Patents by Inventor Lorenzo Berti
Lorenzo Berti 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: 20240132954Abstract: An example of a resin composition includes a free radical curable resin matrix including an acrylate and a siloxane, and a free radical photoinitiator. When cured, the resin composition has low or no autofluorescence when exposed to blue excitation wavelengths ranging from about 380 nm to about 480 nm or green excitation wavelengths ranging from about 510 nm to about 560 nm.Type: ApplicationFiled: December 29, 2023Publication date: April 25, 2024Inventors: Timothy J. Merkel, Wayne N. George, Andrew A. Brown, Audrey Zak, Gianluca Andrea Artioli, Julia Morrison, Nikolai Romanov, Lorenzo Berti, Graham Boud
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Publication number: 20240124920Abstract: A method of conducting an assay for a set of targets, the method comprising: providing a set of targets; subjecting each target of the set of targets to a recognition event, in which each target is uniquely recognized by and bound to a recognition element associated with a code from a set of codes, thereby yielding a set of coded targets comprising the target and the recognition element; subjecting each recognition element of the set of coded targets to a transformation event, in which a molecular transformation of each recognition element produces a modified recognition element, thereby yielding a set of modified recognition elements comprising the code; subjecting each code of the set of modified recognition elements to an amplifying event, in which each code is amplified, thereby yielding a set of amplified codes; subjecting each amplified code of the set of amplified codes to a detection event, thereby determining the nucleic acid sequence of the code.Type: ApplicationFiled: November 23, 2021Publication date: April 18, 2024Inventors: Pieter VAN ROOYEN, Lorenzo BERTI, Jeffrey BRODIN, Donald Brian EIDSON, Gavin STONE, Michael POLLACK, Allen ECKHARDT
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Publication number: 20240117418Abstract: A microarray is designed to capture one or more molecules of interest at each of a plurality of sites on a substrate. The sites comprise base pads, such as polymer base pads, that promote the attachment of the molecules at the sites. The microarray may be made by one or more patterning techniques to create a layout of base pads in a desired pattern. Further, the microarrays may include features to encourage clonality at the sites.Type: ApplicationFiled: November 13, 2023Publication date: April 11, 2024Inventors: M. Shane Bowen, Kevin L. Gunderson, Shengrong Lin, Maria Candelaria Rogert Bacigalupo, Kandaswamy Vijayan, Yir-Shyuan Wu, Bala Murali Venkatesan, James Tsay, John M. Beierle, Lorenzo Berti, Sang Ryul Park
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Patent number: 11884976Abstract: An example of a resin composition includes a free radical curable resin matrix including an acrylate and a siloxane, and a free radical photoinitiator. When cured, the resin composition has low or no autofluorescence when exposed to blue excitation wavelengths ranging from about 380 nm to about 480 nm or green excitation wavelengths ranging from about 510 nm to about 560 nm.Type: GrantFiled: July 18, 2019Date of Patent: January 30, 2024Assignees: Illumina, Inc., Illumina Cambridge LimitedInventors: Timothy J. Merkel, Wayne N. George, Andrew A. Brown, Audrey Zak, Gianluca Andrea Artioli, Julia Morrison, Nikolai Romanov, Lorenzo Berti, Graham Boud
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Patent number: 11834704Abstract: A method includes forming a patterned substrate including a plurality of base pads, using a nano-imprint lithography process. A capture substance is attached to each of the plurality of base pads, optionally through a linker, the capture substance being adapted to promote capture of a target molecule.Type: GrantFiled: December 7, 2020Date of Patent: December 5, 2023Assignee: Illumina, Inc.Inventors: M. Shane Bowen, Kevin L. Gunderson, Shengrong Lin, Maria Candelaria Rogert Bacigalupo, Kandaswamy Vijayan, Yir-Shyuan Wu, Bala Murali Venkatesan, James Tsay, John M. Beierle, Lorenzo Berti, Sang Ryul Park
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Publication number: 20230313275Abstract: Some embodiments provided herein include methods and compositions for the detection of target ligands on an array. In some embodiments, a capture probe specifically binds to a target ligand from a sample, the location of a bead comprising the capture probe in an array is determined, and the bead is decoded to identify the capture probe and the sample. In some embodiments, a barcode is indicative of a capture probe attached to a bead; and an index is indicative of a subpopulation of beads. In some embodiments, the barcode and the index are determined by sequencing.Type: ApplicationFiled: April 18, 2023Publication date: October 5, 2023Inventors: Darren Segale, Fiona E. Black, Jeffrey Dennis Brodin, Jeffrey Fisher, Lorenzo Berti, Siew Hong Leong
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Publication number: 20230295692Abstract: Methods and systems for detecting the presence of a target nucleic acid sequence in one or more samples of a plurality of samples are described. The methods may comprise the use of linear barcoded nucleic acid probes that, upon hybridization to a target nucleic acid sequence, may be ligated to circularize the probe molecule, amplified, and sequenced. The use of a probe-specific barcode integrated into the nucleic acid probe molecule, and sample-specific barcodes that may be incorporated into the nucleic acid probe molecule or added during the amplification step, enable large-scale multiplexed assay and sample processing.Type: ApplicationFiled: January 30, 2023Publication date: September 21, 2023Inventors: Lorenzo BERTI, Semyon KRUGLYAK, Matthew KELLINGER, Molly HE, Sinan ARSLAN, Junhua ZHAO, Michael PREVITE
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Publication number: 20230296593Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.Type: ApplicationFiled: May 25, 2023Publication date: September 21, 2023Inventors: Michael PREVITE, Molly HE, Junhua ZHAO, Hui Zhen MAH, Chunhong ZHOU, Sinan ARSLAN, Matthew KELLINGER, Lorenzo BERTI, Steve Xiangling CHEN
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Publication number: 20230295739Abstract: Methods are provided for conducting an assay on a set of nucleic acid targets, including: combining a set of dual probes with a sample composition potentially comprising a set of nucleic acid targets to form a set of cleavable ternary nucleic acid complexes; releasing from the cleavable ternary nucleic acid complex a set of recognition element fragments comprising the recognition element sequence; combining the released recognition element fragments with an additional nucleic acid sequence from a set of additional nucleic acid sequences to create a circular nucleic acid, wherein the circular nucleic acid comprises a target-associated code and additional sequence elements; and performing a detection event to identify a set of detected codes of the target-associated codes.Type: ApplicationFiled: January 5, 2023Publication date: September 21, 2023Inventors: Jeffrey BRODIN, Lorenzo BERTI, Brian EIDSON, Christian SCHLEGEL, Angela BLUM, Rachel SCHOWALTER, Ludovic VINCENT, Pieter VAN ROOYEN, Gavin STONE
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Publication number: 20230296592Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.Type: ApplicationFiled: May 25, 2023Publication date: September 21, 2023Inventors: Michael PREVITE, Molly HE, Junhua ZHAO, Hui Zhen MAH, Chunhong ZHOU, Sinan ARSLAN, Matthew KELLINGER, Lorenzo BERTI, Steve Xiangling CHEN
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Publication number: 20230257801Abstract: Methods are provided for conducting a dual-probe assay on a set of nucleic acid targets, including: combining a set of dual probes with a sample composition potentially comprising a set of nucleic acid targets to form a set of cleavable ternary nucleic acid complexes; releasing from the cleavable ternary nucleic acid complex a set of recognition element fragments; hybridizing each of the set of released recognition element fragments to a coded oligonucleotide probe and using resulting hybridized released recognition elements as primers for copying the coded oligonucleotide probe to produce a sect of target-associated codes, wherein each of the coded oligonucleotide probes comprises a code from a set of codes, each code comprises at least one segment encoding one or more symbols that correspond to a sequence of one or more nucleotides; and performing a detection event to identify a set of detected codes of the target-associated codes.Type: ApplicationFiled: January 5, 2023Publication date: August 17, 2023Inventors: Jeffrey BRODIN, Lorenzo BERTI, Brian EIDSON, Christian SCHLEGEL, Angela BLUM, Rachel SCHOWALTER, Ludovic VINCENT, Pieter VAN ROOYEN, Gavin STONE
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Publication number: 20230250248Abstract: Some embodiments described herein relate to a substrate with a surface comprising a silane or a silane derivative covalently attached to optionally substituted cycloalkene or optionally substituted heterocycloalkene for direct conjugation with a functionalized molecule of interest, such as a polymer, a hydrogel, an amino acid, a nucleoside, a nucleotide, a peptide, a polynucleotide, or a protein. In some embodiments, the silane or silane derivative contains optionally substituted norbornene or norbornene derivatives. Method for preparing a functionalized surface and the use in DNA sequencing and other diagnostic applications are also disclosed.Type: ApplicationFiled: March 27, 2023Publication date: August 10, 2023Inventors: Lorenzo Berti, Andrew A. Brown, Wayne N. George
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Patent number: 11667957Abstract: Some embodiments provided herein include methods and compositions for the detection of target ligands on an array. In some embodiments, a capture probe specifically binds to a target ligand from a sample, the location of a bead comprising the capture probe in an array is determined, and the bead is decoded to identify the capture probe and the sample. In some embodiments, a barcode is indicative of a capture probe attached to a bead; and an index is indicative of a subpopulation of beads. In some embodiments, the barcode and the index are determined by sequencing.Type: GrantFiled: October 23, 2019Date of Patent: June 6, 2023Assignee: Illumina, Inc.Inventors: Darren Segale, Fiona E. Black, Jeffrey Dennis Brodin, Jeffrey Fisher, Lorenzo Berti, Siew Hong Leong
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Patent number: 11618808Abstract: Some embodiments described herein relate to a substrate with a surface comprising a silane or a silane derivative covalently attached to optionally substituted cycloalkene or optionally substituted heterocycloalkene for direct conjugation with a functionalized molecule of interest, such as a polymer, a hydrogel, an amino acid, a nucleoside, a nucleotide, a peptide, a polynucleotide, or a protein. In some embodiments, the silane or silane derivative contains optionally substituted norbornene or norbornene derivatives. Method for preparing a functionalized surface and the use in DNA sequencing and other diagnostic applications are also disclosed.Type: GrantFiled: March 5, 2021Date of Patent: April 4, 2023Assignee: Illumina, Inc.Inventors: Lorenzo Berti, Andrew A. Brown, Wayne N. George
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Publication number: 20220170919Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.Type: ApplicationFiled: February 18, 2022Publication date: June 2, 2022Inventors: Michael PREVITE, Molly HE, Junhua ZHAO, Hui Zhen MAH, Chunhong ZHOU, Sinan ARSLAN, Matthew KELLINGER, Lorenzo BERTI, Steve Xiangling CHEN
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Patent number: 11287422Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.Type: GrantFiled: June 24, 2021Date of Patent: March 29, 2022Assignee: ELEMENT BIOSCIENCES, INC.Inventors: Michael Previte, Molly Min He, Junhua Zhao, Hui Zhen Mah, Chunhong Zhou, Sinan Arslan, Matthew Kellinger, Lorenzo Berti, Steve Xiangling Chen
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Publication number: 20210318294Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.Type: ApplicationFiled: June 24, 2021Publication date: October 14, 2021Inventors: Michael PREVITE, Molly Min HE, Junhua ZHAO, Hui Zhen MAH, Chunhong ZHOU, Sinan ARSLAN, Matthew KELLINGER, Lorenzo BERTI, Steve Xiangling CHEN
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Patent number: 11060135Abstract: A method includes forming a patterned substrate including a plurality of base pads, using a nano-imprint lithography process. A capture substance is attached to each of the plurality of base pads, optionally through a linker, the capture substance being adapted to promote capture of a target molecule.Type: GrantFiled: August 30, 2018Date of Patent: July 13, 2021Assignee: Illumina, Inc.Inventors: M. Shane Bowen, Kevin L. Gunderson, Shengrong Lin, Maria Candelaria Rogert Bacigalupo, Kandaswamy Vijayan, Yir-Shyuan Wu, Bala Murali Venkatesan, James Tsay, John M. Beierle, Lorenzo Berti, Sang Ryul Park
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Publication number: 20210187469Abstract: Provided is a nanoparticle including a scaffold, a single template site for bonding a template polynucleotide to the scaffold, and a plurality of accessory sites for bonding accessory oligonucleotides to the scaffold, wherein the scaffold is selected from one or more scaffold DNA molecules and one or more scaffold polypeptides, the single template site for bonding a template polynucleotide to the scaffold is selected from a covalent template bonding site and a noncovalent template bonding site and the plurality of accessory sites for bonding accessory oligonucleotides to the scaffold are selected from covalent accessory oligonucleotide bonding sites and noncovalent accessory oligonucleotide bonding sites. Also provided are methods of using the nanoparticle.Type: ApplicationFiled: December 22, 2020Publication date: June 24, 2021Applicants: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITED, ILLUMINA SINGAPORE PTE. LTD.Inventors: Wayne N. GEORGE, Jonathan Mark BOUTELL, Mathieu LESSARD-VIGER, Saurabh NIRANTAR, Pietro GATTI LAFRANCONI, Seth MCDONALD, Yin Nah TEO, Maria Rogert BACIGALUPO, Sergio PEISAJOVICH, Eric BRUSTAD, Michael HOWARD, Xiangyuan YANG, M. Shane Bowen, Alex NEMIROSKI, Jeffrey BRODIN, Ludovic VINCENT, Lorenzo BERTI, Andrew A. BROWN, Fei SHEN, Lena STORMS, Olivia BENICE
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Publication number: 20210189082Abstract: Some embodiments described herein relate to a substrate with a surface comprising a silane or a silane derivative covalently attached to optionally substituted cycloalkene or optionally substituted heterocycloalkene for direct conjugation with a functionalized molecule of interest, such as a polymer, a hydrogel, an amino acid, a nucleoside, a nucleotide, a peptide, a polynucleotide, or a protein. In some embodiments, the silane or silane derivative contains optionally substituted norbornene or norbornene derivatives. Method for preparing a functionalized surface and the use in DNA sequencing and other diagnostic applications are also disclosed.Type: ApplicationFiled: March 5, 2021Publication date: June 24, 2021Inventors: Lorenzo Berti, Andrew A. Brown, Wayne N. George