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1. 发明申请

US20150376697A1 METHOD AND SYSTEM TO DETERMINE BIOMARKERS RELATED TO ABNORMAL CONDITION 审中-公开
标题翻译：用于确定与异常条件相关的生物标志物的方法和系统
公开(公告)号：US20150376697A1
公开(公告)日：2015-12-31
申请号：US13640448
申请日：2012-08-22
申请人： Shenghui Li , Junjie Qin , Jianfeng Zhu , Dongya Zhang , Zhuye Jie , Jun Wang , Jian Wang , Huanming Yang
发明人： Shenghui Li , Junjie Qin , Jianfeng Zhu , Dongya Zhang , Zhuye Jie , Jun Wang , Jian Wang , Huanming Yang
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6883 , C12Q2600/112
摘要： A method and system to determine biomarkers related to abnormal condition in a subject are provided, comprising:sequencing nucleic acid samples from a first and a second subject in order to obtain multiple sequences respectively consisting of the first and the second sequencing results, wherein the first subject is in the abnormal condition; and the second subject is not in the abnormal condition; and the nucleic acid samples from the first and the second subject are both isolated from the samples of the same type; and the first and the second subject belong to the same species; and determining the biomarkers related to the abnormal condition in the subject based on the difference between the first and the second sequencing results.
摘要翻译：提供了确定与受试者异常状况相关的生物标志物的方法和系统，其包括：对来自第一和第二受试者的核酸样品进行测序，以获得分别由第一和第二测序结果组成的多个序列，其中第一个受试者处于异常状况; 第二个受试者不处于异常状态; 并且来自第一和第二受试者的核酸样品均从相同类型的样品中分离; 第一和第二主题属于同一物种; 并且基于第一和第二测序结果之间的差异来确定与受试者的异常状况相关的生物标志物。

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. 发明授权

US09857377B2 Method for quantification of proteome 有权
公开(公告)号：US09857377B2
公开(公告)日：2018-01-02
申请号：US14369825
申请日：2011-12-31
申请人： Haiyi Zhao , Dahai Jiang , Bo Wen , Jian Wang , Jun Wang , Huanming Yang , Jin Zi , Yan Ren , Siqi Liu
发明人： Haiyi Zhao , Dahai Jiang , Bo Wen , Jian Wang , Jun Wang , Huanming Yang , Jin Zi , Yan Ren , Siqi Liu
IPC分类号： G01N33/68 , G06F19/18 , H01J49/00
CPC分类号： G01N33/6848 , G01N33/68 , G01N2570/00 , G06F19/18 , H01J49/0036
摘要： The present invention relates to a method for quantifying the relative content of a protein in a sample. The present invention also relates to a method for comprising the relative content of a protein in at least two samples.

5. 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。

6. 发明授权

US08751165B2 Error correcting method of test sequence, corresponding system and gene assembly equipment 有权
标题翻译：测试序列错误纠正方法，相应的系统和基因组装设备
公开(公告)号：US08751165B2
公开(公告)日：2014-06-10
申请号：US13132038
申请日：2009-12-11
申请人： Jun Wang , Huanming Yang , Jian Wang
发明人： Jun Wang , Huanming Yang , Jian Wang
IPC分类号： G01N33/48 , G06F19/00 , G06F19/24
CPC分类号： G06F19/24 , C12Q1/6874 , G06F19/22
摘要： The present invention provides an error correcting method of test sequence, which involves receiving test sequences, configuring high frequency short string list based on a preset high frequency threshold value, traversing each received test sequence, searching an area with the largest number of continuous high frequency short strings on each test sequence in combination with high frequency short string list, configuring whole left sequence and/or right sequence of high frequency short strings at left side and/or right side of searched area according to corresponding received test sequence and high frequency short string list, and constituting corresponding test sequence according to configured left and/or right sequence and searched area. The present invention also provides corresponding error correcting system of test sequence and gene assembly equipment.
摘要翻译：本发明提供一种测试序列的纠错方法，其包括接收测试序列，基于预设的高频阈值配置高频短串列表，遍历每个接收的测试序列，搜索具有最大数目的连续高频区域每个测试序列上的短串组合高频短串列表，根据相应的接收测试序列和高频短信配置搜索区域的左侧和/或右侧的全部左序列和/或右序列的高频短串字符串列表，并根据配置的左和/或右序列和搜索区域构成对应的测试序列。本发明还提供了相应的测试序列和基因组装设备的纠错系统。

7. 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。

8. 发明申请

US20140323320A1 METHOD OF DETECTING FUSED TRANSCRIPTS AND SYSTEM THEREOF 审中-公开
公开(公告)号：US20140323320A1
公开(公告)日：2014-10-30
申请号：US14369566
申请日：2011-12-31
申请人： Wenlong Jia , Kunlong Qiu , Guangwu Guo , Minghui He , Jun Wang , Jian Wang , Huanming Yang
发明人： Wenlong Jia , Kunlong Qiu , Guangwu Guo , Minghui He , Jun Wang , Jian Wang , Huanming Yang
IPC分类号： G06F19/22
CPC分类号： G16B30/00 , C12Q1/6869 , C12Q2535/122
摘要： Provided is a method of detecting method of detecting fusion transcripts in a sample to be analyzed. The method may comprises: subjecting the sample to be analyzed containing a RNA transcriptome to paired-end sequencing, to obtain paired-end RNA-Seq data of the sample to be analyzed; aligning the paired-end RNA-Seq data to a human reference genome sequence, to obtain first paired-end mapped reads, first single-end mapped reads, and first unmapped reads; evaluating an insertsize between two ends of the paired-end mapped reads by means of the first paired-end mapped reads, to obtain a proportion of paired-end mapped reads with overlapped 3′-ends; aligning the first unmapped reads to annotated transcripts, to obtain second single-end mapped reads and second unmapped reads; aligning the second unmapped reads to the annotated transcripts, to filter out unmapped reads caused by indel and obtain third unmapped reads; merging all single-end mapped reads, to obtain a set of single-end mapped reads; obtaining a gene pair linked by a cross-read as a primary set of candidate gene pairs based on the set of single-end mapped reads and combining with a relationship of the mapped paired-end reads; subjecting the primary set of candidate gene pairs to a filtration, to obtain a candidate set of fused gene pairs; bisecting the third unmapped read, to obtain a half-unmapped read; aligning the half-unmapped read to a gene-junction sequence in the candidate set of fused gene pairs, to obtain a potent region of a fused junction site in the gene in which the half-unmap read locates; outputting original reads of mapped half-unmapped reads, to obtain useful unmapped reads; subjecting the candidate set of fused gene pairs to a fusion simulation; aligning the useful unmapped reads to a junction library, to obtain a fused gene supported by the useful unmapped reads; calculating and gathering the fused sequence supported by the useful unmapped reads, to obtain information of the fused gene. And a system for detecting fusion transcripts is also provided.

9. 发明申请

US20110295784A1 ERROR CORRECTING METHOD OF TEST SEQUENCE, CORRESPONDING SYSTEM AND GENE ASSEMBLY EQUIPMENT 有权
标题翻译：测试顺序错误校正方法，相应系统和基因组装设备
公开(公告)号：US20110295784A1
公开(公告)日：2011-12-01
申请号：US13132038
申请日：2009-12-11
申请人： Jun Wang , Huanming Yang , Jian Wang
发明人： Jun Wang , Huanming Yang , Jian Wang
IPC分类号： G06N3/12
CPC分类号： G06F19/24 , C12Q1/6874 , G06F19/22
摘要： The present invention provides an error correcting method of test sequence, which involves receiving test sequences, configuring high frequency short string list based on a preset high frequency threshold value, traversing each received test sequence, searching an area with the largest number of continuous high frequency short strings on each test sequence in combination with high frequency short string list, configuring whole left sequence and/or right sequence of high frequency short strings at left side and/or right side of searched area according to corresponding received test sequence and high frequency short string list, and constituting corresponding test sequence according to configured left and/or right sequence and searched area. The present invention also provides corresponding error correcting system of test sequence and gene assembly equipment.
摘要翻译：本发明提供一种测试序列的纠错方法，其包括接收测试序列，基于预设的高频阈值配置高频短串列表，遍历每个接收的测试序列，搜索具有最大数目的连续高频区域每个测试序列上的短串组合高频短串列表，根据相应的接收测试序列和高频短信配置搜索区域的左侧和/或右侧的全部左序列和/或右序列的高频短串字符串列表，并根据配置的左和/或右序列和搜索区域构成对应的测试序列。本发明还提供了相应的测试序列和基因组装设备的纠错系统。

10. 发明授权

US10395757B2 Parental genome assembly method 有权
公开(公告)号：US10395757B2
公开(公告)日：2019-08-27
申请号：US14361865
申请日：2011-12-02
申请人： Weiming He , Shancen Zhao , Xuemei Zhang , Yingrui Li , Jun Wang , Jian Wang , Huanming Yang
发明人： Weiming He , Shancen Zhao , Xuemei Zhang , Yingrui Li , Jun Wang , Jian Wang , Huanming Yang
IPC分类号： G16B20/00 , C12Q1/6869 , C12Q1/6895 , G16C99/00
摘要： Provided is a parental genome assembly method, comprising: using the sequencing data of parental selfing line progeny population to assemble and perfect the parental genome data. Also provided is a device for implementing the method.

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