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：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：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.

公开(公告)号：US20140080718A1

公开(公告)日：2014-03-20

申请号：US14024878

申请日：2013-09-12

Applicant: Life Technologies Corporation

Inventor： Fiona Hyland ,  Heinz Breu

IPC: G06F19/18

CPC classification number: G16B20/00

Abstract: 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.

Abstract translation: 用于鉴定与遗传疾病相关的变体的系统和方法可以包括获得针对变体位置的列表的多个个体的呼叫。 可以将呼叫进行比较，以确定在受影响的个体中发现的变体，并且在不受影响的个体中不存在。 这样的变体可以包括杂合性的丧失，反式复合杂合子，增加的频率线粒体变体，纯合隐性变体，从头变体，性别连锁的变体及其组合。

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：US20230282306A1

公开(公告)日：2023-09-07

申请号：US18170797

申请日：2023-02-17

Applicant: Life Technologies Corporation

Inventor： Fiona Hyland ,  Asha Kamat ,  Timothy Looney

IPC: G16B20/20 ,  G06F16/2457 ,  G06F16/248 ,  G06N3/126

CPC classification number: G16B20/20 ,  G06F16/24575 ,  G06F16/248 ,  G06N3/126

Abstract: The method includes compressing numbers of reads data for targeted genes of a gene expression assay performed on a test sample. The targeted genes are organized into categories. Each category represents a functional context associated with the targeted genes in that category. The numbers of reads corresponding to targeted genes each category is compressed to form a compressed value for the category. The compressed value is compared to a baseline value for the category to determine an enrichment or a loss of a signature corresponding to the functional context of the category. The method may include analyzing information from multiple assays performed on the test sample, assigning a score value to each assay result and predicting a response to immune-oncology treatment based on the assigned scores.

公开(公告)号：US20210173842A1

公开(公告)日：2021-06-10

申请号：US17124846

申请日：2020-12-17

Applicant: Life Technologies Corporation

Inventor： Liviu Popescu ,  Fiona Hyland

IPC: G06F16/2457 ,  G06F16/2455 ,  G06F16/248 ,  G16B50/00 ,  G16B40/00

Abstract: 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.

公开(公告)号：US11021734B2

公开(公告)日：2021-06-01

申请号：US15952463

申请日：2018-04-13

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Dumitru Brinza ,  Fiona Hyland

IPC: C12Q1/6869 ,  C12Q1/6858 ,  C12Q1/6806 ,  G16B30/00

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：US20190385698A1

公开(公告)日：2019-12-19

申请号：US16445477

申请日：2019-06-19

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Rajesh Gottimukkala ,  Fiona Hyland

IPC: G16B30/00

Abstract: 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.