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1. 发明申请

WO2012142611A3 SEQUENCING SMALL AMOUNTS OF COMPLEX NUCLEIC ACIDS 审中-公开
标题翻译：序列复合核酸的小数量
公开(公告)号：WO2012142611A3
公开(公告)日：2016-03-03
申请号：PCT/US2012033832
申请日：2012-04-16
申请人： COMPLETE GENOMICS INC , DRMANAC RADOJE , PETERS BROCK A , KERMANI BAHRAM GHAFFARZADEH
发明人： DRMANAC RADOJE , PETERS BROCK A , KERMANI BAHRAM GHAFFARZADEH
IPC分类号： C12Q1/68
CPC分类号： G06F19/22 , C12Q1/6869 , C12Q2537/159 , C12Q2549/10
摘要： The present invention provides methods and compositions for sequencing small amounts of complex nucleic acids (as defined herein) and for analyzing the resulting sequence information in order to reduce errors and perform haplotype phasing, among other things. As one example, even after amplifying complex nucleic acids more than 1 000-fold- starting, for example, with genomic DNA from 5- human cells- highly accurate whole genome sequences that are fully haplotyped have been produced.
摘要翻译：本发明提供了用于测序小量复合核酸（如本文所定义）的方法和组合物，并用于分析所得序列信息以减少错误并执行单倍型定相等。作为一个示例，即使在扩增了多于1000倍的复合核酸之后，例如，使用来自5个人细胞的基因组DNA，已经产生了完全单体型的高度准确的全基因组序列。

2. 发明申请

WO2012142531A3 PROCESSING AND ANALYSIS OF COMPLEX NUCLEIC ACID SEQUENCE DATA 审中-公开
标题翻译：复杂核酸序列数据的处理和分析
公开(公告)号：WO2012142531A3
公开(公告)日：2014-05-08
申请号：PCT/US2012033686
申请日：2012-04-13
申请人： COMPLETE GENOMICS INC , DRMANAC RADOJE , PETERS BROCK A , KERMANI BAHRAM GHAFFARZADEH
发明人： DRMANAC RADOJE , PETERS BROCK A , KERMANI BAHRAM GHAFFARZADEH
IPC分类号： G06F19/10
CPC分类号： G06F19/22
摘要： The present invention is directed to logic for analysis of nucleic acid sequence data that employs algorithms that lead to a substantial improvement in sequence accuracy and that can be used to phase sequence variations, e.g., in connection with the use of the long fragment read (LFR) process.
摘要翻译：本发明涉及用于分析核酸序列数据的逻辑，其使用导致序列精度的实质性改进并且可用于相序变化的算法，例如结合使用长片段读取（LFR ）过程。

3. 发明申请

WO2007005749A3 SYSTEMS AND METHODS FOR AUTOMATED QUALITY CONTROL OF POLYMER SYNTHESIS 审中-公开
标题翻译：用于自动质量控制聚合物合成的系统和方法
公开(公告)号：WO2007005749A3
公开(公告)日：2009-04-30
申请号：PCT/US2006025843
申请日：2006-06-30
申请人： ILLUMINA INC , KERMANI BAHRAM GHAFFARZADEH , REN HONGJI , KOTSEROGLOU THEO , OLSON NELS A
发明人： KERMANI BAHRAM GHAFFARZADEH , REN HONGJI , KOTSEROGLOU THEO , OLSON NELS A
IPC分类号： C12Q1/68 , G01N33/53
CPC分类号： C40B99/00 , B01J2219/00693
摘要： The invention provides systems and methods for evaluating synthetic reactions such as polymer synthesis reactions. Evaluation of a synthetic reaction product can be based on a quantitative measure of synthesis such as coupling efficiency or yield, and various parameters determined from a separation record obtained for the synthetic reaction product. The invention further provides methods for evaluating a separation method based on various parameters determined from a separation record. The invention can be used to select an appropriate treatment for a synthetic reaction product such as a separation treatment or treatments related to further processing for the desired product. The methods are particularly useful for automated selection of treatments for synthetic reaction products.
摘要翻译：本发明提供用于评价合成反应如聚合物合成反应的系统和方法。合成反应产物的评估可以基于合成的定量测量，例如偶合效率或产率，以及由合成反应产物获得的分离记录确定的各种参数。本发明还提供了基于从分离记录确定的各种参数来评估分离方法的方法。本发明可用于选择合成反应产物的合适处理，例如分离处理或与所需产物的进一步加工有关的处理。该方法对于自动选择合成反应产物的处理特别有用。

4. 发明申请

WO2007005749A2 SYSTEMS AND METHODS FOR AUTOMATED QUALITY CONTROL OF POLYMER SYNTHESIS 审中-公开
标题翻译：用于自动质量控制聚合物合成的系统和方法
公开(公告)号：WO2007005749A2
公开(公告)日：2007-01-11
申请号：PCT/US2006/025843
申请日：2006-06-30
申请人： ILLUMINA, INC. ET AL. , KERMANI, Bahram, Ghaffarzadeh , REN, Hongji , KOTSEROGLOU, Theo , OLSON, Nels, A.
发明人： KERMANI, Bahram, Ghaffarzadeh , REN, Hongji , KOTSEROGLOU, Theo , OLSON, Nels, A.
IPC分类号： C12Q1/68 , G06F19/00
CPC分类号： C40B99/00 , B01J2219/00693
摘要： The invention provides systems and methods for evaluating synthetic reactions such as polymer synthesis reactions. Evaluation of a synthetic reaction product can be based on a quantitative measure of synthesis such as coupling efficiency or yield, and various parameters determined from a separation record obtained for the synthetic reaction product. The invention further provides methods for evaluating a separation method based on various parameters determined from a separation record. The invention can be used to select an appropriate treatment for a synthetic reaction product such as a separation treatment or treatments related to further processing for the desired product. The methods are particularly useful for automated selection of treatments for synthetic reaction products.
摘要翻译：本发明提供用于评价合成反应如聚合物合成反应的系统和方法。合成反应产物的评估可以基于合成的定量测量，例如偶合效率或产率，以及由合成反应产物获得的分离记录确定的各种参数。本发明还提供了基于从分离记录确定的各种参数来评估分离方法的方法。本发明可用于选择合成反应产物的合适处理，例如分离处理或与所需产物的进一步加工有关的处理。该方法对于自动选择合成反应产物的处理特别有用。

5. 发明申请

WO2003069333A1 AUTOMATED INFORMATION PROCESSING IN RANDOMLY ORDERED ARRAYS 审中-公开
标题翻译：随机排序阵列中的自动信息处理
公开(公告)号：WO2003069333A1
公开(公告)日：2003-08-21
申请号：PCT/US2003/004570
申请日：2003-02-14
申请人： ILLUMINA, INC. , KERMANI, Bahram, Ghaffarzadeh , HAAS, Juergen
发明人： KERMANI, Bahram, Ghaffarzadeh , HAAS, Juergen
IPC分类号： G01N33/48
CPC分类号： G01N21/6428 , G01N21/6452 , G01N2021/6484 , G01N2021/772 , G01N2021/7786 , G01N2201/0846 , G06T7/0012 , G06T7/337 , G06T2207/30072
摘要： The invention relates to the use of a computer system to compare images generated from a randomly ordered array. This system preserves the relative position of each site within the array so that the same site can be compared in different images.
摘要翻译：本发明涉及使用计算机系统来比较从随机排序阵列产生的图像。该系统保留了阵列中每个站点的相对位置，以便可以在不同的图像中比较同一站点。

6. 发明申请

WO2018152267A1 RELIABLE AND SECURE DETECTION TECHNIQUES FOR PROCESSING GENOME DATA IN NEXT GENERATION SEQUENCING (NGS) 审中-公开
公开(公告)号：WO2018152267A1
公开(公告)日：2018-08-23
申请号：PCT/US2018/018264
申请日：2018-02-14
申请人： KERMANI, Bahram Ghaffarzadeh
发明人： KERMANI, Bahram Ghaffarzadeh
IPC分类号： G01N33/50 , C12Q1/68 , C40B40/06 , C40B40/00
CPC分类号： G16B30/00 , C12Q1/6806 , C12Q1/6869 , C12Q1/6883 , C12Q2600/156 , C40B40/00 , G16B20/00 , G16B30/10 , G16H50/20 , G16H50/30 , C12Q2535/122 , C12Q2537/101 , C12Q2537/165
摘要： Genetic samples are obtained from separate people, and at least a portion of each are purposefully combined before testing to form a pooled genetic sample. The pooled genetic sample is tested for the presence of a signature for a given known ailment. DNA identification uses discovered InDels in a region of InDel variation in a genetic sample. A pair-wise comparison is performed to reference InDels, and a distance is measured between the first InDel and the reference Indel. Reference kmers are identified in a reference genome, and in a test sample. The plurality of sample kmers are filtered to those which have a 1 edit distance from a corresponding one of the plurality of reference kmers. Reads that have kmers that do not have a 1 edit distance from the corresponding one of the plurality of reference kmers are identified, and multiple single-mutations are eliminated from candidate InDel reads.

7. 发明申请

WO2013028739A1 PHASING OF HETEROZYGOUS LOCI TO DETERMINE GENOMIC HAPLOTYPES 审中-公开
标题翻译：异位定位法测定基因组HAPLOTYPES
公开(公告)号：WO2013028739A1
公开(公告)日：2013-02-28
申请号：PCT/US2012/051825
申请日：2012-08-22
申请人： COMPLETE GENOMICS , KERMANI, Bahram, Ghaffarzadeh , DRMANAC, Radoje
发明人： KERMANI, Bahram, Ghaffarzadeh , DRMANAC, Radoje
IPC分类号： C40B20/00 , C40B20/04
CPC分类号： G06F19/18 , G06F19/22
摘要： Sequencing information is used to correlate alleles at certain locations to alleles at other locations. The statistical information from the reads of fragments in a sample can be used to determine the phasing of haplotypes and to correct or confirm based calls at the locations. In one example, a confidence value (strength score) is determined for a particular hypothesis, which can include whether two alleles are on a same haplotype at two particular loci, as well as what the alleles are on another haplotype (e.g. for a diploid organism). The strength can include a positive contribution from data that is consistent with the hypothesis and a negative contribution from data is that inconsistent with the hypothesis, where both values can be used in a formula to determine the strength.
摘要翻译：测序信息用于将某些位置处的等位基因与其他位置处的等位基因相关联。来自样本中片段读取的统计信息可用于确定单倍型的定相并且在该位置校正或确认基于呼叫。在一个示例中，对于特定假设确定置信度值（强度分数），其可以包括两个等位基因是否在两个特定基因座处于同一单倍型，以及等位基因在另一个单倍型上（例如二倍体生物体）。实力可以包括与假设一致的数据的积极贡献，数据的负面贡献是与假设不一致，其中两个值都可以在公式中用于确定强度。

8. 发明申请

WO2012142611A2 SEQUENCING SMALL AMOUNTS OF COMPLEX NUCLEIC ACIDS 审中-公开
标题翻译：序列复合核酸的小数量
公开(公告)号：WO2012142611A2
公开(公告)日：2012-10-18
申请号：PCT/US2012/033832
申请日：2012-04-16
申请人： COMPLETE GENOMICS, INC. , DRMANAC, Radoje , PETERS, Brock A. , KERMANI, Bahram Ghaffarzadeh
发明人： DRMANAC, Radoje , PETERS, Brock A. , KERMANI, Bahram Ghaffarzadeh
CPC分类号： G06F19/22 , C12Q1/6869 , C12Q2537/159 , C12Q2549/10
摘要： The present invention provides methods and compositions for sequencing small amounts of complex nucleic acids such as human genomes and for analyzing the resulting sequence information in order to reduce sequencing errors and perform haplotype phasing, for example.
摘要翻译：本发明提供了用于测序少量复合核酸如人类基因组的方法和组合物，并且用于分析所得序列信息以减少测序误差并进行例如单倍型定相。

9. 发明申请

WO2013055955A1 IDENTIFICATION OF DNA FRAGMENTS AND STRUCTURAL VARIATIONS 审中-公开
标题翻译：鉴定DNA片段和结构变异
公开(公告)号：WO2013055955A1
公开(公告)日：2013-04-18
申请号：PCT/US2012/059806
申请日：2012-10-11
申请人： COMPLETE GENOMICS, INC. , KERMANI, Bahram Ghaffarzadeh , DRMANAC, Radoje , ALFEROV, Oleg
发明人： KERMANI, Bahram Ghaffarzadeh , DRMANAC, Radoje , ALFEROV, Oleg
IPC分类号： G06F19/14
CPC分类号： G06F19/22
摘要： Various short reads can be grouped and identified as coming from a same long DNA fragment (e.g., by using wells with a relatively low-concentration of DNA). A histogram of the genomic coverage of a group of short reads can provide the edges of the corresponding long fragment (pulse). The knowledge of these pulses can provide an ability to determine the haploid genome and to identify structural variations
摘要翻译：可以将各种短读数分组并鉴定为来自相同的长DNA片段（例如，通过使用具有相对低浓度的DNA的孔）。一组短读取的基因组覆盖率的直方图可以提供对应的长片段（脉冲）的边缘。这些脉冲的知识可以提供确定单倍体基因组并鉴定结构变化的能力

10. 发明申请

WO2012142531A2 PROCESSING AND ANALYSIS OF COMPLEX NUCLEIC ACID SEQUENCE DATA 审中-公开
标题翻译：复合核酸序列数据的处理和分析
公开(公告)号：WO2012142531A2
公开(公告)日：2012-10-18
申请号：PCT/US2012/033686
申请日：2012-04-13
申请人： COMPLETE GENOMICS, INC. , DRMANAC, Radoje , PETERS, Brock A. , KERMANI, Bahram Ghaffarzadeh
发明人： DRMANAC, Radoje , PETERS, Brock A. , KERMANI, Bahram Ghaffarzadeh
CPC分类号： G06F19/22
摘要： The present invention is directed to logic for analysis of nucleic acid sequence data that employs algorithms that lead to a substantial improvement in sequence accuracy and that can be used to phase sequence variations, e.g., in connection with the use of the long fragment read (LFR) process.
摘要翻译：本发明涉及用于分析核酸序列数据的逻辑，其使用导致序列精度的实质性改进并且可用于相序变化的算法，例如结合使用长片段读取（LFR ）过程。

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