公开(公告)号：US20090280492A1

公开(公告)日：2009-11-12

申请号：US12413485

申请日：2009-03-27

申请人： Roland Stoughton ,  Ravi Kapur ,  Barb Ariel Cohen

发明人： Roland Stoughton ,  Ravi Kapur ,  Barb Ariel Cohen

IPC分类号： C12Q1/68

CPC分类号： G01N1/30 ,  C12Q1/6883 ,  C12Q2600/156 ,  C12Q2600/158 ,  C12Q2600/16 ,  G16B20/00

摘要： The present invention provides systems, apparatuses, and methods to detect the presence of fetal cells when mixed with a population of maternal cells in a sample and to test fetal abnormalities, i.e. aneuploidy. In addition, the present invention provides methods to determine when there are insufficient fetal cells for a determination and report a non-informative case. The present invention involves quantifying regions of genomic DNA from a mixed sample. More particularly the invention involves quantifying DNA polymorphisms from the mixed sample.

摘要翻译： 本发明提供了当与样品中的母体细胞群混合时检测胎儿细胞的存在并测试胎儿异常（即非整倍体）的系统，装置和方法。 此外，本发明提供了确定何时胎儿细胞不足以确定并报告非信息性病例的方法。 本发明涉及量化来自混合样品的基因组DNA的区域。 更具体地，本发明涉及从混合样品中定量DNA多态性。

公开(公告)号：US20080187909A1

公开(公告)日：2008-08-07

申请号：US10591800

申请日：2005-03-07

申请人： Hongyue Dai ,  Laura J. Van't Veer ,  John Lamb ,  Roland Stoughton ,  Stephen H. Friend ,  Yudong He

发明人： Hongyue Dai ,  Laura J. Van't Veer ,  John Lamb ,  Roland Stoughton ,  Stephen H. Friend ,  Yudong He

IPC分类号： C12Q1/68 ,  C40B40/06

CPC分类号： G01N33/57415 ,  C12Q1/6886 ,  C12Q2600/106 ,  C12Q2600/112 ,  C12Q2600/118 ,  Y10T436/143333

摘要： The present invention provides prognostic methods for conditions such as cancer, for example, breast cancer, comprising classifying an individual by a plurality of phenotypic, genotypic or clinical characteristics of the condition into a plurality of patient subsets, and analyzing the pattern of expression of prognosis-informative genes identified for that subset in a sample from the individual. The present invention also provides methods for constructing such patient subsets and of identifying prognosis-informative genesets for such subsets. The invention further provides methods of assigning a therapeutic regimen to an individual, microarrays useful for performing prognosis, kits comprising these microarrays, and computer systems and programs for implementing the methods of the invention.

摘要翻译： 本发明提供了诸如癌症例如乳腺癌的病症的预后方法，包括将个体的多个表型，基因型或临床特征分类为多个患者子集，并分析预后表达模式 在来自个体的样品中识别该子集的信息基因。 本发明还提供了用于构建这样的患者子集以及鉴定这样的子集的预后信息性基因组的方法。 本发明进一步提供了将个体的治疗方案分配给用于进行预后的微阵列，包括这些微阵列的试剂盒以及用于实施本发明的方法的计算机系统和程序的方法。

公开(公告)号：US20080070792A1

公开(公告)日：2008-03-20

申请号：US11763133

申请日：2007-06-14

申请人： Roland Stoughton ,  Ravi Kapur ,  Barb Cohen

发明人： Roland Stoughton ,  Ravi Kapur ,  Barb Cohen

IPC分类号： C40B30/04 ,  C12Q1/68

CPC分类号： C12Q1/6874 ,  C12Q1/6883 ,  C12Q2600/156

摘要： The present invention provides apparatus and methods for enriching components or cells from a sample and conducting genetic analysis, such as SNP genotyping to provide diagnostic results for fetal disorders or conditions.

摘要翻译： 本发明提供了用于从样品中富集组分或细胞并进行遗传分析的装置和方法，例如SNP基因分型以提供胎儿障碍或病症的诊断结果。

公开(公告)号：US20070275407A1

公开(公告)日：2007-11-29

申请号：US11879161

申请日：2007-07-16

申请人： Matthew Marton ,  Roland Stoughton

发明人： Matthew Marton ,  Roland Stoughton

IPC分类号： C12Q1/68 ,  C12Q1/18 ,  G01N33/566

CPC分类号： C12Q1/6883 ,  C12Q1/025 ,  C12Q1/18 ,  C12Q2600/106 ,  C12Q2600/158 ,  G01N33/5005 ,  G01N33/5088 ,  G06F19/20 ,  G06F19/70

摘要： This invention provides methods for determining drug specificity, therapeutic index and effective doses for individual patients. According to the methods of the invention, graded levels of drug are applied to a biological sample or a patient. A plurality of cellular constituents are measured to determine the activity of the drug on a target pathway and at least one off-target pathway. A drug specificity is determined by comparing the target and off target activities of the drug. A therapeutic concentration (or dose) is defined as a concentration (or dose) of the drug that induces certain response in the target pathway. A toxic concentration (or dose) is defined as a concentration (or dose) of the drug that induces certain response in the off target pathway. Therapeutic index is the ratio of the toxic concentration over therapeutic concentration. Methods are also provided to determine an effective dose of a drug for a patient by measuring the activity of the drug on the particular patient.

公开(公告)号：US20070009884A1

公开(公告)日：2007-01-11

申请号：US11399192

申请日：2006-04-06

申请人： Roland Stoughton ,  Michael Meyer ,  Daniel Shoemaker

发明人： Roland Stoughton ,  Michael Meyer ,  Daniel Shoemaker

IPC分类号： C12Q1/70 ,  C12Q1/68 ,  C12M1/34

CPC分类号： C12Q1/6813 ,  B82Y5/00 ,  B82Y10/00 ,  Y02A50/52 ,  Y02A50/53 ,  Y02A50/54 ,  Y02A50/55 ,  Y02A50/59 ,  Y02A50/60

摘要： The present invention provides methods and apparatuses for detection of pathogens or toxins in a sample. The invention also provides kits comprises reagents, including probes sets, and other consumables, such as surfaces, which can be used for detection of pathogens or toxins in a sample.

摘要翻译： 本发明提供了用于检测样品中病原体或毒素的方法和装置。 本发明还提供了包括试剂，包括探针组和其它可用于检测样品中的病原体或毒素的消耗品，例如表面的试剂盒。

公开(公告)号：US20060141501A1

公开(公告)日：2006-06-29

申请号：US11282025

申请日：2005-11-16

申请人： Stephen Friend ,  Roland Stoughton ,  Peter Linsley ,  Julia Burchard

发明人： Stephen Friend ,  Roland Stoughton ,  Peter Linsley ,  Julia Burchard

IPC分类号： C12Q1/68

CPC分类号： G16B25/00

摘要： Methods and compositions are provided that are useful for detecting and reporting a plurality of different target polynucleotide sequences in a sample, such as polynucleotides corresponding to a plurality of different genes expressed by a cell or cells. In particular, the invention provides methods for screening a plurality of candidate polynucleotide probes to evaluate both the sensitivity and the specificity with which each candidate probe hybridizes to a target polynucleoide sequence. Candidate polynucleotide probes can then be ranked according to both their sensitivity and specificity, and probes that have optimal sensitivity and specificity for a target polynucleotide sequence can be selected. In one embodiment, polynucleotide probes can be selected according to the methods described herein to prepare “screening chips” wherein a large number of target polynucleotide sequences are detected using a single microarray have a few (e.g., 1-5) probes for each target polynucleotide sequence. In a particularly preferred embodiment, the invention provides a screening chip that can detect genetic transcripts from the entire genome of an organism. In an alternative embodiment, polynucleotide probes can be selected according to the methods described herein to prepare “signature chips” to more accurately detect certain selected “signature genes” using several polynucleotide probes (e:g., 10-20) for each signature gene. The invention additionally provides microarrays containing polynucleotide probes for a large number of genes expressed by a cell or organism. Further, methods for detecting a plurality of polynucleotide molecules, including a large number of genes expressed by a cell or organism, are also provided.

摘要翻译： 提供了可用于检测和报告样品中多个不同靶多核苷酸序列的方法和组合物，例如对应于由细胞或细胞表达的多种不同基因的多核苷酸。 特别地，本发明提供了筛选多个候选多核苷酸探针以评估每个候选探针与目标多核苷酸序列杂交的灵敏度和特异性的方法。 然后可以根据其灵敏度和特异性对候选多核苷酸探针进行排序，并且可以选择对靶多核苷酸序列具有最佳敏感性和特异性的探针。 在一个实施方案中，可以根据本文所述的方法选择多核苷酸探针以制备“筛选芯片”，其中使用单个微阵列检测大量目标多核苷酸序列，其中每个靶多核苷酸具有少量（例如1-5）探针 序列。 在一个特别优选的实施方案中，本发明提供了可以检测来自生物体的整个基因组的遗传转录物的筛选芯片。 在替代实施方案中，可以根据本文所述的方法选择多核苷酸探针，以制备“签名芯片”，以使用每个签名基因的多个多核苷酸探针（例如，10-20）更准确地检测某些所选择的“签名基因” 。 本发明另外提供含有由细胞或生物表达的大量基因的多核苷酸探针的微阵列。 此外，还提供了用于检测多个多核苷酸分子的方法，包括由细胞或生物体表达的大量基因。

公开(公告)号：US07013221B1

公开(公告)日：2006-03-14

申请号：US09561487

申请日：2000-04-28

申请人： Stephen H. Friend ,  Roland Stoughton ,  Peter S. Linsley ,  Julja Burchard

发明人： Stephen H. Friend ,  Roland Stoughton ,  Peter S. Linsley ,  Julja Burchard

IPC分类号： G01N33/48 ,  C12Q1/68

CPC分类号： G06F19/20

摘要： Methods and compositions are provided that are useful for detecting and reporting a plurality of different target polynucleotide sequences in a sample, such as polynucleotides corresponding to a plurality of different genes expressed by a cell or cells. In particular, the invention provides methods for screening a plurality of candidate polynucleotide probes to evaluate both the sensitivity and the specificity with which each candidate probe hybridizes to a target polynucleoide sequence. Candidate polynucleotide probes can then be ranked according to both their sensitivity and specificity, and probes that have optimal sensitivity and specificity for a target polynucleotide sequence can be selected. In one embodiment, polynucleotide probes can be selected according to the methods described herein to prepare “screening chips” wherein a large number of target polynucleotide sequences are detected using a single microarray have a few (e.g., 1–5) probes for each target polynucleotide sequence. In a particularly preferred embodiment, the invention provides a screening chip that can detect genetic transcripts from the entire genome of an organism. In an alternative embodiment, polynucleotide probes can be selected according to the methods described herein to prepare “signature chips” to more accurately detect certain selected “signature genes” using several polynucleotide probes (e.g., 10–20) for each signature gene. The invention additionally provides microarrays containing polynucleotide probes for a large number of genes expressed by a cell or organism. Further, methods for detecting a plurality of polynucleotide molecules, including a large number of genes expressed by a cell or organism, are also provided.

摘要翻译： 提供了可用于检测和报告样品中多个不同靶多核苷酸序列的方法和组合物，例如对应于由细胞或细胞表达的多种不同基因的多核苷酸。 特别地，本发明提供了筛选多个候选多核苷酸探针以评估每个候选探针与目标多核苷酸序列杂交的灵敏度和特异性的方法。 然后可以根据其灵敏度和特异性对候选多核苷酸探针进行排序，并且可以选择对靶多核苷酸序列具有最佳敏感性和特异性的探针。 在一个实施方案中，可以根据本文所述的方法选择多核苷酸探针以制备“筛选芯片”，其中使用单个微阵列检测大量目标多核苷酸序列，其中每个靶多核苷酸具有少量（例如1-5）探针 序列。 在一个特别优选的实施方案中，本发明提供了可以检测来自生物体的整个基因组的遗传转录物的筛选芯片。 在替代实施方案中，可以根据本文所述的方法选择多核苷酸探针以通过使用每个特征基因的多个多核苷酸探针（例如10-20）来制备“签名芯片”以更精确地检测某些所选择的“特征基因”。 本发明另外提供含有由细胞或生物表达的大量基因的多核苷酸探针的微阵列。 此外，还提供了用于检测多个多核苷酸分子的方法，包括由细胞或生物体表达的大量基因。

公开(公告)号：US20050130215A1

公开(公告)日：2005-06-16

申请号：US11042653

申请日：2005-01-24

申请人： Roland Stoughton ,  Hongyue Dai

发明人： Roland Stoughton ,  Hongyue Dai

IPC分类号： G01N33/53 ,  C12N15/09 ,  C12Q1/68 ,  C12Q1/6837 ,  G01N33/48 ,  G01N33/566 ,  G01N33/58 ,  G01N37/00 ,  G06F17/18 ,  G06F19/20 ,  G06F19/00 ,  G01N33/50

CPC分类号： C12Q1/6837 ,  G16B25/00 ,  Y10T436/10

摘要： A method for fluorophore bias removal in microarray experiments in which the fluorophores used in microarray experiment pairs are reversed. Further, a method for calculating the individual errors associated with each measurement made in nominally repeated microarray experiments. This error measurement is optionally coupled with rank based methods in order to determine a probability that a cellular constituent is up or down regulated in response to a perturbation. Finally, a method for determining the confidence in the weighted average of the expression level of a cellular constituent in nominally repeated microarray experiments.

摘要翻译： 用于微阵列实验对中的荧光团的微阵列实验中的荧光团偏置去除方法是相反的。 此外，一种用于计算与名义上重复的微阵列实验中进行的每个测量相关联的各个错误的方法。 该误差测量可选地与基于秩的方法耦合，以便确定响应于扰动的细胞成分向上或向下调节的概率。 最后，在名义上重复的微阵列实验中确定细胞成分的表达水平的加权平均的置信度的方法。

公开(公告)号：US06370478B1

公开(公告)日：2002-04-09

申请号：US09222595

申请日：1998-12-28

申请人： Roland Stoughton ,  Sergey Stepaniants

发明人： Roland Stoughton ,  Sergey Stepaniants

IPC分类号： G01N3348

CPC分类号： G06F19/20 ,  G06F19/00 ,  G06F19/18 ,  G06F19/24 ,  G16H50/50

摘要： This invention provides methods for detecting and predicting drug interaction. In one embodiment of the invention, a plurality of cellular constituents in a biological sample is monitored as the sample is subject to various drug treatments. The response of the cellular constituents are analyzed to detect interactions. This method is particularly useful for predicting drug interaction using a model organism. It is also useful for analyzing interaction between any perturbations to a biological system.

摘要翻译： 本发明提供了检测和预测药物相互作用的方法。 在本发明的一个实施方案中，当样品进行各种药物治疗时，监测生物样品中的多种细胞成分。 分析细胞成分的反应以检测相互作用。 该方法对于使用模型生物体预测药物相互作用特别有用。 它也可用于分析与生物系统的任何扰动之间的相互作用。

公开(公告)号：US20130210644A1

公开(公告)日：2013-08-15

申请号：US13863992

申请日：2013-04-16

申请人： Roland Stoughton ,  Ravi Kapur ,  Mehmet Toner ,  Ronald Davis ,  Barb Ariel Cohen

发明人： Roland Stoughton ,  Ravi Kapur ,  Mehmet Toner ,  Ronald Davis ,  Barb Ariel Cohen

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6874 ,  C12Q1/6883 ,  C12Q2600/156

摘要： The present invention provides apparatus and methods for enriching components or cells from a sample and conducting genetic analysis, such as SNP genotyping to provide diagnostic results for fetal disorders or conditions.

摘要翻译： 本发明提供了用于从样品中富集组分或细胞并进行遗传分析的装置和方法，例如SNP基因分型以提供胎儿障碍或病症的诊断结果。