公开(公告)号：US11783911B2

公开(公告)日：2023-10-10

申请号：US15329016

申请日：2015-07-29

申请人： SEQUENOM, INC.

发明人： Chen Zhao ,  Cosmin Deciu ,  Dirk Johannes Van Den Boom

IPC分类号： G16B20/10 ,  G16B40/00 ,  G16B30/00 ,  C12Q1/6883 ,  G16B20/00 ,  G16B20/20 ,  G16B30/10

CPC分类号： G16B20/10 ,  C12Q1/6883 ,  G16B20/00 ,  G16B20/20 ,  G16B30/00 ,  G16B30/10 ,  G16B40/00 ,  C12Q2600/112 ,  C12Q2600/156

摘要： Methods for non-invasive assessment of genetic variations that make use of nucleic acid fragment length information, in particular length of fragments in circulating cell-free nucleic acids and compares the number of counts from fragments with different length.

公开(公告)号：US11200963B2

公开(公告)日：2021-12-14

申请号：US15661804

申请日：2017-07-27

申请人： Sequenom, Inc.

发明人： Amin Mazloom ,  Cosmin Deciu ,  Chen Zhao ,  Tong Liu ,  Yijin Wu

IPC分类号： G16B20/10 ,  G16B40/00 ,  G16B20/00 ,  G16B20/20 ,  G06N7/00

摘要： Technology provided herein relates in part to non-invasive classification of one or more genetic copy number alterations (CNAs) for a test sample. Certain methods include sampling a quantification of sequence reads from parts of a genome, generating a confidence determination, and using the confidence determination to enhance classification. Technology provided herein is useful for classifying a genetic CNA for a sample as part of non-invasive pre-natal (NIPT) testing and oncology testing, for example.

公开(公告)号：US10930368B2

公开(公告)日：2021-02-23

申请号：US14781987

申请日：2014-04-02

申请人： SEQUENOM, INC.

发明人： Zeljko Dzakula ,  Chen Zhao ,  Cosmin Deciu

IPC分类号： G16B20/00 ,  G16B30/00 ,  G16B40/00 ,  G06F17/18

摘要： A method and system for analyzing circulating cell-free nucleic acids from a pregnant female with reduced bias, Counts of sequence reads mapped to portions of a reference genome are obtained. A regression model is generated that models the relationship between the counts and the GC content. The read counts are normalized according to the regression model to remove the GC bias. The normalized counts are used for further analysis, such as the detection of fetal aneuploidy.

公开(公告)号：US20220093207A1

公开(公告)日：2022-03-24

申请号：US17544537

申请日：2021-12-07

申请人： Sequenom, Inc.

发明人： Amin Mazloom ,  Cosmin Deciu ,  Chen Zhao ,  Tong Liu ,  Yijin Wu

IPC分类号： G16B20/10 ,  G16B40/00 ,  G16B20/00 ,  G16B20/20 ,  G06N7/00

摘要： Technology provided herein relates in part to non-invasive classification of one or more genetic copy number alterations (CNAs) for a test sample. Certain methods include sampling a quantification of sequence reads from parts of a genome, generating a confidence determination, and using the confidence determination to enhance classification. Technology provided herein is useful for classifying a genetic CNA for a sample as part of non-invasive pre-natal (NIPT) testing and oncology testing, for example.

公开(公告)号：US20210272650A1

公开(公告)日：2021-09-02

申请号：US17140426

申请日：2021-01-04

申请人： Sequenom, Inc.

发明人： Cosmin Deciu ,  Chen Zhao

IPC分类号： G16B30/00 ,  C12Q1/6869

摘要： Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations that make use of nucleic acid fragments from circulating cell free nucleic acid. Also provided herein are methods for partitioning one or more genomic regions of a reference genome into a plurality of portions according to one or more features.

公开(公告)号：US11462298B2

公开(公告)日：2022-10-04

申请号：US16862324

申请日：2020-04-29

申请人： SEQUENOM, INC.

发明人： Chen Zhao ,  Zeljko Dzakula ,  Cosmin Deciu ,  Sung Kyun Kim ,  Amin R. Mazloom ,  Gregory Hannum ,  Mathias Ehrich

IPC分类号： G16B20/10 ,  C12Q1/6869 ,  C12Q1/6883 ,  G16B30/10 ,  G16B30/00 ,  G16B40/00 ,  G16B25/10

摘要： Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations that make use of decision analyses. The decision analyses sometimes include segmentation analyses and/or odds ratio analyses.

公开(公告)号：US20180282801A1

公开(公告)日：2018-10-04

申请号：US15965350

申请日：2018-04-27

申请人： Sequenom, Inc.

发明人： Chen Zhao ,  Cosmin Deciu

IPC分类号： C12Q1/6869 ,  G06F19/00 ,  G16H50/30 ,  C12Q1/6827 ,  G06F19/18 ,  G06F19/22 ,  G06F19/24

摘要： Technology described herein pertains in part to diagnostic tests that make use of sequence reads generated by a sequencing process. In some embodiments, a component used to generate a chromosome representation can be based on counts of sequence reads not aligned to a reference genome.

公开(公告)号：US20240141422A1

公开(公告)日：2024-05-02

申请号：US18500812

申请日：2023-11-02

申请人： Sequenom, Inc.

发明人： Chen Zhao ,  Cosmin Deciu ,  Eyad Almasri ,  Tong Liu

IPC分类号： C12Q1/6869 ,  C12Q1/6827 ,  G16B20/00 ,  G16B20/10 ,  G16B20/20 ,  G16B30/00 ,  G16B30/10 ,  G16B40/00 ,  G16H50/30

CPC分类号： C12Q1/6869 ,  C12Q1/6827 ,  G16B20/00 ,  G16B20/10 ,  G16B20/20 ,  G16B30/00 ,  G16B30/10 ,  G16B40/00 ,  G16H50/30 ,  C12Q2535/122

摘要： Techniques are described for identifying a genetic variant in a test sample by comparing sequences reads obtained from the test sample to unique k-mers that are representative of a target genomic region. In one particular aspect, a method is described that includes generating a dictionary of a target genomic region having a set of unique k-mers by: accessing a sequence of the target genomic region, determining a set of k-mers for the target genomic region, comparing the set of k-mers for the target genomic region with one or more sets of k-mers for non-target genomic regions, and selecting the unique k-mers that do not appear in the one or more sets of k-mers for non-target genomic regions. The dictionary can then be used to identify a genetic variant in a test sample by comparing sequences reads obtained from the test sample to the unique k-mers in the dictionary.

公开(公告)号：US10892035B2

公开(公告)日：2021-01-12

申请号：US15517107

申请日：2015-10-09

申请人： Sequenom, Inc.

发明人： Cosmin Deciu ,  Chen Zhao

IPC分类号： G16B30/00 ,  C12Q1/6869

摘要： Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations that make use of nucleic acid fragments from circulating cell free nucleic acid. Also provided herein are methods for partitioning one or more genomic regions of a reference genome into a plurality of portions according to one or more features.

公开(公告)号：US10699800B2

公开(公告)日：2020-06-30

申请号：US14892782

申请日：2014-05-23

申请人： SEQUENOM, INC.

发明人： Chen Zhao ,  Zeljko Dzakula ,  Cosmin Deciu ,  Sung Kyun Kim ,  Amin R. Mazloom ,  Gregory Hannum ,  Mathias Ehrich

IPC分类号： G16B20/10 ,  C12Q1/6883 ,  C12Q1/6869 ,  G16B30/00 ,  G16B40/00

摘要： Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations that make use of decision analyses. The decision analyses sometimes include segmentation analyses and/or odds ratio analyses.