公开(公告)号：US20250084470A1

公开(公告)日：2025-03-13

申请号：US18896256

申请日：2024-09-25

Applicant: Life Technologies Corporation

Inventor： Rajesh Gottimukkala ,  Amir Marcovitz ,  Jeoffrey Schageman ,  Varun Bagai ,  Jian Gu ,  James Veitch ,  Kelli Bramlett ,  Scott Myrand ,  Fiona Hyland ,  Seth Sadis ,  Paul Williams

IPC: C12Q1/6851 ,  G06F17/18 ,  G16B25/10

Abstract: 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.

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：US09970048B2

公开(公告)日：2018-05-15

申请号：US13774648

申请日：2013-02-22

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Jian Gu ,  Kelli Bramlett ,  Christopher Burnett

IPC: C12Q1/68

CPC classification number: C12Q1/6806 ,  C12Q1/6848 ,  C12Q2521/501 ,  C12Q2525/113 ,  C12Q2525/186 ,  C12Q2525/191 ,  C12Q2537/163

Abstract: Disclosed are compositions and methods for the preparation of RNA libraries for sequencing, gene expression profiling, microarray and other uses and for simplification of the library preparation process. The disclosure provides blocking oligonucleotides which bind to byproduct nucleic acid molecules formed during the ligation of adapters to nucleic acid segments prior to sequencing and inhibit or block amplification of the byproduct nucleic acid molecules in subsequent amplification reactions. Methods for library preparation using blocking oligonucleotides are also provided.

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：US12139753B2

公开(公告)日：2024-11-12

申请号：US16825238

申请日：2020-03-20

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Rajesh Gottimukkala ,  Amir Marcovitz ,  Jeoffrey Schageman ,  Varun Bagai ,  Jian Gu ,  James Veitch ,  Kelli Bramlett ,  Scott Myrand ,  Fiona Hyland ,  Seth Sadis ,  Paul Williams

IPC: C12Q1/68 ,  C12Q1/6851 ,  G06F17/18 ,  G16B25/10

Abstract: 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.

公开(公告)号：US11136616B2

公开(公告)日：2021-10-05

申请号：US15950921

申请日：2018-04-11

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Jian Gu ,  Kelli Bramlett ,  Christopher Burnett

IPC: C12Q1/68 ,  C12Q1/6806 ,  C12Q1/6848

Abstract: Disclosed are compositions and methods for the preparation of RNA libraries for sequencing, gene expression profiling, microarray and other uses and for simplification of the library preparation process. The disclosure provides blocking oligonucleotides which bind to byproduct nucleic acid molecules formed during the ligation of adapters to nucleic acid segments prior to sequencing and inhibit or block amplification of the byproduct nucleic acid molecules in subsequent amplification reactions. Methods for library preparation using blocking oligonucleotides are also provided.