Patents by Inventor Michael Y. Lucero
Michael Y. Lucero 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).
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Publication number: 20230372935Abstract: Methods of partition-based analysis. In an exemplary method, a device having a port fluidically connected to a chamber may be selected. A sample-containing fluid may be placed into the port. The sample-containing fluid may be moved from the port to the chamber. Partitions of the sample-containing fluid may be formed. A monolayer of the partitions in the chamber may be created. At least a portion of the monolayer may be imaged.Type: ApplicationFiled: July 31, 2023Publication date: November 23, 2023Inventors: Amy L. Hiddessen, Donald A. Masquelier, Kevin D. Ness, Benjamin J. Hindson, Anthony J. Makarewicz, Erin R. Chia, Billy W. Colston, Serge Saxonov, Svilen S. Tzonev, Michael Y. Lucero, Ryan T. Koehler
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Publication number: 20230287486Abstract: Method of haplotype analysis. In an exemplary method, an aqueous phase containing nucleic acid may be partitioned into a plurality of discrete volumes. At least one allele sequence may be amplified in the volumes from each of a first polymorphic locus and a second polymorphic locus that exhibit sequence variation in the nucleic acid. At least one measure of co-amplification of allele sequences from both loci in the same volumes may be determined. A haplotype of the first and second loci may be selected based on the at least one measure of co-amplification.Type: ApplicationFiled: November 14, 2022Publication date: September 14, 2023Applicant: Bio-Rad Laboratories, Inc.Inventors: John F. REGAN, Serge SAXONOV, Michael Y. LUCERO, Benjamin J. HINDSON, Phillip BELGRADER, Simant DUBE, Austin SO, Jeffrey Clark MELLEN, Nicholas Jack HEREDIA, Kevin D. NESS, Billy W. COLSTON, Jr.
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Publication number: 20220362764Abstract: The present disclosure provides methods and compositions for detecting polynucleotides in a sample and for quantifying polynucleotide load in a sample. The polynucleotides can be associated with a disease, disorder, or condition. In some applications, methylated DNA is quantified, e.g., in order to determine the load of polynucleotides in a sample. The present disclosure also provides methods and compositions for determining the load of fetal polynucleotides in a biological sample, e.g., the load of fetal polynucleotides (e.g., DNA, RNA) in maternal plasma. The present disclosure provides methods and compositions for detecting cellular processes such as cellular viability, growth rates, and infection rates. This disclosure also provides compositions and methods for detecting differences in copy number of a target polynucleotide. In some embodiments, the methods and compositions provided herein are useful for diagnosis of fetal genetic abnormalities, when the starting sample is maternal tissue (e.g.Type: ApplicationFiled: May 20, 2022Publication date: November 17, 2022Applicant: Bio-Rad Laboratories, Inc.Inventors: Benjamin J. HINDSON, Serge SAXONOV, Phillip BELGRADER, Kevin D. NESS, Michael Y. LUCERO, Billy W. COLSTON, JR., Shawn Paul HODGES, Nicholas J. HEREDIA, Jeffrey Clark MELLEN, Camille Bodley TROUP, Paul WYATT
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Patent number: 11499181Abstract: Method of haplotype analysis. In an exemplary method, an aqueous phase containing nucleic acid may be partitioned into a plurality of discrete volumes. At least one allele sequence may be amplified in the volumes from each of a first polymorphic locus and a second polymorphic locus that exhibit sequence variation in the nucleic acid. At least one measure of co-amplification of allele sequences from both loci in the same volumes may be determined. A haplotype of the first and second loci may be selected based on the at least one measure of co-amplification.Type: GrantFiled: December 28, 2018Date of Patent: November 15, 2022Assignee: Bio-Rad Laboratories, Inc.Inventors: John F. Regan, Serge Saxonov, Michael Y. Lucero, Benjamin J. Hindson, Phillip Belgrader, Simant Dube, Austin P. So, Jeffrey C. Mellen, Nicholas J. Heredia, Kevin D. Ness, Billy W. Colston, Jr.
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Publication number: 20220355292Abstract: This invention provides compositions and methods for detecting differences in copy number of a target polynucleotide. In some cases, the methods and compositions provided herein are useful for diagnosis of fetal genetic abnormalities, when the starting sample is maternal tissue (e.g., blood, plasma). The methods and materials described apply techniques for allowing detection of small, but statistically significant, differences in polynucleotide copy number.Type: ApplicationFiled: May 20, 2022Publication date: November 10, 2022Applicant: Bio-Rad Laboratories, Inc.Inventors: Benjamin J. HINDSON, Serge SAXONOV, Phillip BELGRADER, Kevin D. NESS, Michael Y. LUCERO, Billy W. COLSTON, JR.
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Publication number: 20220008914Abstract: Methods of partition-based analysis. In an exemplary method, a device having a port fluidically connected to a chamber may be selected. A sample-containing fluid may be placed into the port. The sample-containing fluid may be moved from the port to the chamber. Partitions of the sample-containing fluid may be formed. A monolayer of the partitions in the chamber may be created. At least a portion of the monolayer may be imaged.Type: ApplicationFiled: September 27, 2021Publication date: January 13, 2022Applicant: Bio-Rad Laboratories, Inc.Inventors: Amy L. Hiddessen, Donald A. Masquelier, Kevin D. Ness, Benjamin J. Hindson, Anthony J. Makarewicz, JR., Erin R. Chia, Billy W. Colston, JR., Serge Saxonov, Svilen S. Tzonev, Michael Y. Lucero, Ryan T. Koehler
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Publication number: 20200086312Abstract: Method of detecting a target nucleic acid. In an exemplary method, at least two thermal zones of different temperature may be created using a heating assembly. A first emulsion and a second emulsion may be formed. The first and second emulsions may be thermally cycled by passing them through tubing in a spaced relation to one another, with the tubing being wound around a central axis of the heating assembly and extending through each thermal zone multiple times. Thermally cycling may promote amplification of the target nucleic acid in droplets of each emulsion. Droplets of each emulsion may be passed through a detection channel located downstream of the tubing. Fluorescence may be detected from the droplets being passed through the detection channel.Type: ApplicationFiled: October 29, 2019Publication date: March 19, 2020Applicant: Bio-Rad Laboratories, Inc.Inventors: Amy L. HIDDESSEN, Donald A. MASQUELIER, Kevin D. NESS, Benjamin J. HINDSON, Anthony J. MAKAREWICZ, JR., Erin R. CHIA, Billy W. COLSTON, JR., Serge SAXONOV, Svilen S. TZONEV, Michael Y. LUCERO, Ryan T. KOEHLER
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Publication number: 20190241947Abstract: Method of haplotype analysis. In an exemplary method, an aqueous phase containing nucleic acid may be partitioned into a plurality of discrete volumes. At least one allele sequence may be amplified in the volumes from each of a first polymorphic locus and a second polymorphic locus that exhibit sequence variation in the nucleic acid. At least one measure of co-amplification of allele sequences from both loci in the same volumes may be determined. A haplotype of the first and second loci may be selected based on the at least one measure of co-amplification.Type: ApplicationFiled: December 28, 2018Publication date: August 8, 2019Applicant: Bio-Rad Laboratories, Inc.Inventors: John F. Regan, Serge Saxonov, Michael Y. Lucero, Benjamin J. Hindson, Phillip Belgrader, Simant Dube, Austin P. So, Jeffrey C. Mellen, Nicholas J. Heredia, Kevin D. Ness, Billy W. Colston, JR.
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Patent number: 10167509Abstract: Provided herein are improved methods, compositions, and kits for analysis of nucleic acids. The improved methods, compositions, and kits can enable copy number estimation of a nucleic acid in a sample. Also provided herein are methods, compositions, and kits for determining the linkage of two or more copies of a target nucleic acid in a sample (e.g. whether the two or more copies are on the same chromosome or different chromosomes) or for phasing alleles.Type: GrantFiled: September 8, 2015Date of Patent: January 1, 2019Assignee: Bio-Rad Laboratories, Inc.Inventors: John F. Regan, Serge Saxonov, Michael Y. Lucero, Benjamin J. Hindson, Phillip Belgrader, Simant Dube, Austin P. So, Jeffrey C. Mellen, Nicholas J. Heredia, Kevin D. Ness, Billy W. Colston, Jr.
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Publication number: 20180147573Abstract: Devices and methods for generating droplets. An exemplary device comprises a substantially planar base portion including a bottom surface having a plurality of microfluidic channels formed therein as recessed regions of the bottom surface. The device also comprises a plurality of protrusions projecting from a top surface of the base portion and each formed integrally with the base portion. The device further comprises a sample well, a carrier well, and a droplet well. Each well has an upper portion created by one of the protrusions. A cover layer is attached to the bottom surface of the base portion and seals a bottom side of each microfluidic channel.Type: ApplicationFiled: September 18, 2017Publication date: May 31, 2018Inventors: Amy L. Hiddessen, Donald A. Masquelier, Kevin D. Ness, Benjamin J. Hindson, Anthony J. Makarewicz, Jr., Erin R. Chia, Billy W. Colston, Jr., Serge Saxonov, Svilen S. Tzonev, Michael Y. Lucero, Ryan T. Koehler
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Publication number: 20180148756Abstract: Aspects of the invention relate to methods and kits for assessing cancer. Some aspects of the invention relate to methods and kits for preparing a sample library for sequencing. Some aspects of the invention relate to methods and kits for allele detection. Some aspects of the invention relate to high efficiency ligation methods and kits. Some aspects of the invention relate to sensitive detection of amplicons.Type: ApplicationFiled: December 1, 2017Publication date: May 31, 2018Inventors: Austin SO, Michael Y. LUCERO
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Publication number: 20170151558Abstract: System, including methods, apparatus, and kits, for forming emulsions. In an exemplary method of generating droplets, a device may be selected that includes a plurality of emulsion-formation units each including a sample well, a continuous-phase well, a droplet well, and a channel network that fluidically interconnects the wells and creates a droplet-generation region. A discrete volume of sample-containing fluid may be placed into the sample well of each emulsion-formation unit, and a discrete volume of continuous-phase fluid into the continuous-phase well of each emulsion-formation unit. Pressure may be applied to the device with a fluidics assembly after the step of placing, such that the plurality of emulsion-formation units generate droplets in parallel with one another. A pressure signal may be detected from the fluidics assembly. Application of the pressure may be stopped when the pressure signal indicates that a sample well is empty.Type: ApplicationFiled: November 14, 2016Publication date: June 1, 2017Inventors: Amy L. Hiddessen, Donald A. Masquelier, Kevin D. Ness, Benjamin J. Hindson, Anthony J. Makarewicz, JR., Erin R. Chia, Billy W. Colston, JR., Serge Saxonov, Svilen S. Tzonev, Michael Y. Lucero, Ryan T. Koehler
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Publication number: 20170101674Abstract: Aspects of the disclosure relate to methods and kits for assessing cancer. Some aspects of the disclosure relate to methods and kits for preparing a sample library for sequencing. Some aspects of the disclosure relate to methods and kits for allele detection. Some aspects of the disclosure relate to high efficiency ligation methods and kits. Some aspects of the disclosure relate to sensitive detection of amplicons.Type: ApplicationFiled: August 19, 2016Publication date: April 13, 2017Inventors: Austin So, Michael Y. Lucero, Francisco M. De La Vega, Federico Goodsaid
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Publication number: 20160281154Abstract: Provided herein are methods for assessing cancer, comprising analysis of sequence data from a set of cancer-related genes in a tumor sample from a subject, followed by monitoring of a subset of the set in circulating tumor-associated DNA in a fluid sample from the subject. Also provided are kits and systems for practicing any of them methods of the invention.Type: ApplicationFiled: April 14, 2016Publication date: September 29, 2016Inventors: Austin So, Michael Y. Lucero
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Publication number: 20160222427Abstract: Aspects of the invention relate to methods and kits for assessing cancer. Some aspects of the invention relate to methods and kits for preparing a sample library for sequencing. Some aspects of the invention relate to methods and kits for allele detection. Some aspects of the invention relate to high efficiency ligation methods and kits. Some aspects of the invention relate to sensitive detection of amplicons.Type: ApplicationFiled: February 10, 2016Publication date: August 4, 2016Inventors: Austin So, Michael Y. Lucero
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Publication number: 20160186267Abstract: Aspects of the invention relate to methods and kits for assessing cancer. Some aspects of the invention relate to methods and kits for preparing a sample library for sequencing. Some aspects of the invention relate to methods and kits for allele detection. Some aspects of the invention relate to high efficiency ligation methods and kits. Some aspects of the invention relate to sensitive detection of amplicons.Type: ApplicationFiled: February 21, 2014Publication date: June 30, 2016Applicant: Toma Biosciences, Inc.Inventors: Austin SO, Michael Y. LUCERO
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Publication number: 20160076099Abstract: Provided herein are improved methods, compositions, and kits for analysis of nucleic acids. The improved methods, compositions, and kits can enable copy number estimation of a nucleic acid in a sample. Also provided herein are methods, compositions, and kits for determining the linkage of two or more copies of a target nucleic acid in a sample (e.g. whether the two or more copies are on the same chromosome or different chromosomes) or for phasing alleles.Type: ApplicationFiled: September 8, 2015Publication date: March 17, 2016Inventors: John F. Regan, Serge Saxonov, Michael Y. Lucero, Benjamin J. Hindson, Phillip Belgrader, Simant Dube, Austin P. So, Jeffrey C. Mellen, Nicholas J. Heredia, Kevin D. Ness, Billy W. Colston, Jr.
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Publication number: 20140287937Abstract: Provided herein are methods for assessing cancer, comprising analysis of sequence data from a set of cancer-related genes in a tumor sample from a subject, followed by monitoring of a subset of the set in circulating tumor-associated DNA in a fluid sample from the subject. Also provided are kits and systems for practicing any of them methods of the invention.Type: ApplicationFiled: February 21, 2014Publication date: September 25, 2014Applicant: TOMA Biosciences, Inc.Inventors: Austin So, Michael Y. LUCERO
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Publication number: 20140200164Abstract: System, including methods and apparatus, for detection of spaced droplets.Type: ApplicationFiled: January 20, 2014Publication date: July 17, 2014Inventors: Anthony J. Makarewicz, JR., Amy L. Hiddessen, Kevin D. Ness, Donald. A. Masquelier, Billy W. Colston, JR., Benjamin J. Hindson, Serge Saxonov, Svilen S. Tzonev, Michael Y. Lucero, Ryan T. Koehler
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Patent number: 8663920Abstract: Methods of characterizing a nucleic acid library by digital assay.Type: GrantFiled: July 30, 2012Date of Patent: March 4, 2014Assignee: Bio-Rad Laboratories, Inc.Inventors: Serge Saxonov, Svilen S. Tzonev, Michael Y. Lucero, Ryan T. Koehler, Benjamin J. Hindson