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1. 发明授权

US08364417B2 System and method to correct out of phase errors in DNA sequencing data by use of a recursive algorithm 有权
标题翻译：通过使用递归算法来纠正DNA测序数据中的相位误差的系统和方法
公开(公告)号：US08364417B2
公开(公告)日：2013-01-29
申请号：US13043063
申请日：2011-03-08
申请人： Yi-Ju Chen , Chiu Tai Andrew Wong
发明人： Yi-Ju Chen , Chiu Tai Andrew Wong
IPC分类号： G06F19/00 , G06F15/00
CPC分类号： G06F19/22 , C12Q1/6869 , G06F19/24 , C12Q2565/301 , C12Q2537/165 , C12Q2535/113
摘要： An embodiment of a method for correcting an error associated with phasic synchrony of sequence data generated from a population of template molecules is described that comprises the steps of detecting signals generated in response to nucleotide species introduced during a sequencing reaction; generating an observed value for the signal detected from each of the nucleotide species; defining positive incorporation values and negative incorporation values from the observed values using a carry forward value and an incomplete extension value; and revising the carry forward value and the incomplete extension value using a noise value that is derived from observed values associated with the negative incorporation values.
摘要翻译：描述了用于校正与从模板分子群体生成的序列数据的相位同步相关联的错误的方法的实施例，其包括以下步骤：检测响应于在测序反应期间引入的核苷酸种类产生的信号; 产生从每个核苷酸物种检测的信号的观察值; 使用结转值和不完全扩展值从观察值中确定正合并值和负并入值; 并且使用从与负合并值相关联的观测值导出的噪声值来修正结转值和不完全扩展值。

2. 发明申请

US20110287432A1 SYSTEM AND METHOD FOR TAILORING NUCLEOTIDE CONCENTRATION TO ENZYMATIC EFFICIENCIES IN DNA SEQUENCING TECHNOLOGIES 审中-公开
标题翻译：在DNA测序技术中将核苷酸浓缩到酶促效率的系统和方法
公开(公告)号：US20110287432A1
公开(公告)日：2011-11-24
申请号：US13110589
申请日：2011-05-18
申请人： Chiu Tai Andrew Wong , Yi-Ju Chen , Vinod Bhagwan Makhijani
发明人： Chiu Tai Andrew Wong , Yi-Ju Chen , Vinod Bhagwan Makhijani
IPC分类号： C12Q1/68 , C12M1/34
CPC分类号： C12Q1/6869 , C12Q2527/137 , C12Q2565/301
摘要： An embodiment of a method for optimizing sequencing performance is described that comprises the steps of calculating a nucleotide species specific degradation rate of an apyrase enzyme for a plurality of nucleotide species; determining a concentration for each of the nucleotide species using the nucleotide species specific degradation rate; iteratively providing the concentration of each of the nucleotide species in a reaction environment comprising a polymerase enzyme and a species of template nucleic acid molecule, wherein one or more molecules of the nucleotide species are incorporated into a nascent molecule in a sequencing reaction and the apyrase enzyme is introduced to the reaction environment to degrade unincorporated nucleotide species molecules; and detecting a signal in response to the incorporation of the nucleotide species.
摘要翻译：描述了用于优化测序性能的方法的实施方案，其包括以下步骤：计算多种核苷酸种类的脱酰酶的核苷酸种类特异性降解速率; 使用核苷酸种类特异性降解速率确定每个核苷酸种类的浓度; 迭代地提供在包含聚合酶和模板核酸分子的种类的反应环境中的每种核苷酸种类的浓度，其中核苷酸种类的一个或多个分子被结合到测序反应中的新生分子中，并且apyrase酶引入反应环境以降解未掺入的核苷酸物质分子; 以及响应于核苷酸种类的掺入而检测信号。

3. 发明申请

US20110213563A1 SYSTEM AND METHOD TO CORRECT OUT OF PHASE ERRORS IN DNA SEQUENCING DATA BY USE OF A RECURSIVE ALGORITHM 有权
标题翻译：通过使用回归算法来校正DNA序列数据中的相位误差的系统和方法
公开(公告)号：US20110213563A1
公开(公告)日：2011-09-01
申请号：US13043063
申请日：2011-03-08
申请人： Yi-Ju Chen , Chiu Tai Andrew Wong
发明人： Yi-Ju Chen , Chiu Tai Andrew Wong
IPC分类号： G06F19/00
CPC分类号： G06F19/22 , C12Q1/6869 , G06F19/24 , C12Q2565/301 , C12Q2537/165 , C12Q2535/113
摘要： An embodiment of a method for correcting an error associated with phasic synchrony of sequence data generated from a population of template molecules is described that comprises the steps of detecting signals generated in response to nucleotide species introduced during a sequencing reaction; generating an observed value for the signal detected from each of the nucleotide species; defining positive incorporation values and negative incorporation values from the observed values using a carry forward value and an incomplete extension value; revising the carry forward value and the incomplete extension value using a noise value that is derived from observed values associated with the negative incorporation values; re-defining the positive incorporation values and the negative incorporation values using the revised carry forward value and the revised incomplete extension value; and repeating the steps of revising and re-defining until convergence of the positive incorporation values and the negative incorporation values
摘要翻译：描述了用于校正与从模板分子群体生成的序列数据的相位同步相关联的错误的方法的实施例，其包括以下步骤：检测响应于在测序反应期间引入的核苷酸种类产生的信号; 产生从每个核苷酸物种检测的信号的观察值; 使用结转值和不完全扩展值从观察值中确定正合并值和负并入值; 使用从与负合并值相关联的观测值导出的噪声值来修正结转值和不完全扩展值; 使用修订的结转值和修订的不完全扩展值重新定义积极的并入价值和负的并入价值; 并重复修正和重新定义的步骤，直到正合并值和负合并值的收敛

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