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1. 发明申请

WO2013155119A1 DETECTION AND QUANTITATION OF SAMPLE CONTAMINATION IN IMMUNE REPERTOIRE ANALYSIS 审中-公开
标题翻译：免疫样品分析中样品污染的检测和定量
公开(公告)号：WO2013155119A1
公开(公告)日：2013-10-17
申请号：PCT/US2013/035857
申请日：2013-04-09
申请人： SEQUENTA, INC. , ASBURY, Thomas , CARLTON, Victoria , FAHAM, Malek , MACEVICZ, Stephen , MOORHEAD, Martin , WILLIS, Thomas , ZHENG, Jianbiao
发明人： ASBURY, Thomas , CARLTON, Victoria , FAHAM, Malek , MACEVICZ, Stephen , MOORHEAD, Martin , WILLIS, Thomas , ZHENG, Jianbiao
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6848 , G06F19/00 , C12Q2525/161 , C12Q2535/122
摘要： The invention is directed to methods for detecting and quantifying nucleic acid contamination in a tissue sample of an individual containing T cells and/or B cells, which is used for generating a sequence-based clonotype profile. In one aspect, the invention is implemented by measuring the presence and/or level of an endogenous or exogenous nucleic acid tag by which nucleic acid from an intended individual can be distinguished from that of unintended individuals. Endogenous tags include genetic identity markers, such as short tandem repeats, rare clonotypes or the like, and exogenous tags include sequence tags employed to determine clonotype sequences from sequence reads.
摘要翻译：本发明涉及用于检测和定量含有T细胞和/或B细胞的个体的组织样品中的核酸污染物的方法，其用于产生基于序列的克隆型谱。在一个方面，本发明通过测量内源或外源核酸标签的存在和/或水平来实现，通过该核酸标签，来自预期个体的核酸可以与非预期个体的核酸区别。内源性标签包括遗传同一性标记，例如短串联重复，罕见克隆型等，外源标签包括用于从序列读数确定克隆型序列的序列标签。

2. 发明申请

WO2018057779A1 COMPOSITIONS OF SYNTHETIC TRANSPOSONS AND METHODS OF USE THEREOF 审中-公开
标题翻译：合成运输体的组合物及其使用方法
公开(公告)号：WO2018057779A1
公开(公告)日：2018-03-29
申请号：PCT/US2017/052776
申请日：2017-09-21
申请人： ZHENG, Jianbiao
发明人： ZHENG, Jianbiao
IPC分类号： C12N15/10 , C12Q1/68
CPC分类号： C12N15/10
摘要： The present invention provides synthetic transposons having two non-complementary regions comprising adapter sequences and linked to each other. The synthetic transposons may further comprise molecular barcodes. Also disclosed are compositions comprising a plurality of the synthetic transposons, methods, and kits for library preparation. The compositions, methods, kits and analysis tools described herein have many applications, including high-quality sequencing, haplotyping, error correction, sequencing of repetitive regions, detection of structural variations and copy number variations, methylation analysis and quantification of target nucleic acids.
摘要翻译：本发明提供了具有两个包含衔接子序列且彼此连接的非互补区的合成转座子。合成转座子可以进一步包含分子条码。还公开了包含多个用于文库制备的合成转座子，方法和试剂盒的组合物。本文所述的组合物，方法，试剂盒和分析工具具有许多应用，包括高质量测序，单元型分型，错误校正，重复区域的测序，结构变异和拷贝数变异的检测，靶核酸的甲基化分析和定量。 / p>

3. 发明申请

WO2013188471A3 METHOD OF SEQUENCE DETERMINATION USING SEQUENCE TAGS 审中-公开
标题翻译：使用序列标签进行序列确定的方法
公开(公告)号：WO2013188471A3
公开(公告)日：2014-04-03
申请号：PCT/US2013045276
申请日：2013-06-11
申请人： SEQUENTA INC , FAHAM MALEK , MOORHEAD MARTIN , WILLIS THOMAS , ZHENG JIANBIAO
发明人： FAHAM MALEK , MOORHEAD MARTIN , WILLIS THOMAS , ZHENG JIANBIAO
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6869 , C12Q2565/514 , C12Q2565/537 , C12Q2525/161 , C12Q2525/179 , C12Q2525/191
摘要： The invention is directed to the use of sequence tags to improve sequence determination of amplicons of related sequences, particularly large and complex amplicons, such as those comprising recombined nucleic acids encoding immune receptor molecules. In one aspect, sequence reads having the same sequence tags are aligned after which final base calls are determined from a (possibly weighted) average base call from sequence read base calls at each position. Similarly, in another aspect, sequence reads comprising series of incorporation signals are aligned by common sequence tags and base calls in homopolymer regions are made as a function incorporation signal values at each "flow" position.
摘要翻译：本发明涉及使用序列标签来改进相关序列扩增子的序列测定，特别是大的和复杂的扩增子，例如包含编码免疫受体分子的重组核酸的扩增子。在一个方面，具有相同序列标签的序列读取被对齐，之后，从每个位置处的来自序列读取基础调用的（可能加权的）平均基本调用确定最终基本调用。类似地，在另一方面，包括一系列并入信号的序列读数由公共序列标签对齐，并且均聚物区域中的碱基调节作为在每个“流动”位置处的函数并入信号值。

4. 发明申请

WO2014018460A1 SINGLE CELL ANALYSIS USING SEQUENCE TAGS 审中-公开
标题翻译：使用序列标签的单细胞分析
公开(公告)号：WO2014018460A1
公开(公告)日：2014-01-30
申请号：PCT/US2013/051539
申请日：2013-07-22
申请人： SEQUENTA, INC. , FAHAM, Malek , WILLIS, Thomas , ZHENG, Jianbiao
发明人： FAHAM, Malek , WILLIS, Thomas , ZHENG, Jianbiao
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6806 , C12Q1/6844 , C12Q2521/301 , C12Q2527/101 , C12Q2563/159 , C12Q2563/179
摘要： The invention provides a method of making measurements on individual cells of a population by forming reactors containing single cells and a predetermined number, usually one, homogeneous sequence tag. In one aspect, the invention provides a method of making multiparameter measurements on individual cells of such a population by carrying out a polymerase cycling assembly (PCA) reaction to link their identifying nucleic acid sequences, such as sequence tag copies derived from a homogeneous sequence tag, to other cellular nucleic acids of interest, thereby forming fusion products. The fusion products of such PCA reactions are then sequenced and tabulated to generate multiparameter data for cells of the population.
摘要翻译：本发明提供了通过形成含有单个细胞的反应器和预定数量的通常为一个均质序列标签来对群体的个体细胞进行测量的方法。一方面，本发明提供了一种通过进行聚合酶循环组件（PCA）反应以连接其鉴定的核酸序列（例如衍生自均质序列标签的序列标签拷贝）来对这样群体的个体细胞进行多参数测量的方法，到目的地的其他细胞核酸，从而形成融合产物。然后对这种PCA反应的融合产物进行测序并列表，以产生群体细胞的多参数数据。

5. 发明申请

WO2013066726A1 T-CELL RECEPTOR CLONOTYPES SHARED AMONG ANKYLOSING SPONDYLITIS PATIENTS 审中-公开
标题翻译：淋巴细胞感染患者共享的T细胞受体克隆
公开(公告)号：WO2013066726A1
公开(公告)日：2013-05-10
申请号：PCT/US2012/061977
申请日：2012-10-25
申请人： SEQUENTA, INC. , FAHAM, Malek , CARLTON, Victoria , MOORHEAD, Martin , ZHENG, Jianbiao , ASBURY, Thomas
发明人： FAHAM, Malek , CARLTON, Victoria , MOORHEAD, Martin , ZHENG, Jianbiao , ASBURY, Thomas
IPC分类号： C12Q1/68 , C12N15/12 , C07K16/18 , A61K39/395
CPC分类号： C12Q1/6883 , C07K14/7051 , C07K16/2809 , C07K2317/34 , C12Q1/6881 , C12Q2600/112 , C12Q2600/156 , C12Q2600/158 , G06F19/00 , G16H50/20
摘要： The invention includes a method for determining the disease status of an individual suffering from ankylosing spondylitis by monitoring the individual's T-cell repertoire for the presence and/or level of clonotypes encoding T-cell receptor chains with segments identical to and/or related to the peptide LCASSLEASGSSYNEQFFGPGTRLTV (SEQ ID NO: 1) or the peptide VYFCASSDSSGSTDTQYFGPGTRLTV (SEQ ID NO: 2). The invention also includes therapeutic antibodies specific for these peptides for ameliorating the effects of ankylosing spondylitis.
摘要翻译：本发明包括一种通过监测个体的T细胞谱来确定编码T细胞受体链的克隆型的存在和/或水平的方法，该方法通过监测个体的T细胞谱，所述片段与T细胞受体链相同和/或相关的片段肽LCASSLEASGSSYNEQFFGPGTRLTV（SEQ ID NO：1）或肽VYFCASSDSSGSTDTQYFGPGTRLTV（SEQ ID NO：2）。本发明还包括对这些肽特异的治疗性抗体，以改善强直性脊柱炎的作用。

6. 发明申请

WO2016191618A1 METHODS OF INSERTING MOLECULAR BARCODES 审中-公开
标题翻译：插入分子杆的方法
公开(公告)号：WO2016191618A1
公开(公告)日：2016-12-01
申请号：PCT/US2016/034480
申请日：2016-05-26
申请人： ZHENG, Jianbiao , SHI, Changping
发明人： ZHENG, Jianbiao , SHI, Changping
IPC分类号： C07H1/00 , C07H21/00 , C07H21/04 , C12N15/10
CPC分类号： C12N15/1068 , C07H1/00 , C07H21/00 , C07H21/04 , C12N15/1065 , C12N15/1082 , C12Q1/6874 , C12Q2525/191 , C12Q2563/179 , C12Q2565/514
摘要： The present invention provides compositions, methods, and kits for inserting a plurality of synthetic transposons each comprising a different nucleic acid sequence (i.e., molecular barcode) in a target nucleic acid of interest to allow extraction of contiguity information in the target nucleic acid. The molecular barcodes are also useful for reducing amplification or sequencing bias and errors, and for guiding accurate sequence assembly of the target nucleic acid from sequencing reads. The compositions, methods, and kits described herein have many applications, including haplotyping, genome assembly, sequencing of repetitive regions, detection of structural variations and copy number variations, chromosomal conformation analysis, and methylation analysis.
摘要翻译：本发明提供用于将各种包含不同核酸序列（即分子条形码）的多个合成转座子插入目的靶核酸中的组合物，方法和试剂盒，以允许提取靶核酸中的毗连信息。分子条形码也可用于减少扩增或测序偏差和错误，并用于从测序读数引导靶核酸的精确序列组装。本文描述的组合物，方法和试剂盒具有许多应用，包括单倍型，基因组装配，重复区域测序，结构变异和拷贝数变异检测，染色体构象分析和甲基化分析。

7. 发明申请

WO2013188471A2 METHOD OF SEQUENCE DETERMINATION USING SEQUENCE TAGS 审中-公开
标题翻译：使用序列标签进行序列确定的方法
公开(公告)号：WO2013188471A2
公开(公告)日：2013-12-19
申请号：PCT/US2013/045276
申请日：2013-06-11
申请人： SEQUENTA, INC. , FAHAM, Malek , MOORHEAD, Martin , WILLIS, Thomas , ZHENG, Jianbiao
发明人： FAHAM, Malek , MOORHEAD, Martin , WILLIS, Thomas , ZHENG, Jianbiao
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6869 , C12Q2565/514 , C12Q2565/537 , C12Q2525/161 , C12Q2525/179 , C12Q2525/191
摘要： The invention is directed to the use of sequence tags to improve sequence determination of amplicons of related sequences, particularly large and complex amplicons, such as those comprising recombined nucleic acids encoding immune receptor molecules. In one aspect, sequence reads having the same sequence tags are aligned after which final base calls are determined from a (possibly weighted) average base call from sequence read base calls at each position. Similarly, in another aspect, sequence reads comprising series of incorporation signals are aligned by common sequence tags and base calls in homopolymer regions are made as a function incorporation signal values at each "flow" position.
摘要翻译：本发明涉及使用序列标签来改进相关序列扩增子的序列测定，特别是大的和复杂的扩增子，例如包含编码免疫受体分子的重组核酸的扩增子。在一个方面，具有相同序列标签的序列读取被对齐，之后，从每个位置处的来自序列读取基础调用的（可能加权的）平均基本调用确定最终基本调用。类似地，在另一方面，包括一系列并入信号的序列读数由公共序列标签对齐，并且均聚物区域中的碱基调节作为在每个“流动”位置处的函数并入信号值。

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