126 patents
Page 5 of 7
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
25 Mar 21
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
Cancer Evolution Detection and Diagnostic
18 Feb 21
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: 3 Sep 20
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
11 Feb 21
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
Detection and Treatment of Disease Exhibiting Disease Cell Heterogeneity and Systems and Methods for Communicating Test Results
11 Feb 21
This disclosure provides, among other things, methods for generating and applying therapeutic interventions.
Helmy ELTOUKHY, AmirAli TALASAZ, Bahram Ghaffarzadeh KERMANI, Nnamdi IHUEGBU
Filed: 21 Aug 20
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
4 Feb 21
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: 12 Oct 20
Utility
Methods and Systems for Improving Patient Monitoring after Surgery
21 Jan 21
In an aspect, a method for detecting the presence or absence of cancer in a subject comprises: (a) obtaining samples from the subject from different time points, wherein a first sample obtained at first time point is a polynucleotide sample from a tumor tissue specimen and a second sample obtained at second time point is a cell-free polynucleotide sample from a blood sample; (b) processing polynucleotides from each of the samples, comprising: i) tagging at least a portion of the polynucleotides, thereby generating tagged parent polynucleotides; ii) amplifying at least a portion of the tagged parent polynucleotides to generate progeny polynucleotides; iii) enriching at least a portion of the progeny polynucleotides for target genomic regions; thereby generating enriched polynucleotides; and iv) sequencing at least a portion of the enriched polynucleotides to generate sequencing reads; and (c) analyzing genomic regions for at least one epigenetic feature from the sequencing reads.
Ariel JAIMOVICH, Yupeng HE, Oscar WESTESSON, William J. GREENLEAF
Filed: 1 Jun 20
Utility
Population Based Treatment Recommender Using Cell Free Dna
16 Dec 20
Systems and methods are disclosed for generating a therapeutic response predict or detecting a disease, by: using a genetic analyzer to generate genetic information; receiving into computer memory a training dataset comprising, for each of a plurality of individuals having a disease, (1) genetic information from the individual generated at first time point and (2) treatment response of the individual to one or more therapeutic interventions determined at a second, later, time point; and implementing a machine learning algorithm using the dataset to generate at least one computer implemented classification algorithm, wherein the classification algorithm, based on genetic information from a subject, predicts therapeutic response of the subject to a therapeutic intervention.
Helmy ELTOUKHY, AmirAli TALASAZ
Filed: 25 Aug 20
Utility
Correcting for Deamination-induced Sequence Errors
2 Dec 20
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: 3 May 20
Utility
Methods and Systems for Adjusting Tumor Mutational Burden by Tumor Fraction and Coverage
25 Nov 20
Provided herein are methods for detecting tumor mutational burden (TMB) in subjects.
Katie Julia QUINN, Elena HELMAN, Darya CHUDOVA
Filed: 29 Jun 20
Utility
Methods and Systems for Detecting Genetic Variants
18 Nov 20
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 Jul 20
Utility
Methods and Systems for Differentiating Somatic and Germline Variants
14 Oct 20
In an aspect, a method of identifying a somatic or germline origin of a nucleic acid variant from a sample of nucleic acid molecules comprises: determining quantitative measures for the nucleic acid variant comprising total allele count and minor allele count for the nucleic acid variant; identifying an associated variable of the nucleic acid variant; determining quantitative value for the associated variable; generating a statistical model for expected germline mutant allele counts at a genomic locus of the nucleic acid variant; generating a probability value (p-value) for the nucleic acid variant based at least in part on the statistical model, the quantitative value, and at least one of the quantitative measures; and classifying the nucleic acid variant as (i) being of somatic origin when the p-value is below a predetermined threshold value, or as (ii) being of germline origin when the p-value is at or above the predetermined threshold value.
Tracy NANCE, Elena HELMAN, Darya CHUDOVA
Filed: 18 Mar 20
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
14 Oct 20
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: 25 Jun 20
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
23 Sep 20
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: 8 Jun 20
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
23 Sep 20
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: 7 May 20
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
16 Sep 20
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: 26 May 20
Utility
Methods of Attaching Adapters to Sample Nucleic Acids
9 Sep 20
Methods of preparing double-stranded nucleic acids with single-stranded overhangs for amplification and sequencing are disclosed.
Andrew KENNEDY, Stefanie Ann Ward MORTIMER
Filed: 20 May 20
Utility
Computational Modeling of Loss of Function Based on Allelic Frequency
26 Aug 20
The disclosure relates to computer technology for precision diagnosis of various states of genetic material such as a gene sequenced from cell-free DNA in a sample.
Catalin BARBACIORU, Marcin SIKORA, Darya CHUDOVA
Filed: 26 Feb 20
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
19 Aug 20
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: 19 Apr 20
Utility
Normalizing Tumor Mutation Burden
19 Aug 20
Values for tumor mutation burden from different samples can be made more comparable to each other or control standards by a normalization regime that takes into account the minor allele fraction of highly rated mutations in a sample.
Darya CHUDOVA
Filed: 3 May 20
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
5 Aug 20
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: 9 Dec 19