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公开(公告)号：US07754428B2
公开(公告)日：2010-07-13
申请号：US11784501
申请日：2007-04-06
申请人： Yuk Ming Dennis Lo , Rossa Wai Kwun Chiu , Stephen Siu Chung Chim , Chunming Ding , Kwan Chee Chan , Hing Nam Ivy Wong , Ka Chun Ryan Yuen
发明人： Yuk Ming Dennis Lo , Rossa Wai Kwun Chiu , Stephen Siu Chung Chim , Chunming Ding , Kwan Chee Chan , Hing Nam Ivy Wong , Ka Chun Ryan Yuen
CPC分类号： C12Q1/68 , C12Q1/6876 , C12Q1/6883 , C12Q2600/154 , C12Q2600/156
摘要： This application describes the discovery that, in a pregnant woman, certain genes (such as RASSF1A, APC, CASP8, RARB, SCGB3A1, DAB2IP, PTPN6, THY1, TMEFF2, and PYCARD) originated from a fetus are highly methylated, whereas the same genes of maternal origin are unmethylated. This discovery allows the easy detection of one or more of these methylated fetal genes in a biological sample from a pregnant woman, serving as a universal indicator of the presence of fetal DNA in the sample. These fetal methylation markers are particularly useful as positive controls for a non-invasive analytical process during which the quality and quantity of fetal DNA are monitored. These newly identified fetal markers can also be measured directly for diagnosis of certain pregnancy-related conditions.
摘要翻译： 该应用描述了在孕妇中发现来自胎儿的某些基因（如RASSF1A，APC，CASP8，RARB，SCGB3A1，DAB2IP，PTPN6，THY1，TMEFF2和PYCARD）高度甲基化，而相同的基因 产妇来源是未甲基化。 该发现允许从孕妇的生物样品中容易地检测这些甲基化胎儿基因中的一种或多种，作为样品中胎儿DNA存在的通用指标。 这些胎儿甲基化标记物作为非侵入性分析过程的阳性对照特别有用，在此过程中监测胎儿DNA的质量和数量。 这些新确定的胎儿标记物也可以直接测量以诊断某些妊娠相关病症。
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公开(公告)号：US20090087847A1
公开(公告)日：2009-04-02
申请号：US12178116
申请日：2008-07-23
申请人： Yuk-Ming Dennis LO , Rossa Wai Kwun Chiu , Kwan Chee Chan , Benny Chung Ying Zee , Ka Chun Chong
发明人： Yuk-Ming Dennis LO , Rossa Wai Kwun Chiu , Kwan Chee Chan , Benny Chung Ying Zee , Ka Chun Chong
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6883 , C12Q1/6827 , C12Q1/6888 , C12Q2600/112 , C12Q2600/154 , C12Q2600/156 , G01N2800/387 , G06F19/18 , G06F19/22 , C12Q2521/331 , C12Q2537/16
摘要： Methods, systems, and apparatus are provided for determining whether a nucleic acid sequence imbalance exists within a biological sample. One or more cutoff values for determining an imbalance of, for example, the ratio of the two sequences (or sets of sequences) are chosen. The cutoff value may be determined based at least in part on the percentage of fetal DNA in a sample, such as maternal plasma, containing a background of maternal nucleic acid sequences. The cutoff value may also be determined based on an average concentration of a sequence per reaction. In one aspect, the cutoff value is determined from a proportion of informative wells that are estimated to contain a particular nucleic acid sequence, where the proportion is determined based on the above-mentioned percentage and/or average concentration. The cutoff value may be determined using many different types of methods, such as sequential probability ratio testing (SPRT).
摘要翻译： 提供了用于确定生物样品中是否存在核酸序列不平衡的方法，系统和装置。 选择用于确定例如两个序列（或序列集合）的比例的不平衡的一个或多个截断值。 截止值可以至少部分地基于含有母体核酸序列背景的样品中的胎儿DNA（例如母体血浆）的百分比来确定。 截止值也可以基于每个反应的序列的平均浓度来确定。 在一个方面，截断值由估计含有特定核酸序列的信息井的比例确定，其中所述比例基于上述百分比和/或平均浓度来确定。 截断值可以使用许多不同类型的方法来确定，例如顺序概率比测试（SPRT）。
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公开(公告)号：US12065704B2
公开(公告)日：2024-08-20
申请号：US13070251
申请日：2011-03-23
IPC分类号： C12Q1/6886 , C12Q1/6809 , C12Q1/6827 , C12Q1/6874 , C12Q1/6883 , G16B20/00 , G16B20/10 , G16B20/20 , G16B30/00 , G16B30/10
CPC分类号： C12Q1/6886 , C12Q1/6809 , C12Q1/6827 , C12Q1/6874 , C12Q1/6883 , G16B20/00 , G16B20/10 , G16B20/20 , G16B30/00 , G16B30/10 , C12Q2600/156 , C12Q1/6827 , C12Q2537/16
摘要： Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. The determination of the relative amounts may count sequences of only certain length. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. Prior to sequencing, the biological sample may be enriched for DNA fragments of a particular sizes.
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公开(公告)号：US20140329695A1
公开(公告)日：2014-11-06
申请号：US14335374
申请日：2014-07-18
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6883 , C12Q1/6827 , C12Q1/6888 , C12Q2600/112 , C12Q2600/154 , C12Q2600/156 , G01N2800/387 , G06F19/18 , G06F19/22 , C12Q2521/331 , C12Q2537/16
摘要： Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists.
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公开(公告)号：US08741811B2
公开(公告)日：2014-06-03
申请号：US13308473
申请日：2011-11-30
CPC分类号： G06F19/22 , C12Q1/6809 , C12Q1/6869 , C12Q1/6886 , C12Q2600/156 , C12Q2600/172 , G06F19/18 , C12Q2535/122 , C12Q2537/165 , C12Q2545/114
摘要： Biological samples including cell-free DNA fragments are analyzed to identify imbalances in chromosomal regions, e.g., due to deletions and/or amplifications in a tumor. Multiple loci are used for each chromosomal region. Such imbalances can then be used to diagnose (screen) a patient for cancer, as well as prognosticate a patient with cancer, or to detect the presence or to monitor the progress of a premalignant condition in a patient. The severity of an imbalance as well as the number of regions exhibiting an imbalance can be used. A systematic analysis of non-overlapping segments of a genome can provide a general screening tool for a sample. Additionally, a patient can be tested over time to track severity of each of one or more chromosomal regions and a number of chromosomal regions to enable screening and prognosticating, as well as monitoring of progress (e.g. after treatment).
摘要翻译： 分析包括无细胞DNA片段的生物样品，以鉴定染色体区域中的不平衡，例如由于肿瘤中的缺失和/或扩增。 每个染色体区域使用多个基因座。 然后可以将这种不平衡用于诊断（筛选）患者癌症，以及预测患有癌症的患者，或者检测病人的存在或监测恶化前状况的进展情况。 可以使用不平衡的严重性以及表现出不平衡的区域的数量。 对基因组的非重叠片段的系统分析可以为样品提供一般的筛选工具。 此外，可以随时间测试患者以跟踪一个或多个染色体区域和多个染色体区域中的每一个的严重性，以使得能够进行筛选和预测，以及监测进展（例如，治疗后）。
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26.发明授权Methods for detecting fetal DNA in a plasma or serum sample from a pregnant woman 有权检测孕妇血浆或血清样品中胎儿DNA的方法公开(公告)号：US08288100B2
公开(公告)日：2012-10-16
申请号：US12791776
申请日：2010-06-01
申请人： Yuk Ming Dennis Lo , Rossa Wai Kwun Chiu , Stephen Siu Chung Chim , Chunming Ding , Kwan Chee Chan , Hing Nam Ivy Wong , Ka Chun Ryan Yuen
发明人： Yuk Ming Dennis Lo , Rossa Wai Kwun Chiu , Stephen Siu Chung Chim , Chunming Ding , Kwan Chee Chan , Hing Nam Ivy Wong , Ka Chun Ryan Yuen
CPC分类号： C12Q1/68 , C12Q1/6876 , C12Q1/6883 , C12Q2600/154 , C12Q2600/156
摘要： This application describes the discovery that, in a pregnant woman, certain genes (such as RASSF1A, APC, CASP8, RARB, SCGB3A1, DAB2IP, PTPN6, THY1, TMEFF2, and PYCARD) originated from a fetus are highly methylated, whereas the same genes of maternal origin are unmethylated. This discovery allows the easy detection of one or more of these methylated fetal genes in a biological sample from a pregnant woman, serving as a universal indicator of the presence of fetal DNA in the sample. These fetal methylation markers are particularly useful as positive controls for a non-invasive analytical process during which the quality and quantity of fetal DNA are monitored. These newly identified fetal markers can also be measured directly for diagnosis of certain pregnancy-related conditions.
摘要翻译： 该应用描述了在孕妇中发现来自胎儿的某些基因（如RASSF1A，APC，CASP8，RARB，SCGB3A1，DAB2IP，PTPN6，THY1，TMEFF2和PYCARD）高度甲基化，而相同的基因 产妇来源是未甲基化。 该发现允许从孕妇的生物样品中容易地检测这些甲基化胎儿基因中的一种或多种，作为样品中胎儿DNA存在的通用指标。 这些胎儿甲基化标记物作为非侵入性分析过程的阳性对照特别有用，在此过程中监测胎儿DNA的质量和数量。 这些新确定的胎儿标记物也可以直接测量以诊断某些妊娠相关病症。
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公开(公告)号：US20080081338A1
公开(公告)日：2008-04-03
申请号：US11861809
申请日：2007-09-26
申请人： Yuk Ming LO , Kwan Chee Chan , Chunming Ding
发明人： Yuk Ming LO , Kwan Chee Chan , Chunming Ding
CPC分类号： C12Q1/6886 , C12Q2600/118 , C12Q2600/154
摘要： The present invention concerns a method for the detection or monitoring of cancer using a biological sample selected from blood, plasma, serum, saliva, urine from an individual, said method comprising: (a) obtaining DNA from the said biological sample; (b) digesting the DNA sample with one or more methylation-sensitive restriction enzymes; (c) quantifying or detecting a DNA sequence of interest after step (b), wherein the target sequence of interest contains at least two methylation-sensitive restriction enzyme recognition sites; and (d) comparing the level of the DNA sequence from the individual to a normal standard, to detect, prognosticate or monitor cancer.
摘要翻译： 本发明涉及使用选自血液，血浆，血清，唾液，个体尿液的生物样品检测或监测癌症的方法，所述方法包括：（a）从所述生物样品中获得DNA; （b）用一种或多种甲基化敏感性限制酶消化DNA样品; （c）在步骤（b）之后量化或检测目标DNA序列，其中所述靶序列含有至少两个甲基化敏感性限制酶识别位点; 和（d）将来自个体的DNA序列的水平与正常标准进行比较，以检测，预测或监测癌症。
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公开(公告)号：US12054780B2
公开(公告)日：2024-08-06
申请号：US13070240
申请日：2011-03-23
IPC分类号： C12Q1/6886 , C12Q1/6809 , C12Q1/6827 , C12Q1/6874 , C12Q1/6883 , G16B20/00 , G16B20/10 , G16B20/20 , G16B30/00 , G16B30/10
CPC分类号： C12Q1/6886 , C12Q1/6809 , C12Q1/6827 , C12Q1/6874 , C12Q1/6883 , G16B20/00 , G16B20/10 , G16B20/20 , G16B30/00 , G16B30/10 , C12Q2600/156 , C12Q1/6827 , C12Q2537/16
摘要： Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. The determination of the relative amounts may count sequences of only certain length. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. Prior to sequencing, the biological sample may be enriched for DNA fragments of a particular sizes.
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公开(公告)号：US12018329B2
公开(公告)日：2024-06-25
申请号：US13070275
申请日：2011-03-23
IPC分类号： G01N33/50 , C12Q1/6809 , C12Q1/6827 , C12Q1/6874 , C12Q1/6883 , C12Q1/6886 , G16B20/00 , G16B20/10 , G16B20/20 , G16B30/00 , G16B30/10
CPC分类号： C12Q1/6886 , C12Q1/6809 , C12Q1/6827 , C12Q1/6874 , C12Q1/6883 , G16B20/00 , G16B20/10 , G16B30/00 , G16B30/10 , C12Q2600/156 , C12Q1/6827 , C12Q2537/16
摘要： Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. The determination of the relative amounts may count sequences of only certain length. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. Prior to sequencing, the biological sample may be enriched for DNA fragments of a particular sizes.
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公开(公告)号：US20140329696A1
公开(公告)日：2014-11-06
申请号：US14335477
申请日：2014-07-18
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6883 , C12Q1/6827 , C12Q1/6888 , C12Q2600/112 , C12Q2600/154 , C12Q2600/156 , G01N2800/387 , G06F19/18 , G06F19/22 , C12Q2521/331 , C12Q2537/16
摘要： Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists.
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