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公开(公告)号：EP3783110A1
公开(公告)日：2021-02-24
申请号：EP20200970.0
申请日：2010-11-05
IPC分类号： C12Q1/68 , C12Q1/6827
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.
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2.发明公开
公开(公告)号：EP3640346A1
公开(公告)日：2020-04-22
申请号：EP19206273.5
申请日：2011-11-30
IPC分类号： C12Q1/6809 , G16B20/00 , C12Q1/6869 , C12Q1/6886
摘要： Progress of chromosomal aberrations in an organism is determined using biological samples including nucleic acid molecules originating from normal cells and potentially from cells associated with a disease, at least some of the nucleic acid molecules being cell-free. Non-overlapping chromosomal regions of a reference genome of the organism are determined. At a plurality of times: for each of plural nucleic acid molecules, a location thereof in the reference genome is determined; and for each chromosomal region: a respective group of nucleic acid molecules is identified as being therefrom based on the identified locations; a respective value defining a property of the nucleic acid molecules is calculated and compared to a reference value to determine a classification of whether the chromosomal region exhibits a deletion or an amplification. The classifications at the plurality of times are used to determine the progress of the chromosomal aberrations in the organism.
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公开(公告)号：EP3202921A1
公开(公告)日：2017-08-09
申请号：EP17161168.4
申请日：2012-02-24
发明人： LO, Yuk Ming Dennis , CHIU, Wai Kwun Rossa , CHAN, Kwan Chee , LEUNG, Tak Yeung , JIANG, Peiyong
CPC分类号： G06F19/18 , C12Q1/6881 , C12Q2600/154 , C12Q2600/156 , C12Q2600/172 , G06F19/24
摘要： A method for analyzing a biological sample of a pregnant female to determine whether at least two fetuses of the pregnant female are dizygotic, the biological sample comprising fetal and maternal DNA, the method comprising: creating a histogram by: for each of a plurality of chromosomal regions: identifying one or more loci in the respective chromosomal region at which a respective first allele and a respective second allele are detected in the biological sample; measuring, at the one or more loci, a first amount of the one or more first alleles and/or a second amount of the one or more second alleles in the biological sample; and obtaining a normalized parameter for the first amount or the second amount; and incrementing counters based on a number of chromosomal regions with specified values for the normalized parameter; identifying chromosomal regions corresponding to loci at which the mother is homozygous and at least one of the fetuses is heterozygous or corresponding to loci at which the mother is heterozygous and at least one of the fetuses is homozygous; fitting a multi-component mixture model to the histogram corresponding to the identified chromosomal regions, the multi-component mixture model including a mixture coefficient for each of a plurality of components; and determining whether at least two of the fetuses are dizygotic using at least two of the mixture coefficients.
摘要翻译： 一种用于分析怀孕女性的生物样本以确定怀孕女性的至少两个胎儿是否是双合子的方法，所述生物样本包含胎儿和母体DNA，所述方法包括：通过以下步骤创建直方图：对于多个染色体 区域：鉴定在生物样品中检测到相应的第一等位基因和相应的第二等位基因的相应染色体区域中的一个或多个基因座; 在所述一个或多个基因座处测量所述生物样品中的所述一种或多种第一等位基因的第一量和/或所述一种或多种第二等位基因的第二量; 并获得第一量或第二量的标准化参数; 并基于具有归一化参数的指定值的多个染色体区域递增计数器; 鉴定对应于母亲是纯合的基因座的染色体区域，并且至少一个胎儿是杂合的或对应于母亲是杂合的基因座，并且至少一个胎儿是纯合的; 将多组分混合物模型拟合至对应于所识别的染色体区域的直方图，所述多组分混合物模型包括用于多个组分中的每一个的混合物系数; 以及使用混合系数中的至少两个确定至少两个胎儿是否是双合子的。
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公开(公告)号：EP2678451A1
公开(公告)日：2014-01-01
申请号：EP12834099.9
申请日：2012-02-24
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.
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5.发明公开METHODS AND KITS FOR SELECTIVELY AMPLIFYING, DETECTING OR QUANTIFYING TARGET DNA WITH SPECIFIC END SEQUENCES 有权METHOD FOR SELECTIVE扩增，检测或低甲基化DNA的定量
公开(公告)号：EP2195449A1
公开(公告)日：2010-06-16
申请号：EP08783612.8
申请日：2008-08-05
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.
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公开(公告)号：EP4212630A1
公开(公告)日：2023-07-19
申请号：EP23160186.5
申请日：2010-11-05
IPC分类号： C12Q1/6809 , C12Q1/6883
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.
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公开(公告)号：EP3882358A1
公开(公告)日：2021-09-22
申请号：EP21172741.7
申请日：2013-03-08
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
摘要： A plasma sample of an organism is analysed. The sample includes cell-free DNA fragments originating from normal cells and potentially from cells associated with cancer. 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 tumor DNA.
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公开(公告)号：EP3489368B1
公开(公告)日：2020-09-09
申请号：EP18213644.0
申请日：2012-02-24
发明人： LO, Yuk Ming Dennis , CHIU, Wai Kwun Rossa , CHAN, Kwan Chee , LEUNG, Tak Yeung , JIANG, Peiyong
IPC分类号： C12Q1/6881 , G16B20/00 , G16B40/00
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公开(公告)号：EP3301193B1
公开(公告)日：2019-04-24
申请号：EP17202838.3
申请日：2013-03-08
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
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公开(公告)号：EP3241914A1
公开(公告)日：2017-11-08
申请号：EP17168527.4
申请日：2010-11-05
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，方法和设备。 可以分析母体样品（母体和胎儿DNA）的DNA片段以鉴定某些基因座的等位基因。 可以一起分析这些基因座处各个等位基因的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倍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定组合的基因座以确定胎儿基因组的区域。 群体中常见的参考单体型可以与母体样品的DNA片段分析一起使用以确定母本和父本基因组。 还可以提供突变的确定，母体样品中分数的胎儿DNA浓度以及母体样品测序覆盖率的比例。
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