126 patents
Page 6 of 7
Utility
Compositions and Methods for Isolating Cell-free Dna
5 Aug 20
Disclosed herein are compositions and methods for isolating DNA, such as cell-free DNA (cfDNA).
Andrew KENNEDY, Ariel JAIMOVICH, Matthew SCHULTZ, William J. GREENLEAF
Filed: 30 Jan 20
Utility
Methods, Compositions, and Systems for Improving Recovery of Nucleic Acid Molecules
22 Jul 20
In an aspect, the present disclosure provides a method for analyzing nucleic acid molecules in a sample of polynucleotides, comprising: (a) adding a subset of fragment size control molecules to the nucleic acid molecules, thereby producing a first spike-in sample; (b) extracting nucleic acids from the first spike-in sample; (c) processing at least a subset of the extracted nucleic acids, thereby producing a processed sample, wherein the processing comprises partitioning, tagging, and/or amplifying at least a subset of the first spike-in sample; (d) enriching for at least a subset of the processed sample, thereby producing an enriched sample; (e) sequencing at least a subset of the enriched sample to generate sequence reads; (0 analyzing the sequence reads to generate fragment size scores of the subset of fragment size control molecules; and (g) comparing the fragment size scores with fragment size thresholds.
Stefanie Ann Ward MORTIMER, Dustin Howard HITE, Laura Michelle MELROY
Filed: 19 Dec 19
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
15 Jul 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: 11 Dec 19
Utility
Determination of a Physiological Condition with Nucleic Acid Fragment Endpoints
24 Jun 20
Methods for diagnosis of one or more physiological conditions using cfDNAs are disclosed.
Matthew William SNYDER, Jason Thaddeus DEAN
Filed: 16 Dec 19
Utility
Identification of Somatic or Germline Origin for Cell-free Dna
24 Jun 20
The present disclosure provides systems and methods to detect somatic or germline variants from cell-free DNA (cfDNA).
Richard B. LANMAN, Geoffrey R. OXNARD
Filed: 7 Nov 19
Utility
Methods for Multi-resolution Analysis of Cell-free Nucleic Acids
10 Jun 20
The present disclosure provides a method for enriching for multiple genomic regions using a first bait set that selectively hybridizes to a first set of genomic regions of a nucleic acid sample and a second bait set that selectively hybridizes to a second set of genomic regions of the nucleic acid sample.
Darya CHUDOVA, Helmy ELTOUKHY, Stefanie Ann Ward MORTIMER
Filed: 17 Dec 19
Utility
Methods to Determine Tumor Gene Copy Number by Analysis of Cell-free Dna
6 May 20
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: 7 Jan 20
Utility
Methods, Compositions and Systems for Calibrating Epigenetic Partitioning Assays
29 Apr 20
In an aspect, a method for evaluating the partitioning of nucleic acid molecules in a sample of polynucleotides based on epigenetic state, comprising: (a) adding a set of epigenetic-control nucleic acid molecules to the nucleic acid molecules in the sample of polynucleotides, whereby producing a spiked-in sample; (b) partitioning nucleic acid molecules of the spiked-in sample into plurality of partitioned sets; (c) enriching a subset of molecules from the plurality of partitioned sets to generate enriched molecules, wherein the enriched molecules comprises a group of epigenetic-control nucleic acid molecules and a group of nucleic acid molecules from the sample of polynucleotides; (d) sequencing the enriched molecules to produce sequencing reads; (e) analyzing the sequencing reads to generate one or more epigenetic partition scores of the epigenetic-control nucleic acid molecules; and (f) comparing the one or more epigenetic partition scores with one or more epigenetic partition cut-offs.
Andrew KENNEDY, Oscar WESTESSON, Yupeng He, Matthew SCHULTZ
Filed: 30 Oct 19
Utility
Methods of Attaching Adapters to Sample Nucleic Acids
29 Apr 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: 7 Oct 19
Utility
Methods and Systems for Detecting Genetic Variants
29 Apr 20
Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample.
AmirAli TALASAZ, Stefanie Ann Ward MORTIMER
Filed: 12 Dec 19
Utility
Methods and Systems for Detecting Genetic Variants
22 Apr 20
Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample.
Helmy ELTOUKHY, AmirAli Talasaz, Stefanie Ann Ward Mortimer
Filed: 13 Oct 19
Utility
Methods and Systems for Detecting Genetic Variants
15 Apr 20
Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample.
AmirAli TALASAZ, Stetanie Ann Ward Mortimer
Filed: 6 Jan 20
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
15 Apr 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: 3 Oct 19
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
18 Mar 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: 17 Sep 19
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
18 Mar 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: 3 Oct 19
Utility
Methods and Systems for Detecting Contamination Between Samples
4 Mar 20
Provided herein are various methods and related systems for detecting the presence/absence of contamination of a first sample with a second sample.
Darya CHUDOVA, Helmy ELTOUKHY, Stephen FAIRCLOUGH, Narsi RAJAGOPALAN, Marcin SIKORA
Filed: 29 Aug 19
Utility
Genetic Variant Detection Based on Merged and Unmerged Reads
4 Mar 20
Methods and systems for improving identification of nucleic acid variants by identifying genetic sequence reads having identical molecular barcodes and sequences among sequence reads from a nucleic acid sequencer, grouping the genetic reads into a family, and processing families comprising split reads to detect the variants in a sample of polynucleotide molecules.
Darya CHUDOVA, Mohammad Reza MOKHTARI
Filed: 2 Sep 19
Utility
Methods and Systems for Detecting Allelic Imbalance In Cell-free Nucleic Acid Samples
4 Mar 20
The present disclosure provides methods and systems for detecting an allelic imbalance in a sample from a subject, comprising: (a) sequencing cell-free DNA molecules from the sample to generate sequence reads; (b) aligning at least a portion of the sequence reads to a reference sequence to produce aligned sequence reads; (c) for at least a portion of the plurality of aligned sequence reads, identifying a germline variant present at a mutant allele fraction (MAF) in the sample, thereby identifying a set of germline variants in the sample, wherein individual germline variants in the set of germline variants have corresponding MAF values; (d) determining a quantitative measure of the set of germline variants that are among a plurality of discrete ranges of MAF values; and (e) detecting the allelic imbalance based on a predetermined criterion by filtering the set of germline variants based on at least the quantitative measure.
Jing Zhao, Stephen FAIRCLOUGH, Tracy NANCE, Jie YIN
Filed: 3 Sep 19
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
29 Jan 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: 17 Sep 19
Utility
Methods for Detecting and Suppressing Alignment Errors Caused by Fusion Events
15 Jan 20
Methods and systems for producing a filtered read sequence information data set by identifying one or more split sequence reads in a set of test sequence reads obtained from cell-free nucleic acid (cfNA) in a biological sample obtained from a subject, wherein each split sequence read comprises at least one breakpoint; and, suppressing, in the set of test sequence reads, (i) at least a portion of one or more of the split sequence reads and/or at least a portion of one or more of the test sequence reads that comprise at least one sequence variant within a selected number of nucleotides from a given breakpoint, thereby producing the filtered sequence information data set, or, (ii) one or more base calls of the split sequence reads and/or one or more base calls of the test sequence reads that comprise at least one sequence variant within a selected number of nucleotides from a given breakpoint, thereby producing the filtered sequence information data set.
Carlo ARTIERI, Marcin SIKORA
Filed: 11 Apr 19