公开(公告)号：US20250011863A1

公开(公告)日：2025-01-09

申请号：US18769897

申请日：2024-07-11

Applicant: Life Technologies Corporation

Inventor： Dumitru Brinza ,  Zheng Zhang ,  Fiona Hyland ,  Rajesh Gottimukkala

IPC: C12Q1/6874 ,  G16B5/00 ,  G16B5/20 ,  G16B30/00 ,  G16B30/10 ,  G16B30/20

Abstract: 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.

公开(公告)号：US20170335387A1

公开(公告)日：2017-11-23

申请号：US15497872

申请日：2017-04-26

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Dumitru Brinza ,  Zheng ZHANG ,  Fiona HYLAND ,  Rajesh GOTTIMUKKALA

IPC: C12Q1/68 ,  G06F19/22 ,  G06F19/12

CPC classification number: C12Q1/6874 ,  G16B5/00 ,  G16B30/00

Abstract: 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.

公开(公告)号：US20180298424A1

公开(公告)日：2018-10-18

申请号：US15952463

申请日：2018-04-13

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Dumitru Brinza ,  Fiona Hyland

IPC: C12Q1/6806 ,  C12Q1/6869 ,  C12Q1/6858 ,  G06F19/22

Abstract: 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.

公开(公告)号：US20250061970A1

公开(公告)日：2025-02-20

申请号：US18816167

申请日：2024-08-27

Applicant: Life Technologies Corporation

Inventor： Sowmi Utiramerur ,  Dumitru Brinza ,  Marcin Sikora ,  Christian Koller ,  Earl Hubbell ,  Chantal Roth ,  Rajesh Gottimukkala

IPC: G16B30/10 ,  G16B20/20 ,  G16B30/00

Abstract: 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.

公开(公告)号：US11124842B2

公开(公告)日：2021-09-21

申请号：US16503262

申请日：2019-07-03

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Kelli Bramlett ,  Dumitru Brinza ,  Richard Chien ,  Dalia Dhingra ,  Jian Gu ,  Ann Mongan

IPC: C12Q1/6886 ,  C12Q1/6874 ,  C12Q1/6827

Abstract: 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.

公开(公告)号：US09957551B2

公开(公告)日：2018-05-01

申请号：US14711501

申请日：2015-05-13

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Dumitru Brinza ,  Fiona Hyland

IPC: C12Q1/68 ,  G06F19/22

CPC classification number: C12Q1/6806 ,  C12Q1/6858 ,  C12Q1/6869 ,  G06F19/22 ,  C12Q2525/161 ,  C12Q2525/173

Abstract: 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.

公开(公告)号：US11817180B2

公开(公告)日：2023-11-14

申请号：US16279315

申请日：2019-02-19

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Zheng Zhang ,  Danwei Guo ,  Yuandan Lou ,  Asim Siddiqui ,  Dumitru Brinza

IPC: G16B30/10 ,  G16B30/00 ,  G16B30/20

CPC classification number: G16B30/10 ,  G16B30/00 ,  G16B30/20

Abstract: 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.

公开(公告)号：US11091811B2

公开(公告)日：2021-08-17

申请号：US16503262

申请日：2019-07-03

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Kelli Bramlett ,  Dumitru Brinza ,  Richard Chien ,  Dalia Dhingra ,  Jian Gu ,  Ann Mongan

IPC: C12Q1/6886 ,  C12Q1/6874 ,  C12Q1/6827

Abstract: 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.

公开(公告)号：US10344336B2

公开(公告)日：2019-07-09

申请号：US15178450

申请日：2016-06-09

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Kelli Bramlett ,  Dumitru Brinza ,  Richard Chien ,  Dalia Dhingra ,  Jian Gu ,  Ann Mongan

IPC: C12Q1/6827 ,  C12Q1/6874 ,  C12Q1/6886 ,  C07H21/02

Abstract: 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.

公开(公告)号：US20240203525A1

公开(公告)日：2024-06-20

申请号：US18531920

申请日：2023-12-07

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Rajesh Gottimukkala ,  Cheng-Zong Bai ,  Dumitru Brinza ,  Jeoffrey Schageman ,  Varun Bagai

IPC: G16B30/00 ,  C12Q1/6853 ,  G16B20/20 ,  G16B30/10 ,  G16B50/50

CPC classification number: G16B30/00 ,  C12Q1/6853 ,  G16B20/20 ,  G16B30/10 ,  G16B50/50

Abstract: 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.