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1. 发明申请

US20130345095A1 METHOD AND DEVICE FOR ASSEMBLING GENOME SEQUENCE 审中-公开
标题翻译：用于组装基因序列的方法和装置
公开(公告)号：US20130345095A1
公开(公告)日：2013-12-26
申请号：US14002374
申请日：2012-03-02
申请人： Changlei Han , Wenbin Chen , Xiuqing Zhang , Huanming Yang
发明人： Changlei Han , Wenbin Chen , Xiuqing Zhang , Huanming Yang
IPC分类号： G06F19/18
CPC分类号： G16B20/00 , G16B30/00
摘要： A method and an apparatus for genome assembly are provided. The method comprises: filtering a short-fragment-sequence output from end sequencing of an large insert-size library to remove unqualified sequence; aligning the filtered short-fragment-sequence onto a reference genome sequence, wherein, the filtered short-fragment-sequences comprise paired short-fragment-sequences; sorting the paired short-fragment-sequence after alignment into soap reads sequence, single reads sequence and unmap reads sequence based on the aligning result, and counting the number of each sort of sequence; calculating a distance between the paired soap reads on a fragment of the reference genome sequence, wherein a pair of the paired soap reads can be aligned onto a same fragment of the reference genome sequence; and counting a distance distribution of each pair of soap reads on the reference genome sequence; and assembling the genome sequence by using the paired single reads upon the distance distribution meeting a requirement of a threshold, wherein a pair of the paired single reads can be aligned onto two different fragments of the reference genome sequence.
摘要翻译：提供了用于基因组装配的方法和装置。该方法包括：从大插入大小库的末端排序中过滤短片段序列输出，以去除不合格序列; 将经过滤的短片段序列对准参考基因组序列，其中，经过滤的短片段序列包含配对的短片段序列; 将对齐后的配对短片段序列排序为soap，读取序列，基于对齐结果的单次读取序列和unmap读取序列，并对每种序列的数量进行计数; 计算参考基因组序列的片段上的成对皂读数之间的距离，其中一对成对的皂读数可以对准参考基因组序列的相同片段; 并计算参考基因组序列上每对皂读数的距离分布; 并且通过在距离分布上使用配对的单个读数来组合基因组序列，满足阈值的要求，其中一对成对的单个读数可以对准参考基因组序列的两个不同片段。

2. 发明申请

US20150094210A1 METHOD, SYSTEM AND COMPUTER READABLE MEDIUM FOR DETERMINING BASE INFORMATION IN PREDETERMINED AREA OF FETUS GENOME 审中-公开
标题翻译：方法，系统和计算机可读介质，用于确定基因组预测区域的基础信息
公开(公告)号：US20150094210A1
公开(公告)日：2015-04-02
申请号：US14395065
申请日：2012-05-14
申请人： Shengpei Chen , Huijuan Ge , Xuchao Li , Shang Yi , Jian Wang , Jun Wang , Huanming Yang , Xiuqing Zhang
发明人： Shengpei Chen , Huijuan Ge , Xuchao Li , Shang Yi , Jian Wang , Jun Wang , Huanming Yang , Xiuqing Zhang
IPC分类号： C12Q1/68 , G06F19/22 , G06F19/00 , G06F19/18
CPC分类号： C12Q1/6883 , C12Q1/6858 , C12Q1/6869 , C12Q2600/118 , C12Q2600/156 , G16B20/00 , G16B30/00 , G16H50/20 , G16H50/30 , C12Q2535/122 , C12Q2537/165
摘要： 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.
摘要翻译：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。

3. 发明申请

US20140336075A1 METHOD AND SYSTEM FOR DETERMININING WHETHER GENOME IS ABNORMAL 审中-公开
标题翻译：用于确定基因组异常的方法和系统
公开(公告)号：US20140336075A1
公开(公告)日：2014-11-13
申请号：US14365847
申请日：2011-12-17
申请人： Yong Qiu , Lifu Liu , Hui Jiang , Fang Chen , Chunlei Zhang , Jian Wang , Jun Wang , Huanming Yang , Xiuqing Zhang
发明人： Yong Qiu , Lifu Liu , Hui Jiang , Fang Chen , Chunlei Zhang , Jian Wang , Jun Wang , Huanming Yang , Xiuqing Zhang
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6806 , C12Q1/6869 , C12Q1/6883 , C12Q2600/156 , G16B30/00
摘要： 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.
摘要翻译：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。

4. 发明申请

US20140249038A1 Method of detecting a pre-determined event in a nucleic acid sample and system thereof 审中-公开
标题翻译：检测核酸样品中的预定事件的方法及其系统
公开(公告)号：US20140249038A1
公开(公告)日：2014-09-04
申请号：US14351468
申请日：2011-12-21
申请人： Hui Jiang , Fang Chen , Huijuan Ge , Peipei Li , Xuchao Li , Jian Wang , Jun Wang , Huanming Yang , Xiuqing Zhang
发明人： Hui Jiang , Fang Chen , Huijuan Ge , Peipei Li , Xuchao Li , Jian Wang , Jun Wang , Huanming Yang , Xiuqing Zhang
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6869 , C12Q1/6883 , C12Q2600/156
摘要： 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.
摘要翻译：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。

5. 发明授权

US09238840B2 Method for single cell genome analysis and kit therefor 有权
标题翻译：单细胞基因组分析方法及其试剂盒
公开(公告)号：US09238840B2
公开(公告)日：2016-01-19
申请号：US13976845
申请日：2011-12-29
申请人： Xuyang Yin , Li Bao , Xun Xu , Hanjie Wu , Xiaoyu Liu , Xiuqing Zhang , Huanming Yang
发明人： Xuyang Yin , Li Bao , Xun Xu , Hanjie Wu , Xiaoyu Liu , Xiuqing Zhang , Huanming Yang
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6888 , C12Q1/6806 , C12Q1/6851 , C12Q1/6869 , C12Q1/6876 , C12Q2600/166 , C12Q2531/119 , C12Q2545/101
摘要： A method for analyzing a genome of a single cell is provided, and a kit is also provided. The method for analyzing the genome of the single cell may comprise separating and lysing the single cell to obtain a whole-genome DNA of the cell; subjecting the whole-genome DNA to a whole-genome amplification to obtain a whole-genome amplification product; performing a PCR amplification using the whole-genome amplification product as template and using housekeeping-gene-specific primers to detect the housekeeping gene of the whole-genome amplification product; and determining whether the whole genome amplification product meets a requirement for sequencing based on the detection result, wherein a uniform distribution of the amplification product in each chromosome is an indication of the amplification product meeting the requirement for sequencing.
摘要翻译：提供了用于分析单细胞的基因组的方法，并且还提供了试剂盒。用于分析单细胞基因组的方法可以包括分离和裂解单细胞以获得细胞的全基因组DNA; 对全基因组DNA进行全基因组扩增以获得全基因组扩增产物; 使用全基因组扩增产物作为模板进行PCR扩增，并使用管家基因特异性引物检测全基因组扩增产物的管家基因; 并且基于检测结果确定全基因组扩增产物是否满足测序要求，其中扩增产物在每个染色体中的均匀分布是满足测序要求的扩增产物的指示。

6. 发明申请

US20140370504A1 METHOD FOR DETECTING GENETIC VARIATION 审中-公开
标题翻译：检测遗传变异的方法
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。

7. 发明申请

US20140017683A1 METHOD FOR SINGLE CELL GENOME ANALYSIS AND KIT THEREFOR 有权
标题翻译：单细胞基因组分析方法及其制备方法
公开(公告)号：US20140017683A1
公开(公告)日：2014-01-16
申请号：US13976845
申请日：2011-12-29
申请人： Xuyang Yin , Li Bao , Xun Xu , Hanjie Wu , Xiaoyu Liu , Xiuqing Zhang , Huanming Yang
发明人： Xuyang Yin , Li Bao , Xun Xu , Hanjie Wu , Xiaoyu Liu , Xiuqing Zhang , Huanming Yang
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6888 , C12Q1/6806 , C12Q1/6851 , C12Q1/6869 , C12Q1/6876 , C12Q2600/166 , C12Q2531/119 , C12Q2545/101
摘要： A method for analyzing a genome of a single cell is provided, and a kit is also provided. The method for analyzing the genome of the single cell may comprise separating and lysing the single cell to obtain a whole-genome DNA of the cell; subjecting the whole-genome DNA to a whole-genome amplification to obtain a whole-genome amplification product; performing a PCR amplification using the whole-genome amplification product as template and using housekeeping-gene-specific primers to detect the housekeeping gene of the whole-genome amplification product; and determining whether the whole genome amplification product meets a requirement for sequencing based on the detection result, wherein a uniform distribution of the amplification product in each chromosome is an indication of the amplification product meeting the requirement for sequencing.
摘要翻译：提供了用于分析单细胞的基因组的方法，并且还提供了试剂盒。用于分析单细胞基因组的方法可以包括分离和裂解单细胞以获得细胞的全基因组DNA; 对全基因组DNA进行全基因组扩增以获得全基因组扩增产物; 使用全基因组扩增产物作为模板进行PCR扩增，并使用管家基因特异性引物检测全基因组扩增产物的管家基因; 并且基于检测结果确定全基因组扩增产物是否满足测序要求，其中扩增产物在每个染色体中的均匀分布是满足测序要求的扩增产物的指示。

8. 发明申请

US20150105264A1 METHOD AND SYSTEM FOR IDENTIFYING TYPES OF TWINS 审中-公开
标题翻译：识别TWINS类型的方法和系统
公开(公告)号：US20150105264A1
公开(公告)日：2015-04-16
申请号：US14395074
申请日：2012-05-23
申请人： Huijuan Ge , Jing Zheng , Shang Yi , Xuchao Li , Jian Wang , Jun Wang , Huanming Yang , Xiuqing Zhang
发明人： Huijuan Ge , Jing Zheng , Shang Yi , Xuchao Li , Jian Wang , Jun Wang , Huanming Yang , Xiuqing Zhang
IPC分类号： C12Q1/68 , C12N15/10
CPC分类号： C12Q1/6876 , C12N15/1003 , C12Q1/6806 , C12Q1/6888 , C12Q2600/156 , C12Q2600/16
摘要： 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.
摘要翻译：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。

9. 发明申请

US20150056619A1 METHOD AND SYSTEM FOR DETERMINING COPY NUMBER VARIATION 审中-公开
标题翻译：用于确定复制数变化的方法和系统
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。

10. 发明授权

US09518295B2 High-throughput sequencing method for methylated DNA and use thereof 有权
标题翻译：甲基化DNA的高通量测序方法及其用途
公开(公告)号：US09518295B2
公开(公告)日：2016-12-13
申请号：US13814925
申请日：2010-08-11
申请人： Yan Wang , Mingzhi Ye , Xu Han , Xiuqing Zhang , Zhongsheng Sun
发明人： Yan Wang , Mingzhi Ye , Xu Han , Xiuqing Zhang , Zhongsheng Sun
IPC分类号： C12Q1/68 , C12N15/10
CPC分类号： C12Q1/6874 , C12N15/1093 , C12Q1/6804 , C12Q1/6806 , C12Q1/6869 , C12Q2523/125 , C12Q2521/331 , C12Q2525/191
摘要： The present invention provides a high-throughput sequencing method for methylated DNA, and use thereof. Particularly, the present invention provides a high-throughput sequencing method for methylated DNA, which combines methylated DNA immunoprecipitation, removal of repetitive sequences, and bisulfite treatment. The site of sequencing library will be decreased, and the cost will be reduced by using the method disclosed in the present invention.
摘要翻译：本发明提供甲基化DNA的高通量测序方法及其用途。特别地，本发明提供了甲基化DNA的高通量测序方法，其结合甲基化DNA免疫沉淀，去除重复序列和亚硫酸氢盐处理。测序库的位置将减少，并且通过使用本发明公开的方法将降低成本。

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