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1. 发明申请

WO2013190441A2 MUTATIONAL ANALYSIS OF PLASMA DNA FOR CANCER DETECTION 审中-公开
标题翻译：用于癌症检测的血浆DNA的突变分析
公开(公告)号：WO2013190441A2
公开(公告)日：2013-12-27
申请号：PCT/IB2013/054898
申请日：2013-06-14
申请人： THE CHINESE UNIVERSITY OF HONG KONG , CHIU, Wai, Kwun, Rossa
发明人： CHIU, Wai, Kwun, Rossa , LO, Yuk-Ming, Dennis , CHAN, Kwan, Chee , JIANG, Peiyong
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6886 , C12Q1/6827 , C12Q2600/112 , C12Q2600/156 , C12Q2535/122 , C12Q2537/16 , C12Q2539/107
摘要： A frequency of somatic mutations in a biological sample (e.g., plasma or serum) of a subject undergoing screening or monitoring for cancer, can be compared with that in the constitutional DNA of the same subject. A parameter can derived from these frequencies and used to determine a classification of a level of cancer. False positives can be filtered out by requiring any variant locus to have at least a specified number of variant sequence reads (tags), thereby providing a more accurate parameter. The relative frequencies for different variant loci can be analyzed to determine a level of heterogeneity of tumors in a patient.
摘要翻译：可以将经历筛选或监测癌症的受试者的生物样品（例如血浆或血清）中的体细胞突变的频率与同一受试者的结构DNA中的体细胞突变的频率进行比较。一个参数可以从这些频率导出，用于确定癌症水平的分类。可以通过要求任何变体轨迹至少具有指定数量的变体序列读取（标签）来过滤掉假阳性，从而提供更准确的参数。可以分析不同变体基因座的相对频率，以确定患者肿瘤异质性水平。

2. 发明申请

WO2012071621A1 DETECTION OF GENETIC OR MOLECULAR ABERRATIONS ASSOCIATED WITH CANCER 审中-公开
标题翻译：检测与癌症相关的遗传或分子遗传异常
公开(公告)号：WO2012071621A1
公开(公告)日：2012-06-07
申请号：PCT/AU2011/001562
申请日：2011-11-30
申请人： THE CHINESE UNIVERSITY OF HONG KONG , LO, Yuk Ming Dennis , CHAN, Kwan Chee , CHIU, Wai Kwun Rossa , JIANG, Peiyong
发明人： LO, Yuk Ming Dennis , CHAN, Kwan Chee , CHIU, Wai Kwun Rossa , JIANG, Peiyong
IPC分类号： C12Q1/68 , G06F19/18 , G06F19/20
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： Systems, apparatus, and methods are provided for determining genetic or molecular aberrations in a biological sample from an organism. 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：提供系统，装置和方法用于确定来自生物体的生物样品中的遗传或分子畸变。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，可以随时间检测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后，以及监测进展（例如，治疗后）

3. 发明申请

WO2013190441A3 MUTATIONAL ANALYSIS OF PLASMA DNA FOR CANCER DETECTION 审中-公开
标题翻译：用于癌症检测的血浆DNA的突变分析
公开(公告)号：WO2013190441A3
公开(公告)日：2014-02-27
申请号：PCT/IB2013054898
申请日：2013-06-14
申请人： UNIV HONG KONG CHINESE , CHIU WAI KWUN ROSSA
发明人： CHIU WAI KWUN ROSSA , LO YUK-MING DENNIS , CHAN KWAN CHEE , JIANG PEIYONG
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6886 , C12Q1/6827 , C12Q2600/112 , C12Q2600/156 , C12Q2535/122 , C12Q2537/16 , C12Q2539/107
摘要： A frequency of somatic mutations in a biological sample (e.g., plasma or serum) of a subject undergoing screening or monitoring for cancer, can be compared with that in the constitutional DNA of the same subject. A parameter can derived from these frequencies and used to determine a classification of a level of cancer. False positives can be filtered out by requiring any variant locus to have at least a specified number of variant sequence reads (tags), thereby providing a more accurate parameter. The relative frequencies for different variant loci can be analyzed to determine a level of heterogeneity of tumors in a patient.
摘要翻译：可以将经历筛选或监测癌症的受试者的生物样品（例如血浆或血清）中的体细胞突变的频率与同一受试者的结构DNA中的体细胞突变的频率进行比较。一个参数可以从这些频率导出，用于确定癌症水平的分类。可以通过要求任何变体轨迹至少具有指定数量的变体序列读取（标签）来过滤掉假阳性，从而提供更准确的参数。可以分析不同变体基因座的相对频率，以确定患者肿瘤异质性水平。

4. 发明申请

WO2012093331A1 NONINVASIVE PRENATAL GENOTYPING OF FETAL SEX CHROMOSOMES 审中-公开
标题翻译：阴性染色体的非侵入性预测基因
公开(公告)号：WO2012093331A1
公开(公告)日：2012-07-12
申请号：PCT/IB2012/000015
申请日：2012-01-05
申请人： THE CHINESE UNIVERSITY OF HONG KONG , LO, Yuk, Ming, Denis , CHIU, Wai, Kwun, Rossa , CHAN, Kwan, Chee , TSUI, Bo, Yin
发明人： LO, Yuk, Ming, Denis , CHIU, Wai, Kwun, Rossa , CHAN, Kwan, Chee , TSUI, Bo, Yin
IPC分类号： C12Q1/68 , G06F19/00
CPC分类号： G06F19/18 , C12Q1/6883 , C12Q2600/156 , C12Q2600/158
摘要： Methods, apparatuses, and system are provided for analyzing a maternal sample to determine whether a male fetus of a pregnant female has inherited an X-linked mutation from the mother. A percentage of fetal DNA in the sample is obtained, and cutoff values for the two possibilities (fetus inherits mutant or normal allele) are determined. A proportion of mutant alleles relative to a normal allele on the X-chromosome can then be compared to the cutoff values to make a classification of which allele is inherited. Alternatively, a number of alleles from a target region on the X-chromosome can be compared to a number of alleles from a reference region on the X-chromosome to identify a deletion or amplification. The fetal DNA percentage can be computed by counting reactions with a fetal-specific allele, and correcting the number to account for a statistical distribution among the reactions.
摘要翻译：提供方法，装置和系统用于分析母体样品以确定怀孕女性的雄性胎儿是否从母亲遗传了X连锁突变。获得样品中胎儿DNA的百分比，确定两种可能性（胎儿遗传突变体或正常等位基因）的临界值。然后将相对于X染色体上的正常等位基因的突变体等位基因的一部分与截断值进行比较，以对哪个等位基因进行遗传分类。或者，可以将来自X染色体上的目标区域的多个等位基因与来自X染色体上的参考区域的多个等位基因进行比较以鉴定缺失或扩增。胎儿DNA百分比可以通过计数与胎儿特异性等位基因的反应来计算，并且校正数量以解释反应之间的统计分布。

5. 发明申请

WO2009030100A1 METHODS AND KITS FOR SELECTIVELY AMPLIFYING, DETECTING OR QUANTIFYING TARGET DNA WITH SPECIFIC END SEQUENCES 审中-公开
标题翻译：用于选择性扩增，检测或定量具有特定末端序列的靶标DNA的方法和工具
公开(公告)号：WO2009030100A1
公开(公告)日：2009-03-12
申请号：PCT/CN2008/001423
申请日：2008-08-05
申请人： THE CHINESE UNIVERSITY OF HONG KONG , LO, Yuk Ming Dennis , TONG, Yu Kwan , CHIU, Wai Kwun Rossa , DING, Chunming
发明人： LO, Yuk Ming Dennis , TONG, Yu Kwan , CHIU, Wai Kwun Rossa , DING, Chunming
IPC分类号： C12Q1/68
CPC分类号： C12Q1/686 , C12Q2525/301 , C12Q2521/331
摘要： Disclosed herein are methods and kits for selectively amplifying, detecting or quantifying a DNA fragment with a specific end sequence, especially generated following restriction enzyme digestion. This method can be used, for example, to detect a hypomethylated DNA fragment. This methods and kits are especially useful in detecting or quantifying a hypomethylated fetal DNA fragment in a maternal plasma sample containing a corresponding hypermethylated maternal DNA fragment.
摘要翻译：本文公开了用于选择性扩增，检测或定量具有特异末端序列的DNA片段的方法和试剂盒，特别是在限制酶消化后产生。该方法可用于例如检测低甲基化DNA片段。该方法和试剂盒特别可用于检测或定量含有相应的高甲基化母体DNA片段的母体血浆样品中的低甲基化胎儿DNA片段。

6. 发明申请

WO2004065629A1 CIRCULATING MRNA AS DIAGNOSTIC MARKERS FOR PREGNANCY-RELATED DISORDERS 审中-公开
标题翻译：将MRNA作为诊断标记循环用于与PREGNNC相关的疾病
公开(公告)号：WO2004065629A1
公开(公告)日：2004-08-05
申请号：PCT/GB2004/000145
申请日：2004-01-16
申请人： THE CHINESE UNIVERSITY OF HONG KONG , LO, Yuk-Ming Dennis , NG, Kai On , TSUI, Bo Yin , CHIU, Wai Kwun Rossa
发明人： LO, Yuk-Ming Dennis , NG, Kai On , TSUI, Bo Yin , CHIU, Wai Kwun Rossa
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6883 , C12Q2600/156 , C12Q2600/158
摘要： Methods and kits are provided for diagnosing, monitoring, or predicting the conditions of pre-eclaimpsia, fetal chromosomal aneuploidy, and pre-term labor in a pregnant woman, as well as for detecting pregnancy in a woman, by quantitatively measuring in the maternal blood the amount of one or more mRNA species encoding human chorionic gonadotropin β subunit (hCG-β), human placental lactogen (hPL), human corticotropin releasing hormone (hCRH), KiSS-1 metastasis-suppressor (KISS1), tissue factor pathway inhibitor 2 (TPFI2), placenta-specific 1 (PLAC1), or glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and comparing the amount of the Methods and kits are provided for diagnosing, monitoring, or predicting the conditions of pre-eclaimpsia, fetal chromosomal aneuploidy, and pre-term labor in a pregnant woman, as well as for detecting pregnancy in a woman, by quantitatively measuring in the maternal blood the amount of one or more mRNA species encoding human chorionic gonadotropin β subunit (hCG-β), human placental lactogen (hPL), human corticotropin releasing hormone (hCRH), KiSS-1 metastasis-suppressor (KISS1), tissue factor pathway inhibitor 2 (TPFI2), placenta-specific 1 (PLAC1), or glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and comparing the amount of the mRNA species with a standard control.
摘要翻译：提供方法和试剂盒，用于诊断，监测或预测怀孕妇女的pre-eclaimpsia，胎儿染色体非整倍性和早产儿的状况，以及通过定量测量孕妇血液中的孕妇检测怀孕情况编码人绒毛膜促性腺激素β亚基（hCG-β），人胎盘乳腺癌（hPL），促皮质激素释放激素（hCRH），KiSS-1转移抑制因子（KISS1），组织因子途径抑制剂2 （TPFI2），胎盘特异性1（PLAC1）或甘油醛-3-磷酸脱氢酶（GAPDH），并比较方法和试剂盒的数量用于诊断，监测或预测前期症状，胎儿染色体非整倍体和孕妇的早产，以及检测女性的怀孕，通过定量测量母体血液中编码人绒毛膜促性腺激素的一种或多种mRNA种类的数量为（hCG-β），人胎盘乳腺癌（hPL），促皮质激素释放激素（hCRH），KiSS-1转移抑制因子（KISS1），组织因子途径抑制剂2（TPFI2），胎盘特异性1（PLAC1）或甘油醛-3-磷酸脱氢酶（GAPDH），并将mRNA种类的量与标准对照进行比较。

7. 发明申请

WO2011057094A1 FETAL GENOMIC ANALYSIS FROM A MATERNAL BIOLOGICAL SAMPLE 审中-公开
标题翻译：来自生物生物样品的基因组分析
公开(公告)号：WO2011057094A1
公开(公告)日：2011-05-12
申请号：PCT/US2010/055655
申请日：2010-11-05
申请人： THE CHINESE UNIVERSITY OF HONG KONG , SEQUENOM, INC. , LO, Yuk Ming Dennis , CHAN, Kwan Chee , CHIU, Wai Kwun Rossa , CANTOR, Charles
发明人： LO, Yuk Ming Dennis , CHAN, Kwan Chee , CHIU, Wai Kwun Rossa , CANTOR, Charles
IPC分类号： C12Q1/68
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元型的相对量，并确定哪些单元型已经从亲本基因组遗传。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。

8. 发明申请

WO2011054936A1 SIZE-BASED GENOMIC ANALYSIS 审中-公开
标题翻译：基于大小的基因分析
公开(公告)号：WO2011054936A1
公开(公告)日：2011-05-12
申请号：PCT/EP2010/066935
申请日：2010-11-05
申请人： THE CHINESE UNIVERSITY OF HONG KONG , LO, Yuk Ming Dennis , CHAN, Kwan Chee , ZHENG, Wenli , CHIU, Wai Kwun Rossa
发明人： LO, Yuk Ming Dennis , CHAN, Kwan Chee , ZHENG, Wenli , CHIU, Wai Kwun Rossa
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6883 , C12Q1/6809 , 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。

9. 发明申请

WO2014107765A1 NONINVASIVE PRENATAL MOLECULAR KARYOTYPING FROM MATERNAL PLASMA 审中-公开
标题翻译：从等离子体分析非离子型分子核糖体
公开(公告)号：WO2014107765A1
公开(公告)日：2014-07-17
申请号：PCT/AU2014/000012
申请日：2014-01-09
申请人： THE CHINESE UNIVERSITY OF HONG KONG , CHIU, Wai Kwun Rossa
发明人： CHIU, Wai Kwun Rossa , LO, Yuk Ming Dennis , CHAN, Kwan Chee , JIANG, Peiyong , YU, Cheuk Yin Jandy
IPC分类号： C12Q1/68
CPC分类号： G06F19/18
摘要： Disclosed herein are methods, systems, and apparatus for detecting microamplifications or microdeletions in the genome of a fetus. In some embodiments, the method comprises receiving sequence tags for each of a plurality of DNA fragments in a biological sample; determining genomic positions for the sequence tags; determining whether the density of DNA in each of a plurality of genomic regions is aberrantly high or low; identifying as a microamplification a set of consecutive genomic regions having aberrantly high density; and identifying as a microdeletion a set of consecutive genomic regions having aberrantly low density. The biological sample may be a blood sample obtained noninvasively from a female subject pregnant with the fetus.
摘要翻译：本文公开了用于检测胎儿基因组中的微量放大或微缺失的方法，系统和装置。在一些实施方案中，所述方法包括接收生物样品中多个DNA片段中的每一个的序列标签; 确定序列标签的基因组位置; 确定多个基因组区域中的每一个中DNA的密度是否异常高或低; 将一组具有异常高密度的连续基因组区域鉴定为微量放大; 并将一组具有异常低密度的连续基因组区域鉴定为微缺失。生物样品可以是从怀孕胎儿的女性受试者非侵入性获得的血液样品。

10. 发明申请

WO2013041921A1 MOLECULAR TESTING OF MULTIPLE PREGNANCIES 审中-公开
标题翻译：多种孕妇的分子检测
公开(公告)号：WO2013041921A1
公开(公告)日：2013-03-28
申请号：PCT/IB2012/000344
申请日：2012-02-24
申请人： THE CHINESE UNIVERSITY OF HONG KONG , LO, Yuk Ming Dennis , CHIU, Wai Kwun Rossa , CHAN, Kwan Chee , LEUNG, Tak Yeung , JIANG, Peiyong
发明人： LO, Yuk Ming Dennis , CHIU, Wai Kwun Rossa , CHAN, Kwan Chee , LEUNG, Tak Yeung , JIANG, Peiyong
IPC分类号： C12Q1/68
CPC分类号： G06F19/18 , C12Q1/6881 , C12Q2600/154 , C12Q2600/156 , C12Q2600/172 , G06F19/24
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本来确定多胎胎儿妊娠的接合度。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，对于主要或次要等位基因的测量的归一化参数可以显示当胎儿分娩时不同染色体区域的差异。如果胎儿在遗传上相同，则可以相对于期望值确定这样的方差。提供统计学方法来分析标准化参数的变化，以确定胎儿DNA浓度和母体胎儿混合基因型在各个位点。亲代基因型和单倍型信息也可用于鉴定不同亲本单元型的遗传，以指示胎儿之间的遗传差异。

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