126 patents
Page 3 of 7
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
30 Jun 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
Filed: 16 Mar 22
Utility
Methods for Isolating Cell-free Dna
23 Jun 22
Disclosed herein are methods for isolating DNA, such as cell-free DNA (cfDNA) or DNA from a tissue sample, e.g., in which the DNA is partitioned into hypermethylated and hypomethylated partitions.
Ariel JAIMOVICH, Sven Jeffrey DUENWALD, Peter Vilem GRAUMAN, Yupeng HE, Charbel Said EID, Haley Dara AXELROD
Filed: 29 Jul 21
Utility
Machine Learning for Somatic Single Nucleotide Variant Detection in Cell-free Tumor Nucleic acid Sequencing Applications
23 Jun 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: 14 Mar 22
Utility
Methods for Early Detection of Cancer
16 Jun 22
Disclosed herein are methods for use in detection of single nucleotide variants (SNVs) or indels.
Stefanie Ann Ward MORTIMER, AmirAli TALASAZ, Darya CHUDOVA, Helmy ELTOUKHY
Filed: 7 Mar 22
Utility
CorrectedSystems and Methods to Detect Rare Mutations and Copy Number Variation
2 Jun 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: 12 Dec 19
Utility
Methods and Systems to Improve the Signal to Noise Ratio of Dna Methylation Partitioning Assays
26 May 22
In an aspect, the present disclosure provides a method for determining a methylation status comprises: providing a biological sample of nucleic acid molecules; partitioning at least a subset of the nucleic acid molecules in the biological sample based on the methylation status of the nucleic acid molecules into a plurality of partitioned sets; digesting at least a subset of the one or more partitioned sets in the plurality of partitioned sets with at least one methylation sensitive restriction enzyme; enriching at least a subset of the nucleic acid molecules in the plurality of partitioned sets for genomic regions of interest, wherein the at least a subset of the nucleic acid molecules comprises digested nucleic acid molecules in the one or more partitioned sets; and determining methylation status at one or more genetic loci of the nucleic acid molecules in at least one of the partitioned sets.
Andrew KENNEDY, William J. GREENLEAF
Filed: 29 Sep 21
Utility
Methods and Systems for Detecting Genetic Variants
12 May 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 Dec 21
Utility
Methods and Systems for Detecting Genetic Variants
21 Apr 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
Filed: 28 Dec 21
Utility
Methods and Systems for Adjusting Tumor Mutational Burden by Tumor Fraction and Coverage
31 Mar 22
Provided herein are methods for detecting tumor mutational burden (TMB) in subjects.
Katie Julia QUINN, Elena HELMAN, Darya CHUDOVA
Filed: 28 Jul 21
Utility
Computational Detection of Copy Number Variation at a Locus In the Absence of Direct Measurement of the Locus
3 Mar 22
Methods and systems are described for improving detection of copy number loss of a locus of interest without requiring direct measurement of the locus of interest.
Stephen FAIRCLOUGH
Filed: 27 Aug 21
Utility
Methods and Systems for Detecting Genetic Variants
17 Feb 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
Filed: 27 Oct 21
Utility
Methods and Systems for Detecting Genetic Variants
17 Feb 22
AmirAli TALASAZ, Helmy ELTOUKHY, Stefanie Ann Ward MORTIMER
Filed: 27 Oct 21
Utility
Methods for Detecting Single Nucleotide Variants or Indels by Deep Sequencing
17 Feb 22
Disclosed herein are methods for use in detection of single nucleotide variants (SNVs) or indels.
Stefanie Ann Ward MORTIMER, AmirAli TALASAZ, Darya CHUDOVA, Helmy ELTOUKHY
Filed: 21 Oct 21
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
10 Feb 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
Filed: 23 Mar 21
Utility
Homologous Recombination Repair Deficiency Detection
27 Jan 22
Provided herein are methods of generating a homologous recombination repair deficiency (HRD) score, determining a reference HRD score, determining a HRD status of a test subject having one or more cancer types, and/or treating a disease based on HRD status.
Jennifer YEN, Elena HELMAN, Arielle YABLONOVITCH
Filed: 14 May 21
Utility
Methods for Computer Processing Sequence Reads to Detect Molecular Residual Disease
27 Jan 22
Disclosed herein are methods for use in detection of molecular residual disease.
Stefanie Ann Ward MORTIMER, AmirAli TALASAZ, Darya CHUDOVA, Helmy ELTOUKHY
Filed: 2 Jul 21
Utility
Methods and Systems for Determining the Cellular Origin of Cell-free Dna
27 Jan 22
Provided herein are methods for determining the cellular origin of cell-free DNA.
OSCAR WESTESSON, ELENA ZOTENKO
Filed: 19 Aug 21
Utility
Determining Tumor Fraction for a Sample Based on Methyl Binding Domain Calibration Data
30 Dec 21
The application is directed to systems and processes to determine an estimate for tumor fraction of a sample.
Oscar WESTESSON, Yupeng He, William J. GREENLEAF, Ariel JAIMOVICH, AmirAli TALASAZ
Filed: 31 Mar 21
Utility
Methods and Systems for Detecting Genetic Variants
23 Dec 21
Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample.
AmirAli TALASAZ, Helmy ELTOUKHY
Filed: 24 Aug 21
Utility
Correcting for Deamination-induced Sequence Errors
23 Dec 21
Sequencing nucleic acids can identify variations associated with presence, susceptibility or prognosis of disease.
Marcin SIKORA, Andrew KENNEDY, Ariel JAIMOVICH, Darya CHUDOVA, Stephen FAIRCLOUGH
Filed: 23 Mar 21