Patents by Inventor Hei-Mun Christina Fan

Hei-Mun Christina Fan has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Publication number: 20240052405
    Abstract: Systems, methods, and compositions for generating a high-resolution spatial map of a distribution of targets of a sample are described. Processes for generating the spatial map can include: receiving the sample at a substrate having a distribution of functionalized particles, each having a stochastic barcode sequence paired with a position on the substrate; promoting interactions between the distribution of targets of the sample and the distribution of functionalized particles upon transmitting heat to a surface of the substrate opposite the distribution of functionalized particles; applying a set of reactions to the sample at the substrate, obtaining a set of sequences of a population of molecules generated from the set of reactions, the set of sequences associated with the distribution of targets labeled using the stochastic barcode sequences of the distribution of functionalized particles, and returning a set of positions of the distribution of targets upon processing the set of sequences.
    Type: Application
    Filed: October 23, 2023
    Publication date: February 15, 2024
    Inventors: Hei Mun Christina FAN, Stephen P.A. FODOR
  • Patent number: 11834714
    Abstract: The disclosure provides compositions, methods, and systems for implementation of highly multiplexed molecular diagnostic assays involving color combinatorics, stimulus-responsive probes, tandem probes, conjugated polymer probes, and other mechanisms for increasing the number of targets that can be simultaneously detected in a digital assay. Multiplexed detection of targets is achieved in a rapid manner, with respect to sample partitioning and target detection using multiple color channels for detection. Implementation of methods described also achieve detection with significantly improved signal-to-noise ratio (SNR) values.
    Type: Grant
    Filed: December 20, 2022
    Date of Patent: December 5, 2023
    Assignee: ENUMERIX, INC.
    Inventors: Eleen Yee Lam Shum, Hei Mun Christina Fan, Stephen P. A. Fodor, Janice Hoiyi Lai, Jung Won Keum, Haeun Grace Lee
  • Patent number: 11814619
    Abstract: This disclosure provides for devices, methods, and systems for generating a plurality of droplets within a collecting container at an extremely high rate (e.g., of at least 1 million droplets per minute, etc.), the plurality of droplets generated from an aqueous mixture comprising a set of single cells and a set of functionalized particles configured for a single cell assay. Upon generation, the plurality of droplets can be stabilized in position within a region of the collecting container, thereby providing a single-tube workflow for single cell analyses. Further, compositions implemented are structured to allow for overloading of partitions with functionalized particles, such that partitioned single-cells are co-localized with a subset of functionalized particles in a manner that allows for discernable tagging and downstream analyses.
    Type: Grant
    Filed: June 7, 2022
    Date of Patent: November 14, 2023
    Assignee: ENUMERIX, INC.
    Inventors: Eleen Yee Lam Shum, Janice Hoiyi Lai, Hei Mun Christina Fan, Stephen P. A. Fodor
  • Publication number: 20230348898
    Abstract: This disclosure provides for devices, methods, and systems for generating a plurality of droplets within a collecting container at an extremely high rate (e.g., of at least 1 million droplets per minute, etc.), the plurality of droplets generated from an aqueous mixture comprising a set of single cells and a set of functionalized particles configured for a single cell assay. Upon generation, the plurality of droplets can be stabilized in position within a region of the collecting container, thereby providing a single-tube workflow for single cell analyses. Further, compositions implemented are structured to allow for overloading of partitions with functionalized particles, such that partitioned single-cells are co-localized with a subset of functionalized particles in a manner that allows for discernable tagging and downstream analyses.
    Type: Application
    Filed: July 6, 2023
    Publication date: November 2, 2023
    Inventors: Eleen Yee Lam Shum, Janice Hoiyi Lai, Hei Mun Christina Fan, Stephen P. A. Fodor
  • Publication number: 20230287503
    Abstract: The present methods are exemplified by a process in which maternal blood containing fetal DNA is diluted to a nominal value of approximately 0.5 genome equivalent of DNA per reaction sample. Digital analysis is then be used to detect aneuploidy, such as the trisomy that causes Down Syndrome. Since aneuploidies do not present a mutational change in sequence, and are merely a change in the number of chromosomes, it has not been possible to detect them in a fetus without resorting to invasive techniques such as amniocentesis or chorionic villi sampling. Digital amplification allows the detection of aneuploidy using massively parallel amplification and detection methods, examining, e.g., 10,000 genome equivalents.
    Type: Application
    Filed: April 26, 2023
    Publication date: September 14, 2023
    Applicant: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Stephen QUAKE, Hei-Mun Christina FAN
  • Publication number: 20230287482
    Abstract: The inventions cover systems and methods for generation of emulsions having suitable clarity without requiring refractive index matching between emulsion components. Systems can include: a substrate including a set of openings; a reservoir facing the substrate at a first side and containing a sample fluid configured for droplet formation upon interacting with the set of openings of the substrate; and a collecting container facing the substrate at a second side and containing a set of fluid layers configured with a density gradient and suitable immiscibility characteristics. One or more components of the system(s) can support methods for emulsion generation, in relation to enabling interactions between multiple continuous phases and a dispersed droplet phase to generate clear emulsions. Applications of the inventions(s) can include performance of droplet-based digital PCR in an improved manner (e.g., without requiring implementation of correction factors based upon Poisson statistics).
    Type: Application
    Filed: November 11, 2022
    Publication date: September 14, 2023
    Inventors: Hei Mun Christina FAN, Eleen Yee Lam SHUM, Janice Hoiyi LAI, Stephen P. A. FODOR
  • Publication number: 20230250477
    Abstract: The invention generally relates to methods for assessing the health of a tissue by characterizing circulating nucleic acids in a biological sample. According to certain embodiments, methods for assessing the health of a tissue include the steps of detecting a sample level of RNA in a biological sample, comparing the sample level of RNA to a reference level of RNA specific to the tissue, determining whether a difference exists between the sample level and the reference level, and characterizing the tissue as abnormal if a difference is detected.
    Type: Application
    Filed: April 18, 2023
    Publication date: August 10, 2023
    Inventors: Lian Chye Winston Koh, Stephen R. Quake, Hei-Mun Christina Fan, Wenying Pan
  • Publication number: 20230212561
    Abstract: The disclosure provides compositions, methods, and systems for extremely accurate generation of nucleic acid libraries, without use of bulk amplification methods. Accurate library preparation is achieved in a rapid manner, with respect to sample partitioning and amplification in a manner that achieves high performance in relation to low levels of amplification bias and low levels of artifact/chimeric sequence generation. Implementation of methods described also achieve library preparation with significantly reduced false positive rates, across a wide variety of applications.
    Type: Application
    Filed: January 5, 2023
    Publication date: July 6, 2023
    Inventors: Eleen Yee Lam SHUM, Hei Mun Christina FAN, Stephen P.A. FODOR
  • Publication number: 20230212659
    Abstract: The invention(s) cover a composition, where units of the composition are configured to interact with each other (e.g., as neighbors) in order enable decoding of positions of captured target material relative to neighboring units of the composition. In embodiments, the composition includes: a body; and a set of molecules coupled to the body, the set of molecules comprising a first subset and a second subset, wherein the first subset is structured for target analyte capture, and wherein the second subset is structured for interactions with one or more neighboring objects. The invention(s) also cover systems incorporating one or more units of the composition and methods implementing units of the composition.
    Type: Application
    Filed: March 9, 2023
    Publication date: July 6, 2023
    Inventors: Hei Mun Christina Fan, Stephen P. A. Fodor
  • Patent number: 11692225
    Abstract: The present methods are exemplified by a process in which maternal blood containing fetal DNA is diluted to a nominal value of approximately 0.5 genome equivalent of DNA per reaction sample. Digital analysis is then be used to detect aneuploidy, such as the trisomy that causes Down Syndrome. Since aneuploidies do not present a mutational change in sequence, and are merely a change in the number of chromosomes, it has not been possible to detect them in a fetus without resorting to invasive techniques such as amniocentesis or chorionic villi sampling. Digital amplification allows the detection of aneuploidy using massively parallel amplification and detection methods, examining, e.g., 10,000 genome equivalents.
    Type: Grant
    Filed: August 3, 2018
    Date of Patent: July 4, 2023
    Assignee: THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY
    Inventors: Stephen Quake, Hei-Mun Christina Fan
  • Publication number: 20230193385
    Abstract: The disclosure provides compositions, methods, and systems for implementation of highly multiplexed molecular diagnostic assays involving color combinatorics, stimulus-responsive probes, tandem probes, conjugated polymer probes, and other mechanisms for increasing the number of targets that can be simultaneously detected in a digital assay. Multiplexed detection of targets is achieved in a rapid manner, with respect to sample partitioning and target detection using multiple color channels for detection. Implementation of methods described also achieve detection with significantly improved signal-to-noise ratio (SNR) values.
    Type: Application
    Filed: December 20, 2022
    Publication date: June 22, 2023
    Inventors: Eleen Yee Lam SHUM, Hei Mun Christina FAN, Stephen P.A. FODOR, Janice Hoiyi LAI, Jung Won KEUM, Haeun Grace LEE
  • Patent number: 11624088
    Abstract: The invention(s) cover a composition, where units of the composition are configured to interact with each other (e.g., as neighbors) in order enable decoding of positions of captured target material relative to neighboring units of the composition. In embodiments, the composition includes: a body; and a set of molecules coupled to the body, the set of molecules comprising a first subset and a second subset, wherein the first subset is structured for target analyte capture, and wherein the second subset is structured for interactions with one or more neighboring objects. The invention(s) also cover systems incorporating one or more units of the composition and methods implementing units of the composition.
    Type: Grant
    Filed: July 15, 2021
    Date of Patent: April 11, 2023
    Assignee: 13.8, Inc.
    Inventors: Hei Mun Christina Fan, Stephen P. A. Fodor
  • Publication number: 20230074085
    Abstract: This disclosure provides for devices, methods, and systems for performing a non-invasive prenatal testing (NIPT) digital assay upon generating at least a large number of counts per chromosome for a set of chromosomes present in a sample, where performing the NIPT digital assay can include: distributing nucleic acids of the sample and materials for an amplification reaction across a plurality of partitions; amplifying the nucleic acids with the materials, within the plurality of partitions; and generating counts per chromosome upon detecting signals from the plurality of partitions. The inventions enable processing of samples for NIPT digital analyses and/or other digital analyses involving other loci of interest, with unprecedented partitioning, reaction, readout, and analytical performance.
    Type: Application
    Filed: September 7, 2022
    Publication date: March 9, 2023
    Inventors: Eleen Yee Lam Shum, Hei Mun Christina Fan, Stephen P. A. Fodor, Haeun Grace LEE
  • Publication number: 20230057339
    Abstract: Systems, methods, and compositions for generating a high-resolution spatial map of a distribution of targets of a sample are described. Processes for generating the spatial map can include: receiving the sample at a substrate having a distribution of functionalized particles, each having a stochastic barcode sequence paired with a position on the substrate; promoting interactions between the distribution of targets of the sample and the distribution of functionalized particles upon transmitting heat to a surface of the substrate opposite the distribution of functionalized particles; applying a set of reactions to the sample at the substrate, obtaining a set of sequences of a population of molecules generated from the set of reactions, the set of sequences associated with the distribution of targets labeled using the stochastic barcode sequences of the distribution of functionalized particles, and returning a set of positions of the distribution of targets upon processing the set of sequences.
    Type: Application
    Filed: August 25, 2022
    Publication date: February 23, 2023
    Inventors: Stephen P.A. Fodor, Hei Mun Christina Fan, Anaram Shahravan, Christina Chang, Jay Levine
  • Patent number: 11542546
    Abstract: The inventions cover systems and methods for generation of emulsions having suitable clarity without requiring refractive index matching between emulsion components. Systems can include: a substrate including a set of openings; a reservoir facing the substrate at a first side and containing a sample fluid configured for droplet formation upon interacting with the set of openings of the substrate; and a collecting container facing the substrate at a second side and containing a set of fluid layers configured with a density gradient and suitable immiscibility characteristics. One or more components of the system(s) can support methods for emulsion generation, in relation to enabling interactions between multiple continuous phases and a dispersed droplet phase to generate clear emulsions. Applications of the inventions(s) can include performance of droplet-based digital PCR in an improved manner (e.g., without requiring implementation of correction factors based upon Poisson statistics).
    Type: Grant
    Filed: February 16, 2022
    Date of Patent: January 3, 2023
    Assignee: Enumerix, Inc.
    Inventors: Hei Mun Christina Fan, Eleen Yee Lam Shum, Janice Hoiyi Lai, Stephen P. A. Fodor
  • Publication number: 20220411857
    Abstract: Described herein are methods for amplifying and detecting a specific nucleic acid in a nucleic acid sample. The methods may comprise amplifying a target nucleic acid and detecting the target nucleic acid in the presence of a fluorescent probe and a probe complement. Also described herein are probe complements for detecting specific nucleic acid sequences with reduced background fluorescence.
    Type: Application
    Filed: June 9, 2022
    Publication date: December 29, 2022
    Inventors: Hei Mun Christina FAN, Eleen Yee Lam SHUM
  • Publication number: 20220389410
    Abstract: This disclosure provides for devices, methods, and systems for generating a plurality of droplets within a collecting container at an extremely high rate (e.g., of at least 1 million droplets per minute, etc.), the plurality of droplets generated from an aqueous mixture comprising a set of single cells and a set of functionalized particles configured for a single cell assay. Upon generation, the plurality of droplets can be stabilized in position within a region of the collecting container, thereby providing a single-tube workflow for single cell analyses. Further, compositions implemented are structured to allow for overloading of partitions with functionalized particles, such that partitioned single-cells are co-localized with a subset of functionalized particles in a manner that allows for discernable tagging and downstream analyses.
    Type: Application
    Filed: June 7, 2022
    Publication date: December 8, 2022
    Inventors: Eleen Yee Lam Shum, Janice Hoiyi Lai, Hei Mun Christina Fan, Stephen P. A. Fodor
  • Patent number: 11447817
    Abstract: The inventions cover systems and methods for generation of emulsions having suitable clarity without requiring refractive index matching between emulsion components. Systems can include: a substrate including a set of openings; a reservoir facing the substrate at a first side and containing a sample fluid configured for droplet formation upon interacting with the set of openings of the substrate; and a collecting container facing the substrate at a second side and containing a set of fluid layers configured with a density gradient and suitable immiscibility characteristics. One or more components of the system(s) can support methods for emulsion generation, in relation to enabling interactions between multiple continuous phases and a dispersed droplet phase to generate clear emulsions. Applications of the inventions(s) can include performance of droplet-based digital PCR in an improved manner (e.g., without requiring implementation of correction factors based upon Poisson statistics).
    Type: Grant
    Filed: December 23, 2021
    Date of Patent: September 20, 2022
    Assignee: Enumerix, Inc.
    Inventors: Hei Mun Christina Fan, Eleen Yee Lam Shum, Janice Hoiyi Lai, Stephen P. A. Fodor
  • Publication number: 20220290236
    Abstract: The present disclosure provides methods and systems directed to cell-free identification and/or monitoring of pregnancy-related states. A method for identifying or monitoring a presence or susceptibility of a pregnancy-related state of a subject may comprise assaying a cell-free biological sample derived from said subject to detect a set of biomarkers, and analyzing the set of biomarkers with an algorithm to determine the presence or susceptibility of the pregnancy-related state.
    Type: Application
    Filed: February 3, 2022
    Publication date: September 15, 2022
    Inventors: Lian Chye Winston Koh, Stephen R. Quake, Hei-Mun Christina Fan, Wenying Pan
  • Publication number: 20220280941
    Abstract: This disclosure provides for devices, methods, and systems for generating a plurality of droplets within a collecting container at an extremely high rate (e.g., of at least 1 million droplets per minute, etc.), each of the plurality of droplets comprising an aqueous mixture for a digital analysis, wherein upon generation, the plurality of droplets is stabilized in position within a region of the collecting container. The inventions enable partitioning of samples for digital analyses at unprecedented rates, where readout of signals from targets within such partitions can still be achieved in accordance with various assays.
    Type: Application
    Filed: March 4, 2022
    Publication date: September 8, 2022
    Inventors: Hei Mun Christina Fan, Janice Hoiyi Lai, Sixing Li, Stephen P.A. Fodor, Eleen Yee Lam Shum