Patents by Inventor Dumitru Brinza
Dumitru Brinza 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: 11894105Abstract: A method for compressing nucleic acid sequence data wherein each sequence read is associated with a molecular tag sequence, wherein a portion of the sequence reads alignments correspond to sequence reads mapped to a targeted fusion reference sequence includes determining a consensus sequence read for each family of sequence reads based on flow space signal measurements corresponding to the family of sequence reads, determining a consensus sequence alignment for each family of sequence reads, wherein a portion of the consensus sequence alignments correspond to the consensus sequence reads aligned with the targeted fusion reference sequence, generating a compressed data structure comprising consensus compressed data, the consensus compressed data including the consensus sequence read and the consensus sequence alignment for each family, and detecting a fusion using the consensus sequence reads and the consensus sequence alignments from the compressed data structure.Type: GrantFiled: September 20, 2018Date of Patent: February 6, 2024Assignee: Life Technologies CorporationInventors: Rajesh Gottimukkala, Cheng-Zong Bai, Dumitru Brinza, Jeoffrey Schageman, Varun Bagai
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Publication number: 20240035094Abstract: A method for detecting large rearrangements in BRCA1 and BRCA2 genes includes amplifying a nucleic acid sample in the presence of a primer pool to produce amplicons, where the primer pool includes target specific primers targeting regions of exons of the BRCA1 and BRCA2 genes. The method further includes sequencing the amplicons to generate a plurality of reads, mapping the reads to a reference sequence, determining a number of reads per amplicon for the amplicons associated with the exons of the BRCA and the BRCA2 genes, determining exon copy numbers for the exons of the BRCA1 and BRCA2 genes based on the number of reads per amplicon, detecting an exon deletion or duplication based on the exon copy numbers, and detecting a whole gene deletion of the BRCA1 or BRCA2 gene based on the number of reads per amplicon associated with the exons of the BRCA1 and BRCA2 genes.Type: ApplicationFiled: August 8, 2023Publication date: February 1, 2024Inventors: Charles SCAFE, Dumitru BRINZA, James VEITCH, Rongsu QI, Fiona HYLAND
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Publication number: 20240027425Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate configured to rotate. The open substrate can comprise an array of immobilized analytes. A solution comprising a plurality of probes may be directed, via centrifugal force, across the array during rotation of the substrate, to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via continuous rotational area scanning of the substrate.Type: ApplicationFiled: July 20, 2023Publication date: January 25, 2024Inventors: Kristopher BARBEE, Nathan BECKETT, Denis PRISTINSKI, Derek SCHULTE, Avishai BARTOV, Jamie SULLIVAN, Dumitru BRINZA, Abizar LAKDAWALLA, Steven MENCHEN, Gilad ALMOGY, Mark PRATT
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Publication number: 20240021272Abstract: Systems and method for determining variants can receive mapped reads, and call variants. In embodiments, flow space information for the reads can be aligned to a flow space representation of a corresponding portion of the reference. Reads spanning a position with a potential variant can be grouped and a score can be calculated for the variant. Based on the scores, a list of probable variants can be provided. In various embodiments, low frequency variants can be identified where multiple potential variants are present at a position.Type: ApplicationFiled: June 7, 2023Publication date: January 18, 2024Inventors: Fiona HYLAND, Eric TSUNG, Vasisht TADIGOTLA, Zheng ZHANG, Dumitru BRINZA, Onur SAKARYA, Xing XU
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Publication number: 20230407385Abstract: Described herein are methods synchronizing sequencing primers within a sequencing cluster and methods of generating long-range sequencing reads. The methods can include hybridizing primers to polynucleotide copies within a sequencing cluster; extending the primers through a first region of the polynucleotide copies using labeled nucleotides according to a sequencing flow order; extending the primers through a second region of the polynucleotide copies using one or more re-phasing flow steps that each include at least two different types of nucleotide bases; and extending the primers through a third region of the polynucleotide copies using labeled nucleotides according to the sequencing cycle. The rephasing flow steps may be initiated after a predetermined number of sequencing flow steps, after a measured sequencing signal strength falls below a predetermined sequencing signal strength threshold, or a measured sequencing signal-to-noise ratio falls below a sequencing signal-to-noise ratio threshold.Type: ApplicationFiled: November 3, 2021Publication date: December 21, 2023Inventors: Omer BARAD, Mark PRATT, Eliane TREPAGNIER, Yoav ETZIONI, Florian OBERSTRASS, Gilad ALMOGY, Dumitru BRINZA
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Patent number: 11817180Abstract: Nucleic acid sequence mapping/assembly methods are disclosed. The methods initially map only a contiguous portion of each read to a reference sequence and then extends the mapping of the read at both ends of the mapped contiguous portion until the entire read is mapped (aligned). In various embodiments, a mapping score can be calculated for the read alignment using a scoring function, score (i, j)=M+mx, where M can be the number of matches in the extended alignment, x can be the number of mismatches in the alignment, and m can be a negative penalty for each mismatch. The mapping score can be utilized to rank or choose the best alignment for each read.Type: GrantFiled: February 19, 2019Date of Patent: November 14, 2023Assignee: Life Technologies CorporationInventors: Zheng Zhang, Danwei Guo, Yuandan Lou, Asim Siddiqui, Dumitru Brinza
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Patent number: 11747323Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate configured to rotate. The open substrate can comprise an array of immobilized analytes. A solution comprising a plurality of probes may be directed, via centrifugal force, across the array during rotation of the substrate, to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via continuous rotational area scanning of the substrate.Type: GrantFiled: October 7, 2022Date of Patent: September 5, 2023Assignee: ULTIMA GENOMICS, INC.Inventors: Kristopher Barbee, Nathan Beckett, Denis Pristinski, Derek Schulte, Avishai Bartov, Jamie Sullivan, Dumitru Brinza, Abizar Lakdawalla, Steven Menchen, Gilad Almogy, Mark Pratt
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Publication number: 20230152300Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate configured to rotate. The open substrate can comprise an array of immobilized analytes. A solution comprising a plurality of probes may be directed, via centrifugal force, across the array during rotation of the substrate, to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via continuous rotational area scanning of the substrate.Type: ApplicationFiled: October 7, 2022Publication date: May 18, 2023Inventors: Kristopher BARBEE, Nathan BECKETT, Denis PRISTINSKI, Derek SCHULTE, Avishai BARTOV, Jamie SULLIVAN, Dumitru BRINZA, Abizar LAKDAWALLA, Steven MENCHEN, Gilad ALMOGY, Mark PRATT
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Publication number: 20230060685Abstract: Described herein are methods of generating a coupled sequencing read pair for a polynucleotide, and methods of analyzing the coupled sequencing read pair. The coupled sequencing read pair can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the coupled sequencing read pair. Other analytical methods can include using coupled sequencing read pairs to construct or validate a consensus sequence. The coupled sequencing read pair may be generated for a polynucleotide by generating sequencing data for a first region by extending a primer using labeled nucleotides; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein primer extension through the second region is faster than primer extension through the first region; and generating sequencing data associated with a sequence of a third region of the polynucleotide by further extending the primer using labeled nucleotides.Type: ApplicationFiled: August 26, 2022Publication date: March 2, 2023Inventors: Mark Pratt, Gilad Almogy, Dumitru Brinza, Eliane Trepagnier, Omer Barad, Yoav Etzioni, Florian Oberstrass
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Patent number: 11499962Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate configured to rotate. The open substrate can comprise an array of immobilized analytes. A solution comprising a plurality of probes may be directed, via centrifugal force, across the array during rotation of the substrate, to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via continuous rotational area scanning of the substrate.Type: GrantFiled: April 29, 2020Date of Patent: November 15, 2022Assignee: ULTIMA GENOMICS, INC.Inventors: Kristopher Barbee, Nathan Beckett, Denis Pristinski, Derek Schulte, Avishai Bartov, Jamie Sullivan, Dumitru Brinza, Abizar Lakdawalla, Steven Menchen, Gilad Almogy, Mark Pratt
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Patent number: 11459609Abstract: Described herein are methods of generating a coupled sequencing read pair for a polynucleotide, and methods of analyzing the coupled sequencing read pair. The coupled sequencing read pair can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the coupled sequencing read pair. Other analytical methods can include using coupled sequencing read pairs to construct or validate a consensus sequence. The coupled sequencing read pair may be generated for a polynucleotide by generating sequencing data for a first region by extending a primer using labeled nucleotides; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein primer extension through the second region is faster than primer extension through the first region; and generating sequencing data associated with a sequence of a third region of the polynucleotide by further extending the primer using labeled nucleotides.Type: GrantFiled: November 3, 2021Date of Patent: October 4, 2022Assignee: Ultima Genomics, Inc.Inventors: Mark Pratt, Gilad Almogy, Dumitru Brinza, Eliane Trepagnier, Omer Barad, Yoav Etzioni, Florian Oberstrass
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Publication number: 20220170089Abstract: Described herein are methods of generating a coupled sequencing read pair for a polynucleotide, and methods of analyzing the coupled sequencing read pair. The coupled sequencing read pair can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the coupled sequencing read pair. Other analytical methods can include using coupled sequencing read pairs to construct or validate a consensus sequence. The coupled sequencing read pair may be generated for a polynucleotide by generating sequencing data for a first region by extending a primer using labeled nucleotides; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein primer extension through the second region is faster than primer extension through the first region; and generating sequencing data associated with a sequence of a third region of the polynucleotide by further extending the primer using labeled nucleotides.Type: ApplicationFiled: November 3, 2021Publication date: June 2, 2022Inventors: Mark PRATT, Gilad ALMOGY, Dumitru BRINZA, Eliane TREPAGNIER, Omer BARAD, Yoav ETZIONI, Florian OBERSTRASS
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Publication number: 20210363596Abstract: In some embodiments, the disclosure relates generally to methods, as well as related systems, compositions, kits, apparatuses and computer-readable media, comprising a multiplex molecular tagging procedure that employs a plurality of tags that are appended to a plurality of polynucleotides. The tags have characteristics, including a sequence, length and/or detectable moiety, or any other characteristic, that uniquely identifies the polynucleotide molecule to which it is appended, and permits tracking individual tagged molecules in a mixture of tagged molecules. For example, the tag having a unique tag sequence, can uniquely identify an individual polynucleotide to which it is appended, and distinguish the individual polynucleotide from other tagged polynucleotides in a mixture. In some embodiments, the multiplex molecular tagging procedure can be used for generating error-corrected sequencing data and for detecting a target polynucleotide which is present at low abundance in a nucleic acid sample.Type: ApplicationFiled: July 29, 2021Publication date: November 25, 2021Inventors: Kelli BRAMLETT, Dumitru BRINZA, Richard CHIEN, Dalia DHINGRA, Jian GU, Ann MONGAN
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Patent number: 11124842Abstract: In some embodiments, the disclosure relates generally to methods, as well as related systems, compositions, kits, apparatuses and computer-readable media, comprising a multiplex molecular tagging procedure that employs a plurality of tags that are appended to a plurality of polynucleotides. The tags have characteristics, including a sequence, length and/or detectable moiety, or any other characteristic, that uniquely identifies the polynucleotide molecule to which it is appended, and permits tracking individual tagged molecules in a mixture of tagged molecules. For example, the tag having a unique tag sequence, can uniquely identify an individual polynucleotide to which it is appended, and distinguish the individual polynucleotide from other tagged polynucleotides in a mixture. In some embodiments, the multiplex molecular tagging procedure can be used for generating error-corrected sequencing data and for detecting a target polynucleotide which is present at low abundance in a nucleic acid sample.Type: GrantFiled: July 3, 2019Date of Patent: September 21, 2021Assignee: Life Technologies CorporationInventors: Kelli Bramlett, Dumitru Brinza, Richard Chien, Dalia Dhingra, Jian Gu, Ann Mongan
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Patent number: 11091811Abstract: In some embodiments, the disclosure relates generally to methods, as well as related systems, compositions, kits, apparatuses and computer-readable media, comprising a multiplex molecular tagging procedure that employs a plurality of tags that are appended to a plurality of polynucleotides. The tags have characteristics, including a sequence, length and/or detectable moiety, or any other characteristic, that uniquely identifies the polynucleotide molecule to which it is appended, and permits tracking individual tagged molecules in a mixture of tagged molecules. For example, the tag having a unique tag sequence, can uniquely identify an individual polynucleotide to which it is appended, and distinguish the individual polynucleotide from other tagged polynucleotides in a mixture. In some embodiments, the multiplex molecular tagging procedure can be used for generating error-corrected sequencing data and for detecting a target polynucleotide which is present at low abundance in a nucleic acid sample.Type: GrantFiled: July 3, 2019Date of Patent: August 17, 2021Assignee: Life Technologies CorporationInventors: Kelli Bramlett, Dumitru Brinza, Richard Chien, Dalia Dhingra, Jian Gu, Ann Mongan
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Publication number: 20210217491Abstract: Systems and method for determining variants can receive mapped reads and determine a distribution of matched-filter residuals distribution from a plurality of reads at a homopolymer region. The distribution of matched-filter residuals can be fit to uni-modal and bi-modal models. Based on the model that best fits the distribution of matched-filter residuals, the heterozygosity of the sample and the absence or presence of an insertion/deletion in the homopolymer can be determined.Type: ApplicationFiled: January 8, 2021Publication date: July 15, 2021Inventors: Sowmi Utiramerur, Dumitru Brinza, Marcin Sikora, Christian Koller, Earl Hubbell, Chantal Roth, Rajesh Gottimukkala
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Patent number: 11021734Abstract: Systems and method for validation of sequencing results can amplify a target region of a nucleic acid sample in the presence of a primer pool including target specific and variant specific primers. The variant specific primers can include variant specific barcodes and variant specific sequences. An amplicon can be sequenced to determine the sequence of the variant specific barcode. The variant can be identified based on the sequence of the variant specific barcode, and the location of the variant can be determined by mapping the amplicon to a reference sequence.Type: GrantFiled: April 13, 2018Date of Patent: June 1, 2021Assignee: Life Technologies CorporationInventors: Dumitru Brinza, Fiona Hyland
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Publication number: 20210108264Abstract: Systems and method for determining variants can receive mapped reads, align flow space information to a flow space representation of a corresponding portion of the reference. Reads spanning a position with a potential variant can be evaluated in a context specific manner. A list of probable variants can be provided.Type: ApplicationFiled: October 6, 2020Publication date: April 15, 2021Inventors: Dumitru BRINZA, Zheng ZHANG, Fiona HYLAND, Rajesh GOTTIMUKKALA
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Publication number: 20210054442Abstract: Described herein are methods of generating a coupled sequencing read pair for a polynucleotide, and methods of analyzing the coupled sequencing read pair. The coupled sequencing read pair can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the coupled sequencing read pair. Other analytical methods can include using coupled sequencing read pairs to construct or validate a consensus sequence. The coupled sequencing read pair may be generated for a polynucleotide by generating sequencing data for a first region by extending a primer using labeled nucleotides; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein primer extension through the second region is faster than primer extension through the first region; and generating sequencing data associated with a sequence of a third region of the polynucleotide by further extending the primer using labeled nucleotides.Type: ApplicationFiled: October 30, 2020Publication date: February 25, 2021Applicant: Ultima Genomics, Inc.Inventors: Mark PRATT, Gilad ALMOGY, Dumitru BRINZA, Eliane TREPAGNIER, Omer BARAD, Yoav ETZIONI, Florian OBERSTRASS
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Publication number: 20200377937Abstract: Described herein are methods of generating a coupled sequencing read pair for a polynucleotide, and methods of analyzing the coupled sequencing read pair. The coupled sequencing read pair can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the coupled sequencing read pair. Other analytical methods can include using coupled sequencing read pairs to construct or validate a consensus sequence. The coupled sequencing read pair may be generated for a polynucleotide by generating sequencing data for a first region by extending a primer using labeled nucleotides; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein primer extension through the second region is faster than primer extension through the first region; and generating sequencing data associated with a sequence of a third region of the polynucleotide by further extending the primer using labeled nucleotides.Type: ApplicationFiled: May 1, 2020Publication date: December 3, 2020Inventors: Mark PRATT, Gilad ALMOGY, Dumitru BRINZA, Eliane TREPAGNIER, Omer BARAD, Yoav ETZIONI, Florian OBERSTRASS