公开(公告)号：US20150056619A1

公开(公告)日：2015-02-26

申请号：US14389898

申请日：2012-04-05

申请人： Xuchao Li ,  Shengpei Chen ,  Fang Chen ,  Weiwei Xie ,  Jian Wang ,  Jun Wang ,  Huanming Yang ,  Xiuqing Zhang

发明人： Xuchao Li ,  Shengpei Chen ,  Fang Chen ,  Weiwei Xie ,  Jian Wang ,  Jun Wang ,  Huanming Yang ,  Xiuqing Zhang

IPC分类号： C12Q1/68

CPC分类号： C12Q1/68 ,  C12Q1/6869 ,  C12Q2535/122 ,  C12Q2537/165 ,  G16B15/00 ,  G16B30/00 ,  G16C99/00

摘要： Disclosed are a method and a system for determining genome copy number variation, which relates to the technical field of bioinformatics. The method comprises obtaining reads; determining sequence labels according to the reads; counting the number of sequence labels falling into each window; performing GC correction on the sequence label number of each window and a correction according to an expected sequence label number adjusted by a control set to obtain a corrected sequence label number; selecting a demarcation point with a small significance value as a candidate CNV breaking point; rejecting the least significant candidate CNV breaking point at every turn, updating difference significance values of two candidate CNV breaking points on the left and right of the rejected candidate CNV breaking point and performing cyclic iteration until difference significance values of all candidate CNV breaking points are smaller than a termination threshold value, thereby determining a CNV breaking point. The method and the system the present invention have clinical feasibility, and can precisely detect a micro-deletion/micro-duplication area of 0.5 M under the situation of using data of about 50 M.

摘要翻译： 公开了用于确定与生物信息学技术领域有关的基因组拷贝数变异的方法和系统。 该方法包括获取读数; 根据读数确定序列标签; 计算落入每个窗口的序列标签的数量; 对每个窗口的序列标签号执行GC校正，并根据由控制集调整的预期序列标号进行校正，以获得校正的序列标号; 选择具有较小重要性值的分界点作为候选CNV断点; 拒绝每一回合中最不重要的候选CNV断点，更新拒绝的候选CNV断点左侧和右侧的两个候选CNV断点的差异有效值，并执行循环迭代，直到所有候选CNV断点的差值显着值较小 比终止阈值，从而确定CNV断点。 本发明的方法和系统具有临床可行性，并且可以在使用约50M的数据的情况下精确地检测到0.5M的微缺失/微复制区域。

公开(公告)号：US20140370504A1

公开(公告)日：2014-12-18

申请号：US14369615

申请日：2011-12-31

申请人： Shengpei Chen ,  Chunlei Zhang ,  Fang Chen ,  Weiwei Xie ,  Xiaoyu Pan ,  Jian Wang ,  Jun Wang ,  Huanming Yang ,  Xiuqing Zhang

发明人： Shengpei Chen ,  Chunlei Zhang ,  Fang Chen ,  Weiwei Xie ,  Xiaoyu Pan ,  Jian Wang ,  Jun Wang ,  Huanming Yang ,  Xiuqing Zhang

IPC分类号： G06F19/22 ,  G06F17/18 ,  C12Q1/68

CPC分类号： G16B30/00 ,  C12Q1/6809 ,  C12Q1/6869 ,  G06F17/18 ,  C12Q2535/122 ,  C12Q2537/16 ,  C12Q2537/165

摘要： The present invention relates to a method for detecting genetic variation, comprising the following steps: acquiring reads from a test sample; aligning said reads with a reference genome sequence; dividing said reference genome sequence into windows, calculating the number of said reads which are aligned to each window, and acquiring the statistic for each window on the basis of the number of said reads; and for a fragment of the reference genome sequence, acquiring the genetic variation sites on the basis of the change in the statistics of all the windows thereon in the fragment of the reference genome sequence.

摘要翻译： 本发明涉及一种检测遗传变异的方法，包括以下步骤：从测试样品获取读数; 将所述读数与参考基因组序列对齐; 将所述参考基因组序列划分为窗口，计算与每个窗口对齐的所述读取的数量，并且基于所述读取的数量获取每个窗口的统计量; 并且对于参考基因组序列的片段，基于参考基因组序列的片段中所有窗口的统计学变化来获取遗传变异位点。