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    Analyzing genome sequencing information to determine likelihood of co-segregating alleles on haplotypes
    81.
    发明授权
    Analyzing genome sequencing information to determine likelihood of co-segregating alleles on haplotypes 有权
    分析基因组测序信息，以确定单倍型上共分离等位基因的可能性

    公开(公告)号：US08880456B2

    公开(公告)日：2014-11-04

    申请号：US13591741

    申请日：2012-08-22

    申请人： Bahram Ghaffarzadeh Kermani ,  Radoje Drmanac

    发明人： Bahram Ghaffarzadeh Kermani ,  Radoje Drmanac

    IPC分类号： G06F9/44 ,  G06N7/02 ,  G06N7/08 ,  G06F19/18 ,  G06F19/22

    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。

    Nucleic acid sequencing and process
    82.
    发明授权
    Nucleic acid sequencing and process 有权
    核酸测序和过程

    公开(公告)号：US08518640B2

    公开(公告)日：2013-08-27

    申请号：US12573697

    申请日：2009-10-05

    申请人： Radoje Drmanac ,  Matthew Callow

    发明人： Radoje Drmanac ,  Matthew Callow

    IPC分类号： C12Q1/68

    CPC分类号： C12Q1/6874 ,  C12Q2533/107 ,  C12Q2525/185 ,  C12Q2525/151

    摘要： The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods.

    摘要翻译： 本发明涉及用于核酸鉴定和检测的组合物和方法。 本发明的组合物和方法包括从样品中提取和分离靶核酸，使用片段化的靶核酸产生靶核酸模板，并使这些靶核酸模板进行扩增方法以形成核酸纳米棒。 本发明还包括使用各种测序应用检测和鉴定序列的方法，包括通过连接方法测序。

    IDENTIFICATION OF DNA FRAGMENTS AND STRUCTURAL VARIATIONS
    83.
    发明申请
    IDENTIFICATION OF DNA FRAGMENTS AND STRUCTURAL VARIATIONS 有权
    鉴定DNA片段和结构变异

    公开(公告)号：US20130096841A1

    公开(公告)日：2013-04-18

    申请号：US13649966

    申请日：2012-10-11

    申请人： Complete Genomics, Inc.

    发明人： Bahram Ghaffarzadeh Kermani ,  Radoje Drmanac ,  Oleg Alferov

    IPC分类号： G06F17/18

    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。

    EFFICIENT SHOTGUN SEQUENCING METHODS
    85.
    发明申请
    EFFICIENT SHOTGUN SEQUENCING METHODS 审中-公开
    有效的射击测序方法

    公开(公告)号：US20130059737A1

    公开(公告)日：2013-03-07

    申请号：US13647338

    申请日：2012-10-08

    申请人： Complete Genomics, Inc.

    发明人： Radoje Drmanac ,  Clifford Reid

    IPC分类号： C40B20/00

    CPC分类号： C12Q1/6869 ,  C12Q1/6874 ,  C12Q2549/119 ,  C12Q2537/149 ,  C12Q2565/137

    摘要： Methods are provided for efficient shotgun sequencing to allow efficient selection and sequencing of nucleic acids of interest contained in a library. The nucleic acids of interest can be defined any time before or after preparation of the library. One example of nucleic acids of interest is missing or low confidence genome sequences resulting from an initial sequencing procedure. Other nucleic acids of interest include subsets of genomic DNA, RNA or cDNAs (exons, genes, gene sets, transciptomes). By designing an efficient (simple to implement, speedy, high specificity, low cost) selection procedure, a more complete sequence is achieved with less effort than by using highly redundant shotgun sequencing in an initial sequencing procedure

    摘要翻译： 提供了有效的霰弹枪测序的方法，以允许文库中包含的感兴趣的核酸的有效选择和测序。 感兴趣的核酸可以在文库制备之前或之后的任何时间进行定义。 感兴趣的核酸的一个实例是由初始测序程序产生的缺失或低置信基因组序列。 感兴趣的其他核酸包括基因组DNA，RNA或cDNAs（外显子，基因，基因组，转录本）的子集。 通过设计一种高效（简单实施，快速，高特异性，低成本）选择程序，通过在初始测序程序中使用高度冗余的霰弹枪测序，以更少的努力实现更完整的顺序

    METHOD AND SYSTEM FOR IMAGING HIGH DENSITY BIOCHEMICAL ARRAYS WITH SUB-PIXEL ALIGNMENT
    87.
    发明申请
    METHOD AND SYSTEM FOR IMAGING HIGH DENSITY BIOCHEMICAL ARRAYS WITH SUB-PIXEL ALIGNMENT 有权
    用于用子像素对准成像高密度生物化学阵列的方法和系统

    公开(公告)号：US20120200692A1

    公开(公告)日：2012-08-09

    申请号：US13451678

    申请日：2012-04-20

    申请人： Bryan P. Staker ,  Craig E. Uhrich

    发明人： Bryan P. Staker ,  Craig E. Uhrich

    IPC分类号： H04N7/18

    CPC分类号： G02B21/365 ,  G01B11/272 ,  G02B21/002 ,  G02B21/025 ,  G02B21/361 ,  H04N5/37206 ,  H04N7/18

    摘要： A method and associated system for imaging high density biochemical arrays comprises one or more imaging channels that share a common objective lens and a corresponding one or more time delay integration-type imaging cameras with optical alignment mechanisms that permit independent inter-channel and intra-channel adjustment of each of four degrees: X, Y, rotation and scale. The imaging channels are configured to independently examine different spectra of the image of the biochemical arrays.

    摘要翻译： 用于高密度生物化学阵列成像的方法和相关系统包括共享共同物镜的一个或多个成像通道和具有光学对准机构的相应的一个或多个时间延迟积分型成像相机，其允许独立的通道间和通道内 四度调整：X，Y，旋转和刻度。 成像通道被配置为独立地检查生物化学阵列的图像的不同光谱。

    Method and system for imaging high density biochemical arrays with sub-pixel alignment
    88.
    发明授权
    Method and system for imaging high density biochemical arrays with sub-pixel alignment 有权
    用于对具有亚像素对准的高密度生物化学阵列进行成像的方法和系统

    公开(公告)号：US08175452B1

    公开(公告)日：2012-05-08

    申请号：US12912641

    申请日：2010-10-26

    申请人： Bryan P. Staker ,  Craig E. Uhrich

    发明人： Bryan P. Staker ,  Craig E. Uhrich

    IPC分类号： G02B21/36

    CPC分类号： G02B21/365 ,  G01B11/272 ,  G02B21/002 ,  G02B21/025 ,  G02B21/361 ,  H04N5/37206 ,  H04N7/18

    摘要： A system and associated method for imaging high density biochemical arrays comprises one or more imaging channels that share a common objective lens and a corresponding one or more time delay integration-type imaging cameras with optical alignment mechanisms that permit independent inter-channel and intra-channel adjustment of each of four degrees: X, Y, rotation and scale. The imaging channels are configured to independently examine different spectra of the image of the biochemical arrays.

    摘要翻译： 用于对高密度生物化学阵列进行成像的系统和相关方法包括共享共同物镜的一个或多个成像通道和具有光学对准机构的相应的一个或多个时间延迟积分型成像相机，其允许独立的通道间和通道内 四度调整：X，Y，旋转和刻度。 成像通道被配置为独立地检查生物化学阵列的图像的不同光谱。

    METHOD AND SYSTEM FOR ACCURATE ALIGNMENT AND REGISTRATION OF ARRAY FOR DNA SEQUENCING
    89.
    发明申请
    METHOD AND SYSTEM FOR ACCURATE ALIGNMENT AND REGISTRATION OF ARRAY FOR DNA SEQUENCING 有权
    用于DNA序列的精确对准和阵列注册的方法和系统

    公开(公告)号：US20110268347A1

    公开(公告)日：2011-11-03

    申请号：US13092618

    申请日：2011-04-22

    申请人： Bryan P. Staker

    发明人： Bryan P. Staker

    IPC分类号： G06K9/00 ,  C40B60/10

    CPC分类号： C12Q1/6874 ,  G06K9/32 ,  G06K9/42 ,  G06K2209/07 ,  G06T7/0012 ,  G06T7/32 ,  G06T7/337 ,  G06T7/74 ,  G06T2207/10056 ,  G06T2207/30072

    摘要： In a genome sequencing system and methodology, a protocol is provided to achieve precise alignment and accurate registration of an image of a planar array of nanoballs subject to optical analysis. Precise alignment correcting for fractional offsets is achieved by correcting for errors in subperiod x-y offset, scale and rotation by use of minimization techniques and Moiré averaging. In Moiré averaging, magnification is intentionally set so that the pixel period of the imaging element is a noninteger multiple of the site period. Accurate registration is achieved by providing for pre-defined pseudo-random sets of sites, herein deletion or reserved sites, where nanoballs are prevented from attachment to the substrate so that the sites of the array can be used in a pattern matching scheme as registration markers for absolute location identification. Information can be extracted with a high degree of confidence that it is correlated to a known location, while at the same time the amount of information that can be packed on a chip is maximized.

    摘要翻译： 在基因组测序系统和方法学中，提供了一种协议，以实现经受光学分析的纳米棒的平面阵列的图像的精确对准和精确配准。 通过使用最小化技术和莫尔平均来校正子周期x-y偏移，刻度和旋转中的误差来实现分数偏移的精确对准校正。 在莫尔平均中，有意地设置放大率，使得成像元件的像素周期是站点周期的非整数倍。 通过提供预定义的伪随机组的位点（这里是删除或保留位点）来实现精确的注册，其中防止了纳米线附着到基底，使得阵列的位点可以以模式匹配方案用作对准标记 用于绝对位置识别。 可以高信度地提取信息，使其与已知位置相关联，同时可将芯片上打包的信息量最大化。