Patents by Inventor Joel Pel
Joel Pel 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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Patent number: 11905556Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two or more template nucleic acids are joined together by a linking molecule, such as a PEG derivative. Identical copies of a nucleic acid fragment or both strands of a duplex fragment may be linked together. The linked nucleic acids are amplified, creating linked amplicons. Emulsion PCR with linked primers creates linked template nucleic acids for seeding sequencing clusters and errors can be readily identified by their presence on only one of the linked fragments.Type: GrantFiled: February 18, 2021Date of Patent: February 20, 2024Assignee: NCAN Genomics, Inc.Inventors: Joel Pel, Andrea Marziali
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Publication number: 20240052403Abstract: The invention generally relates to capturing, amplifying, and sequencing nucleic acids. In certain embodiments, copies of the sense and antisense strands of a duplex template nucleic acid are captured using linked capture probes and multiple binding and extension steps to improve specificity over traditional single binding target capture techniques. Methods of seeding sequencing clusters with sense and antisense strands of a target nucleic acid are also disclosed including identifying the strands using sense-specific barcodes and confirming base calls using two sense-specific sequencing reads. Linked adapters may be used to increase adapter ligation selectively or efficiency and yield.Type: ApplicationFiled: October 17, 2023Publication date: February 15, 2024Inventors: Andrea Marziali, Joel Pel
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Patent number: 11898196Abstract: The invention includes methods and apparatus for separating mutations, especially rare and unknown mutations, using heteroduplex binding proteins. Nucleic acids may optionally be nicked at or near the mutation in order to promote heteroduplex binding protein recognition and binding. In particular, using the disclosed methods, it is possible to separate heteroduplexed nucleic acid strand pair from homoduplexed nucleic acid strand pairs having similar sequences and being at a much higher concentration. Once the heteroduplexed nucleic acids are isolated and recovered, it is straightforward to analyze the sequences of the heteroduplexed nucleic acids, e.g., using sequencing or hybrid assays.Type: GrantFiled: August 18, 2021Date of Patent: February 13, 2024Assignee: Quantum-Si IncorporatedInventors: Andrea Marziali, Milenko Despotovic, Matthew Wiggin, Joel Pel
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Publication number: 20240043921Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two template nucleic acids are joined together by a linking molecule, such as a PEG derivative. The linked template nucleic acids is amplified, creating linked amplicons.Type: ApplicationFiled: October 18, 2023Publication date: February 8, 2024Inventors: Milenko Despotovic, Joel Pel, Andrea Marziali
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Patent number: 11879151Abstract: The invention generally relates to capturing, amplifying, and sequencing nucleic acids. In certain embodiments, copies of the sense and antisense strands of a duplex template nucleic acid are captured using linked capture probes and multiple binding and extension steps to improve specificity over traditional single binding target capture techniques. Methods of seeding sequencing clusters with sense and antisense strands of a target nucleic acid are also disclosed including identifying the strands using sense-specific barcodes and confirming base calls using two sense-specific sequencing reads. Linked adapters may be used to increase adapter ligation selectively or efficiency and yield.Type: GrantFiled: March 7, 2022Date of Patent: January 23, 2024Assignee: NCAN GENOMICS, INC.Inventors: Andrea Marziali, Joel Pel
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Patent number: 11827930Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two template nucleic acids are joined together by a linking molecule, such as a PEG derivative. The linked template nucleic acids is amplified, creating linked amplicons.Type: GrantFiled: October 1, 2020Date of Patent: November 28, 2023Assignee: NCAN Genomics, Inc.Inventors: Milenko Despotovic, Joel Pel, Andrea Marziali
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Patent number: 11795497Abstract: Methods and apparatus providing for the isolation of an unknown mutation from a sample comprising wild type nucleic acids and mutated nucleic acids through the application of time-varying driving fields and periodically varying mobility-altering fields to the sample within in an affinity matrix.Type: GrantFiled: April 9, 2021Date of Patent: October 24, 2023Assignee: Quantum-Si IncorporatedInventors: Andrea Marziali, Milenko Despotovic, Joel Pel
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Publication number: 20220340967Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two or more template nucleic acids are joined together by a linking molecule, such as a PEG derivative. Identical copies of a nucleic acid fragment or both strands of a duplex fragment may be linked together. The linked nucleic acids are amplified, creating linked amplicons. Emulsion PCR with linked primers creates linked template nucleic acids for seeding sequencing clusters and errors can be readily identified by their presence on only one of the linked fragments.Type: ApplicationFiled: June 16, 2022Publication date: October 27, 2022Inventors: Joel Pel, Andrea Marziali
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Patent number: 11473136Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two or more template nucleic acids are joined together by a linking molecule, such as a PEG derivative. Identical copies of a nucleic acid fragment or both strands of a duplex fragment may be linked together. The linked nucleic acids are amplified, creating linked amplicons. Emulsion PCR with linked primers creates linked template nucleic acids for seeding sequencing clusters and errors can be readily identified by their presence on only one of the linked fragments.Type: GrantFiled: January 3, 2020Date of Patent: October 18, 2022Assignee: NCAN Genomics, Inc.Inventors: Joel Pel, Andrea Marziali
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Publication number: 20220315997Abstract: The invention generally relates to using linked target capture probes to profile the adaptive immune system of a subject, detect pathogens, perform spatial sequencing, and isolate mutant sequences.Type: ApplicationFiled: April 5, 2022Publication date: October 6, 2022Inventors: Joel Pel, Andrea Marziali
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Publication number: 20220228206Abstract: The invention generally relates to using linked target capture probes to evaluate genome editing efficiency and specificity.Type: ApplicationFiled: June 10, 2020Publication date: July 21, 2022Inventors: Joel Pel, Andrea Marziali
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Publication number: 20220186298Abstract: The invention generally relates to capturing, amplifying, and sequencing nucleic acids. In certain embodiments, copies of the sense and antisense strands of a duplex template nucleic acid are captured using linked capture probes and multiple binding and extension steps to improve specificity over traditional single binding target capture techniques. Methods of seeding sequencing clusters with sense and antisense strands of a target nucleic acid are also disclosed including identifying the strands using sense-specific barcodes and confirming base calls using two sense-specific sequencing reads. Linked adapters may be used to increase adapter ligation selectively or efficiency and yield.Type: ApplicationFiled: March 7, 2022Publication date: June 16, 2022Inventors: Andrea Marziali, Joel Pel
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Publication number: 20220081713Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two or more template nucleic acids are joined together by a linking molecule, such as a PEG derivative. Identical copies of a nucleic acid fragment or both strands of a duplex fragment may be linked together. The linked nucleic acids are amplified, creating linked amplicons. Emulsion PCR with linked primers creates linked template nucleic acids for seeding sequencing clusters and errors can be readily identified by their presence on only one of the linked fragments.Type: ApplicationFiled: January 3, 2020Publication date: March 17, 2022Applicants: Boreal Genomics, Inc., Boreal Genomics, Inc.Inventors: Joel Pel, Andrea Marziali
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Patent number: 11268137Abstract: The invention generally relates to capturing, amplifying, and sequencing nucleic acids. In certain embodiments, copies of the sense and antisense strands of a duplex template nucleic acid are captured using linked capture probes and multiple binding and extension steps to improve specificity over traditional single binding target capture techniques. Methods of seeding sequencing clusters with sense and antisense strands of a target nucleic acid are also disclosed including identifying the strands using sense-specific barcodes and confirming base calls using two sense-specific sequencing reads. Linked adapters may be used to increase adapter ligation selectively or efficiency and yield.Type: GrantFiled: December 7, 2017Date of Patent: March 8, 2022Assignee: Boreal Genomics, Inc.Inventors: Andrea Marziali, Joel Pel
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Publication number: 20220056506Abstract: The invention includes methods and apparatus for separating mutations, especially rare and unknown mutations, using heteroduplex binding proteins. Nucleic acids may optionally be nicked at or near the mutation in order to promote heteroduplex binding protein recognition and binding. In particular, using the disclosed methods, it is possible to separate heteroduplexed nucleic acid strand pair from homoduplexed nucleic acid strand pairs having similar sequences and being at a much higher concentration. Once the heteroduplexed nucleic acids are isolated and recovered, it is straightforward to analyze the sequences of the heteroduplexed nucleic acids, e.g., using sequencing or hybrid assays.Type: ApplicationFiled: August 18, 2021Publication date: February 24, 2022Applicant: Quantum-Si IncorporatedInventors: Andrea Marziali, Milenko Despotovic, Matthew Wiggin, Joel Pel
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Patent number: 11130986Abstract: The invention includes methods and apparatus for separating mutations, especially rare and unknown mutations, using heteroduplex binding proteins. Nucleic acids may optionally be nicked at or near the mutation in order to promote heteroduplex binding protein recognition and binding. In particular, using the disclosed methods, it is possible to separate heteroduplexed nucleic acid strand pair from homoduplexed nucleic acid strand pairs having similar sequences and being at a much higher concentration. Once the heteroduplexed nucleic acids are isolated and recovered, it is straightforward to analyze the sequences of the heteroduplexed nucleic acids, e.g., using sequencing or hybrid assays.Type: GrantFiled: May 19, 2016Date of Patent: September 28, 2021Assignee: Quantum-Si IncorporatedInventors: Andrea Marziali, Milenko Despotovic, Matthew Wiggin, Joel Pel
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Publication number: 20210246500Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two or more template nucleic acids are joined together by a linking molecule, such as a PEG derivative. Identical copies of a nucleic acid fragment or both strands of a duplex fragment may be linked together. The linked nucleic acids are amplified, creating linked amplicons. Emulsion PCR with linked primers creates linked template nucleic acids for seeding sequencing clusters and errors can be readily identified by their presence on only one of the linked fragments.Type: ApplicationFiled: February 18, 2021Publication date: August 12, 2021Inventors: Joel Pel, Andrea Marziali
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Publication number: 20210238663Abstract: Methods and apparatus providing for the isolation of an unknown mutation from a sample comprising wild type nucleic acids and mutated nucleic acids through the application of time-varying driving fields and periodically varying mobility-altering fields to the sample within in an affinity matrix.Type: ApplicationFiled: April 9, 2021Publication date: August 5, 2021Applicant: Quantum-Si IncorporatedInventors: Andrea Marziali, Milenko Despotovic, Joel Pel
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Publication number: 20210198731Abstract: The invention generally relates to capturing, amplifying, and sequencing nucleic acids. In certain embodiments, linked capture probes and multiple binding and extension steps improve specificity over traditional single binding target capture techniques. Methods of seeding sequencing clusters with captured target nucleic acids are also disclosed. Linked adapters may be used to increase adapter ligation selectively or efficiency and yield. Ligation adapters and primers can be linked to various sequence-specific or feature-specific molecules to selectively bind targets for ligation or amplification with universal adapters or primers.Type: ApplicationFiled: August 23, 2019Publication date: July 1, 2021Inventors: Joel Pel, Andrea Marziali
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Patent number: 11021742Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two or more template nucleic acids are joined together by a linking molecule, such as a PEG derivative. Identical copies of a nucleic acid fragment or both strands of a duplex fragment may be linked together. The linked nucleic acids are amplified, creating linked amplicons. Emulsion PCR with linked primers creates linked template nucleic acids for seeding sequencing clusters and errors can be readily identified by their presence on only one of the linked fragments.Type: GrantFiled: March 28, 2017Date of Patent: June 1, 2021Assignee: Boreal Genomics, Inc.Inventors: Andrea Marziali, Joel Pel