公开(公告)号：US20180340234A1

公开(公告)日：2018-11-29

申请号：US15989359

申请日：2018-05-25

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Charles Scafe ,  Dumitru Brinza ,  James Veitch ,  Rongsu Qi ,  Fiona Hyland

IPC: C12Q1/6886 ,  C12Q1/6851 ,  C12Q1/6869 ,  G06F19/22 ,  G06F19/24

Abstract: A method for detecting large rearrangements in BRCA1 and BRCA2 genes includes amplifying a nucleic acid sample in the presence of a primer pool to produce amplicons, where the primer pool includes target specific primers targeting regions of exons of the BRCA1 and BRCA2 genes. The method further includes sequencing the amplicons to generate a plurality of reads, mapping the reads to a reference sequence, determining a number of reads per amplicon for the amplicons associated with the exons of the BRCA and the BRCA2 genes, determining exon copy numbers for the exons of the BRCA1 and BRCA2 genes based on the number of reads per amplicon, detecting an exon deletion or duplication based on the exon copy numbers, and detecting a whole gene deletion of the BRCA1 or BRCA2 gene based on the number of reads per amplicon associated with the exons of the BRCA1 and BRCA2 genes.

公开(公告)号：US20180276338A1

公开(公告)日：2018-09-27

申请号：US15928202

申请日：2018-03-22

Applicant: LIFE TECHNOLOGIES CORPORATION

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

IPC: G06F19/22

CPC classification number: G16B30/00

Abstract: Systems and methods are used to identify an exon junction from a single read of a transcript. A transcript sample is interrogated and a read sequence is produced using a nucleic acid sequencer. A first exon sequence and a second exon sequence are obtained using the processor. The first exon sequence is mapped to a prefix of the read sequence using the processor. The second exon sequence is mapped to a suffix of the read sequence using the processor. A sum of a number of sequence elements of the first exon sequence that overlap the prefix of the read sequence, of a number of sequence elements of the second exon sequence that overlap the suffix of the read sequence, and of a constant is calculated using the processor. If the sum equals a length of the read sequence, a junction is identified in the read using the processor.

公开(公告)号：US20180268103A1

公开(公告)日：2018-09-20

申请号：US15866578

申请日：2018-01-10

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Fiona Hyland ,  Rajesh Gottimukkala

IPC: G06F19/22 ,  C12Q1/6809 ,  G06F19/18

CPC classification number: G16B30/00 ,  C12Q1/6809 ,  G16B20/00 ,  C12Q2535/122 ,  C12Q2537/16 ,  C12Q2537/165

Abstract: In one aspect, a system for implementing a copy number variation analysis method, is disclosed. The system can include a nucleic acid sequencer and a computing device in communications with the nucleic acid sequencer. The nucleic acid sequencer can be configured to interrogate a sample to produce a nucleic acid sequence data file containing a plurality of nucleic acid sequence reads. In various embodiments, the computing device can be a workstation, mainframe computer, personal computer, mobile device, etc. The computing device can comprise a sequencing mapping engine, a coverage normalization engine, a segmentation engine and a copy number variation identification engine.

公开(公告)号：US20160019340A1

公开(公告)日：2016-01-21

申请号：US14802595

申请日：2015-07-17

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Rajesh Kumar Gottimukkala ,  Fiona Hyland

IPC: G06F19/22

CPC classification number: G16B30/00 ,  C12Q1/6869 ,  C12Q2535/122 ,  C12Q2563/116

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.

Abstract translation: 用于鉴定基因融合物的系统和方法可以从核酸样品获得多个扩增子的测序信息。 排序信息可以包括最初部分地映射到参考序列的多个读取。 可以通过将部分映射的读取分割成映射和未映射的片段来生成片段，并且片段可以被重新映射到参考序列。 基因融合可以基于第一片段与第一个基因的读数相关，第二个片段映射到第二个基因。

公开(公告)号：US20140051154A1

公开(公告)日：2014-02-20

申请号：US13965944

申请日：2013-08-13

Applicant: Life Technologies Corporation

Inventor： Fiona Hyland ,  Rajesh Gottimukkala

IPC: G06F19/22

CPC classification number: G16B30/00 ,  C12Q1/6809 ,  G16B20/00 ,  C12Q2535/122 ,  C12Q2537/16 ,  C12Q2537/165

Abstract: In one aspect, a system for implementing a copy number variation analysis method, is disclosed. The system can include a nucleic acid sequencer and a computing device in communications with the nucleic acid sequencer. The nucleic acid sequencer can be configured to interrogate a sample to produce a nucleic acid sequence data file containing a plurality of nucleic acid sequence reads. In various embodiments, the computing device can be a workstation, mainframe computer, personal computer, mobile device, etc.

Abstract translation: 一方面，公开了一种用于实现副本号变更分析方法的系统。 该系统可以包括与核酸测序仪通信的核酸测序仪和计算设备。 核酸测序仪可配置成询问样品以产生含有多个核酸序列读数的核酸序列数据文件。 在各种实施例中，计算设备可以是工作站，大型计算机，个人计算机，移动设备等。