Natera, Inc.

Synta Pharmaceuticals Corporation

Zachary Demko

Milena Banjevic

Matthew Rabinowitz

Allison Ryan

George Gemelos

Matthew Micah Hill

Lijun Sun

Bernhard Zimmermann

Styrmir Sigurjonsson

David Walter Johnson

David James

Dusan Kijacic

Mitsunori Ono

Kevin M Foley

Johan Baner

Howard P Ng

Dinesh U Chimmanamada

Hao Li

Teresa Przewloka

Shijie Zhang

Weiwen Ying

Jing Xu

Dimitri Petrov

Joshua Sweetkind-Singer

Kevin Paul Foley

Zhenjian Du

Junghyun Chae

Dan Zhou

Shuzhen Qin

Shoujun Chen

Yumiko Wada

Keizo Koya

Teresa Kowalczyk-Przewloka

Christopher Borella

Elena Kostik

David Scott Johnson

Joseph A Burlison

Chi-Wan Lee

Minghu Song

Stefan M Schweizer

Bernhard Zimmerman

Huseyin Eser Kirkizlar

Onur Sakarya

Joshua Babiarz

Tudor Pompiliu Constantin

Zhi-Qiang Xia

Lane A Eubank

Naresh Vankayalapati

Teresa Kowalczyk-Prezewloka

Josh Sweetkind-Singer

Stefan Michael Schweizer

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

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

Provided herein are improved methods for detecting aneuploidy in a sample. The methods in certain embodiments are used for the analysis of circulating DNA in serum samples, such as circulating fetal DNA or circulating tumor DNA. In certain embodiments, chromosome or chromosome segments of interest are used to set a bias model and/or a control value for a z-score determination, in illustrative examples without the use of a control chromosome.

Systems and methods for detection of aneuploidy

Methods for non-invasive prenatal ploidy calling

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

Methods for preparing a DNA fraction from a biological sample for analyzing genotypes of cell-free DNA

Methods for non-invasive prenatal paternity testing

Growing community of inventors

San Francisco, CA, United States of America

Zachary Demko