Patents by Inventor Alex Aravanis
Alex Aravanis 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: 20240084376Abstract: The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index (UMI) sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the UMIs include both physical UMIs and virtual UMIs. In some implementations, the unique molecular index sequences include non-random sequences. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.Type: ApplicationFiled: August 8, 2023Publication date: March 14, 2024Inventors: Sante Gnerre, Byoungsok Jung, Emrah Kostem, Alex Aravanis, Alex So, Xuyu Cai, Zhihong Zhang, Frank J. Steemers
-
Publication number: 20240084289Abstract: Methods for preparing enriched sequencing libraries from test samples that contain double-stranded deoxyribonucleic acid (dsDNA) are provided.Type: ApplicationFiled: November 15, 2023Publication date: March 14, 2024Inventors: Byoungsok Jung, Alex Aravanis
-
Publication number: 20240068016Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.Type: ApplicationFiled: November 9, 2023Publication date: February 29, 2024Applicants: 10x Genomics Sweden AB, Illumina, Inc.Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
-
Patent number: 11866777Abstract: The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index (UMI) sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the UMIs include both physical UMIs and virtual UMIs. In some implementations, the unique molecular index sequences include non-random sequences. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.Type: GrantFiled: October 21, 2020Date of Patent: January 9, 2024Assignee: Illumina, Inc.Inventors: Sante Gnerre, Byoungsok Jung, Emrah Kostem, Alex Aravanis, Alex So, Xuyu Cai, Zhihong Zhang, Frank J. Steemers
-
Publication number: 20240001361Abstract: Systems and methods for conducting designated reactions that include a fluidic network having a sample channel, a reaction chamber, and a reservoir. The sample channel is in flow communication with a sample port. The system also includes a rotary valve that has a flow channel and is configured to rotate between first and second valve positions. The flow channel fluidically couples the reaction chamber and the sample channel when the rotary valve is in the first valve position and fluidically couples the reservoir and the reaction chamber when the rotary valve is in the second valve position. A pump assembly induces a flow of a biological sample toward the reaction chamber when the rotary valve is in the first valve position and induces a flow of a reaction component from the reservoir toward the reaction chamber when the rotary valve is in the second valve position.Type: ApplicationFiled: September 18, 2023Publication date: January 4, 2024Inventors: Sebastian Bohm, Alex Aravanis, Alexander Hsiao, Behnam Javanmardi, Tarun Kumar Khurana, Hai Quang Tran, Majid Aghababazadeh, M. Shane Bowen, Boyan Boyanov, Dale Buermann
-
Patent number: 11851650Abstract: Methods for preparing enriched sequencing libraries from test samples that contain double-stranded deoxyribonucleic acid (dsDNA) are provided.Type: GrantFiled: September 28, 2018Date of Patent: December 26, 2023Assignee: GRAIL, LLCInventors: Byoungsok Jung, Alex Aravanis
-
Patent number: 11786898Abstract: Systems and methods for conducting designated reactions that include a fluidic network having a sample channel, a reaction chamber, and a reservoir. The sample channel is in flow communication with a sample port. The system also includes a rotary valve that has a flow channel and is configured to rotate between first and second valve positions. The flow channel fluidically couples the reaction chamber and the sample channel when the rotary valve is in the first valve position and fluidically couples the reservoir and the reaction chamber when the rotary valve is in the second valve position. A pump assembly induces a flow of a biological sample toward the reaction chamber when the rotary valve is in the first valve position and induces a flow of a reaction component from the reservoir toward the reaction chamber when the rotary valve is in the second valve position.Type: GrantFiled: March 13, 2020Date of Patent: October 17, 2023Assignee: ILLUMINA, INC.Inventors: Sebastian Bohm, Alex Aravanis, Alexander Hsiao, Behnam Javanmardi, Tarun Khurana, Hai Quang Tran, Majid Aghababazadeh, M. Shane Bowen, Boyan Boyanov, Dale Buermann
-
Publication number: 20230304078Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.Type: ApplicationFiled: May 9, 2023Publication date: September 28, 2023Applicants: Spatial Transcriptomics AB, Illumina, Inc.Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
-
Publication number: 20230272375Abstract: Provided herein are methods of enriching mutated cell free nucleic acids for detection and diagnosis of cancer. Also provided are methods using a CRISPR-Cas system to target and deplete unwanted more abundant cell free nucleic acid sequences thereby enriching for less abundant sequences.Type: ApplicationFiled: April 10, 2023Publication date: August 31, 2023Inventors: Gordon Cann, Alex Aravanis, Arash Jamshidi, Rick Klausner, Richard Rava
-
Patent number: 11739372Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.Type: GrantFiled: February 9, 2023Date of Patent: August 29, 2023Assignees: Spatial Transcriptomics AB, Illumina, Inc.Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
-
Publication number: 20230183785Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.Type: ApplicationFiled: February 9, 2023Publication date: June 15, 2023Applicants: Spatial Transcriptomics AB, Illumina, Inc.Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
-
Publication number: 20230151417Abstract: Aspects of the invention include methods for preparing sequencing libraries, performing sequencing procedures that can correct for process-related errors, and identifying rare variants that are or may be indicative of cancer.Type: ApplicationFiled: January 23, 2023Publication date: May 18, 2023Applicant: GRAIL, LLCInventors: Arash JAMSHIDI, Gordon CANN, Hamed AMINI, Alex ARAVANIS
-
Publication number: 20230145389Abstract: Systems and methods for conducting designated reactions utilizing a base instrument and a removable cartridge. The removable cartridge includes a fluidic network that receives and fluidically directs a biological sample to conduct the designated reactions. The removable cartridge also includes a flow-control valve that is operably coupled to the fluidic network and is movable relative to the fluidic network to control flow of the biological sample therethrough. The removable cartridge is configured to separably engage a base instrument. The base instrument includes a valve actuator that engages the flow-control valve of the removable cartridge. A detection assembly held by at least one of the removable cartridge or the base instrument may be used to detect the designated reactions.Type: ApplicationFiled: December 22, 2022Publication date: May 11, 2023Inventors: Alex Aravanis, Boyan Boyanov, M. Shane Bowen, Dale Buermann, Alexander Hsiao, Behnam Javanmardi, Tarun Khurana, Poorya Sabounchi, Hai Quang Tran
-
Patent number: 11624064Abstract: Provided herein are methods of enriching mutated cell free nucleic acids for detection and diagnosis of cancer. Also provided are methods using a CRISPR-Cas system to target and deplete unwanted more abundant cell free nucleic acid sequences thereby enriching for less abundant sequences.Type: GrantFiled: June 13, 2017Date of Patent: April 11, 2023Assignee: GRAIL, LLCInventors: Gordon Cann, Alex Aravanis, Arash Jamshidi, Rick Klausner, Richard Rava
-
Patent number: 11613773Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.Type: GrantFiled: June 7, 2022Date of Patent: March 28, 2023Assignees: Spatial Transcriptomics AB, Illumina, Inc.Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
-
Patent number: 11590494Abstract: Systems and methods for conducting designated reactions utilizing a base instrument and a removable cartridge. The removable cartridge includes a fluidic network that receives and fluidically directs a biological sample to conduct the designated reactions. The removable cartridge also includes a flow-control valve that is operably coupled to the fluidic network and is movable relative to the fluidic network to control flow of the biological sample therethrough. The removable cartridge is configured to separably engage a base instrument. The base instrument includes a valve actuator that engages the flow-control valve of the removable cartridge. A detection assembly held by at least one of the removable cartridge or the base instrument may be used to detect the designated reactions.Type: GrantFiled: June 6, 2019Date of Patent: February 28, 2023Assignee: ILLUMINA, INC.Inventors: Alex Aravanis, Boyan Boyanov, M. Shane Bowen, Dale Buermann, Alexander Hsiao, Behnam Javanmardi, Tarun Khurana, Poorya Sabounchi, Hai Quang Tran
-
Patent number: 11584958Abstract: Aspects of the invention include methods for preparing sequencing libraries, performing sequencing procedures that can correct for process-related errors, and identifying rare variants that are or may be indicative of cancer.Type: GrantFiled: March 30, 2018Date of Patent: February 21, 2023Assignee: GRAIL, LLCInventors: Arash Jamshidi, Gordon Cann, Hamed Amini, Alex Aravanis
-
Publication number: 20220298560Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.Type: ApplicationFiled: June 7, 2022Publication date: September 22, 2022Applicants: Spatial Transcriptomics AB, Illumina, Inc.Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
-
Patent number: 11390912Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.Type: GrantFiled: March 11, 2022Date of Patent: July 19, 2022Assignees: Spatial Transcriptomics AB, Illumina, Inc.Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
-
Publication number: 20220195505Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.Type: ApplicationFiled: March 11, 2022Publication date: June 23, 2022Applicants: Spatial Transcriptomics AB, Illumina, Inc.Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis