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：US12040048B2

公开(公告)日：2024-07-16

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：US11566281B2

公开(公告)日：2023-01-31

申请号：US16145373

申请日：2018-09-28

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Sowmi Utiramerur ,  Simon Cawley ,  Yongming Sun ,  Fiona Hyland

IPC: C12Q1/6869 ,  G16B30/00 ,  G16B30/10

Abstract: Systems and methods for analyzing overlapping sequence information can obtain first and second overlapping sequence information for a polynucleotide, align the first and second sequence information, determine a degree of agreement between the first and second sequence information for a location along the polynucleotide, and determine a base call and a quality value for the location.

公开(公告)号：US20220284986A1

公开(公告)日：2022-09-08

申请号：US17699439

申请日：2022-03-21

Applicant: Life Technologies Corporation

Inventor： Paolo Vatta ,  Onur Sakarya ,  Heinz Breu ,  Liviu Popescu ,  Asim Siddiqui ,  Fiona Hyland

IPC: G16B30/10 ,  G16B30/00

Abstract: Identification of exon junctions includes obtaining a first read sequence based on a detected plurality of signals of a first sequence. A list of exon prefix and suffix sequences are generated by identifying exons of the human genome with a prefix sequence mapping to a suffix sequence of the first read sequence and by identifying exons with a suffix sequence mapping to a prefix sequence of the first read sequence. A pair of exon sequences is selected, with a first exon sequence being one of the exon suffix sequences and a second exon sequence being one of the exon prefix sequences. Summing a number of sequence elements of the first exon sequence that overlap the prefix of the first read sequence, a number of sequence elements of the second exon sequence that overlap the suffix of the first read sequence, and a constant is used to identify a fusion junction.

公开(公告)号：US20200027527A1

公开(公告)日：2020-01-23

申请号：US16530015

申请日：2019-08-02

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Fiona Hyland ,  Eric TSUNG ,  Vasisht TADIGOTLA ,  Zheng ZHANG ,  Dumitru BRINZA ,  Onur SAKARYA ,  Xing XU

IPC: G16B30/00

Abstract: Systems and method for determining variants can receive mapped reads, and call variants. In embodiments, flow space information for the reads can be aligned to a flow space representation of a corresponding portion of the reference. Reads spanning a position with a potential variant can be grouped and a score can be calculated for the variant. Based on the scores, a list of probable variants can be provided. In various embodiments, low frequency variants can be identified where multiple potential variants are present at a position.

公开(公告)号：US20170132359A1

公开(公告)日：2017-05-11

申请号：US15295114

申请日：2016-10-17

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Alexander Joyner ,  Fiona Hyland ,  Heinz Breu

IPC: G06F19/22

CPC classification number: G16B30/00

Abstract: Systems and method for identifying somatic mutations can receive first and second sequence information, determine if a variant present in the first sequencing information is also present in the second sequence information, and identify variants present in the first sequence information are somatic mutations when the variant is either not present in the second sequence information or the presence of the variant in the second sequence information is likely due to a sequencing error.

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：US20250037797A1

公开(公告)日：2025-01-30

申请号：US18786945

申请日：2024-07-29

Applicant: Life Technologies Corporation

Inventor： Rajesh Gottimukkala ,  Fiona Hyland

IPC: G16B30/10 ,  C12Q1/6869 ,  G16B20/20 ,  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.

公开(公告)号：US20230395192A1

公开(公告)日：2023-12-07

申请号：US18450468

申请日：2023-08-16

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Fiona Hyland ,  Heinz Breu

IPC: G16B20/20 ,  G16B20/00

CPC classification number: G16B20/20 ,  G16B20/00

Abstract: Systems and method for identifying variants associated with a genetic disease can include obtaining sequencing reads for a plurality of individuals for a list of variant positions. The reads 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.

公开(公告)号：US11610648B2

公开(公告)日：2023-03-21

申请号：US16851472

申请日：2020-04-17

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Fiona Hyland ,  Asha Kamat ,  Timothy Looney

IPC: G16B20/20 ,  G06F16/2457 ,  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.