149 patents
Utility
Methods and systems for detecting genetic variants
21 Mar 23
Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample.
AmirAli Talasaz, Helmy Eltoukhy, Stefanie Ann Ward Mortimer
Filed: 28 Jun 22
Utility
Methods for Early Detection of Cancer
16 Mar 23
Disclosed herein are methods, compositions, and devices for use in the early detection of cancer.
Stefanie Ann Ward MORTIMER, AmirAli TALASAZ, Darya CHUDOVA, Helmy ELTOUKHY
Filed: 19 Oct 22
Utility
Systems and methods to detect rare mutations and copy number variation
14 Feb 23
The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides.
AmirAli Talasaz
Filed: 16 Mar 22
Utility
Methods and Related Aspects for Analyzing Molecular Response
29 Dec 22
Provided herein are methods of determining a molecular response score.
Katie Julia QUINN, Allysia Jade MAK, Elena HELMAN, Tingting JIANG, Justin I. ODEGAARD, Darya CHUDOVA, Kyle Lik Ming CHANG, Han-Yu CHUANG, Daniel GAILE
Filed: 4 Mar 22
Utility
Locked Nucleic Acids for Capturing Fusion Genes
29 Dec 22
Provided herein is a method for enriching a sample for polynucleotides comprising a breakpoint of a fusion gene, comprising: a) contacting a probe set comprising a plurality of polynucleotide probes, each probe configured to specifically hybridize to a fusion gene, wherein the set comprises one or more high affinity polynucleotide probes (e.g., a polynucleotide comprising one or more locked nucleic acid nucleotides), with a mixture of polynucleotides under hybridization conditions to produce probe-captured polynucleotides; and b) isolating the probe-captured polynucleotides from the mixture, to produce a sample enriched with polynucleotides comprising breakpoint fragments of the fusion gene.
Stefanie Ann Ward MORTIMER
Filed: 14 Mar 22
Utility
Determining Cell Type Origin of Circulating Cell-free Dna with Molecular Counting
22 Dec 22
Provided herein are compounds, methods, and compositions for use in determining the cellular origin of circulating cell-free DNA.
Matthew William SNYDER
Filed: 28 Feb 22
Utility
Machine learning for somatic single nucleotide variant detection in cell-free tumor nucleic acid sequencing applications
13 Dec 22
Systems and methods are disclosed to detect single-nucleotide variations (SNVs) from somatic sources in a cell-free biological sample of a subject by generating training data with class labels; in computer memory, generating a machine learning unit comprising one output for each of adenine (A), cytosine (C), guanine (G), and thymine (T) calls; training the machine learning unit; and applying the machine learning unit to detect the SNVs from somatic sources in the cell-free biological sample of the subject, wherein the cell-free biological sample comprises a mixture of nucleic acid molecules from somatic and germline sources.
Bahram Ghaffarzadeh Kermani, Helmy Eltoukhy
Filed: 17 Feb 21
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
8 Dec 22
The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides.
AmirAli TALASAZ, Stefanie Ann Ward MORTIMER
Filed: 22 Mar 22
Utility
Methods and systems for analyzing nucleic acid molecules
6 Dec 22
The disclosure provides methods for processing nucleic acid populations containing different forms (e.g., RNA and DNA, single-stranded or double-stranded) and/or extents of modification (e.g., cytosine methylation, association with proteins).
Andrew Kennedy, Stefanie Ann Ward Mortimer, Helmy Eltoukhy, AmirAli Talasaz
Filed: 24 Jun 19
Utility
Methods for computer processing sequence reads to detect molecular residual disease
6 Dec 22
Disclosed herein are methods for use in detection of molecular residual disease.
Stefanie Ann Ward Mortimer, AmirAli Talasaz, Darya Chudova, Helmy Eltoukhy
Filed: 10 Jun 22
Utility
Methods and Systems for Detecting Genetic Variants
1 Dec 22
Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample.
AmirAli TALASAZ, Helmy ELTOUKHY, Stefanie Ann Ward MORTIMER
Filed: 30 Jun 22
Utility
Methods to Determine Tumor Gene Copy Number by Analysis of Cell-free Dna
10 Nov 22
Methods are provided herein to improve automatic detection of copy number variation in nucleic acid samples.
Helmy Eltoukhy, AmirAli Talasaz, Darya Chudova, Diana Abdueva
Filed: 16 Dec 21
Utility
Cancer Evolution Detection and Diagnostic
10 Nov 22
The present disclosure provides methods for determining a probability that after any of a number of therapeutic interventions, an initial state of a subject, such as somatic cell mutational status of a subject with cancer, will develop a subsequent state.
Helmy ELTOUKHY, AmirAli TALASAZ
Filed: 25 Jul 22
Utility
Use of Cell Free Bacterial Nucleic Acids for Detection of Cancer
27 Oct 22
Disclosed herein are compositions and methods for detecting the presence or absence of cancer or a specific cancer type in a subject.
Helmy ELTOUKHY
Filed: 8 Apr 22
Utility
Detecting the Presence of a Tumor Based on Off-target Polynucleotide Sequencing Data
27 Oct 22
In implementations described herein, information derived from a sample that is derived from off-target sequences can be used to determine estimates for the copy number of tumor cells and/or the tumor fraction of a sample.
Catalin BARBACIORU, Darya CHUDOVA, Aliaksandr ARTSIOMENKA, Daniel GAILE, Hao WANG
Filed: 9 Mar 22
Utility
Methods and Systems for Detecting Genetic Variants
13 Oct 22
Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample.
AmirAli TALASAZ, Helmy ELTOUKHY, Stefanie Ann Ward MORTIMER
Filed: 28 Jun 22
Utility
Methods for Computer Processing Sequence Reads to Detect Molecular Residual Disease
13 Oct 22
Disclosed herein are methods for use in detection of molecular residual disease.
Stefanie Ann Ward MORTIMER, AmirAli TALASAZ, Darya CHUDOVA, Helmy ELTOUKHY
Filed: 10 Jun 22
Utility
Systems and methods to detect rare mutations and copy number variation
20 Sep 22
The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides.
AmirAli Talasaz, Stefanie Ann Ward Mortimer
Filed: 13 Oct 20
Utility
Methods for 3′ overhang repair
20 Sep 22
Methods of repairing a partially double-stranded DNA fragment are provided.
Eleen Shum
Filed: 23 Oct 20
Utility
Systems and methods to detect rare mutations and copy number variation
6 Sep 22
The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides.
AmirAli Talasaz, Stefanie Ann Ward Mortimer
Filed: 26 Jun 20