84 patents
Page 4 of 5
Utility
Anomalous Fragment Detection and Classification
29 Jul 20
A system and method for determining a presence of cancer in a test sample from a test subject comprising a set of fragments of deoxyribonucleic acid (DNA).
Samuel S. Gross, Oliver Claude Venn, Alexander P. Fields, Gordon Cann, Arash Jamshidi
Filed: 19 Dec 19
Utility
Source of Origin Deconvolution Based on Methylation Fragments In Cell-free Dna Samples
29 Jul 20
A method and system for determining one or more sources of a cell free deoxyribonucleic acid (cfDNA) test sample from a test subject.
Alexander P. Fields, Oliver Claude Venn, Gordon Cann, Samuel S. Gross, Arash Jamshidi
Filed: 19 Dec 19
Utility
Systems and Methods for Using Fragment Lengths As a Predictor of Cancer
8 Jul 20
Systems and methods are provided for determining relevant medical information about a cancer based on the distribution of fragment lengths of cell-free DNA sequenced from a biological fluid sample.
Earl Hubbell
Filed: 19 Dec 19
Utility
Methods for Detecting Disease Using Analysis of Rna
24 Jun 20
Methods for measuring subpopulations of ribonucleic acid (RNA) molecules are provided.
Wenying Pan, Matthew Larson, H. John Kim, Arash Jamshidi
Filed: 17 Dec 19
Utility
Cell-free Dna End Characteristics
24 Jun 20
The present disclosure describes techniques for measuring quantities (e.g., relative frequencies) of sequence end motifs of cell-free DNA fragments in a biological sample of an organism for measuring a property of the sample (e.g., fractional concentration of clinically-relevant DNA) and/or determining a condition of the organism based on such measurements.
Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Wing Yan Chan, Kun Sun
Filed: 18 Dec 19
Utility
Cancer Tissue Source of Origin Prediction with Multi-tier Analysis of Small Variants In Cell-free Dna Samples
24 Jun 20
A predictive cancer model generates a prediction of cancer tissue source of origin for a subject of interest by analyzing values of one or more types of features that are derived from cfDNA obtained from the individual.
Earl Hubbell, Qinwen Liu
Filed: 17 Dec 19
Utility
Needle-based Devices and Methods for In Vivo Diagnostics of Disease Conditions
10 Jun 20
Diagnostic devices and methods are provided for screening for a disease condition, include a cancer condition or a mendelian disease.
M. Cyrus Maher
Filed: 14 Nov 19
Utility
Systems and Methods for Classifying Patients with Respect to Multiple Cancer Classes
10 Jun 20
Technical solutions for classifying patients with respect to multiple cancer classes are provided.
M. Cyrus Maher, Anton Valouev, Darya Filippova, Virgil Nicula, Karthik Jagadeesh, Oliver Claude Venn, Samuel S. Gross, John F. Beausang, Robert Abe Paine Calef
Filed: 9 Dec 19
Utility
Diagnostic applications using nucleic acid fragments
27 Apr 20
Various embodiments are directed to applications (e.g., classification of biological samples) of the analysis of the count, the fragmentation patterns, and size of cell-free nucleic acids, e.g., plasma DNA and serum DNA, including nucleic acids from pathogens, such as viruses.
Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Wai Kei Lam
Filed: 24 Jan 18
Utility
Methods of analyzing nucleic acid fragments
20 Apr 20
Provided herein are methods for enriching a biological sample for a target nucleic acid, and analyzing the nucleic acid.
Eugeni Namsaraev, Maneesh Jain
Filed: 9 Aug 17
Utility
Models for Targeted Sequencing of Rna
1 Apr 20
Systems and methods for processing sequencing data of ribonucleic acid (RNA) molecules from a test sample include obtaining a plurality of sequence reads each derived from a RNA molecule obtained from the test sample, filtering the plurality of sequence reads, identifying one or more candidate variants from the filtered plurality of sequence reads, determining a quality score for each of the identified one or more candidate variants, the quality score indicating a likelihood that the candidate variant is a false positive detection of a mutation in the RNA molecule, and outputting the one or more candidate variants having a quality score greater than a threshold quality score.
WENYING PAN, HYUNSUNG JOHN KIM, MATTHEW H. LARSON, ALEXANDER W. BLOCKER, EARL HUBBELL, ARASH JAMSHIDI
Filed: 25 Sep 19
Utility
Mixture Model for Targeted Sequencing
1 Apr 20
Systems and methods for determining a source of a variant in a cell free nucleic acid sample include identifying a candidate variant in the cell free nucleic acid sample, determining a numerical score using a measure of first properties of a distribution of novel somatic mutations compared to a measure of second properties of a distribution of somatic variants matched in genomic nucleic acid, and determining a classification of the candidate variant using the numerical score, the classification indicating whether the candidate variant is more likely to be a new novel somatic mutation than a new somatic variant matched in genomic nucleic acid.
EARL HUBBELL, ARCHANA S. SHENOY
Filed: 22 Sep 19
Utility
Methods of Preparing and Analyzing Cell-free Nucleic Acid Sequencing Libraries
19 Feb 20
Aspects of the invention relate to methods for preparing and analyzing a sequencing library from a mixed cell-free DNA (cfDNA) sample, wherein the mixed sample includes double-stranded DNA (dsDNA), damaged dsDNA (e.g., nicked dsDNA), and single-stranded DNA (ssDNA) molecules.
Matthew H. Larson, Hyunsung John Kim, Nick Eattock, Xiao Yang
Filed: 23 Oct 19
Utility
Cell-free Dna Damage Analysis and Its Clinical Applications
19 Feb 20
Cell-free DNA fragments often include jagged ends, where one end of one strand of double-stranded DNA extends beyond the other end of the other strand.
Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Suk Hang Cheng
Filed: 22 Jul 19
Utility
Machine Learning Variant Source Assignment
8 Jan 20
Systems and methods for determining a source of a variant include receiving a plurality of variants obtained from a biological sample, the variants being of unknown source upon receipt, and receiving, for each of the variants, a plurality of values for a plurality of covariates from the biological sample.
Archana Shenoy, Earl Hubbell
Filed: 1 Jul 19
Utility
Methods for Managing Sequencing Pileups
8 Jan 20
In comparison to conventional sequencing pileup algorithms, the process described herein generates sequencing pileups that contains additional information not typically reported by conventional algorithms while also consuming fewer computational resources (e.g., time, processing power, and memory).
Christopher Chang
Filed: 10 Jun 19
Utility
Nucleic Acid Rearrangement and Integration Analysis
1 Jan 20
Provided herein are methods and systems for identifying chimeric nucleic acid fragments, e.g., organism-pathogen chimeric nucleic acid fragments and chromosomal rearrangement chimeric nucleic acid fragments.
Yuk-Ming Dennis LO, Rossa Wai Kwun CHIU, Kwan Chee CHAN, Peiyong JIANG, Wai Kei LAM, Haiqiang ZHANG
Filed: 27 Jun 19
Utility
Convolutional Neural Network Systems and Methods for Data Classification
1 Jan 20
Classification of cancer condition, in a plurality of different cancer conditions, for a species, is provided in which, for each training subject in a plurality of training subjects, there is obtained a cancer condition and a genotypic data construct including genotypic information for the respective training subject.
Virgil Nicula, Anton Valouev, Darya Filippova, Matthew H. Larson, M. Cyrus Maher, Monica Portela dos Santos Pimentel, Robert Abe Paine Calef, Collin Melton
Filed: 30 May 19
Utility
Tissue-specific Methylation Marker
25 Dec 19
Provided herein are compositions comprising tissue-specific markers for identifying a tissue of origin of a cell-free nucleic acid, e.g., a cell-free DNA molecule.
Yuk-Ming Dennis LO, Rossa Wai Kwun CHIU, Kwan Chee CHAN, Wanxia GAI, Lu Ji
Filed: 14 Mar 19
Utility
Methods of preparing and analyzing cell-free nucleic acid sequencing libraries
25 Nov 19
Aspects of the invention relate to methods for preparing and analyzing a sequencing library from a mixed cell-free DNA (cfDNA) sample, wherein the mixed sample includes double-stranded DNA (dsDNA), damaged dsDNA (e.g., nicked dsDNA), and single-stranded DNA (ssDNA) molecules.
Matthew H. Larson, Hyunsung John Kim, Nick Eattock, Xiao Yang
Filed: 21 Sep 17