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公开(公告)号：US20110153222A1
公开(公告)日：2011-06-23
申请号：US12963076
申请日：2010-12-08
申请人： Todd Richmond , Jason Norton , Emile F. Nuwaysir , Roland Green , Kate Nuwaysir
发明人： Todd Richmond , Jason Norton , Emile F. Nuwaysir , Roland Green , Kate Nuwaysir
CPC分类号： C12Q1/6837 , C12Q1/6811 , G16B25/00 , C12Q2537/165
摘要： The present invention provides methods for optimizing oligonucleotide hybridization probes for use in basic and clinical research. Specifically, the invention involves hybridizing serially diluted genomic sample to the oligonucleotide probes on the array, such that a signal intensity is produced for each of the probes; computationally identifying optimized probes which exhibit signal intensities that correspond to the serial dilutions of genomic sample and are reproducibly strong relative to non-optimized probes.
摘要翻译： 本发明提供用于优化用于基础和临床研究的寡核苷酸杂交探针的方法。 具体地，本发明包括将序列稀释的基因组样品与阵列上的寡核苷酸探针杂交，使得为每个探针产生信号强度; 计算识别优化的探针，其显示对应于基因组样品的系列稀释度的信号强度，并且相对于未优化的探针是可重现的。
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公开(公告)号：US07636637B2
公开(公告)日：2009-12-22
申请号：US11156439
申请日：2005-06-20
申请人： Thomas Albert , Jason Norton , Roland Green
发明人： Thomas Albert , Jason Norton , Roland Green
CPC分类号： G06F19/20 , C12Q1/6837 , C12Q1/6874 , C12Q2527/107 , C12Q2525/185
摘要： The present invention provides novel method for increasing the efficiency and accuracy of high-throughput mutation mapping and genome resequencing by using a variable length probe selection algorithm to rationally select probes used in designing oligonucleotide arrays synthesized by Maskless Array Synthesis (MAS) technology. Also disclosed is a variable length probe selection algorithm used in designing such oligonucleotide arrays.
摘要翻译： 本发明提供了通过使用可变长度探针选择算法合理选择用于设计通过无掩模阵列合成（MAS）技术合成的寡核苷酸阵列的探针的探针来提高高通量突变图谱和基因组重排序的效率和准确性的新方法。 还公开了用于设计这种寡核苷酸阵列的可变长度探针选择算法。
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13.发明授权Correction for illumination non-uniformity during the synthesis of arrays of oligomers 失效在寡聚体阵列的合成期间校正照明不均匀性公开(公告)号：US07422851B2
公开(公告)日：2008-09-09
申请号：US10061577
申请日：2002-01-31
申请人： Roland Green , Francesco Cerrina , Jasjit J. Singh
发明人： Roland Green , Francesco Cerrina , Jasjit J. Singh
CPC分类号： B82Y30/00 , B01J19/0046 , B01J2219/00434 , B01J2219/00439 , B01J2219/00527 , B01J2219/00529 , B01J2219/00585 , B01J2219/0059 , B01J2219/00596 , B01J2219/00605 , B01J2219/00608 , B01J2219/00612 , B01J2219/00617 , B01J2219/00637 , B01J2219/00659 , B01J2219/00675 , B01J2219/00689 , B01J2219/00693 , B01J2219/00711 , B01J2219/00722 , C40B40/06 , C40B50/14 , C40B60/14
摘要： The present invention provides an apparatus and a method for the synthesis of arrays of oligomers that have tight illumination intensity requirement. The apparatus and the method contains a mechanism to correct for illumination nonuniformity during the oligomer array synthesis process. To correct for illumination nonuniformity, the illumination intensity of different oligomer synthesis positions across an area in which oligomers are synthesized are determined first. Then, the difference in illumination intensity among the positions are evaluated mathematically. Next, any nonuniformity in illumination intensity is corrected by either reducing the intensity of the light for the brighter positions before the light reaches the illumination area or reducing the illumination time of the brighter positions during one protection group deprotection period.
摘要翻译： 本发明提供了一种具有紧密照明强度要求的合成低聚物阵列的装置和方法。 该装置和方法包含在低聚物阵列合成过程中校正照明不均匀性的机理。 为了校正照明不均匀性，首先确定在合成低聚物的区域上的不同低聚物合成位置的照射强度。 然后，数学地评价位置之间的照度的差异。 接下来，通过在光到达照明区域之间减少用于较亮位置的光的强度或者减少在一个保护组去保护期间的较亮位置的照明时间来校正照明强度的任何不均匀性。
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公开(公告)号：US20080194414A1
公开(公告)日：2008-08-14
申请号：US11970949
申请日：2008-01-08
申请人： Thomas J. Albert , Roland Green , Todd Richmond , Michael Molla , Jeffrey Jeddeloh , Jason Patrick Affourtit , Mathreyan Srinivasan , Brian Christopher Godwin , Matthew Rodesch
发明人： Thomas J. Albert , Roland Green , Todd Richmond , Michael Molla , Jeffrey Jeddeloh , Jason Patrick Affourtit , Mathreyan Srinivasan , Brian Christopher Godwin , Matthew Rodesch
CPC分类号： C12N15/1093 , C12Q1/6834
摘要： The present invention provides novel methods for reducing the complexity of preferably a genomic sample for further analysis such as direct DNA sequencing, resequencing or SNP calling. The methods use pre-selected immobilized oligonucleotide probes to capture target nucleic acid molecules from a sample containing denatured, fragmented (genomic) nucleic acids for reducing the genetic complexity of the original population of nucleic acid molecules.
摘要翻译： 本发明提供了用于降低优选用于进一步分析的基因组样品的复杂性的新方法，例如直接DNA测序，再测序或SNP呼叫。 该方法使用预先选择的固定化寡核苷酸探针从含有变性，片段（基因组）核酸的样品中捕获靶核酸分子，以降低核酸分子的原始群体的遗传复杂性。
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公开(公告)号：US20070037274A1
公开(公告)日：2007-02-15
申请号：US11497407
申请日：2006-10-27
申请人： Roland Green , Alan Pitas , Francesco Cerrina
发明人： Roland Green , Alan Pitas , Francesco Cerrina
CPC分类号： B82Y30/00 , B01J19/0046 , B01J2219/00286 , B01J2219/00353 , B01J2219/00436 , B01J2219/00439 , B01J2219/0045 , B01J2219/00527 , B01J2219/00585 , B01J2219/00596 , B01J2219/00605 , B01J2219/00612 , B01J2219/00637 , B01J2219/00659 , B01J2219/00675 , B01J2219/00711 , B01J2219/00722 , C40B40/06 , C40B50/14 , C40B60/14
摘要： During the light illumination period of a monomer addition cycle in synthesizing an DNA microarray, undesirable reflections of illumination light from various interfaces that the illumination light passes through near the synthesis surface of the substrate may reduce the light-dark contrast, and negatively affect the precision and resolution of the microarray synthesis. The present invention provides an flow cell that reduces the undesired reflections by constructing certain flow cell structures with materials that have similar refractive indexes as that of the solution that is in the oligomer synthesis chamber during the illumination period and/or constructing certain flow cell structures or covering the structures with a layer of a material that has a high extinction coefficient.
摘要翻译： 在合成DNA微阵列的单体添加循环的光照射期间，照明光在基板的合成面附近通过的各种界面的照明光的不期望的反射可能会降低亮暗对比度，并且不利地影响精度 和微阵列合成的分辨率。 本发明提供了一种流动池，其通过使用具有与在照射期间的低聚物合成室中的溶液具有相似折射率的材料构建某些流动池结构和/或构建某些流动池结构或减少不期望的反射来减少不期望的反射， 用具有高消光系数的材料层覆盖结构。
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公开(公告)号：US08030477B2
公开(公告)日：2011-10-04
申请号：US11524082
申请日：2006-09-20
申请人： Francesco Cerrina , Michael R. Sussman , Frederick R. Blattner , Sangeet Singh-Gasson , Roland Green
发明人： Francesco Cerrina , Michael R. Sussman , Frederick R. Blattner , Sangeet Singh-Gasson , Roland Green
CPC分类号： B82Y30/00 , B01J19/0046 , B01J2219/00439 , B01J2219/00527 , B01J2219/00529 , B01J2219/00585 , B01J2219/0059 , B01J2219/00596 , B01J2219/00605 , B01J2219/00608 , B01J2219/00612 , B01J2219/00626 , B01J2219/00637 , B01J2219/00641 , B01J2219/00659 , B01J2219/00689 , B01J2219/00711 , B01J2219/00722 , C07B2200/11 , C07H21/00 , C40B40/00 , C40B40/06 , C40B60/14 , G02B26/0841 , G03F7/2002
摘要： The synthesis of arrays of DNA probes sequences, polypeptides, and the like is carried out using a patterning process on an active surface of a substrate. An image is projected onto the active surface of the substrate utilizing reflective projection optics. The projection optics project a light image onto the active surface of the substrate to deprotect linker molecules thereon. A first level of bases may then be applied to the substrate, followed by development steps, and subsequent exposure of the substrate utilizing a different light image, with further repeats until the elements of a two dimensional array on the substrate surface have an appropriate base bound thereto.
摘要翻译： DNA探针序列，多肽等的阵列的合成使用在底物的活性表面上的图案化方法进行。 使用反射投影光学器件将图像投影到基板的有源表面上。 投影光学器件将光图像投影到衬底的有源表面上以使其上的接头分子去保护。 然后可以将第一水平的碱基施加到基底，随后进行显影步骤，并且随后使用不同光图像曝光基底，进一步重复，直到基底表面上的二维阵列的元件具有适当的基底界限 到此。
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公开(公告)号：US07869959B2
公开(公告)日：2011-01-11
申请号：US11346927
申请日：2006-02-03
申请人： Todd Richmond , Jason Norton , Emile F. Nuwaysir , Roland Green , Kate Nuwaysir
发明人： Todd Richmond , Jason Norton , Emile F. Nuwaysir , Roland Green , Kate Nuwaysir
CPC分类号： C12Q1/6837 , C12Q1/6811 , G06F19/20 , C12Q2537/165
摘要： The present invention provides methods for optimizing oligonucleotide hybridization probes for use in basic and clinical research. Specifically, the invention involves hybridizing serially diluted genomic sample to the oligonucleotide probes on the array, such that a signal intensity is produced for each of the probes; computationally identifying optimized probes which exhibit signal intensities that correspond to the serial dilutions of genomic sample and are reproducibly strong relative to non-optimized probes.
摘要翻译： 本发明提供用于优化用于基础和临床研究的寡核苷酸杂交探针的方法。 具体地，本发明包括将序列稀释的基因组样品与阵列上的寡核苷酸探针杂交，使得为每个探针产生信号强度; 计算识别优化的探针，其显示对应于基因组样品的系列稀释度的信号强度，并且相对于未优化的探针是可重现的。
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公开(公告)号：US20100227780A1
公开(公告)日：2010-09-09
申请号：US11524082
申请日：2006-09-20
申请人： Francesco Cerrina , Michael R. Sussman , Frederick R. Blattner , Sangeet Singh-Gasson , Roland Green
发明人： Francesco Cerrina , Michael R. Sussman , Frederick R. Blattner , Sangeet Singh-Gasson , Roland Green
CPC分类号： B82Y30/00 , B01J19/0046 , B01J2219/00439 , B01J2219/00527 , B01J2219/00529 , B01J2219/00585 , B01J2219/0059 , B01J2219/00596 , B01J2219/00605 , B01J2219/00608 , B01J2219/00612 , B01J2219/00626 , B01J2219/00637 , B01J2219/00641 , B01J2219/00659 , B01J2219/00689 , B01J2219/00711 , B01J2219/00722 , C07B2200/11 , C07H21/00 , C40B40/00 , C40B40/06 , C40B60/14 , G02B26/0841 , G03F7/2002
摘要： The synthesis of arrays of DNA probes sequences, polypeptides, and the like is carried out using a patterning process on an active surface of a substrate. An image is projected onto the active surface of the substrate utilizing reflective projection optics. The projection optics project a light image onto the active surface of the substrate to deprotect linker molecules thereon. A first level of bases may then be applied to the substrate, followed by development steps, and subsequent exposure of the substrate utilizing a different light image, with further repeats until the elements of a two dimensional array on the substrate surface have an appropriate base bound thereto.
摘要翻译： DNA探针序列，多肽等的阵列的合成使用在底物的活性表面上的图案化方法进行。 使用反射投影光学器件将图像投影到基板的有源表面上。 投影光学器件将光图像投影到衬底的有源表面上以使其上的接头分子去保护。 然后可以将第一水平的碱基施加到基底，随后进行显影步骤，并且随后使用不同的光图像曝光基底，进一步重复，直到基底表面上的二维阵列的元件具有适当的基底界限 到此。
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公开(公告)号：US20100222232A1
公开(公告)日：2010-09-02
申请号：US12754308
申请日：2010-04-05
申请人： Thomas J. Albert , Roland Green , Todd Richmond , Michael Molla , Jeffrey Jeddeloh , Jason Patrick Affourtit , Mathreyan Srinivasan , Brian Christopher Godwin , Matthew Rodesch
发明人： Thomas J. Albert , Roland Green , Todd Richmond , Michael Molla , Jeffrey Jeddeloh , Jason Patrick Affourtit , Mathreyan Srinivasan , Brian Christopher Godwin , Matthew Rodesch
CPC分类号： C12N15/1093 , C12Q1/6834
摘要： The present invention provides novel methods for reducing the complexity of preferably a genomic sample for further analysis such as direct DNA sequencing, resequencing or SNP calling. The methods use pre-selected immobilized oligonucleotide probes to capture target nucleic acid molecules from a sample containing denatured, fragmented (genomic) nucleic acids for reducing the genetic complexity of the original population of nucleic acid molecules.
摘要翻译： 本发明提供了用于降低优选用于进一步分析的基因组样品的复杂性的新方法，例如直接DNA测序，再测序或SNP呼叫。 该方法使用预先选择的固定化寡核苷酸探针从含有变性，片段（基因组）核酸的样品中捕获靶核酸分子，以降低核酸分子的原始群体的遗传复杂性。
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公开(公告)号：US20060177858A1
公开(公告)日：2006-08-10
申请号：US11346927
申请日：2006-02-03
申请人： Todd Richmond , Jason Norton , Emile Nuwaysir , Roland Green , Kate Nuwaysir
发明人： Todd Richmond , Jason Norton , Emile Nuwaysir , Roland Green , Kate Nuwaysir
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6837 , C12Q1/6811 , G06F19/20 , C12Q2537/165
摘要： The present invention provides methods for optimizing oligonucleotide hybridization probes for use in basic and clinical research. Specifically, the invention involves hybridizing serially diluted genomic sample to the oligonucleotide probes on the array, such that a signal intensity is produced for each of the probes; computationally identifying optimized probes which exhibit signal intensities that correspond to the serial dilutions of genomic sample and are reproducibly strong relative to non-optimized probes.
摘要翻译： 本发明提供用于优化用于基础和临床研究的寡核苷酸杂交探针的方法。 具体地，本发明包括将序列稀释的基因组样品与阵列上的寡核苷酸探针杂交，使得为每个探针产生信号强度; 计算识别优化的探针，其显示对应于基因组样品的系列稀释度的信号强度，并且相对于未优化的探针是可重现的。
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