公开(公告)号：EP2977455B1

公开(公告)日：2020-04-15

申请号：EP15166986.8

申请日：2010-06-15

申请人： Complete Genomics, Inc.

发明人： Drmanac, Radoje ,  Peters, Brock, A. ,  Alexeev, Andrei ,  Hong, Peter

IPC分类号： C12Q1/6806 ,  C12N15/10

公开(公告)号：EP1907571B1

公开(公告)日：2017-04-26

申请号：EP06760745.7

申请日：2006-06-13

申请人： Complete Genomics Inc.

发明人： DRMANAC, Radoje

IPC分类号： C12Q1/68 ,  C07H21/02

CPC分类号： C12Q1/6874 ,  C07H21/04 ,  C07K1/047 ,  C12Q1/6806 ,  C12Q1/682 ,  C12Q1/6837 ,  C12Q1/6869 ,  C12Q2525/151 ,  C12Q2525/313 ,  C12Q2531/125 ,  C12Q2565/513 ,  G01N15/1404 ,  G01N15/1434 ,  Y10S977/778 ,  Y10S977/789 ,  Y10S977/792 ,  Y10S977/88 ,  Y10S977/882 ,  C12Q2521/307 ,  C12Q2525/161 ,  C12Q2535/122 ,  C12Q2563/179 ,  C12Q2565/514

摘要： The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered. In one aspect, this process is carried out in a hierarchical fashion until the one or more target polynucleotides are characterized, e.g. by their nucleic acid sequences, or by an ordering of sequence segments, or by an ordering of single nucleotide polymorphisms (SNPs), or the like.

摘要翻译： 本发明提供了用于对从一个或多个靶多核苷酸衍生的序列信息进行排序的方法和试剂盒。 在一个方面中，生成一个或多个分层和等分的层或等级，之后从最终等级或等级中的片段获得序列信息。 最后一层中的每个片段都来自一个特定的等分部分，而这个等分部分又来自前一层的特定等分部分，依此类推。 对于最后一层中的等分部分的每一个片段，其在之前的每一层中从其得到的等分部分是已知的，或可以被辨别。 因此，来自不同等分部分的重叠片段的相同序列可以被区分并分组为源自与之前等级相同或不同的片段。 当对最后一层中的片段进行测序时，使用不同等分部分的片段的重叠序列区域来记录片段，使得非重叠区域被排序。 在一个方面，该过程以分层方式进行，直到一个或多个靶多核苷酸被表征，例如， 通过它们的核酸序列，或通过序列区段的排序，或通过单核苷酸多态性（SNP）的排序等等。

公开(公告)号：EP2859397A4

公开(公告)日：2016-03-30

申请号：EP13799902

申请日：2013-06-05

申请人： COMPLETE GENOMICS INC

发明人： STAKER BRYAN P ,  UHRICH CRAIG E

IPC分类号： G02B21/36 ,  G02B27/64

CPC分类号： H04N5/2251 ,  G02B21/16 ,  G02B21/367 ,  G02B27/646

摘要： An imaging system is provided wherein a positioning stage is translated with respect to an objective lens component and a scan mirror is repositioned while a two-dimensional image is made of a biochemical site on a substrate. In an example embodiment, an imaging system comprises a camera, an objective lens component, a positioning stage, and a scan mirror controllable by a servo system that synchronizes movement of the positioning stage and the tilting of the scan mirror so that the substrate image is maintained stable during imaging of the continuously moving positioning stage.

公开(公告)号：EP2859397A1

公开(公告)日：2015-04-15

申请号：EP13799902.5

申请日：2013-06-05

申请人： Complete Genomics, Inc.

发明人： STAKER, Bryan P. ,  UHRICH, Craig E.

IPC分类号： G02B21/36

CPC分类号： H04N5/2251 ,  G02B21/16 ,  G02B21/367 ,  G02B27/646

摘要： An imaging system is provided wherein a positioning stage is translated with respect to an objective lens component and a scan mirror is repositioned while a two-dimensional image is made of a biochemical site on a substrate. In an example embodiment, an imaging system comprises a camera, an objective lens component, a positioning stage, and a scan mirror controllable by a servo system that synchronizes movement of the positioning stage and the tilting of the scan mirror so that the substrate image is maintained stable during imaging of the continuously moving positioning stage.

公开(公告)号：EP2844771A1

公开(公告)日：2015-03-11

申请号：EP13784660.6

申请日：2013-05-06

申请人： Complete Genomics, Inc.

发明人： HALPERN, Aaron ,  PANT, Krishna

IPC分类号： C12Q1/68

CPC分类号： G06F19/22 ,  C12Q1/6827 ,  C12Q1/6886 ,  C12Q2600/156 ,  G06F19/18 ,  C12Q2535/122 ,  C12Q2537/16 ,  C12Q2537/165

摘要： Methods for interpreting absolute copy number of complex tumors and for determining the copy number of a genomic region at a detection position of a target sequence in a sample are disclosed. In certain aspects, genomic regions of a target sequence in a sample are sequenced and measurement data for sequence coverage is obtained. Sequence coverage bias is corrected and may be normalized against a baseline sample. Hidden Markov Model (HMM) segmentation, scoring, and output are performed, and in some embodiments population-based no-calling and identification of low-confidence regions may also be performed. A total copy number value and region-specific copy number value for a plurality of regions are then estimated.

公开(公告)号：EP2430441A4

公开(公告)日：2014-02-19

申请号：EP10770290

申请日：2010-04-28

申请人： COMPLETE GENOMICS INC

发明人： CARNEVALI PAOLO ,  BACCASH JONATHAN M ,  NAZARENKO IGOR ,  HALPERN AARON L ,  NILSEN GEOFFREY ,  MARTIN BRUCE ,  DRMANAC RADOJE

IPC分类号： G06F19/18 ,  G06F19/22

CPC分类号： G06F19/22 ,  G06F19/18

摘要： Embodiments for calling variations in a sample polynucleotide sequence compared to a reference polynucleotide sequence are provided. Aspects of the embodiments include executing an application on at least one computer that locates local areas in the reference polynucleotide sequence where a likelihood exists that one or more bases of the sample polynucleotide sequence are changed from corresponding bases in the reference polynucleotide sequence, where the likelihood is determined at least in part based on mapped mated reads of the sample polynucleotide sequence; generating at least one sequence hypothesis for each of the local areas, and optimizing the at least one sequence hypothesis for at least a portion of the local areas to find one or more optimized sequence hypotheses of high probability for the local areas; and analyzing the optimized sequence hypotheses to identify a series of variation calls in the sample polynucleotide sequence.

摘要翻译： 提供了用于调用与参考多核苷酸序列的样品多核苷酸序列中的变异的实施例。 实施例的方面包括至少一个计算机上应用程序执行并定位在一个似然存在没有样品多核苷酸序列的一个或多个碱基被从对应的碱在所述参考多核苷酸序列改变的参考多核苷酸序列，其中所述似然性的局部区域 是确定性的基于映射配合样品多核苷酸序列的一部分中读取开采至少; 生成至少一个序列假设为每个局部区域的，和优化所述至少一个序列假设为局部区域的至少一部分以查找一个或多个优化的高概率的局部区域的序列假设; 和分析该优化的序列假设以识别序列变化的调用在样品多核苷酸序列。

公开(公告)号：EP2394165A4

公开(公告)日：2013-12-11

申请号：EP10739027

申请日：2010-02-02

申请人： COMPLETE GENOMICS INC

发明人： HALPERN AARON L ,  NAZARENKO IGOR

IPC分类号： G06F19/22 ,  G01N33/48 ,  G01N33/50

CPC分类号： G06F19/22

公开(公告)号：EP2393944A4

公开(公告)日：2013-11-27

申请号：EP10739026

申请日：2010-02-02

申请人： COMPLETE GENOMICS INC

发明人： HALPERN AARON L ,  NAZARENKO IGOR

IPC分类号： G06F19/22 ,  G06F17/30

CPC分类号： G06F19/22 ,  G06F17/30312

公开(公告)号：EP2511843A2

公开(公告)日：2012-10-17

申请号：EP12165247.3

申请日：2010-04-28

申请人： Complete Genomics, Inc.

发明人： Carnevali, Paolo ,  Baccash, Jonathan, M. ,  Nazarenko,, Igor ,  Halpern, Aaron, L. ,  Nilsen Geoffrey ,  Martin, Bruce ,  Drmanac, Radoje

IPC分类号： G06F19/22

CPC分类号： G06F19/22 ,  G06F19/18

摘要： Embodiments for calling variations in a sample polynucleotide sequence compared to a reference polynucleotide sequence are provided. Aspects of the embodiments include executing an application on at least one computer that locates local areas in the reference polynucleotide sequence where a likelihood exists that one or more bases of the sample polynucleotide sequence are changed from corresponding bases in the reference polynucleotide sequence, where the likelihood is determined at least in part based on mapped mated reads of the sample polynucleotide sequence; generating at least one sequence hypothesis for each of the local areas, and optimizing the at least one sequence hypothesis for at least a portion of the local areas to find one or more optimized sequence hypotheses of high probability for the local areas; and analyzing the optimized sequence hypotheses to identify a series of variation calls in the sample polynucleotide sequence.

摘要翻译： 提供了用于调用与参考多核苷酸序列的样品多核苷酸序列中的变异的实施例。 实施例的方面包括至少一个计算机上应用程序执行并定位在一个似然存在没有样品多核苷酸序列的一个或多个碱基被从对应的碱在所述参考多核苷酸序列改变的参考多核苷酸序列，其中所述似然性的局部区域 是确定性的基于映射配合样品多核苷酸序列的一部分中读取开采至少; 生成至少一个序列假设为每个局部区域的，和优化所述至少一个序列假设为局部区域的至少一部分以查找一个或多个优化的高概率的局部区域的序列假设; 和分析该优化的序列假设以识别序列变化的调用在样品多核苷酸序列。

公开(公告)号：EP2215209A4

公开(公告)日：2012-08-29

申请号：EP08844709

申请日：2008-10-30

申请人： COMPLETE GENOMICS INC

发明人： OLIPHANT ARNOLD

IPC分类号： C12M1/00 ,  C12Q1/68 ,  G01N35/00

CPC分类号： C12Q1/6874 ,  G01N21/6486 ,  G01N35/0099 ,  G01N2035/00158 ,  G01N2201/0461

摘要： A scalable reaction and detection system for automated high throughput sequencing of nucleic acids involving a combination of chemical processes and observation processes independent of the chemistry processes. Discrete functional units may be configured in a manner that allows the system to interchangeably utilize different sequencing reaction components in conjunction with discrete apparatus components for optical image collection and/or analysis.

摘要翻译： 用于自动化高通量测序的可扩展的反应和检测系统，涉及独立于化学过程的化学过程和观察过程的组合。 离散功能单元可以以允许系统与用于光学图像收集和/或分析的分立装置组件可互换地利用不同排序反应组件的方式来配置。