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1. 发明申请

WO2010028366A3 METHODS AND SYSTEMS FOR NUCLEIC ACID SEQUENCING VALIDATION, CALIBRATION AND NORMALIZATION 审中-公开
公开(公告)号：WO2010028366A3
公开(公告)日：2010-03-11
申请号：PCT/US2009/056225
申请日：2009-09-08
申请人： LIFE TECHNOLOGIES CORPORATION , GREINER, Douglas, P. , GJERSTAD, Carmen , ZIEGLE, Janet, S. , JONES, Lee, W. , SHEN, Min-Yi , CHIN, Jason , BREU, Heinz
发明人： GREINER, Douglas, P. , GJERSTAD, Carmen , ZIEGLE, Janet, S. , JONES, Lee, W. , SHEN, Min-Yi , CHIN, Jason , BREU, Heinz
IPC分类号： C12Q1/68 , C12N15/10
摘要： A system for performing quality control for nucleic acid sample sequencing is disclosed. The system has a set of solid supports, each support having attached thereto a plurality of nucleic acid sequences. The set has plural groups of solid supports and each group contains solid supports having the same nucleic acid sequences attached thereto. The nucleic acid sequences of each group differ from each other. The nucleic acid sequences are synthetically derived. A method of preparing a quality control for performing nucleic acid sample sequencing and a method of validating a nucleic acid sequencing instrument are also disclosed.

2. 发明申请

WO2011143525A2 COMPUTATIONAL METHODS FOR TRANSLATING A SEQUENCE OF MULTI-BASE COLOR CALLS TO A SEQUENCE OF BASES 审中-公开
标题翻译：用于将多基色颜色调用序列转换为基数序列的计算方法
公开(公告)号：WO2011143525A2
公开(公告)日：2011-11-17
申请号：PCT/US2011/036393
申请日：2011-05-13
申请人： LIFE TECHNOLOGIES CORPORATION , BREU, Heinz , GUO, Danwei
发明人： BREU, Heinz , GUO, Danwei
IPC分类号： C12Q1/68 , G06F19/10 , G06F19/22
CPC分类号： C12Q1/6869 , G06F19/22 , C12Q2535/131 , C12Q2565/1025
摘要： Disclosed are systems and methods for resequencing using color calls. A DNA sample is encoded and sequenced according to a multi-base code producing a string of read color calls for a fragment of the sample. A reference sequence is obtained. The string of read color calls is mapped to the reference sequence. A base sequence is extracted from the reference sequence. The base sequence is encoded as a string of reference color codes according to the multi-base code. The string of read color calls is aligned with the string of reference color codes and mismatches in the alignment are detected. One or more mismatches of the string of read color calls are annotated as inconsistent. The one or more inconsistent mismatches of the string of read color calls are corrected. The string of corrected read color calls is decoded to bases producing a read sequence.
摘要翻译：公开了使用颜色调用重新测序的系统和方法。 DNA样本根据多基因码进行编码和排序，产生样本片段的一系列读取颜色调用。得到参考序列。读取颜色调用的字符串映射到参考序列。从参考序列中提取碱基序列。基本序列根据多基本码被编码为参考颜色码串。读取颜色调用的字符串与参考颜色代码的字符串对齐，并且检测到对齐中的不匹配。读取颜色调用字符串的一个或多个不匹配被注释为不一致。读取颜色调用串的一个或多个不一致的不匹配被更正。将经校正的读取颜色调用的字符串解码为产生读取序列的基准。

3. 发明申请

WO2011137356A2 SYSTEMS AND METHODS FOR IDENTIFYING EXON JUNCTIONS 审中-公开
标题翻译：用于识别EXON JUNCTIONS的系统和方法
公开(公告)号：WO2011137356A2
公开(公告)日：2011-11-03
申请号：PCT/US2011/034592
申请日：2011-04-29
申请人： LIFE TECHNOLOGIES CORPORATION , VATTA, Paolo , SAKARYA, Onur , BREU, Heinz , POPESCU, Liviu , SIDDIQUI, Asim , HYLAND, Fiona
发明人： VATTA, Paolo , SAKARYA, Onur , BREU, Heinz , POPESCU, Liviu , SIDDIQUI, Asim , HYLAND, Fiona
IPC分类号： G06F19/22 , G06F19/28 , C12Q1/68
CPC分类号： G06F19/22
摘要： Systems and methods are used to identify an exon junction from a single read of a transcript. A transcript sample is interrogated and a read sequence is produced using a nucleic acid sequencer. A first exon sequence and a second exon sequence are obtained using the processor. The first exon sequence is mapped to a prefix of the read sequence using the processor. The second exon sequence is mapped to a suffix of the read sequence using the processor. A sum of a number of sequence elements of the first exon sequence that overlap the prefix of the read sequence, of a number of sequence elements of the second exon sequence that overlap the suffix of the read sequence, and of a constant is calculated using the processor. If the sum equals a length of the read sequence, a junction is identified in the read using the processor.
摘要翻译：系统和方法用于从单次阅读誊本中鉴定出外显子连接。询问转录物样品，并使用核酸测序仪产生读序列。使用处理器获得第一外显子序列和第二外显子序列。使用处理器将第一个外显子序列映射到读取序列的前缀。第二个外显子序列使用处理器映射到读序列的后缀。与第一外显子序列的序列元素的数量重叠，读取序列的前缀，与重写序列的后缀重叠的第二外显子序列的多个序列元件的数目和一个常数的序列元素的总和是使用处理器。如果总和等于读取序列的长度，则使用处理器在读取中识别结。

4. 发明申请

WO2011100617A2 NUCLEIC ACID, BIOMOLECULE AND POLYMER IDENTIFIER CODES 审中-公开
标题翻译：核酸，生物分子和聚合物鉴定码
公开(公告)号：WO2011100617A2
公开(公告)日：2011-08-18
申请号：PCT/US2011/024631
申请日：2011-02-11
申请人： LIFE TECHNOLOGIES CORPORATION , BODEAU, John , BREU, Heinz , GILLES, Patrick (deceased) , PERRY, Kathleen , HARRIS, Adam
发明人： BODEAU, John , BREU, Heinz , GILLES, Patrick (deceased) , PERRY, Kathleen , HARRIS, Adam
IPC分类号： C40B30/04 , C12Q1/68
CPC分类号： C12Q1/6869 , C12N15/1065 , C12Q1/6876 , C12Q2600/166 , C12Q2565/102 , C12Q2533/107 , C12Q2563/179 , C12Q2565/514
摘要： Provided herein are systems, compositions and methods for tracking, sorting and/or identifying sample polynucleotides using nucleic acid barcodes. The barcodes provided herein are oligonucleotides that are designed to be uniquely identifiable. The nucleic acid barcodes have properties that permit them to be sequenced with high accuracy and/or reduced error rates. In some embodiments, the nucleic acid barcodes are designed to have certain nucleotide sequences that make up overlapping dibase color positions (also called color positions). The order of the overlapping dibase color positions can be determined using fluorophore-encoded dibase probes in a fluorophore color calling scheme to give high fidelity reads.
摘要翻译：本文提供了使用核酸条形码跟踪，分选和/或鉴定样品多核苷酸的系统，组合物和方法。本文提供的条形码是被设计为唯一可识别的寡核苷酸。核酸条形码具有允许以高精度和/或降低的错误率排序的性质。在一些实施方案中，将核酸条形码设计为具有构成重叠二碱基色素位置（也称为色素位置）的某些核苷酸序列。可以使用荧光团编码的二酶探针在荧光团颜色调用方案中确定重叠二碱基色素位置的顺序，以提供高保真读数。

5. 发明申请

WO2014043298A1 SYSTEMS AND METHODS FOR IDENTIFYING SEQUENCE VARIATION ASSOCIATED WITH GENETIC DISEASES 审中-公开
标题翻译：用于识别与遗传病相关的序列变异的系统和方法
公开(公告)号：WO2014043298A1
公开(公告)日：2014-03-20
申请号：PCT/US2013/059365
申请日：2013-09-12
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： HYLAND, Fiona , BREU, Heinz
IPC分类号： G06F19/18
CPC分类号： G06F19/18
摘要： Systems and method for identifying variants associated with a genetic disease can include obtaining calls for a plurality of individuals for a list of variant positions. The calls can be compared to identify variants that are found in affected individuals and absent in non-affected individuals. Such variants can include loss of heterozygosity, trans-phased compound heterozygotes, increased frequency mitochondrial variants, homozygous recessive variants, de novo variants, sex-linked variants, and combinations thereof.
摘要翻译：用于识别与遗传疾病相关的变体的系统和方法可以包括获得针对变体位置的列表的多个个体的呼叫。可以将呼叫进行比较，以确定在受影响的个体中发现的变体，并且在不受影响的个体中不存在。这样的变体可以包括杂合性的丧失，反式复合杂合子，增加的频率线粒体变体，纯合隐性变体，从头变体，性别连锁的变体及其组合。

6. 发明申请

WO2013055822A2 SYSTEMS AND METHODS FOR ANALYSIS AND INTERPRETATION OF NUCLEIC ACID SEQUENCE DATA 审中-公开
标题翻译：用于核酸序列数据分析和解释的系统和方法
公开(公告)号：WO2013055822A2
公开(公告)日：2013-04-18
申请号：PCT/US2012/059601
申请日：2012-10-10
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： KRISHNASWAMI, Brijesh , JANDHYALA, Srikanth , LOU, Yuandan , SIDDIQUI, Asim , AGATE, Mrunal , DHAPULKAR, Ameet , BREU, Heinz , SHUKLA, Amitabh , KUHLMANN, Karl , HYLAND, Fiona , ALTUN, Gulsah , THOMAS, Daryl
IPC分类号： G06F19/18
CPC分类号： G06F19/18 , G06F17/30991 , G06F19/28
摘要： Systems and method for annotating variants within a genome can call variants from reads or receive called variants directly and associate the called variants with functional annotations and interpretive annotations. A summary report of the called variants, the associated functional annotations, and the associated interpretive annotations can be generated.
摘要翻译：用于在基因组内注释变体的系统和方法可以直接从读取或接收所调用的变体调用变体，并将被叫变体与功能注释和解释性注释相关联。可以生成所调用的变体，关联的功能注释和相关联的解释性注释的总结报告。

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