71 patents
Page 4 of 4
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
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
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
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
Inferring Selection In White Blood Cell Matched Cell-free Dna Variants And/or In Rna Variants
20 Nov 19
Methods and systems for detecting positive, neutral, or negative selection at a locus include obtaining a test sample of cell-free nucleic acids from a subject, preparing a sequencing library of the cell-free nucleic acids, sequencing the library to obtain a plurality of sequence reads, analyzing the sequence reads to detect and quantify one or more somatic mutations at the locus, determining a selection coefficient for the locus, and comparing the selection coefficient with a threshold value to detect positive, neutral, or negative selection at the locus.
Oliver Claude Venn, Earl Hubbell
Filed: 19 May 19
Utility
Methods and Systems for High Fidelity Sequencing
6 Nov 19
Systems and methods for high fidelity sequencing and identification of rare mutations at dilute concentrations in a sample are described herein.
Oliver Claude Venn, Alexander Tilo Dilthey
Filed: 21 Jan 17
Utility
Size-tagged Preferred Ends and Orientation-aware Analysis for Measuring Properties of Cell-free Mixtures
6 Nov 19
Various applications can use fragmentation patterns related of cell-free DNA, e.g., plasma DNA and serum DNA.
Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Kun Sun
Filed: 2 May 19
Utility
Multi-Assay Prediction Model for Cancer Detection
16 Oct 19
A predictive cancer model generates a cancer prediction for an individual of interest by analyzing values of one or more types of features that are derived from cfDNA obtained from the individual.
Earl Hubbell, Samuel S. Gross, Darya Filippova, Ling Shen, Oliver Claude Venn, Alexander Weaver Blocker, Nan Zhang, Tara Maddala, Alex Aravanis, Qinwen Liu, Anton Valouev, Virgil Nicula
Filed: 14 Apr 19