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: 20170335387Abstract: 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: April 26, 2017Publication date: November 23, 2017Inventors: Dumitru Brinza, Zheng ZHANG, Fiona HYLAND, Rajesh GOTTIMUKKALA
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Publication number: 20170132359Abstract: 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: October 17, 2016Publication date: May 11, 2017Inventors: Alexander Joyner, Fiona Hyland, Heinz Breu
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Publication number: 20160140291Abstract: 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: January 20, 2016Publication date: May 19, 2016Inventors: Zheng ZHANG, Sowmi UTIRAMERUR, Fiona HYLAND
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Publication number: 20160078094Abstract: 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: September 21, 2015Publication date: March 17, 2016Inventors: Liviu Popescu, Fiona HYLAND
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Patent number: 9268903Abstract: 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: GrantFiled: July 6, 2011Date of Patent: February 23, 2016Assignee: Life Technologies CorporationInventors: Zheng Zhang, Sowmi Utiramerur, Fiona Hyland
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Publication number: 20160026753Abstract: Systems and method for annotating variants within a genome can call variants from reads or receive called variants directly and associate the called variants with functional annotations and interpretive annotations. A summary report of the called variants, the associated functional annotations, and the associated interpretive annotations can be generated.Type: ApplicationFiled: June 24, 2015Publication date: January 28, 2016Inventors: Brijesh Krishnaswami, Srikanth JANDHYALA, Yuandan LOU, Asim SIDDIQUI, Mrunal AGATE, Ameet DHAPULKAR, Heinz BREU, Amitabh SHUKLA, Karl KUHLMANN, Fiona HYLAND, Gulsah ALTUN, Daryl THOMAS
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Publication number: 20160019340Abstract: Systems and method for identifying gene fusions can obtain sequencing information for a plurality of amplicons from a nucleic acid sample. The sequencing information can include a plurality of reads that are initially partially mapped to a reference sequence. Fragments may be generated by splitting the partially mapped reads into mapped and unmapped fragments, and the fragments may be remapped to the reference sequence. Gene fusions can be identified based on reads where the first fragment maps to a first gene and the second fragment maps to a second gene.Type: ApplicationFiled: July 17, 2015Publication date: January 21, 2016Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Rajesh Kumar Gottimukkala, Fiona Hyland
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Publication number: 20150094212Abstract: 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: ApplicationFiled: October 1, 2014Publication date: April 2, 2015Inventors: Rajesh Gottimukkala, Fiona Hyland, Sowmi Utiramerur, Jeoffrey Schageman, Susan Magdaleno
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Publication number: 20140080718Abstract: 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: ApplicationFiled: September 12, 2013Publication date: March 20, 2014Applicant: Life Technologies CorporationInventors: Fiona Hyland, Heinz Breu
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Publication number: 20140051154Abstract: 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.Type: ApplicationFiled: August 13, 2013Publication date: February 20, 2014Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Fiona Hyland, Rajesh Gottimukkala
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Publication number: 20130345066Abstract: 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: May 9, 2013Publication date: December 26, 2013Applicant: Life Technologies CorporationInventors: Dumitru BRINZA, Zheng ZHANG, Fiona HYLAND, Rajesh GOTTIMUKKALA
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Publication number: 20130288902Abstract: 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: March 6, 2013Publication date: October 31, 2013Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Sowmi UTIRAMERUR, Simon CAWLEY, Yongming SUN, Fiona HYLAND
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Publication number: 20130268207Abstract: Systems and method for identifying somatic mutations can receive first ans 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: March 8, 2013Publication date: October 10, 2013Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Alexander JOYNER, Fiona HYLAND, Heinz BREU
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Publication number: 20130073214Abstract: 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: September 20, 2012Publication date: March 21, 2013Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Fiona HYLAND, Eric TSUNG, Vasisht TADIGOTLA, Zheng ZHANG, Dumitru BRINZA, Onur SAKARYA, Xing XU
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Publication number: 20120203792Abstract: 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: February 1, 2012Publication date: August 9, 2012Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Zheng ZHANG, Fiona HYLAND, Sowmi UTIRAMERUR
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Publication number: 20120102054Abstract: 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: October 25, 2011Publication date: April 26, 2012Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Liviu POPESCU, Fiona Hyland
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Publication number: 20120046877Abstract: 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. The sequence mapping engine can be configured to align the plurality of nucleic acid sequence reads to a reference sequence, wherein the aligned nucleic acid sequence reads merge to form a plurality of chromosomal regions.Type: ApplicationFiled: July 5, 2011Publication date: February 23, 2012Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Fiona HYLAND, Rajesh Gottimukkala
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Publication number: 20120011086Abstract: 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: July 6, 2011Publication date: January 12, 2012Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Zheng ZHANG, Sowmi Utiramerur, Fiona Hyland
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Publication number: 20110270532Abstract: Systems and methods are used to identify an exon junction from a single read of a transcript. A transcript sample is interrogated and a read sequence is produced using a nucleic acid sequencer. A first exon sequence and a second exon sequence are obtained using the processor. The first exon sequence is mapped to a prefix of the read sequence using the processor. The second exon sequence is mapped to a suffix of the read sequence using the processor. A sum of a number of sequence elements of the first exon sequence that overlap the prefix of the read sequence, of a number of sequence elements of the second exon sequence that overlap the suffix of the read sequence, and of a constant is calculated using the processor. If the sum equals a length of the read sequence, a junction is identified in the read using the processor.Type: ApplicationFiled: April 29, 2011Publication date: November 3, 2011Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Paolo VATTA, Onur Sakarya, Heinz Breu, Liviu Popescu, Asim Siddiqui, Fiona Hyland