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    SEQUENCE CAPTURE METHOD USING SPECIALIZED CAPTURE PROBES (HEATSEQ)
    2.
    发明申请
    SEQUENCE CAPTURE METHOD USING SPECIALIZED CAPTURE PROBES (HEATSEQ) 审中-公开
    使用专用捕获探测器的序列捕获方法（HEATSEQ）

    公开(公告)号：US20150141257A1

    公开(公告)日：2015-05-21

    申请号：US14338921

    申请日：2014-07-23

    申请人： Roche NimbleGen, Inc.

    发明人： Thomas Albert ,  Michael Brockman ,  Daniel Lee Burgess ,  Victor Lyamichev ,  Jason Norton ,  Jigar Patel

    IPC分类号： C12Q1/68

    CPC分类号： C12Q1/6876 ,  C12Q1/6813 ,  C12Q1/6874 ,  C12Q2525/161 ,  C12Q2525/179 ,  C12Q2537/159 ,  C12Q2563/179

    摘要： The present invention is a novel protocol for the massively parallel production of improved MIPs. The molecular improvements to the MIP cover the manufacturing of the probes, the workflow, the addition of unique sequence elements which connote sample specificity, and a sequence tag which uniquely identifies a specific molecule present in the initial sample population. Lastly, this invention also is combined with an empirical optimization strategy that overcomes issues of both locus representation and allelic bias. This improved technique is scalable and can be utilized to amplify targets comprised of a single locus' amplicon up to targeting more than 1 million loci.

    摘要翻译： 本发明是用于大规模并行生产改进的MIP的新方案。 对MIP的分子改进涵盖探针的制造，工作流程，添加独特序列元件，其指示样品特异性，以及唯一识别初始样品群体中存在的特定分子的序列标签。 最后，本发明还结合经验优化策略，其克服了轨迹表示和等位基因偏差的问题。 这种改进的技术是可扩展的，并且可以用于放大由单个基因座扩增子组成的靶，其靶向超过100万个位点。

    COMPOSITIONS AND METHODS FOR BISULFITE CONVERTED SEQUENCE CAPTURE
    3.
    发明申请
    COMPOSITIONS AND METHODS FOR BISULFITE CONVERTED SEQUENCE CAPTURE 审中-公开
    双相转换序列捕获的组合物和方法

    公开(公告)号：US20150141256A1

    公开(公告)日：2015-05-21

    申请号：US14338748

    申请日：2014-07-23

    申请人： Roche NimbleGen, Inc.

    发明人： Daniel Burgess ,  Jeffrey Jeddeloh

    IPC分类号： C12Q1/68

    CPC分类号： C12Q1/6876 ,  C12Q1/6869 ,  C12Q2523/125 ,  C12Q2600/154

    摘要： This invention relates generally to composition and methods for characterizing a methylome which comprises all or substantially all methylation states of a genome. In particular, a plurality of oligonucleotides, each representing nearly every possible methylation state of the cytosine position of each CG dinucleotide pair within a target nucleic acid of interest, and methods of using the plurality are provided herein.

    摘要翻译： 本发明一般涉及用于表征甲基化的组合物和方法，其包含基因组的全部或基本上全部的甲基化状态。 特别地，本文提供了多个寡核苷酸，其各自表示感兴趣的目标核酸中每个CG二核苷酸对的胞嘧啶位置的几乎每个可能的甲基化状态。

    METHODS OF ASSESSING EPIGENETIC REGULATION OF GENOME FUNCTION VIA DNA METHYLATION STATUS AND SYSTEMS AND KITS THEREFOR
    5.
    发明申请
    METHODS OF ASSESSING EPIGENETIC REGULATION OF GENOME FUNCTION VIA DNA METHYLATION STATUS AND SYSTEMS AND KITS THEREFOR 审中-公开
    通过DNA甲基化状态及其系统及其作用的基因功能评估方法

    公开(公告)号：US20150259743A1

    公开(公告)日：2015-09-17

    申请号：US14577680

    申请日：2014-12-19

    申请人： Roche NimbleGen, Inc.

    发明人： Daniel Lee Burgess ,  Jason Norton ,  Todd Richmond ,  Jennifer Wendt

    IPC分类号： C12Q1/68

    CPC分类号： C12Q1/6883 ,  C12Q1/6827 ,  C12Q1/6869 ,  C12Q1/6886 ,  C12Q2600/154 ,  C12Q2523/125 ,  C12Q2535/131 ,  C12Q2537/143

    摘要： Systems, kits and methods are disclosed for assessing epigenetic regulation of genome function via deoxyribonucleic acid (DNA) methylation status. The systems, kits and methods rely on a covert then capture concept in which unmethylated cytosine residues in a nucleic acid sequence are first converted to uracil residues and then captured for subsequent analysis. The systems, kits and method use a solution-phase capture probe pool having a mixture of at least three (3) types of capture probes. One type is “wobble” probes, in which some cytosine residues in a nucleic acid sequence are randomly assumed to be unmethylated and thus converted to uracil residues, while other cytosine residues are assumed to be methylated and thus conserved as cytosine residues. Moreover, each type of probe can include a mixture of probes that bind/hybridize to one or the other strand of a nucleic acid sequence of interest, thereby improving sequencing depth and reliability.

    摘要翻译： 公开了用于通过脱氧核糖核酸（DNA）甲基化状态来评估基因组功能的表观遗传调节的系统，试剂盒和方法。 系统，试剂盒和方法依赖于隐蔽的捕获概念，其中核酸序列中的未甲基化的胞嘧啶残基首先转化为尿嘧啶残基，然后捕获用于随后的分析。 系统，试剂盒和方法使用具有至少三种（3）种捕获探针混合物的溶液相捕获探针池。 一种类型是“摆动”探针，其中核酸序列中的一些胞嘧啶残基被随机假定为未甲基化并因此转化为尿嘧啶残基，而其它胞嘧啶残基被假定为甲基化并因此被保守为胞嘧啶残基。 此外，每种类型的探针可以包括与感兴趣的核酸序列的一条或另一条链结合/杂交的探针的混合物，从而改善测序深度和可靠性。

    Multiplexed Microarray Assembly and Method for Fabricating a Multiplexed Microarray
    7.
    发明申请
    Multiplexed Microarray Assembly and Method for Fabricating a Multiplexed Microarray 审中-公开
    复用微阵列装配和复制微阵列的制作方法

    公开(公告)号：US20140303040A1

    公开(公告)日：2014-10-09

    申请号：US14271942

    申请日：2014-05-07

    申请人： Roche NimbleGen, Inc.

    发明人： John A. Luckey

    IPC分类号： B01L3/00

    CPC分类号： B01L3/502707 ,  B01L3/5085 ,  B01L9/527 ,  B01L2200/021 ,  B01L2200/025 ,  B01L2300/0636 ,  B01L2300/0829 ,  B01L2300/0887

    摘要： Multiplexed microarrays, multiplexed microarray cassettes, and methods for fabricating multiplexed microarrays are disclosed. In some embodiments, the multiplexed microarrays include a substrate, a chamber layer, and at least one channel layer. The topmost channel layer forms a port layer and may be compressible. The multiplexed microarrays may also include a compressible or non-compressible cover or sealing film. The multiplexed microarray cassette includes a base and may also include a cover. The base of the multiplexed microarray cassette includes a plurality of tracks to receive corresponding multiplexed microarrays.

    摘要翻译： 公开了复用微阵列，复用微阵列盒和制造多路复用微阵列的方法。 在一些实施例中，复用的微阵列包括基底，腔室层和至少一个通道层。 最上面的通道层形成端口层并且可以是可压缩的。 复用的微阵列还可以包括可压缩或不可压缩的覆盖物或密封膜。 复用的微阵列盒包括底座并且还可以包括盖。 复用的微阵列盒的基底包括多个轨道以接收相应的多路复用微阵列。

    WHOLE PROTEOME TILING MICROARRAYS
    10.
    发明申请
    WHOLE PROTEOME TILING MICROARRAYS 审中-公开
    全面保护倾斜微波

    公开(公告)号：US20150377898A1

    公开(公告)日：2015-12-31

    申请号：US14469686

    申请日：2014-08-27

    申请人： Roche NimbleGen, Inc.

    发明人： Tom Albert ,  Todd Richmond ,  Matthew Rodesch ,  Klaus-Peter Stengele ,  Jochen Buehler

    IPC分类号： G01N33/68 ,  C07K1/04

    CPC分类号： G01N33/6842 ,  C07K1/047 ,  G01N33/6845 ,  G01N2570/00

    摘要： The present invention relates to a microarray comprising at least 50,000 oligopeptide features per cm2 where the oligopeptide features represent at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 99%, or 100% of the proteome of a virus or an organism. The present invention further relates to methods for the synthesis of such microarrays and methods of using microarrays comprising at least 50,000 oligopeptide features per cm2. In an embodiment of the invention, the oligopeptide features represent proteins expressed in the same species, wherein the oligopeptide features are presented in a tiling pattern representing at least about 5,000, at least about 10,000, at least about 15,000, at least about 20,000, or at least about 25,000 proteins expressed in a species. In some embodiments, the oligopeptide microarray features represent proteins expressed in the same species, wherein the microarray features are present in a tiling pattern that represents between about 5,000 and 50,000 expressed proteins, between about 10,000 and 50,000 expressed proteins, between about 15,000 and 50,000 expressed proteins, between about 20,000 and 50,000 expressed proteins, or between about 25,000 and 50,000 expressed proteins.

    摘要翻译： 本发明涉及包含至少50,000个寡肽特征/ cm 2的微阵列，其中寡肽特征表示至少50％，至少60％，至少70％，至少80％，至少90％，至少95％ 至少99％或100％的病毒或生物体的蛋白质组。 本发明还涉及用于合成这种微阵列的方法和使用每cm 2包含至少50,000个寡肽特征的微阵列的方法。 在本发明的一个实施方案中，寡肽特征表示在相同物种中表达的蛋白质，其中所述寡肽特征呈现为代表至少约5,000，至少约10,000，至少约15,000，至少约20,000或 至少约25,000个蛋白质在一个物种中表达。 在一些实施方案中，寡肽微阵列特征表示在相同物种中表达的蛋白质，其中微阵列特征以平铺图案存在，其表示约5,000至50,000表达的蛋白质，约10,000至50,000表达的蛋白质之间，约15,000至50,000表达 约20,000至50,000个表达的蛋白质之间，或约25,000至50,000个表达蛋白质之间的蛋白质。