidy status of a chromosome in a fetus (such as a gestating fetus or a POC sample) 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. In some embodiments, 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.

Methods For Non-Invasive Prenatal Paternity Testing

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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.

Methods For Cell Genotyping

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US Patent:
20110033862, Feb 10, 2011
Filed:
Feb 19, 2009
Appl. No.:
12/918445
Inventors:
Matthew Rabinowitz - Portola Valley CA, US
David S. Johnson - San Francisco CA, US
Johan Baner - Palo Alto CA, US
Zachary Demko - Somerville MA, US
Cengiz Cinnioglu - Sunnyvale CA, US
International Classification:
C12Q 1/68
C12P 19/34
US Classification:
435 6, 435 915
Abstract:
Methods for cell genotyping are disclosed herein. A method for determining the genomic data of one or a small number of cells, or from fragmentary DNA, where a limited quantity of genetic data is available may include adding one or more targeted primers to a whole genome amplification of a cell, increasing the accuracy with which key alleles are measured in the context of a whole genome amplification. The genetic material from a single cell may be divided into fractions, each of which may be separately genotyped, allowing the reconstruction of the cells haplotype. The genetic material from a single cell may be divided into fractions, each of which may be separately genotyped, and the distribution of the various alleles in the different fractions may be used to determine the ploidy state of one or a plurality of chromosomes in the cell.

Methods For Simultaneous Amplification Of Target Loci

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US Patent:
20220411875, Dec 29, 2022
Filed:
Jul 19, 2022
Appl. No.:
17/868141
Inventors:
- San Carlos CA, US
Matthew Micah HILL - Belmont CA, US
Bernhard ZIMMERMANN - Manteca CA, US
Johan BANER - San Francisco CA, US
George GEMELOS - Portland OR, US
Milena BANJEVIC - Los Altos Hills CA, US
Allison RYAN - Belmont CA, US
Styrmir SIGURJONSSON - San Jose CA, US
Zachary DEMKO - San Francisco CA, US
Assignee:
Natera, Inc. - San Carlos CA
International Classification:
C12Q 1/6883
C12Q 1/6811
C12Q 1/6848
C12Q 1/6809
C12Q 1/6851
C12Q 1/6844
C12Q 1/6869
C12Q 1/6855
C12Q 1/6874
Abstract:
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.
Johan Baner from Palo Alto, CA, age ~52 Get Report