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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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32.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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公开(公告)号：US08620593B2
公开(公告)日：2013-12-31
申请号：US12940992
申请日：2010-11-05
CPC分类号： C12Q1/6809 , C12Q1/6883 , C12Q2600/112 , C12Q2600/156 , C12Q2600/172 , G06F19/18
摘要： Systems, methods, and apparatuses for performing a prenatal diagnosis of a sequence imbalance are provided. A shift (e.g. to a smaller size distribution) can signify an imbalance in certain circumstances. For example, a size distribution of fragments of nucleic acids from an at-risk chromosome can be used to determine a fetal chromosomal aneuploidy. A size ranking of different chromosomes can be used to determine changes of a rank of an at-risk chromosome from an expected ranking. Also, a difference between a statistical size value for one chromosome can be compared to a statistical size value of another chromosome to identify a significant shift in size. A genotype and haplotype of the fetus may also be determined using a size distribution to determine whether a sequence imbalance occurs in a maternal sample relative to a genotypes or haplotype of the mother, thereby providing a genotype or haplotype of the fetus.
摘要翻译： 提供了用于执行序列不平衡的产前诊断的系统，方法和装置。 在某些情况下，偏移（例如，到更小的分布）可以表示不平衡。 例如，可以使用来自高危染色体的核酸片段的大小分布来确定胎儿染色体非整倍体。 可以使用不同染色体的大小排序来从预期排名中确定危险染色体的等级的变化。 而且，一个染色体的统计大小值之间的差异可以与另一个染色体的统计大小值进行比较，以确定大小的显着变化。 也可以使用大小分布来确定胎儿的基因型和单倍型，以确定相对于母体的基因型或单倍型，母体样品中是否发生序列不平衡，从而提供胎儿的基因型或单倍型。
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公开(公告)号：US08467976B2
公开(公告)日：2013-06-18
申请号：US12940993
申请日：2010-11-05
CPC分类号： C12Q1/6876 , C12Q1/6827 , G06F19/18 , G06F19/22 , G06F19/24 , Y10T436/143333 , C12Q2537/165 , C12Q2535/101 , C12Q2527/125
摘要： Systems, methods, and apparatus for determining at least a portion of fetal genome are provided. DNA fragments from a maternal sample (maternal and fetal DNA) can be analyzed to identify alleles at certain loci. The amounts of DNA fragments of the respective alleles at these loci can be analyzed together to determine relative amounts of the haplotypes for these loci and determine which haplotypes have been inherited from the parental genomes. Loci where the parents are a specific combination of homozygous and heterozygous can be analyzed to determine regions of the fetal genome. Reference haplotypes common in the population can be used along with the analysis of the DNA fragments of the maternal sample to determine the maternal and paternal genomes. Determination of mutations, a fractional fetal DNA concentration in a maternal sample, and a proportion of coverage of a sequencing of the maternal sample can also be provided.
摘要翻译： 提供了用于确定胎儿基因组的至少一部分的系统，方法和装置。 可以分析来自母体样品（母体和胎儿DNA）的DNA片段，以鉴定某些位点处的等位基因。 可以一起分析在这些位点处各个等位基因的DNA片段的量，以确定这些基因座的单倍型的相对量，并确定哪些单元型已经从亲代基因组遗传。 可以分析父母是纯合子和杂合子的特异性组合的位点，以确定胎儿基因组的区域。 可以在群体中常见的参考单倍型与母体样品的DNA片段的分析一起使用，以确定母体和父系的基因组。 也可以提供母体样品中突变的确定，胎儿DNA分数的分数以及母体样品测序的覆盖率。
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公开(公告)号：US08442774B2
公开(公告)日：2013-05-14
申请号：US13433110
申请日：2012-03-28
IPC分类号： G01N33/50
CPC分类号： C12Q1/6886 , C12Q1/6809 , C12Q1/6827 , C12Q1/6874 , C12Q1/6883 , C12Q2600/156 , G06F19/18 , G06F19/22 , 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.
摘要翻译： 本发明的实施方案提供了用于确定从怀孕女性获得的生物样品中是否存在胎儿染色体非整倍性的方法，系统和装置。 对生物样品的核酸分子进行测序，使得对基因组的一部分进行测序。 根据测序结果确定相应量的临床相关染色体和背景染色体。 相对量的确定可以计算一定长度的序列。 将来自这些量（例如比例）的参数与一个或多个截断值进行比较，从而确定是否存在胎儿染色体非整倍性的分类。 在测序之前，生物样品可以富集特定大小的DNA片段。
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公开(公告)号：US20130059733A1
公开(公告)日：2013-03-07
申请号：US13405073
申请日：2012-02-24
CPC分类号： C12Q1/6881 , C12Q2600/154 , C12Q2600/156 , C12Q2600/172 , G16B20/00 , G16B40/00
摘要： Methods, systems, and apparatus are provided for determining zygosity of a multiple-fetus pregnancy using a biological sample taken from the mother. The fetal and maternal DNA in the sample (e.g. plasma) can be analyzed for a particular chromosomal region to identify genetic differences in the fetuses. For example, a normalized parameter for the measure of a primary or secondary allele can show variances for different chromosomal regions when fetuses are dizygotic. Such a variance can be determined relative to an expected value if the fetuses were genetically identical. Statistical methods are provided for analyzing the variation of the normalized parameters to determine fetal DNA concentration and the maternal-fetal mixed genotype at various loci. Parental genotype and haplotype information can also be used to identify inheritance of different parental haplotypes to indicate genetic differences among the fetuses.
摘要翻译： 提供了方法，系统和装置，用于使用从母亲取得的生物样品来确定多胎胎儿怀孕的接合性。 可以分析样品中的胎儿和母体DNA（例如血浆）以获得特定的染色体区域，以鉴定胎儿中的遗传差异。 例如，当胎儿分娩时，用于测量初级或次级等位基因的归一化参数可以显示不同染色体区域的方差。 如果胎儿在遗传上相同，则可以相对于期望值确定这种变化。 提供统计方法用于分析标准化参数的变化，以确定胎儿DNA浓度和各种基因座的母体 - 胎儿混合基因型。 亲代基因型和单倍型信息也可用于鉴定不同亲代单倍型的遗传，以指示胎儿之间的遗传差异。
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