126 patents
Utility
Methods and Systems for Predicting an Origin of a Variant
18 Jan 24
Provided herein are methods for differentiating tumor and non-tumor (e.g., clonal hematopoiesis of indeterminate potential (CHIP)) origin nucleic acid variants from one another in a test sample obtained from a test subject at least partially using a computer.
Ross Keating EPPLER
Filed: 22 Feb 23
Utility
Methods and Systems for Detecting Genetic Variants
18 Jan 24
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: 12 May 23
Utility
Methods for Simultaneous Molecular and Sample Barcoding
4 Jan 24
The present application provides methods of sequencing populations of nucleic acids within multiple pooled samples with tracking of individual molecules and their samples of origin.
Andrew KENNEDY
Filed: 27 Jun 23
Utility
Methods and Systems for Improving Patient Monitoring after Surgery
4 Jan 24
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: 28 Oct 22
Utility
Methods for Identifying Druggable Targets and Treating Cancer
4 Jan 24
This disclosure provides methods, sets, and kits for predicting and identifying druggable targets for treating cancer.
Scott R. Bortner
Filed: 17 May 23
Utility
Methods and Systems for Detecting Insertions and Deletions
4 Jan 24
Methods and systems for improving callings of insertions and/or deletions 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 insertion and/or deletion in a sample of polynucleotide molecules.
Marcin Sikora, Mohammad R Mokhtari, Darya Chudova
Filed: 18 Sep 23
Utility
Microsatellite Instability Detection In Cell-free Dna
28 Dec 23
Provided herein are methods for determining the microsatellite instability status of samples.
Aliaksandr ARTSIOMENKA, Marcin SIKORA, Catalin BARBACIORU, Darya CHUDOVA, Martina I. LEFTEROVA
Filed: 25 Aug 23
Utility
Methods of Detecting Genomic Rearrangements Using Cell Free Nucleic Acids
7 Dec 23
Disclosed are methods of detecting the presence or absence of a genomic rearrangement in which a sample of tagged DNA molecules is divided into aliquots.
Anna Vilborg HARTWIG, Jordan Emily Halsig BURKE
Filed: 9 Jan 23
Utility
Detecting Degradation Based on Strand Bias
9 Nov 23
During operation, a computer system may receive information corresponding to identified molecules of deoxyribonucleic acid (DNA) in a tissue sample.
Zachary Scott BOHANNAN
Filed: 9 May 23
Utility
Computational Modeling of Loss of Function Based on Allelic Frequency
9 Nov 23
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: 6 Jul 23
Utility
Methods and Systems for Analyzing Nucleic Acid Molecules
19 Oct 23
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, DIANA ABDUEVA
Filed: 5 Dec 22
Utility
Methods and Systems for Detecting Insertions and Deletions
19 Oct 23
Methods and systems for improving callings of insertions and/or deletions 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 insertion and/or deletion in a sample of polynucleotide molecules.
Marcin Sikora, Mohammad R. Mokhtari, Darya Chudova
Filed: 22 Jun 23
Utility
Compositions and Methods for Isolating Cell-free Dna
12 Oct 23
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: 8 May 23
Utility
Systems and Methods to Detect Rare Mutations and Copy Number Variation
12 Oct 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: 12 Jun 23
Utility
Methods for Sequence Determination Using Partitioned Nucleic Acids
5 Oct 23
DNA damage (e.g., cytosine deamination) can appear more frequently in hypermethylated partitions of DNA (e.g., cell-free DNA) samples, than in hypomethylated partitions.
Carlo ARTIERI, Yu KONG, Ariel JAIMOVICH, Jessica Setsuko KURATA
Filed: 28 Oct 22
Utility
Methods for Early Detection of Cancer
5 Oct 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 Jan 23
Utility
Methods and Systems for Detecting Genetic Variants
31 Aug 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: 12 May 23
Utility
Methods for Multi-resolution Analysis of Cell-free Nucleic Acids
17 Aug 23
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, DIANA ABDUEVA
Filed: 17 Jan 23
Utility
Methods for Multi-resolution Analysis of Cell-free Nucleic Acids
10 Aug 23
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, DIANA ABDUEVA
Filed: 14 Nov 22
Utility
Methods for 3' Overhang Repair
6 Jul 23
Methods of repairing a partially double-stranded DNA fragment are provided.
Eleen SHUM
Filed: 15 Jun 22