公开(公告)号：US20150094212A1

公开(公告)日：2015-04-02

申请号：US14503461

申请日：2014-10-01

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Rajesh Gottimukkala ,  Fiona Hyland ,  Sowmi Utiramerur ,  Jeoffrey Schageman ,  Susan Magdaleno

IPC: C12Q1/68 ,  G06F19/18

CPC classification number: G06F19/18 ,  C12Q1/6858 ,  C12Q1/6869 ,  C12Q2535/101 ,  C12Q2537/143 ,  C12Q2539/105

Abstract: 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.

Abstract translation: 用于识别长缺失的系统和方法可以获得核酸样品的潜在区域内和周围的多个扩增子的测序信息。 排序信息可以包括可以映射到参考序列的多个读取。 使用诸如读数映射到扩增子的参考序列和相对丰度的信息的信息，可以鉴定结构变体，并且如果核酸样品对于结构变体是纯合的或杂合的，则可以进行确定。

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：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.

公开(公告)号：US11894105B2

公开(公告)日：2024-02-06

申请号：US16136463

申请日：2018-09-20

Applicant: LIFE TECHNOLOGIES CORPORATION

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

IPC: G16B30/00 ,  C12Q1/6853 ,  G16B30/10 ,  G16B20/20 ,  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.

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：US10984887B2

公开(公告)日：2021-04-20

申请号：US15921812

申请日：2018-03-15

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Rajesh Gottimukkala ,  Fiona Hyland ,  Sowmi Utiramerur ,  Jeoffrey Schageman ,  Susan Magdaleno

IPC: C12Q1/6858 ,  C12Q1/6869 ,  G16B20/00

Abstract: 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.

公开(公告)号：US20180276335A1

公开(公告)日：2018-09-27

申请号：US15921812

申请日：2018-03-15

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Rajesh Gottimukkala ,  Fiona Hyland ,  Sowmi Utiramerur ,  Jeoffrey Schageman ,  Susan Magdaleno

IPC: G06F19/18 ,  C12Q1/6858 ,  C12Q1/6869

CPC classification number: G16B20/00 ,  C12Q1/6858 ,  C12Q1/6869 ,  C12Q2535/101 ,  C12Q2537/143 ,  C12Q2539/105

Abstract: 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.

公开(公告)号：US09953130B2

公开(公告)日：2018-04-24

申请号：US14503461

申请日：2014-10-01

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Rajesh Gottimukkala ,  Fiona Hyland ,  Sowmi Utiramerur ,  Jeoffrey Schageman ,  Susan Magdaleno

IPC: C12Q1/68 ,  G06F19/18

CPC classification number: G06F19/18 ,  C12Q1/6858 ,  C12Q1/6869 ,  C12Q2535/101 ,  C12Q2537/143 ,  C12Q2539/105

Abstract: 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.