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71. 发明公开

EP3456843A1 MUTATIONAL ANALYSIS OF PLASMA DNA FOR CANCER DETECTION 有权
公开(公告)号：EP3456843A1
公开(公告)日：2019-03-20
申请号：EP18185290.6
申请日：2013-06-14
申请人： The Chinese University Of Hong Kong
发明人： CHIU, Wai Kwun Rossa , LO, Yuk-Ming Dennis , CHAN, Kwan Chee , JIANG, Peiyong
IPC分类号： C12Q1/68
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.

72. 发明授权

EP3202921B1 MOLECULAR TESTING OF MULTIPLE PREGNANCIES 有权转让
公开(公告)号：EP3202921B1
公开(公告)日：2019-02-13
申请号：EP17161168.4
申请日：2012-02-24
申请人： The Chinese University of Hong Kong
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 , G06F19/18 , G06F19/24

73. 发明公开

EP3406737A1 SIZE-BASED GENOMIC ANALYSIS 有权转让
公开(公告)号：EP3406737A1
公开(公告)日：2018-11-28
申请号：EP18182983.9
申请日：2010-11-05
申请人： The Chinese University of Hong Kong
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： C12Q1/6809 , 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.

74. 发明授权

EP3178945B1 METHOD OF ANALYZING A BIOLOGICAL SAMPLE FROM A FEMALE SUBJECT PREGNANT WITH A FETUS 有权
公开(公告)号：EP3178945B1
公开(公告)日：2018-10-17
申请号：EP17154021.4
申请日：2013-04-08
申请人： The Chinese University Of Hong Kong
发明人： CHIU, Wai Kwun Rossa , LIAO, Jiawei , CHAN, Kwan Chee , LO, Yuk Ming Dennis
IPC分类号： C12Q1/6883 , C12Q1/6827 , G06F19/18
CPC分类号： C12Q1/6883 , C12Q1/6827 , C12Q2600/156 , C12Q2600/158 , G06F19/20 , G06F19/22 , C12Q2537/16
摘要： Whether a fetus has an aneuploidy associated with a first chromosome is detected using ratios of alleles detected in a maternal sample having a mixture of maternal and fetal DNA. DNA from the sample is enriched for target regions associated with polymorphic loci and then sequenced. Polymorphic loci (e.g., single nucleotide polymorphisms) in the target regions with fetal-specific alleles are identified on a first chromosome and on one or more reference chromosomes. A first ratio of the fetal-specific alleles and shared alleles is determined for the loci on the first chromosome. A second ratio of the fetal-specific alleles and shared alleles is determined for the loci on the reference chromosome(s). A third ratio of the first and second ratio can be compared to a cutoff to determine whether an aneuploidy is present, and whether the aneuploidy is maternally-derived or paternally-derived.

75. 发明公开

EP3334843A1 SINGLE-MOLECULE SEQUENCING OF PLASMA DNA 审中-实审
公开(公告)号：EP3334843A1
公开(公告)日：2018-06-20
申请号：EP16834683.1
申请日：2016-08-12
申请人： The Chinese University Of Hong Kong
发明人： LO, Yuk-Ming Dennis , CHIU, Rossa Wai Kwun , CHENG, Suk Hang
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6806 , C12Q1/6869 , G01N33/48721 , G06F19/22 , C12Q2525/151 , C12Q2565/631 , C12Q2521/501 , C12Q2525/191 , C12Q2525/197
摘要： Embodiments may include a method of determining a nucleic acid sequence. The method may include receiving a plurality of DNA fragments. The method may also include concatemerizing a first set of the DNA fragments to obtain a concatemer. The method may include performing single-molecule sequencing of the concatemer to obtain a first sequence of the concatemer. In some embodiments, single-molecule sequencing may be performed using a nanopore, and the method may include passing the concatemer through a nanopore. A first electrical signal may then be detected as the concatemer passes through the nanopore. The first electrical signal may correspond to a first sequence of the concatemer. In addition, the method may include analyzing the first electrical signal to determine the first sequence. Subsequences of the first sequence may be aligned to identify sequences corresponding to each of the first set of the DNA fragments.

76. 发明公开

EP3325663A1 METHYLATION PATTERN ANALYSIS OF HAPLOTYPES IN TISSUES IN DNA MIXTURE 有权
公开(公告)号：EP3325663A1
公开(公告)日：2018-05-30
申请号：EP16827235.9
申请日：2016-07-20
申请人： The Chinese University Of Hong Kong
发明人： LO, Yuk-Ming Dennis , CHAN, Kwan Chee , CHIU, Rossa Wai Kwun , JIANG, Peiyong , SUN, Kun
IPC分类号： C12Q1/68
摘要： Systems, apparatuses, and method are provided for determining the contributions of different tissues to a biological sample that includes a mixture of cell-free DNA molecules from various tissues types, e.g., as occurs in plasma or serum and other body fluids. Embodiments can analyze the methylation patterns of the DNA mixture (e.g., methylation levels at particular loci) for a particular haplotype and determine fractional contributions of various tissue types to the DNA mixture, e.g., of fetal tissue types or tissue types of specific organs that might have a tumor. Such fractional contributions determined for a haplotype can be used in a variety of ways.

77. 发明公开

EP3301193A1 SIZE-BASED ANALYSIS OF FETAL DNA FRACTION IN MATERNAL PLASMA 有权
标题翻译：母婴血浆中胎儿DNA分数的基于尺度的分析
公开(公告)号：EP3301193A1
公开(公告)日：2018-04-04
申请号：EP17202838.3
申请日：2013-03-08
申请人： The Chinese University Of Hong Kong
发明人： LO, Yuk Ming Dennis , CHAN, Kwan Chee , ZHENG, Wenli , JIANG, Peiyong , LIAO, Jiawei , CHIU, Wai Kwun Rossa
IPC分类号： C12Q1/68
CPC分类号： G06F19/22 , C12Q1/6809 , C12Q1/6816 , C12Q1/6827 , C12Q1/6869 , G06F19/00 , G06F19/18 , G16H10/40 , G16H50/20 , G16H50/30 , C12Q2535/122 , C12Q2537/16 , C12Q2537/165 , C12Q2539/107 , C12Q2525/204
摘要： A maternal plasma sample of a pregnant woman is analysed. The sample includes cell-free DNA fragments originating from maternal cells and fetal cells. For each of a plurality of DNA fragments: one or more sequence reads is received, including both ends of the DNA fragment; the sequence reads are aligned to a reference genome to obtain aligned locations for both ends; and the aligned locations are used to determine a size of the DNA fragment. For each of a plurality of sizes, an amount of a set of the plurality of DNA fragments from the plasma sample corresponding to the size is determined. There is calculated a value of a first parameter based on the amounts of DNA fragments at multiple sizes, providing a statistical measure of a size profile of DNA fragments. The value is compared to a calibration value to estimate a fractional concentration of fetal DNA.
摘要翻译：分析孕妇的母亲血浆样品。样品包括源自母体细胞和胎儿细胞的无细胞DNA片段。对于多个DNA片段中的每一个：接收一个或多个序列读段，包括DNA片段的两个末端; 将序列读数与参考基因组进行比对以获得两端的比对位置; 并且对齐的位置用于确定DNA片段的大小。对于多个尺寸中的每一个尺寸，确定来自血浆样品的与该尺寸对应的一组多个DNA片段的量。基于多个大小的DNA片段的量计算第一个参数的值，提供DNA片段的大小轮廓的统计测量。将该值与校准值进行比较以估计胎儿DNA的分数浓度。

78. 发明授权

EP2823062B1 SIZE-BASED ANALYSIS OF FETAL DNA FRACTION IN MATERNAL PLASMA 有权转让
标题翻译：母婴血浆中胎儿DNA分数的基于尺度的分析
公开(公告)号：EP2823062B1
公开(公告)日：2018-01-03
申请号：EP13757943.9
申请日：2013-03-08
申请人： The Chinese University of Hong Kong
发明人： LO, Yuk Ming Dennis , CHAN, Kwan Chee , ZHENG, Wenli , JIANG, Peiyong , LIAO, Jiawei , CHIU, Wai Kwun Rossa
IPC分类号： C12Q1/68
CPC分类号： G06F19/22 , C12Q1/6809 , C12Q1/6816 , C12Q1/6827 , C12Q1/6869 , G06F19/00 , G06F19/18 , G16H10/40 , G16H50/20 , G16H50/30 , C12Q2535/122 , C12Q2537/16 , C12Q2537/165 , C12Q2539/107 , C12Q2525/204
摘要： A method of analyzing a biological sample of an organism, the biological sample including DNA originating from normal cells and potentially from cells associated with cancer, wherein at least some of the DNA is cell-free in the biological sample, the method comprising: for each size of a plurality of sizes: measuring an amount of a first set of DNA fragments from the biological sample corresponding to the size; calculating a first value of a first parameter based on the amounts of DNA fragments at multiple sizes, the first parameter providing a statistical measure of a size profile of DNA fragments in the biological sample; comparing the first value to a reference value; and determining a classification of a level of cancer in the organism based on the comparison.

79. 发明公开

EP3245299A1 USING SIZE AND NUMBER ABERRATIONS IN PLASMA DNA FOR DETECTING CANCER 有权转让
标题翻译：用等离子体DNA中的大小和数字区分检测癌症
公开(公告)号：EP3245299A1
公开(公告)日：2017-11-22
申请号：EP16737075.8
申请日：2016-01-13
申请人： The Chinese University Of Hong Kong
发明人： LO, Yuk-Ming Dennis , CHIU, Rossa Wai Kwun , CHAN, Kwan Chee , JIANG, Peiyong
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6886 , C12Q1/6869 , C12Q2600/112 , C12Q2600/156 , G06F19/24 , C12Q2535/122 , C12Q2537/16
摘要： Analysis of tumor-derived circulating cell-free DNA opens up new possibilities for performing liquid biopsies for solid tumor assessment or cancer screening. However, many aspects of the biological characteristics of tumor-derived cell-free DNA remain unclear. Regarding the size profile of plasma DNA molecules, some studies reported increased integrity of tumor-derived plasma DNA while others reported shorter tumor-derived plasma DNA molecules. We performed an analysis of the size profiles of plasma DNA in patients with cancer using massively parallel sequencing at single base resolution and in a genomewide manner. Tumor-derived plasma DNA molecules were further identified using chromosome arm-level z-score analysis (CAZA). We showed that populations of aberrantly short and long DNA molecules co-existed in the plasma of patients with cancer. The short ones preferentially carried the tumor-associated copy number aberrations. These results show the ability to use plasma DNA as a molecular diagnostic tool.

80. 发明公开

EP3178945A1 METHOD OF ANALYZING A BIOLOGICAL SAMPLE FROM A FEMALE SUBJECT PREGNANT WITH A FETUS 有权
标题翻译：程序是用于分析一个女的人的生物样品与胎儿怀孕
公开(公告)号：EP3178945A1
公开(公告)日：2017-06-14
申请号：EP17154021.4
申请日：2013-04-08
申请人： The Chinese University Of Hong Kong
发明人： CHIU, Wai Kwun Rossa , LIAO, Jiawei , CHAN, Kwan Chee , LO, Yuk Ming Dennis
IPC分类号： C12Q1/68 , G06F19/18
CPC分类号： C12Q1/6883 , C12Q1/6827 , C12Q2600/156 , C12Q2600/158 , G06F19/20 , G06F19/22 , C12Q2537/16
摘要： Whether a fetus has an aneuploidy associated with a first chromosome is detected using ratios of alleles detected in a maternal sample having a mixture of maternal and fetal DNA. DNA from the sample is enriched for target regions associated with polymorphic loci and then sequenced. Polymorphic loci (e.g., single nucleotide polymorphisms) in the target regions with fetal-specific alleles are identified on a first chromosome and on one or more reference chromosomes. A first ratio of the fetal-specific alleles and shared alleles is determined for the loci on the first chromosome. A second ratio of the fetal-specific alleles and shared alleles is determined for the loci on the reference chromosome(s). A third ratio of the first and second ratio can be compared to a cutoff to determine whether an aneuploidy is present, and whether the aneuploidy is maternally-derived or paternally-derived.
摘要翻译：是否胎儿具有非整倍性与第一染色体相关联的使用具有母体和胎儿DNA的混合物的母体样品中检测到的等位基因的比率进行检测。从样品DNA富集与多态性位点相关联，并进行测序的靶区域。与胎儿特异性等位基因的目标区域多态位点（例如，单核苷酸多态性）的标识的第一染色体上和一个或多个参考染色体。胎儿特异性等位基因和共享的等位基因的第一比例确定开采第一染色体上的基因座。胎儿特异性等位基因和共享的等位基因的第二比例确定开采参考染色体上基因座。第一和第二比率的第三比率可以相比于截止到确定性矿无论非整倍体是目前，以及是否非整倍性母系衍生的或父本衍生。

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