Patents by Inventor Fiona Hyland
Fiona Hyland 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: 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: 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: 20230410946Abstract: A computer-implemented method for classifying alignments of paired nucleic acid sequence reads is disclosed. A plurality of paired nucleic acid sequence reads is received, wherein each read is comprised of a first tag and a second tag separated by an insert region. Potential alignments for the first and second tags of each read to a reference sequence is determined, wherein the potential alignments satisfies a minimum threshold mismatch constraint. Potential paired alignments of the first and second tags of each read are identified, wherein a distance between the first and second tags of each potential paired alignment is within an estimated insert size range. An alignment score is calculated for each potential paired alignment based on a distance between the first and second tags and a total number of mismatches for each tag.Type: ApplicationFiled: June 21, 2023Publication date: December 21, 2023Inventors: Zheng ZHANG, Sowmi UTIRAMERUR, Fiona HYLAND
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Publication number: 20230395192Abstract: Systems and method for identifying variants associated with a genetic disease can include obtaining sequencing reads for a plurality of individuals for a list of variant positions. The reads can be compared to identify variants that are found in affected individuals and absent in non-affected individuals. Such variants can include loss of heterozygosity, trans-phased compound heterozygotes, increased frequency mitochondrial variants, homozygous recessive variants, de novo variants, sex-linked variants, and combinations thereof.Type: ApplicationFiled: August 16, 2023Publication date: December 7, 2023Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Fiona Hyland, Heinz Breu
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Publication number: 20230340586Abstract: Systems and methods for analyzing overlapping sequence information can obtain first and second overlapping sequence information for a polynucleotide, align the first and second sequence information, determine a degree of agreement between the first and second sequence information for a location along the polynucleotide, and determine a base call and a quality value for the location.Type: ApplicationFiled: January 11, 2023Publication date: October 26, 2023Inventors: Sowmi UTIRAMERUR, Simon CAWLEY, Yongming SUN, Fiona HYLAND
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Publication number: 20230282306Abstract: The method includes compressing numbers of reads data for targeted genes of a gene expression assay performed on a test sample. The targeted genes are organized into categories. Each category represents a functional context associated with the targeted genes in that category. The numbers of reads corresponding to targeted genes each category is compressed to form a compressed value for the category. The compressed value is compared to a baseline value for the category to determine an enrichment or a loss of a signature corresponding to the functional context of the category. The method may include analyzing information from multiple assays performed on the test sample, assigning a score value to each assay result and predicting a response to immune-oncology treatment based on the assigned scores.Type: ApplicationFiled: February 17, 2023Publication date: September 7, 2023Inventors: Fiona Hyland, Asha Kamat, Timothy Looney
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Patent number: 11749376Abstract: Systems and method for identifying variants associated with a genetic disease can include obtaining calls for a plurality of individuals for a list of variant positions. The calls can be compared to identify variants that are found in affected individuals and absent in non-affected individuals. Such variants can include loss of heterozygosity, trans-phased compound heterozygotes, increased frequency mitochondrial variants, homozygous recessive variants, de novo variants, sex-linked variants, and combinations thereof.Type: GrantFiled: June 7, 2019Date of Patent: September 5, 2023Assignee: LIFE TECHNOLOGIES CORPORATIONInventors: Fiona Hyland, Heinz Breu
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Patent number: 11610648Abstract: The method includes compressing numbers of reads data for targeted genes of a gene expression assay performed on a test sample. The targeted genes are organized into categories. Each category represents a functional context associated with the targeted genes in that category. The numbers of reads corresponding to targeted genes each category is compressed to form a compressed value for the category. The compressed value is compared to a baseline value for the category to determine an enrichment or a loss of a signature corresponding to the functional context of the category. The method may include analyzing information from multiple assays performed on the test sample, assigning a score value to each assay result and predicting a response to immune-oncology treatment based on the assigned scores.Type: GrantFiled: April 17, 2020Date of Patent: March 21, 2023Assignee: Life Technologies CorporationInventors: Fiona Hyland, Asha Kamat, Timothy Looney
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Publication number: 20230083827Abstract: Systems and method for identifying somatic mutations can receive first and second sequence information, determine if a variant present in the first sequencing information is also present in the second sequence information, and identify variants present in the first sequence information are somatic mutations when the variant is either not present in the second sequence information or the presence of the variant in the second sequence information is likely due to a sequencing error.Type: ApplicationFiled: September 16, 2022Publication date: March 16, 2023Inventors: Alexander Joyner, Fiona HYLAND, Heinz BREU
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Patent number: 11566281Abstract: Systems and methods for analyzing overlapping sequence information can obtain first and second overlapping sequence information for a polynucleotide, align the first and second sequence information, determine a degree of agreement between the first and second sequence information for a location along the polynucleotide, and determine a base call and a quality value for the location.Type: GrantFiled: September 28, 2018Date of Patent: January 31, 2023Assignee: Life Technologies CorporationInventors: Sowmi Utiramerur, Simon Cawley, Yongming Sun, Fiona Hyland
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Patent number: 11468968Abstract: Systems and method for identifying somatic mutations can receive first and second sequence information, determine if a variant present in the first sequencing information is also present in the second sequence information, and identify variants present in the first sequence information are somatic mutations when the variant is either not present in the second sequence information or the presence of the variant in the second sequence information is likely due to a sequencing error.Type: GrantFiled: June 7, 2019Date of Patent: October 11, 2022Assignee: Life Technologies CorporationInventors: Alexander Joyner, Fiona Hyland, Heinz Breu
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Publication number: 20220284986Abstract: Identification of exon junctions includes obtaining a first read sequence based on a detected plurality of signals of a first sequence. A list of exon prefix and suffix sequences are generated by identifying exons of the human genome with a prefix sequence mapping to a suffix sequence of the first read sequence and by identifying exons with a suffix sequence mapping to a prefix sequence of the first read sequence. A pair of exon sequences is selected, with a first exon sequence being one of the exon suffix sequences and a second exon sequence being one of the exon prefix sequences. Summing a number of sequence elements of the first exon sequence that overlap the prefix of the first read sequence, a number of sequence elements of the second exon sequence that overlap the suffix of the first read sequence, and a constant is used to identify a fusion junction.Type: ApplicationFiled: March 21, 2022Publication date: September 8, 2022Applicant: Life Technologies CorporationInventors: Paolo Vatta, Onur Sakarya, Heinz Breu, Liviu Popescu, Asim Siddiqui, Fiona Hyland
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Publication number: 20220251669Abstract: The present disclosure provides compositions and methods, as well as combinations, kits, and systems that include the compositions and methods, for amplification, detection, characterization, assessment, profiling and/or measurement of nucleic acids in samples, particularly biological samples. Compositions and methods provided herein include combinations of microbial species target-specific nucleic acid primers for selective amplification and/or combinations of primers for amplification of nucleic acids from a large group of taxonomically related microorganisms. In one aspect, amplified nucleic acids obtained using the compositions and methods can be used in various processes including nucleic acid sequencing and used to detect the presence of microbial species and assess microbial populations in a variety of samples.Type: ApplicationFiled: April 8, 2022Publication date: August 11, 2022Inventors: Shrutii SARDA, Anna MCGEACHY, Rajesh GOTTIMUKKALA, David MERRILL, Heesun SHIN, Aren EWING, Wing LEE, Birgit DREWS, Fiona HYLAND, Janice AU-YOUNG
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Publication number: 20210343367Abstract: A targeted panel with low sample input requirements from a tumor only sample may be processed to estimate mutation load in a tumor sample. The method may include detecting variants in nucleic acid sequence reads corresponding to targeted locations in the tumor sample genome; annotating detected variants with an annotation information from a population database; filtering the detected variants, wherein the filtering rule set retains the somatic variants and removes germ-line variants; counting the identified somatic variants to give a number of somatic variants; determining a number of bases in covered regions of the targeted locations in the tumor sample genome; and calculating a number of somatic variants per megabase, provides an estimate of the mutation load per megabase in the tumor sample genome.Type: ApplicationFiled: July 9, 2021Publication date: November 4, 2021Inventors: Ruchi Chaudhary, Fiona HYLAND
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Publication number: 20210292831Abstract: In one aspect, a system for implementing a copy number variation analysis method, is disclosed. The system can include a nucleic acid sequencer and a computing device in communications with the nucleic acid sequencer. The nucleic acid sequencer can be configured to interrogate a sample to produce a nucleic acid sequence data file containing a plurality of nucleic acid sequence reads. In various embodiments, the computing device can be a workstation, mainframe computer, personal computer, mobile device, etc. The computing device can comprise a sequencing mapping engine, a coverage normalization engine, a segmentation engine and a copy number variation identification engine.Type: ApplicationFiled: April 8, 2021Publication date: September 23, 2021Inventors: Fiona Hyland, Rajesh Gottimukkala
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Patent number: 11101019Abstract: A targeted panel with low sample input requirements from a tumor only sample may be processed to estimate mutation load in a tumor sample. The method may include: detecting variants in nucleic acid sequence reads corresponding to targeted locations in the tumor sample genome; annotating detected variants with an annotation information from a population database; filtering the detected variants, wherein the filtering rule set retains the somatic variants and removes germ-line variants; counting the identified somatic variants to give a number of somatic variants; determining a number of bases in covered regions of the targeted locations in the tumor sample genome; and calculating a number of somatic variants per megabase, provides an estimate of the mutation load per megabase in the tumor sample genome.Type: GrantFiled: December 7, 2017Date of Patent: August 24, 2021Assignee: Life Technologies CorporationInventors: Ruchi Chaudhary, Fiona Hyland
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Publication number: 20210210164Abstract: Systems, methods, and computer program products for aligning a fragment sequence to a target sequencing. The alignment is allowed at most one gap, such as an insertion or a deletion. In some embodiments, both a gapped alignment and an ungapped alignment can be produced. A selection can be made between the gapped alignment and the ungapped alignment based on a quality value for each alignment.Type: ApplicationFiled: December 29, 2020Publication date: July 8, 2021Inventors: Zheng ZHANG, Fiona HYLAND, Sowmi UTIRAMERUR
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Publication number: 20210173842Abstract: Systems, methods, software and computer-usable media for annotating biomolecule-related data are disclosed. In certain exemplified embodiments, the biomolecules can be nucleic acids and the data can be sequence-related data. In various embodiments, systems can include one or more public or private biological attributes (e.g., annotation information databases, data storage devices and systems, etc.) sources, one or more genomic features data sources (e.g., genomic variant tools, genomic variant databases, genomic variant data storage devices and systems, etc.), a computing device (e.g., workstation, server, personal computer, mobile device, etc.) hosting an annotations module and/or a reporting module, and a client terminal.Type: ApplicationFiled: December 17, 2020Publication date: June 10, 2021Inventors: Liviu Popescu, Fiona Hyland
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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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Patent number: 10984887Abstract: Systems and method for identifying long deletions can obtain sequencing information for a plurality of amplicons in and around a potential region from a nucleic acid sample. The sequencing information can include a plurality of reads that can be mapped to a reference sequence. Using information, such as where reads map to a reference sequence and relative abundance of reads for the amplicons, structural variants can be identified and a determination can be made if the nucleic acid sample is homozygous or heterozygous for the structural variant.Type: GrantFiled: March 15, 2018Date of Patent: April 20, 2021Assignee: Life Technologies CorporationInventors: Rajesh Gottimukkala, Fiona Hyland, Sowmi Utiramerur, Jeoffrey Schageman, Susan Magdaleno