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公开(公告)号：EP4259817A1
公开(公告)日：2023-10-18
申请号：EP21902599.6
申请日：2021-12-07
发明人： LO, Yuk-Ming Dennis , CHAN, Kwan Chee , JIANG, Peiyong , CHENG, Suk Hang , ZHOU, Ze , XIE, Tingting , WANG, Guangya , DING, Chen
IPC分类号： C12Q1/68
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公开(公告)号：EP4413151A1
公开(公告)日：2024-08-14
申请号：EP22877903.9
申请日：2022-09-29
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6883 , C12Q1/701 , C12Q2600/11820130101
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公开(公告)号：EP4320269A1
公开(公告)日：2024-02-14
申请号：EP22784117.8
申请日：2022-04-08
发明人： LO, Yuk-Ming Dennis , CHIU, Rossa Wai Kwun , CHAN, Kwan Chee , JIANG, Peiyong , CHAN, Wing Yan , NI, Meng , HAN, Diana Siao Cheng , SIN, Tsz Kwan
IPC分类号： C12Q1/6827 , C12Q1/6886 , C12Q1/6883 , C12Q1/6869
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公开(公告)号：EP4418274A2
公开(公告)日：2024-08-21
申请号：EP24186490.9
申请日：2016-01-13
IPC分类号： G16B20/00
CPC分类号： C12Q1/6869 , C12Q1/6883 , C12Q1/6886 , G16B20/00 , G16B40/00 , G16B20/20
摘要： An amount of mitochondrial DNA molecules relative to an amount of nuclear DNA molecules is determined in a biological sample, and the relative amount is used for various purposes, e.g., screening, detection, prognostication or monitoring of various physiological and pathological conditions. As examples, an amount of mitochondrial DNA can be used to estimate a concentration of DNA of a tissue type, such as a fetal DNA concentration, tumor DNA concentration, or a concentration of DNA in the biological sample derived from a non-hematopoietic tissue source. Sequencing techniques can be used to determine a mitochondrial DNA concentration in a sample for an accurate detection of a level of cancer. A level of an auto-immune disease is also determined using a relative amount of mitochondrial DNA molecules compared nuclear DNA molecules.
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公开(公告)号：EP4357461A3
公开(公告)日：2024-07-03
申请号：EP24151722.6
申请日：2020-08-17
发明人： LO, Yuk-Ming Dennis , CHIU, Rossa Wai Kwun , CHAN, Kwan Chee , JIANG, Peiyong , CHENG, Suk Hang , PENG, Wenlei , TSE, On Yee
摘要： We describe a method for detection of a methylation of a nucleotide in a nucleic acid molecule. The method comprises receiving a first plurality of first data structures, each first data structure including information measured at nucleotide positions. Then, a plurality of first training samples, each including one of the first plurality of first data structures and a first label is stored. The model is trained using the plurality of first training samples by optimizing parameters of the model based on outputs of the model matching or not matching corresponding labels of the first labels. An output of the model specifies whether the nucleotide has the methylation.
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公开(公告)号：EP4324937A3
公开(公告)日：2024-05-15
申请号：EP23214529.2
申请日：2017-05-30
IPC分类号： C12Q1/68 , C12Q1/6883 , G16B20/40
CPC分类号： C12Q1/6883 , C12Q2600/15420130101 , G16B30/00
摘要： Techniques are provided for detecting hematological disorders using cell-free DNA in a blood sample, e.g., using plasma or serum. For example, an assay can target one or more differentially-methylated regions specific to a particular hematological cell lineage (e.g., erythroblasts). A methylation level can be quantified from the assay to determine an amount of methylated or unmethylated DNA fragments in a cell-free mixture of the blood sample. The methylation level can be compared to one or more cutoff values, e.g., that correspond to a normal range for the particular hematological cell lineage as part of determining a level of a hematological disorder.
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公开(公告)号：EP4357461A2
公开(公告)日：2024-04-24
申请号：EP24151722.6
申请日：2020-08-17
发明人： LO, Yuk-Ming Dennis , CHIU, Rossa Wai Kwun , CHAN, Kwan Chee , JIANG, Peiyong , CHENG, Suk Hang , PENG, Wenlei , TSE, On Yee
IPC分类号： C12Q1/6869
摘要： We describe a method for detection of a methylation of a nucleotide in a nucleic acid molecule. The method comprises receiving a first plurality of first data structures, each first data structure including information measured at nucleotide positions. Then, a plurality of first training samples, each including one of the first plurality of first data structures and a first label is stored. The model is trained using the plurality of first training samples by optimizing parameters of the model based on outputs of the model matching or not matching corresponding labels of the first labels. An output of the model specifies whether the nucleotide has the methylation.
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公开(公告)号：EP4056712A1
公开(公告)日：2022-09-14
申请号：EP22171427.2
申请日：2013-09-20
发明人： CHIU, Rossa Wai Kwun , CHAN, Kwan Chee , LO, Yuk-Ming Dennis , LUN, Miu Fan , JIANG, Peiyong , CHAN, Wai Man
IPC分类号： C12Q1/68 , C12Q1/6869
摘要： Systems, methods, and apparatuses can determine and use methylation profiles of various tissues and samples. Examples are provided. A methylation profile can be deduced for fetal/tumor tissue based on a comparison of plasma methylation (or other sample with cell-free DNA) to a methylation profile of the mother/patient. A methylation profile can be determined for fetal/tumor tissue using tissue-specific alleles to identify DNA from the fetus/tumor when the sample has a mixture of DNA. A methylation profile can be used to determine copy number variations in genome of a fetus/tumor. Methylation markers for a fetus have been identified via various techniques. The methylation profile can be determined by determining a size parameter of a size distribution of DNA fragments, where reference values for the size parameter can be used to determine methylation levels. Additionally, a methylation level can be used to determine a level of cancer.
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公开(公告)号：EP3245300A1
公开(公告)日：2017-11-22
申请号：EP16737076.6
申请日：2016-01-13
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6869 , C12Q1/6883 , C12Q1/6886 , G06F19/18 , G06F19/24 , C12Q2537/165
摘要： An amount of mitochondrial DNA molecules relative to an amount of nuclear DNA molecules is determined in a biological sample, and the relative amount is used for various purposes, e.g., screening, detection, prognostication or monitoring of various physiological and pathological conditions. As examples, an amount of mitochondrial DNA can be used to estimate a concentration of DNA of a tissue type, such as a fetal DNA concentration, tumor DNA concentration, or a concentration of DNA in the biological sample derived from a non-hematopoietic tissue source. Sequencing techniques can be used to determine a mitochondrial DNA concentration in a sample for an accurate detection of a level of cancer. A level of an auto-immune disease is also determined using a relative amount of mitochondrial DNA molecules compared nuclear DNA molecules.
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10.发明公开SEQUENCING ANALYSIS OF CIRCULATING DNA TO DETECT AND MONITOR AUTOIMMUNE DISEASES 审中-公开SEQUENZIERUNGSANALYSE VON ZIRKULIERENDER DNA ZUM NACHWEIS UND ZURÜBERWACHUNGVON AUTOIMMUNKRANKHEITEN
公开(公告)号：EP3047038A1
公开(公告)日：2016-07-27
申请号：EP14845937.3
申请日：2014-09-20
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6883 , C12Q2600/154 , G06F19/18 , G06F19/20
摘要： Systems, methods, and apparatuses are provided for diagnosing auto-immune diseases such as systemic lupus erythematosus (SLE) based on the sizes, methylation levels, and/or genomic characteristics of circulating DNA molecules. Patients provide blood or other tissue samples containing cell-free nucleic molecules for analysis. Massively parallel and/or methylation-aware sequencing can be used to determine the sizes and methylation levels of individual DNA molecules and identify the number of molecules originating from different genomic regions. A level of SLE can be estimated based on: the amount of molecules having sizes below a threshold value; the methylation level(s) of the entire genome or portions of the genome; correlations between the sizes and methylation levels of DNA molecules; and/or comparing the representation of DNA molecules in each of a plurality of genomic regions with a reference value for that region, and determining an amount of genomic regions having increased or decreased measured genomic representation.
摘要翻译： 基于循环DNA分子的大小，甲基化水平和/或基因组特征，提供系统，方法和装置用于诊断诸如系统性红斑狼疮（SLE）的自身免疫性疾病。 患者提供含有无细胞核酸分子的血液或其他组织样本用于分析。 可以使用大规模平行和/或甲基化感知测序来确定个体DNA分子的大小和甲基化水平，并确定源于不同基因组区域的分子数。 可以基于以下尺寸估计SLE的水平：具有低于阈值的分子的量; 整个基因组或基因组部分的甲基化水平; DNA分子的大小和甲基化水平之间的相关性; 和/或将多个基因组区域中的每一个中的DNA分子的表示与该区域的参考值进行比较，以及确定具有增加或减少的测量的基因组表达的基因组区域的量。
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