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    Method for detecting hydroxylmethylation modification in nucleic acid and use thereof
    1.
    发明授权
    Method for detecting hydroxylmethylation modification in nucleic acid and use thereof 有权
    检测核酸中羟基甲基化修饰的方法及其用途

    公开(公告)号：US09567633B2

    公开(公告)日：2017-02-14

    申请号：US14360594

    申请日：2012-11-21

    申请人： BGI TECH SOLUTIONS CO., LTD.

    发明人： Fei Gao ,  Junwen Wang ,  Xiuqing Zhang ,  Huanming Yang

    IPC分类号： C12Q1/68 ,  C12Q1/54 ,  C12P19/18 ,  C12M1/34 ,  C12N15/74 ,  G01N31/22 ,  G01N33/52 ,  C07H21/04 ,  C40B40/06

    CPC分类号： C12Q1/6874 ,  C12Q1/683 ,  C12Q2600/154 ,  C12Q2521/501 ,  C12Q2521/531 ,  C12Q2525/197 ,  C12Q2537/164 ,  C12Q2563/131 ,  C12Q2521/331

    摘要： A method for detecting hydroxymethylation modification in nucleic acid comprises: glycosylating the nucleic acid, digesting with MspI, ligating the digested fragments to a biotin-labeled linker at both ends thereof, digesting with NlaIII; capturing the digested fragments using streptavidin magnetic beads to produce fragments having the biotin-labeled linker at one end and a CATG 4-base sticky end at the other end, wherein these fragments reveal modification information of their adjacent CCGG sites; ligating the CATG sticky end to a linker containing a recognition site of MmeI or Ecop15I, digesting with corresponding restriction endonuclease to produce short sequence fragments that can reveal modification information of their adjacent CCGG sites; and performing a tag number comparison to obtain information about methylation and hydroxymethylation modification relative levels. A use of the method is also provided.

    摘要翻译： 用于检测核酸中羟基甲基化修饰的方法包括：使核酸糖基化，用MspI消化，将消化的片段两端连接到生物素标记的接头，用NlaIII消化; 使用链霉抗生物素蛋白磁珠捕获消化的片段，以在另一端产生具有生物素标记的接头的片段和另一端的CATG 4-碱基粘性末端，其中这些片段揭示其相邻CCGG位点的修饰信息; 将CATG粘性末端连接到含有MmeI或Ecop15I的识别位点的接头，用相应的限制性内切核酸酶消化以产生可以揭示其相邻CCGG位点的修饰信息的短序列片段; 并进行标签号比较以获得关于甲基化和羟甲基化修饰相关水平的信息。 还提供了该方法的使用。

    METHOD OF DETECTING FUSED TRANSCRIPTS AND SYSTEM THEREOF
    2.
    发明申请
    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.

    WHOLE GENOME AMPLIFICATION METHOD AND APPLICATION THEREOF
    4.
    发明申请
    WHOLE GENOME AMPLIFICATION METHOD AND APPLICATION THEREOF 审中-公开
    全基因扩增方法及其应用

    公开(公告)号：US20150299753A1

    公开(公告)日：2015-10-22

    申请号：US14378935

    申请日：2012-03-30

    申请人： Kui WU ,  Hanjie WU ,  Yong HOU ,  Xun XU ,  Jun WANG

    发明人： Kui WU ,  Hanjie WU ,  Yong HOU ,  Xun XU ,  Jun WANG

    IPC分类号： C12P19/34 ,  C12Q1/68

    CPC分类号： C12P19/34 ,  C12Q1/6806 ,  C12Q1/686 ,  C12Q2537/149

    摘要： Provided are a whole genome sample amplification method, a whole genome sequencing method, and a method for determining whether an abnormal state occurs in a whole genome, a whole genome sample amplification apparatus, a whole genome sequencing device, and a system for determining whether an abnormal state occurs in a whole genome. The whole genome sample amplification method comprises: subjecting a whole genome sample to a first amplification reaction, so as to obtain a first amplification product; and subjecting the first amplification product to a second amplification reaction, so as to obtain a second amplification product. The first amplification reaction is one of the PCR-based amplification reaction and the isothermal amplification reaction, and the second amplification reaction is the other of the PCR-based amplification reaction and the isothermal amplification reaction.

    摘要翻译： 提供了全基因组样品扩增方法，全基因组测序方法以及用于确定全基因组中是否发生异常状态的方法，全基因组样品扩增装置，全基因组测序装置和用于确定是否 异常状态发生在整个基因组中。 全基因组样品扩增方法包括：对全基因组样品进行第一次扩增反应，得到第一扩增产物; 并对第一扩增产物进行第二次扩增反应，得到第二扩增产物。 第一次扩增反应是基于PCR的扩增反应和等温扩增反应之一，第二次扩增反应是基于PCR的扩增反应和等温扩增反应中的另一个。

    METHOD FOR ASSEMBLING SEQUENCED SEGMENTS
    5.
    发明申请
    METHOD FOR ASSEMBLING SEQUENCED SEGMENTS 审中-公开
    组装序列部分的方法

    公开(公告)号：US20140136121A1

    公开(公告)日：2014-05-15

    申请号：US14130706

    申请日：2011-07-05

    申请人： Xun Xu ,  Ye Tao ,  Zequn Zheng ,  Jun Wang

    发明人： Xun Xu ,  Ye Tao ,  Zequn Zheng ,  Jun Wang

    IPC分类号： G06F19/22

    CPC分类号： G16B30/00 ,  G16B40/00

    摘要： The present invention relates to a method for optimizing the assembled result of sequencing data using a genetic map. In particular, provided in the present invention is a new method for assembling individual sequenced segments, which comprises the step of constructing the genetic map with a genetic marker. Furthermore, also provided in the present invention is a method for assembling the individual sequenced segments into a genome sequence, such as a chromosome sequence.

    摘要翻译： 本发明涉及使用遗传图谱优化测序数据的组合结果的方法。 特别地，本发明提供了一种用于组装单个测序片段的新方法，其包括用遗传标记构建遗传图谱的步骤。 此外，本发明还提供了将各个测序片段组装成基因组序列（例如染色体序列）的方法。

    Method and device for genetic map construction, method and device for haplotype analysis
    7.
    发明授权
    Method and device for genetic map construction, method and device for haplotype analysis 有权
    用于遗传图谱构建的方法和装置，用于单倍型分析的方法和装置

    公开(公告)号：US09309570B2

    公开(公告)日：2016-04-12

    申请号：US14240955

    申请日：2012-08-24

    申请人： Luting Song ,  Di Shao ,  Zequn Zheng ,  Zhijun Zheng ,  Kui Wu ,  Shuheng Liang ,  Ye Tao ,  Yong Hou

    发明人： Luting Song ,  Di Shao ,  Zequn Zheng ,  Zhijun Zheng ,  Kui Wu ,  Shuheng Liang ,  Ye Tao ,  Yong Hou

    IPC分类号： C12Q1/68 ,  C12M1/34 ,  G01N33/48 ,  G06F19/20 ,  G06F19/22

    CPC分类号： C12Q1/6869 ,  C12Q1/6874 ,  C12Q1/6881 ,  C12Q2600/172 ,  G06F19/20 ,  G06F19/22

    摘要： Provided are the method and device for genetic map construction and the method and device for haplotype determination of a single cell. Wherein the method for genetic map construction includes: whole genome sequencing for at least a single cell from a same species, aligning the sequencing data to reference sequences respectively to determine genotypes of SNP sites, determining male parent a/female parent b typing results of SNP genotypes of a single cell based on the genotypes of SNP sites, dividing the chromosome of the species into linkage regions based on the male parent a/female parent b typing results of SNP genotypes, determining the variation ratio of a/b between two linkage regions to obtain recombination rate between every two continuous linkage regions, determining recombination map of a single cell according to the recombination rate, wherein the boundary site of a and b is the recombination site, determining the recombination rate of each recombination rate based on the recombination map to construct a genetic map of the species.

    摘要翻译： 提供遗传图谱构建的方法和装置以及单细胞单体型确定的方法和装置。 遗传图谱构建方法包括：对同一物种的至少一个细胞进行全基因组测序，分别将测序数据与参照序列进行比对，以确定SNP位点的基因型，确定SNP的雄性亲本a /雌性亲本B分型结果 基于SNP位点基因型的单细胞基因型，根据SNP基因型的雄性亲本a /雌性亲本B分型结果将该物种的染色体分为连锁区，确定两个连锁区之间a / b的变异比 以获得每两个连续连锁区域之间的重组率，根据复合率确定单个细胞的重组图谱，其中a和b的边界位点是重组位点，基于重组图确定每个重组速率的重组率 构建该物种的遗传图谱。

    Error correcting method of test sequence, corresponding system and gene assembly equipment
    8.
    发明授权
    Error correcting method of test sequence, corresponding system and gene assembly equipment 有权
    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。

    METHOD AND DEVICE FOR ASSEMBLING GENOME SEQUENCE
    9.
    发明申请
    METHOD AND DEVICE FOR ASSEMBLING GENOME SEQUENCE 审中-公开
    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。