公开(公告)号：US20150094210A1

公开(公告)日：2015-04-02

申请号：US14395065

申请日：2012-05-14

Applicant: Shengpei Chen ,  Huijuan Ge ,  Xuchao Li ,  Shang Yi ,  Jian Wang ,  Jun Wang ,  Huanming Yang ,  Xiuqing Zhang

Inventor： Shengpei Chen ,  Huijuan Ge ,  Xuchao Li ,  Shang Yi ,  Jian Wang ,  Jun Wang ,  Huanming Yang ,  Xiuqing Zhang

IPC: C12Q1/68 ,  G06F19/22 ,  G06F19/00 ,  G06F19/18

CPC classification number: C12Q1/6883 ,  C12Q1/6858 ,  C12Q1/6869 ,  C12Q2600/118 ,  C12Q2600/156 ,  G16B20/00 ,  G16B30/00 ,  G16H50/20 ,  G16H50/30 ,  C12Q2535/122 ,  C12Q2537/165

Abstract: Provided are a method, system and computer readable medium for determining the base information in a predetermined area of a fetus genome, the method comprising following steps: constructing a sequence library for the DNA samples of the fetus genome; sequencing the sequence library to obtain the sequencing result of the fetus, the sequencing result of the fetus comprised of a plurality of sequencing data; and based on the sequencing result of the fetus, determining the base information in the predetermined area according to the hidden Markov model in conjunction with the genetic information of an individual related hereditarily to the fetus.

Abstract translation: 提供了一种用于确定胎儿基因组的预定区域中的基础信息的方法，系统和计算机可读介质，所述方法包括以下步骤：构建胎儿基因组的DNA样品的序列文库; 对序列库进行测序以获得胎儿的测序结果，由多个测序数据组成的胎儿的测序结果; 并且基于胎儿的测序结果，结合遗传信息与胎儿相关的遗传信息，根据隐马尔可夫模型确定预定区域中的基础信息。

公开(公告)号：US20140336075A1

公开(公告)日：2014-11-13

申请号：US14365847

申请日：2011-12-17

Applicant: Yong Qiu ,  Lifu Liu ,  Hui Jiang ,  Fang Chen ,  Chunlei Zhang ,  Jian Wang ,  Jun Wang ,  Huanming Yang ,  Xiuqing Zhang

Inventor： Yong Qiu ,  Lifu Liu ,  Hui Jiang ,  Fang Chen ,  Chunlei Zhang ,  Jian Wang ,  Jun Wang ,  Huanming Yang ,  Xiuqing Zhang

IPC: C12Q1/68

CPC classification number: C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6869 ,  C12Q1/6883 ,  C12Q2600/156 ,  G16B30/00

Abstract: The present invention provides a method and system for determining whether a genomic abnormality exists. The method for determining whether a genomic abnormality exists includes the steps of: separating fetal nucleated red blood cells from a sample from a pregnant woman; sequencing at least a part of the genome of the nucleated red blood cells, so as to obtain a sequencing result; and on the basis of the sequencing result, determining whether a genomic abnormality exists in the nucleated red blood cells.

Abstract translation: 本发明提供了确定基因组异常是否存在的方法和系统。 用于确定是否存在基因组异常的方法包括以下步骤：从孕妇中分离胎儿有核的红细胞与样品; 对有核红细胞的至少一部分基因组进行测序，以获得测序结果; 并在测序结果的基础上，确定有核红细胞中是否存在基因组异常。

公开(公告)号：US20140370504A1

公开(公告)日：2014-12-18

申请号：US14369615

申请日：2011-12-31

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

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

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

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

Abstract: 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.

Abstract translation: 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。

公开(公告)号：US20140249038A1

公开(公告)日：2014-09-04

申请号：US14351468

申请日：2011-12-21

Applicant: Hui Jiang ,  Fang Chen ,  Huijuan Ge ,  Peipei Li ,  Xuchao Li ,  Jian Wang ,  Jun Wang ,  Huanming Yang ,  Xiuqing Zhang

Inventor： Hui Jiang ,  Fang Chen ,  Huijuan Ge ,  Peipei Li ,  Xuchao Li ,  Jian Wang ,  Jun Wang ,  Huanming Yang ,  Xiuqing Zhang

IPC: C12Q1/68

CPC classification number: C12Q1/6874 ,  C12Q1/6869 ,  C12Q1/6883 ,  C12Q2600/156

Abstract: Disclosed are a method of detecting a pre-determined event in a nucleic acid sample and a system thereof. The method of detecting the pre-determined event in the nucleic acid sample comprises the following steps: constructing a sequencing-library for the nucleic acid sample; sequencing the sequencing-library to obtain a sequencing result consisting of a plurality of sequencing data; determining the sequencing data from a pre-determined region; and determining an occurrence of the pre-determined event in the nucleic acid sample based on a composition of the sequencing data from the pre-determined region.

Abstract translation: 公开了一种在核酸样品及其系统中检测预定事件的方法。 检测核酸样品中预先确定事件的方法包括以下步骤：构建核酸样品的测序文库; 测序序列库以获得由多个测序数据组成的测序结果; 确定来自预定区域的测序数据; 以及基于来自预定区域的测序数据的组成确定核酸样品中预定事件的发生。

公开(公告)号：US20150105264A1

公开(公告)日：2015-04-16

申请号：US14395074

申请日：2012-05-23

Applicant: Huijuan Ge ,  Jing Zheng ,  Shang Yi ,  Xuchao Li ,  Jian Wang ,  Jun Wang ,  Huanming Yang ,  Xiuqing Zhang

Inventor： Huijuan Ge ,  Jing Zheng ,  Shang Yi ,  Xuchao Li ,  Jian Wang ,  Jun Wang ,  Huanming Yang ,  Xiuqing Zhang

IPC: C12Q1/68 ,  C12N15/10

CPC classification number: C12Q1/6876 ,  C12N15/1003 ,  C12Q1/6806 ,  C12Q1/6888 ,  C12Q2600/156 ,  C12Q2600/16

Abstract: Provided are a method and a system for identifying whether the twins are dizygotic twins, the method comprising: typing at least one polymorphic loci of the twins fetuses to obtain the fetal polymorphism types, comparing the fetal polymorphism types with the corresponding polymorphism types of their parents, determining whether the twins are dizygotic twins on the basis of the comparison result.

Abstract translation: 提供了一种用于识别双胞胎是否是双卵双胞胎的方法和系统，所述方法包括：输入双胎胎儿的至少一个多态性位点以获得胎儿多态性类型，将胎儿多态性类型与其父母的相应多态性类型进行比较 根据比较结果确定双胞胎是否是异卵双胞胎。

公开(公告)号：US20150056619A1

公开(公告)日：2015-02-26

申请号：US14389898

申请日：2012-04-05

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

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

IPC: C12Q1/68

CPC classification number: C12Q1/68 ,  C12Q1/6869 ,  C12Q2535/122 ,  C12Q2537/165 ,  G16B15/00 ,  G16B30/00 ,  G16C99/00

Abstract: 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.

Abstract translation: 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：US20150012252A1

公开(公告)日：2015-01-08

申请号：US14373072

申请日：2012-01-20

Applicant: Xuyang Yin ,  Chunlei Zhang ,  Shengpei Chen ,  Chunsheng Zhang ,  Xiaoyu Pan ,  Hui Jiang ,  Xiuqing Zhang

Inventor： Xuyang Yin ,  Chunlei Zhang ,  Shengpei Chen ,  Chunsheng Zhang ,  Xiaoyu Pan ,  Hui Jiang ,  Xiuqing Zhang

IPC: G06F19/12 ,  G06F17/50

CPC classification number: G16B5/00 ,  C12Q1/6809 ,  G06F17/5009 ,  G16B30/00 ,  C12Q2535/122 ,  C12Q2537/16 ,  C12Q2537/165

Abstract: Provided are a method, system, and computer-readable medium for determining whether a copy number variation exists in a sample genome. The method includes sequencing a sample genome to obtain a sequencing result formed by multiple reads; comparing the sequencing result with a reference genome sequence to determine the distribution of the reads on the reference genome sequence; determining, based on the distribution of the reads on the reference genome sequence, multiple breakpoints on the reference genome sequence, wherein the number of the reads on either side of each breakpoint are significantly different; determining, based on the plurality of breakpoints, a detection window on the reference genome; determining, based on the reads falling in the detection window, a parameter; and determining, based on the difference between the first parameter and a preset threshold, whether a copy number variation exists in the sample genome against the detection window.

Abstract translation: 提供了用于确定样本基因组中是否存在拷贝数变异的方法，系统和计算机可读介质。 该方法包括对样品基因组进行测序以获得通过多次读取形成的测序结果; 将测序结果与参考基因组序列进行比较，以确定参考基因组序列上读数的分布; 基于参考基因组序列上的读数的分布来确定参考基因组序列上的多个断点，其中每个断点的任一侧的读数显着不同; 基于所述多个断点确定所述参考基因组上的检测窗口; 基于落在检测窗口中的读取来确定参数; 以及基于所述第一参数和预设阈值之间的差来确定所述样本基因组中是否存在根据所述检测窗口的拷贝数变异。

公开(公告)号：US20140274745A1

公开(公告)日：2014-09-18

申请号：US14354109

申请日：2011-10-28

Applicant: Fang Chen ,  Xiaoyu Pan ,  Shengpei Chen ,  Xuchao Li ,  Hui Jiang ,  Xiuqing Zhang

Inventor： Fang Chen ,  Xiaoyu Pan ,  Shengpei Chen ,  Xuchao Li ,  Hui Jiang ,  Xiuqing Zhang

IPC: C12Q1/68 ,  G06F19/22

CPC classification number: C12Q1/6874 ,  C12Q1/6883 ,  C12Q2600/156 ,  G16B30/00

Abstract: The present invention relates to the field of genomic mutation detection, and in particular, to the detection of the copy number variation (CNV) in cellular chromosomal DNA fragments. The present invention also relates to the detection of diseases related to the copy number variation in the cellular chromosomal DNA fragments.

Abstract translation: 本发明涉及基因组突变检测领域，特别涉及检测细胞染色体DNA片段中的拷贝数变异（CNV）。 本发明还涉及与细胞染色体DNA片段的拷贝数变异相关的疾病的检测。