Natera, Inc.

Rosum Corporation

Trueposition, Inc.

Leland Stanford Junior University

Rosom Corporation

Gene Security Network, Inc.

Matthew Rabinowitz

George Gemelos

Milena Banjevic

Zachary Demko

Bernhard Zimmermann

Matthew Micah Hill

Styrmir Sigurjonsson

Allison Ryan

Johan Baner

Huseyin Eser Kirkizlar

Onur Sakarya

Joshua Babiarz

Lane A Eubank

James J Spilker, Jr

Tudor Pompiliu Constantin

David Walter Johnson

Joshua Sweetkind-Singer

Jing Xu

Dimitri Petrov

Dusan Kijacic

Jimmy Kazuhiro Omura

Guttorm Ringstad Opshaug

Andy Lee

Ryan Swenerton

Himanshu Sethi

Apratim Ganguly

Scott Furman

Ju-Yong Do

Dimitri Rubin

David Scott Johnson

David Burgess

Matthew Dalton Pierce

Matthew Hill

Bernhard Zimmerman

Jim Omura

Harvind Samra

David G Lawrence

Clark Emerson Cohen

Michael John Sabin

George Flammer

Bradford W Parkinson

Johan Banér

David I Gotwisner

John Croswell

Josh Sweetkind-Singer

Tudor Popiliu Constantin

Todd Young

Miro Sarbaev

Wayne Chambliss

Zachary Paul Demko

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.

Detecting mutations and ploidy in chromosomal segments

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

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.

Methods for simultaneous amplification of target loci

Methods for preparing a biological sample obtained from an individual for use in a genetic testing assay

Provided herein are methods for determining the ploidy state of one or more chromosome in a developing fetus. The subject methods provide for increased accuracy by utilizing information about the mosaicism level of one or more chromosomes of interest in the mother of fetus. The mosaicism level of one or more chromosomes of interest is determined for the maternal tissue that is used as the source of nucleic acid for genetic analysis that are used to determine the ploidy state of the fetal chromosome or chromosomes of interest. Utilization of the mosaicism data can be used to increase the reliability and accuracy of the determination of the ploidy state of a chromosome of interest.

Method for non-invasive prenatal testing using parental mosaicism data

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.

System and method for cleaning noisy genetic data and determining chromosome copy number

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 amplification of cell-free DNA using ligated adaptors and universal and inner target-specific primers for multiplexed nested PCR

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.

Compositions and methods for identifying nucleic acid molecules

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San Francisco, CA, United States of America

Matthew Rabinowitz