Patents by Inventor Rajesh Gottimukkala
Rajesh Gottimukkala 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: 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: 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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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: 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
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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: 20200318175Abstract: A method for detecting a gene fusion includes amplifying a nucleic acid sample in the presence of primer pool to produce a plurality of amplicons. The primer pool includes primers targeting a plurality of exon-exon junctions of a driver gene. The amplicons correspond to the exon-exon junctions. The amplicons are sequenced and aligned to a reference sequence. The number of reads corresponding to each amplicon is normalized to give a normalized read count. A baseline correction is applied to the normalized read counts for the amplicons to form corrected read counts. A binary segmentation score is calculated for each corrected read count. A predicted breakpoint for the gene fusion is determined based on the amplicon index corresponding to the maximum absolute binary segmentation score. Gene fusion events may be detected in a partner agnostic manner, i.e. without prior knowledge of the specific fusion partner genes or specific breakpoint information.Type: ApplicationFiled: March 20, 2020Publication date: October 8, 2020Inventors: Rajesh GOTTIMUKKALA, Amir MARCOVITZ, Jeoffrey SCHAGEMAN, Varun BAGAI, Jian GU, James VEITCH, Kelli BRAMLETT, Scott MYRAND, Fiona HYLAND, Seth SADIS, Paul WILLIAMS
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Publication number: 20190385698Abstract: 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: June 19, 2019Publication date: December 19, 2019Inventors: Rajesh Gottimukkala, Fiona Hyland
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Publication number: 20190087539Abstract: 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: ApplicationFiled: September 20, 2018Publication date: March 21, 2019Inventors: Rajesh GOTTIMUKKALA, Cheng-Zong BAI, Dumitru BRINZA, Jeoffrey SCHAGEMAN, Varun BAGAI
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Publication number: 20180276335Abstract: 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: March 15, 2018Publication date: September 27, 2018Inventors: Rajesh Gottimukkala, Fiona Hyland, Sowmi Utiramerur, Jeoffrey Schageman, Susan Magdaleno
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Publication number: 20180268103Abstract: 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: January 10, 2018Publication date: September 20, 2018Inventors: Fiona Hyland, Rajesh Gottimukkala
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Patent number: 9953130Abstract: 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: October 1, 2014Date of Patent: April 24, 2018Assignee: Life Technologies CorporationInventors: Rajesh Gottimukkala, Fiona Hyland, Sowmi Utiramerur, Jeoffrey Schageman, Susan Magdaleno
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Publication number: 20180068061Abstract: 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: August 9, 2017Publication date: March 8, 2018Inventors: Sowmi Utiramerur, Dumitru Brinza, Marcin Sikora, Christian Koller, Earl Hubbell, Chantal Roth, Rajesh Gottimukkala
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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: 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: 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: 20140052381Abstract: 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: August 14, 2013Publication date: February 20, 2014Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Sowmi UTIRAMERUR, Dumitru BRINZA, Marcin SIKORA, Christian KOLLER, Earl HUBBELL, Chantal ROTH, 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: 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