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：EP2511843B1

公开(公告)日：2016-12-21

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： G06F19/18 ,  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.

公开(公告)号：EP2511843A3

公开(公告)日：2014-02-19

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： G06F19/18 ,  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.