Natera, Inc.

Sequenom, Inc.

Fluidigm Corporation

Ucl Business Plc

Bernhard Zimmermann

Matthew Rabinowitz

George Gemelos

Matthew Micah Hill

Styrmir Sigurjonsson

Huseyin Eser Kirkizlar

Tudor Pompiliu Constantin

Joshua Babiarz

Allison Ryan

Onur Sakarya

Lane A Eubank

Zachary Demko

Milena Banjevic

Johan Baner

Ryan Swenerton

Himanshu Sethi

Philippe Lacroute

Raheleh Salari

Michael Dodd

Alexander Wong

Apratim Ganguly

Ramesh Ramakrishnan

Sinuhe Hahn

Naresh Vankayalapati

Marc Alexander Unger

Andrew Paul May

Ying Li

Alain Mir

Wolfgang Holzgreve

Simant Dube

Lesley Suzanne Weaver

Hsin-Ta Wu

Robert Charles Swanton

Christopher Abbosh

Prashanthi Natarajan

Gareth Wilson

Mariam Jamal-hanjani

Dina M Hafez

Tudor Popiliu Constantin

Felipe Acosta Archila

Solomon Moshkevich

Philippe Gilbert Lacroute

Scott Dashner

Fei Lu

Mariam Jamal-Hanjani

Wolfgang Prof Holzgreve

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

The invention provides methods for detecting single nucleotide variants in breast cancer, bladder cancer, or colorectal cancer. Additional methods and compositions, such as reaction mixtures and solid supports comprising clonal populations of nucleic acids, are provided. For example, provided here is a method for monitoring and detection of early relapse or metastasis of breast cancer, bladder cancer, or colorectal cancer, comprising generating a set of amplicons by performing a multiplex amplification reaction on nucleic acids isolated from a sample of blood or urine or a fraction thereof from a patient who has been treated for a breast cancer, bladder cancer, or colorectal cancer, wherein each amplicon of the set of amplicons spans at least one single nucleotide variant locus of a set of patient-specific single nucleotide variant loci associated with the breast cancer, bladder cancer, or colorectal cancer; and determining the sequence of at least a segment of each amplicon of the set of amplicons that comprises a patient-specific single nucleotide variant locus, wherein detection of one or more patient-specific single nucleotide variants is indicative of early relapse or metastasis of breast cancer, bladder cancer, or colorectal cancer.

Methods for cancer detection and monitoring

The disclosure herein provides methods and compositions for detecting or monitoring immune cell populations in biological samples. The methods and compositions disclosed herein are particularly useful for detecting or monitoring immune cell populations in patients suffering from a disease or undergoing treatment of a disease resulting in depletion of immune cells. In particular, the present disclosure provides method for using multiplex PCR combined with next-generation DNA sequencing to detect DNA containing recombined V(D)J gene segments which can be used to detect immune cells.

Methods for detecting immune cell DNA and monitoring immune system

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

The present disclosure provides methods for determining the status of an allograft within a transplant recipient from genotypic data measured from a mixed sample of DNA comprising DNA from both the transplant recipient and from the donor. 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 detection of donor-derived cell-free DNA

The invention provides methods for detecting single nucleotide variants in lung cancer, especially stage 3a lung adenocarcinoma and lung squamous cell carcinoma. Additional methods and compositions, such as reaction mixtures and solid supports comprising clonal populations of nucleic acids, are provided.

Methods for lung cancer detection

Growing community of inventors

Manteca, CA, United States of America

Bernhard Zimmermann