CN117402950A - 确定导致无细胞dna的产生的组织和/或细胞类型的方法以及使用其鉴定疾病或紊乱的方法 - Google Patents

确定导致无细胞dna的产生的组织和/或细胞类型的方法以及使用其鉴定疾病或紊乱的方法 Download PDF

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CN117402950A
CN117402950A CN202311109971.5A CN202311109971A CN117402950A CN 117402950 A CN117402950 A CN 117402950A CN 202311109971 A CN202311109971 A CN 202311109971A CN 117402950 A CN117402950 A CN 117402950A
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cfdna
nucleosome
tissue
fragments
biological sample
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杰·什杜尔
马修·斯奈德
马丁·基尔舍
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University of Washington
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University of Washington
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CN202311109971.5A 2014-07-25 2015-07-27 确定导致无细胞dna的产生的组织和/或细胞类型的方法以及使用其鉴定疾病或紊乱的方法 Pending CN117402950A (zh)

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Application Number Priority Date Filing Date Title
US201462029178P 2014-07-25 2014-07-25
US62/029,178 2014-07-25
US201462087619P 2014-12-04 2014-12-04
US62/087,619 2014-12-04
PCT/US2015/042310 WO2016015058A2 (en) 2014-07-25 2015-07-27 Methods of determining tissues and/or cell types giving rise to cell-free dna, and methods of identifying a disease or disorder using same
CN201580052170.7A CN107002122B (zh) 2014-07-25 2015-07-27 确定导致无细胞dna的产生的组织和/或细胞类型的方法以及使用其鉴定疾病或紊乱的方法

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CN202311109971.5A Pending CN117402950A (zh) 2014-07-25 2015-07-27 确定导致无细胞dna的产生的组织和/或细胞类型的方法以及使用其鉴定疾病或紊乱的方法

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EP (2) EP4358097A1 (enExample)
JP (3) JP2017522908A (enExample)
KR (2) KR102441391B1 (enExample)
CN (2) CN107002122B (enExample)
AU (2) AU2015292311B2 (enExample)
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Families Citing this family (119)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2012129363A2 (en) 2011-03-24 2012-09-27 President And Fellows Of Harvard College Single cell nucleic acid detection and analysis
US9892230B2 (en) 2012-03-08 2018-02-13 The Chinese University Of Hong Kong Size-based analysis of fetal or tumor DNA fraction in plasma
US11261494B2 (en) 2012-06-21 2022-03-01 The Chinese University Of Hong Kong Method of measuring a fractional concentration of tumor DNA
US20160040229A1 (en) 2013-08-16 2016-02-11 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number variation
US10876152B2 (en) 2012-09-04 2020-12-29 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number variation
US11913065B2 (en) 2012-09-04 2024-02-27 Guardent Health, Inc. Systems and methods to detect rare mutations and copy number variation
ES2769241T5 (es) 2012-09-04 2023-05-30 Guardant Health Inc Sistemas y métodos para detectar variación en el número de copias
CN111534580B (zh) 2013-12-28 2024-06-04 夸登特健康公司 用于检测遗传变异的方法和系统
TWI727156B (zh) 2014-07-18 2021-05-11 香港中文大學 Dna混合物中之組織甲基化模式分析
WO2016015058A2 (en) 2014-07-25 2016-01-28 University Of Washington Methods of determining tissues and/or cell types giving rise to cell-free dna, and methods of identifying a disease or disorder using same
US10364467B2 (en) 2015-01-13 2019-07-30 The Chinese University Of Hong Kong Using size and number aberrations in plasma DNA for detecting cancer
WO2016123698A1 (en) * 2015-02-06 2016-08-11 Uti Limited Partnership Diagnostic assay for post-transplant assessment of potential rejection of donor organs
SG11201706529TA (en) 2015-02-10 2017-09-28 Univ Hong Kong Chinese Detecting mutations for cancer screening and fetal analysis
DK3325664T3 (da) 2015-07-23 2022-03-07 Univ Hong Kong Chinese Analyse af fragmenteringsmønstre for cellefrit DNA
EP4180532A1 (en) * 2015-11-09 2023-05-17 Roche Molecular Systems, Inc. Methods for determining the origin of dna molecules
CA3008651A1 (en) 2015-12-17 2017-06-22 Guardant Health, Inc. Methods to determine tumor gene copy number by analysis of cell-free dna
US11514289B1 (en) 2016-03-09 2022-11-29 Freenome Holdings, Inc. Generating machine learning models using genetic data
JP7448310B2 (ja) 2016-07-06 2024-03-12 ガーダント ヘルス, インコーポレイテッド セルフリー核酸のフラグメントームプロファイリングのための方法
EP3485035B1 (en) 2016-07-15 2024-07-03 The Regents of the University of California Methods of producing nucleic acid libraries
WO2018027176A1 (en) 2016-08-05 2018-02-08 The Broad Institute, Inc. Methods for genome characterization
US9850523B1 (en) 2016-09-30 2017-12-26 Guardant Health, Inc. Methods for multi-resolution analysis of cell-free nucleic acids
KR102344635B1 (ko) 2016-09-30 2021-12-31 가던트 헬쓰, 인크. 무세포 핵산의 다중-해상도 분석 방법
EP4656736A2 (en) * 2016-10-12 2025-12-03 Bellwether Bio, Inc. Determining cell type origin of circulating cell-free dna with molecular counting
WO2018072705A1 (en) 2016-10-19 2018-04-26 The Chinese University Of Hong Kong Gestational age assessment by methylation and size profiling of maternal plasma dna
TWI797095B (zh) 2016-10-24 2023-04-01 美商格瑞爾有限責任公司 腫瘤檢測之方法及系統
US11435339B2 (en) 2016-11-30 2022-09-06 The Chinese University Of Hong Kong Analysis of cell-free DNA in urine
EP3555311B1 (en) 2016-12-13 2024-06-26 Bellwether Bio, Inc. Determining a physiological condition in an individual by analyzing cell-free dna fragment endpoints in a biological sample
AU2017382439B2 (en) 2016-12-22 2024-08-08 Guardant Health, Inc. Methods and systems for analyzing nucleic acid molecules
MX2019008227A (es) 2017-01-10 2020-08-17 Juno Therapeutics Inc Analisis epigenetico de terapia celular y metodos relacionados.
ES2990117T3 (es) 2017-01-25 2024-11-28 Univ Hong Kong Chinese Aplicaciones de diagnóstico que utilizan fragmentos de ácido nucleico
EP3635138B1 (en) 2017-05-15 2024-07-03 Katholieke Universiteit Leuven Method for analysing cell-free nucleic acids
EP3635134A4 (en) * 2017-06-09 2021-03-03 Bellwether Bio, Inc. DIAGNOSTIC CANCER OR OTHER PHYSIOLOGICAL CONDITIONS USING CIRCULATING NUCLEIC ACID FRAGMENT SENTINEL END POINTS
EP3635133A4 (en) * 2017-06-09 2021-03-03 Bellwether Bio, Inc. DETERMINATION OF THE TYPE OF CANCER IN A SUBJECT BY PROBABILISTIC MODELING OF END POINTS OF CIRCULATING NUCLEIC ACID FRAGMENT
US10636512B2 (en) 2017-07-14 2020-04-28 Cofactor Genomics, Inc. Immuno-oncology applications using next generation sequencing
ES2959360T3 (es) 2017-07-26 2024-02-23 Univ Hong Kong Chinese Mejora del cribado del cáncer mediante ácidos nucleicos víricos acelulares
US11810672B2 (en) * 2017-10-12 2023-11-07 Nantomics, Llc Cancer score for assessment and response prediction from biological fluids
CN107545153B (zh) * 2017-10-25 2021-06-11 桂林电子科技大学 一种基于卷积神经网络的核小体分类预测方法
WO2019024341A1 (zh) * 2017-11-27 2019-02-07 深圳华大生命科学研究院 一种体液游离dna的文库构建方法及其应用
CN108061794B (zh) * 2017-12-25 2020-03-27 苏州大学 一种无染色、无探针、无损检测细胞或类细胞结构微生物的类型及其周期的方法
JP7296969B2 (ja) 2018-01-12 2023-06-23 クラレット バイオサイエンス, エルエルシー 核酸を解析するための方法および組成物
US11781183B2 (en) * 2018-03-13 2023-10-10 Yissum Research Development Company Of The Hebrew University Of Jerusalem Ltd. Diagnostic use of cell free DNA chromatin immunoprecipitation
EP3775198A4 (en) 2018-04-02 2022-01-05 Grail, Inc. METHYLATION MARKERS AND TARGETED METHYLATION PROBE PANELS
WO2019209884A1 (en) * 2018-04-23 2019-10-31 Grail, Inc. Methods and systems for screening for conditions
EP3794348A4 (en) 2018-05-18 2022-03-09 The Johns Hopkins University ACELLULAR DNA FOR ASSESSING AND/OR TREATING CANCER
JP2021526791A (ja) * 2018-06-04 2021-10-11 ガーダント ヘルス, インコーポレイテッド セルフリー核酸の細胞起源を決定するための方法およびシステム
WO2019236726A1 (en) 2018-06-06 2019-12-12 The Regents Of The University Of California Methods of producing nucleic acid libraries and compositions and kits for practicing same
CN108796056A (zh) * 2018-06-28 2018-11-13 元码基因科技(北京)股份有限公司 基于游离dna的目标基因捕获技术进行组织溯源的方法
WO2020006369A1 (en) * 2018-06-29 2020-01-02 Guardant Health, Inc. Methods and systems for analysis of ctcf binding regions in cell-free dna
CN108913682A (zh) * 2018-07-05 2018-11-30 上海奥测医疗科技有限公司 一种制备cfDNA参考品的方法
CA3107359A1 (en) * 2018-07-23 2020-01-30 The Chinese University Of Hong Kong Cell-free dna damage analysis and its clinical applications
CN109448783B (zh) * 2018-08-07 2022-05-13 清华大学 一种染色质拓扑结构域边界的分析方法
CN113286881A (zh) 2018-09-27 2021-08-20 格里尔公司 甲基化标记和标靶甲基化探针板
CA3107948A1 (en) * 2018-10-08 2020-04-16 Freenome Holdings, Inc. Transcription factor profiling
CN111172263A (zh) * 2018-11-12 2020-05-19 北京医院 一种应用于无创产前检测的参考物质及其制备方法
BR112021009706A2 (pt) * 2018-11-21 2021-08-17 Karius, Inc. detecção e predição de doença infecciosa
US20200199685A1 (en) 2018-12-17 2020-06-25 Guardant Health, Inc. Determination of a physiological condition with nucleic acid fragment endpoints
AU2019410635A1 (en) * 2018-12-19 2021-06-17 Grail, Inc. Cell-free DNA end characteristics
US11657897B2 (en) * 2018-12-31 2023-05-23 Nvidia Corporation Denoising ATAC-seq data with deep learning
WO2020154402A1 (en) * 2019-01-24 2020-07-30 Illumina, Inc. Methods and systems for monitoring organ health and disease
AU2020216438A1 (en) 2019-01-31 2021-07-29 Guardant Health, Inc. Compositions and methods for isolating cell-free DNA
CN109841265B (zh) * 2019-02-22 2021-09-21 清华大学 使用片段化模式确定血浆游离核酸分子组织来源的方法和系统及应用
WO2020198942A1 (zh) * 2019-03-29 2020-10-08 中国科学技术大学 基于峰聚类的单细胞染色质可及性测序数据分析方法和系统
EP3976822A1 (en) 2019-05-31 2022-04-06 Guardant Health, Inc. Methods and systems for improving patient monitoring after surgery
CN110272985B (zh) * 2019-06-26 2021-08-17 广州市雄基生物信息技术有限公司 基于外周血血浆游离dna高通量测序技术的肿瘤筛查试剂盒及其系统与方法
WO2021067484A1 (en) 2019-09-30 2021-04-08 Guardant Health, Inc. Compositions and methods for analyzing cell-free dna in methylation partitioning assays
CN110739027B (zh) * 2019-10-23 2023-04-18 深圳吉因加医学检验实验室 一种基于染色质区域覆盖深度的癌症组织定位方法及系统
WO2021108708A1 (en) 2019-11-26 2021-06-03 Guardant Health, Inc. Methods, compositions and systems for improving the binding of methylated polynucleotides
CN115298324A (zh) * 2019-12-18 2022-11-04 香港中文大学 游离dna断裂和核酸酶
WO2021126091A1 (en) * 2019-12-19 2021-06-24 Agency For Science, Technology And Research A method of estimating a circulating tumor dna burden and related kits and methods
CN115151657A (zh) * 2019-12-20 2022-10-04 安可济控股有限公司 用于疾病检测的方法和系统
EP4081655A1 (en) 2019-12-24 2022-11-02 Vib Vzw Disease detection in liquid biopsies
CN115087745A (zh) * 2020-01-08 2022-09-20 香港中文大学 无细胞样品中的双末端dna片段类型及其用途
US20230053409A1 (en) * 2020-01-09 2023-02-23 Seoul National University R&Db Foundation Atac-seq data normalization and method for utilizing same
CN111254194B (zh) * 2020-01-13 2021-09-07 东南大学 基于cfDNA的测序及数据分析的癌症相关生物标记及其在cfDNA样品分类中的应用
CN115428088A (zh) * 2020-02-13 2022-12-02 10X基因组学有限公司 用于基因表达和dna染色质可及性的联合交互式可视化的系统和方法
US11211147B2 (en) 2020-02-18 2021-12-28 Tempus Labs, Inc. Estimation of circulating tumor fraction using off-target reads of targeted-panel sequencing
US11211144B2 (en) 2020-02-18 2021-12-28 Tempus Labs, Inc. Methods and systems for refining copy number variation in a liquid biopsy assay
US11475981B2 (en) 2020-02-18 2022-10-18 Tempus Labs, Inc. Methods and systems for dynamic variant thresholding in a liquid biopsy assay
CN113362897A (zh) * 2020-03-06 2021-09-07 福建和瑞基因科技有限公司 基于核小体分布特征的肿瘤标志物筛选方法及应用
WO2021222828A1 (en) 2020-04-30 2021-11-04 Guardant Health, Inc. Methods for sequence determination using partitioned nucleic acids
IL298458A (en) * 2020-05-22 2023-01-01 Aqtual Inc Methods for characterizing cell-free nucleic acid fragments
CN111724860B (zh) * 2020-06-18 2021-03-16 深圳吉因加医学检验实验室 一种基于测序数据识别染色质开放区域的方法及装置
EP4407042A3 (en) 2020-07-10 2024-09-18 Guardant Health, Inc. Methods of detecting genomic rearrangements using cell free nucleic acids
WO2023282916A1 (en) 2021-07-09 2023-01-12 Guardant Health, Inc. Methods of detecting genomic rearrangements using cell free nucleic acids
CN111881418B (zh) * 2020-07-27 2023-05-16 中国农业科学院农业信息研究所 一种基于二分法的大豆气象产量预测方法及系统
ES3018032T3 (en) 2020-07-30 2025-05-14 Guardant Health Inc Methods for isolating cell-free dna
CN112085067B (zh) * 2020-08-17 2022-07-12 浙江大学 一种高通量筛选dna损伤反应抑制剂的方法
JP2023540221A (ja) 2020-08-25 2023-09-22 ガーダント ヘルス, インコーポレイテッド バリアントの起源を予測するための方法およびシステム
WO2022061080A1 (en) * 2020-09-17 2022-03-24 The Regents Of The University Of Colorado, A Body Corporate Signatures in cell-free dna to detect disease, track treatment response, and inform treatment decisions
WO2022073011A1 (en) 2020-09-30 2022-04-07 Guardant Health, Inc. Methods and systems to improve the signal to noise ratio of dna methylation partitioning assays
JP2023547620A (ja) 2020-10-23 2023-11-13 ガーダント ヘルス, インコーポレイテッド 分配および塩基変換を使用してdnaを解析するための組成物および方法
EP4251765A1 (en) 2020-11-30 2023-10-04 Guardant Health, Inc. Compositions and methods for enriching methylated polynucleotides
EP4267757A1 (en) 2020-12-23 2023-11-01 Guardant Health, Inc. Methods and systems for analyzing methylated polynucleotides
TW202242145A (zh) * 2020-12-29 2022-11-01 比利時商比利時意志有限公司 核小體耗盡循環無細胞染色質片段之轉錄因子結合位點分析
CN115667543A (zh) * 2021-02-09 2023-01-31 因美纳有限公司 用于监测器官健康和疾病的方法和系统
WO2022174109A1 (en) 2021-02-12 2022-08-18 Guardant Health, Inc. Methods and compositions for detecting nucleic acid variants
WO2022204730A1 (en) 2021-03-25 2022-09-29 Guardant Health, Inc. Methods and compositions for quantifying immune cell dna
EP4320277A4 (en) * 2021-04-08 2025-03-05 Delfi Diagnostics, Inc. CANCER DETECTION METHOD USING GENOME-WIDE CELL-FREE DNA FRAGMENTATION PROFILES
EP4320618A4 (en) * 2021-04-08 2025-08-27 Fred Hutchinson Cancer Center METHOD FOR ANALYZING CELL-FREE DNA SEQUENCE DATA TO EXAMINE NUCLEOSOME PROTECTION AND CHROMATIN ACCESSIBILITY
WO2022271730A1 (en) 2021-06-21 2022-12-29 Guardant Health, Inc. Methods and compositions for copy-number informed tissue-of-origin analysis
WO2023056065A1 (en) 2021-09-30 2023-04-06 Guardant Health, Inc. Compositions and methods for synthesis and use of probes targeting nucleic acid rearrangements
CA3246524A1 (en) 2022-04-07 2023-10-12 Guardant Health, Inc. TUMOR PRESENCE DETECTION BASED ON THE METHYLATION STATE OF ACELLULAR NUCLEIC ACID MOLECULES
GB202205710D0 (en) 2022-04-19 2022-06-01 Univ Of Essex Enterprises Limited Cell-free DNA-based methods
JP2025522763A (ja) 2022-06-30 2025-07-17 ガーダント ヘルス, インコーポレイテッド 異常にメチル化されたdnaの富化
WO2024056720A1 (en) 2022-09-13 2024-03-21 Medizinische Universität Graz Determining of health status and treatment monitoring with cell-free dna
EP4594522A2 (en) 2022-09-27 2025-08-06 Guardant Health, Inc. Methods for quantifying immune cell dna
EP4638782A2 (en) 2022-12-22 2025-10-29 Guardant Health, Inc. Integrated targeted and whole genome somatic and dna methylation sequencing workflows
EP4638781A2 (en) 2022-12-22 2025-10-29 Guardant Health, Inc. Methods involving methylation preserving amplification with error correction
WO2024233502A1 (en) 2023-05-05 2024-11-14 Guardant Health, Inc. Cell-free dna blood-based test for cancer screening
WO2025029475A1 (en) 2023-07-28 2025-02-06 Guardant Health, Inc. Methods to enrich nucleotide variants by negative selection
WO2025038399A1 (en) 2023-08-11 2025-02-20 Guardant Health, Inc. Methylated enrichment methods for single-molecule genetic and epigenetic sequencing
CN117230165A (zh) * 2023-09-01 2023-12-15 深圳湾实验室 一种无创产前检测胎儿染色体拷贝数异常的优化方法
WO2025064706A1 (en) 2023-09-19 2025-03-27 Guardant Health, Inc. Detecting the presence of a tumor based on methylation status of cell-free nucleic acid molecules
WO2025076452A1 (en) 2023-10-06 2025-04-10 Guardant Health, Inc. Detecting tumor-related information based on methylation status of cell-free nucleic acid molecules
WO2025137389A2 (en) 2023-12-22 2025-06-26 Guardant Health, Inc. Methods for targeted single-molecule genetic and epigenetic sequencing
WO2025207817A1 (en) 2024-03-26 2025-10-02 Guardant Health, Inc. Method of determining the likelihood of a disease by combining biomarkers and imaging
WO2025208044A1 (en) 2024-03-28 2025-10-02 Guardant Health, Inc. Methods for cancer detection using molecular patterns
WO2025235889A1 (en) 2024-05-10 2025-11-13 Guardant Health, Inc. Methods involving multiplexed pooled pcr
WO2025250544A1 (en) 2024-05-31 2025-12-04 Guardant Health, Inc. Methods for analyzing chromatin architecture in tissue to boost detection of cancer associated signals in cell-free dna

Family Cites Families (56)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
GB0016742D0 (en) * 2000-07-10 2000-08-30 Simeg Limited Diagnostic method
JP2002272497A (ja) 2001-03-15 2002-09-24 Venture Link Co Ltd 癌の診断方法、およびその診断用ベクター
US6927028B2 (en) 2001-08-31 2005-08-09 Chinese University Of Hong Kong Non-invasive methods for detecting non-host DNA in a host using epigenetic differences between the host and non-host DNA
AU2004217872B2 (en) 2003-03-05 2010-03-25 Genetic Technologies Limited Identification of fetal DNA and fetal cell markers in maternal plasma or serum
ATE435301T1 (de) 2003-10-16 2009-07-15 Sequenom Inc Nicht invasiver nachweis fötaler genetischer merkmale
US20070122823A1 (en) 2005-09-01 2007-05-31 Bianchi Diana W Amniotic fluid cell-free fetal DNA fragment size pattern for prenatal diagnosis
EP2423334A3 (en) 2006-02-02 2012-04-18 The Board of Trustees of The Leland Stanford Junior University Non-invasive fetal genetic screening by digital analysis
AU2007220991C1 (en) 2006-02-28 2013-08-15 University Of Louisville Research Foundation Detecting fetal chromosomal abnormalities using tandem single nucleotide polymorphisms
TWI335354B (en) 2006-09-27 2011-01-01 Univ Hong Kong Chinese Methods for the detection of the degree of the methylation of a target dna and kits
US7842482B2 (en) 2007-02-26 2010-11-30 The Chinese University Of Hong Kong Methods and kits for diagnosis, prognosis or monitoring of Epstein-Barr virus (EBV)-associated cancer
US12180549B2 (en) 2007-07-23 2024-12-31 The Chinese University Of Hong Kong Diagnosing fetal chromosomal aneuploidy using genomic sequencing
CN106886688B (zh) 2007-07-23 2020-07-10 香港中文大学 用于分析癌症相关的遗传变异的系统
US9218449B2 (en) 2007-07-23 2015-12-22 The Chinese University Of Hong Kong Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis
US20090053719A1 (en) 2007-08-03 2009-02-26 The Chinese University Of Hong Kong Analysis of nucleic acids by digital pcr
US8748100B2 (en) 2007-08-30 2014-06-10 The Chinese University Of Hong Kong Methods and kits for selectively amplifying, detecting or quantifying target DNA with specific end sequences
WO2009051842A2 (en) 2007-10-18 2009-04-23 The Johns Hopkins University Detection of cancer by measuring genomic copy number and strand length in cell-free dna
US20100041048A1 (en) 2008-07-31 2010-02-18 The Johns Hopkins University Circulating Mutant DNA to Assess Tumor Dynamics
US8476013B2 (en) * 2008-09-16 2013-07-02 Sequenom, Inc. Processes and compositions for methylation-based acid enrichment of fetal nucleic acid from a maternal sample useful for non-invasive prenatal diagnoses
ES2620012T3 (es) 2008-09-20 2017-06-27 The Board Of Trustees Of The Leland Stanford Junior University Diagnóstico no invasivo de la aneuploidia fetal por secuenciación
WO2010053980A2 (en) 2008-11-04 2010-05-14 The Johns Hopkins University Dna integrity assay (dia) for cancer diagnostics, using confocal fluorescence spectroscopy
WO2010112316A1 (en) 2009-03-31 2010-10-07 Oridis Biomed Forschungs- Und Entwicklungs Gmbh Method for diagnosis of cancer and monitoring of cancer treatments
WO2011053790A2 (en) 2009-10-30 2011-05-05 Fluidigm Corporation Assay of closely linked targets in fetal diagnosis and coincidence detection assay for genetic analysis
WO2011057094A1 (en) 2009-11-05 2011-05-12 The Chinese University Of Hong Kong Fetal genomic analysis from a maternal biological sample
AU2010317019B2 (en) 2009-11-06 2014-10-30 The Chinese University Of Hong Kong Size-based genomic analysis
WO2011090556A1 (en) 2010-01-19 2011-07-28 Verinata Health, Inc. Methods for determining fraction of fetal nucleic acid in maternal samples
US9260745B2 (en) 2010-01-19 2016-02-16 Verinata Health, Inc. Detecting and classifying copy number variation
US20130210645A1 (en) * 2010-02-18 2013-08-15 The Johns Hopkins University Personalized tumor biomarkers
CN103370456A (zh) * 2010-08-24 2013-10-23 比奥Dx股份有限公司 限定母体循环血液中保守的游离浮动胎儿dna的诊断性和治疗性靶物
EP2426217A1 (en) 2010-09-03 2012-03-07 Centre National de la Recherche Scientifique (CNRS) Analytical methods for cell free nucleic acids and applications
EP4269623A3 (en) 2010-11-30 2024-03-06 The Chinese University Of Hong Kong Analysis of a biological sample of an organism for chromosomal deletions or amplifications associated with cancer
WO2013043922A1 (en) 2011-09-22 2013-03-28 ImmuMetrix, LLC Compositions and methods for analyzing heterogeneous samples
US10196681B2 (en) 2011-10-06 2019-02-05 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
WO2013060762A1 (en) 2011-10-25 2013-05-02 Roche Diagnostics Gmbh Method for diagnosing a disease based on plasma-dna distribution
US9757458B2 (en) 2011-12-05 2017-09-12 Immunomedics, Inc. Crosslinking of CD22 by epratuzumab triggers BCR signaling and caspase-dependent apoptosis in hematopoietic cancer cells
EP2807277A4 (en) 2012-01-27 2016-02-17 Univ Leland Stanford Junior PROCESS FOR PROFILING AND QUANTIFYING cell-free RNA
EP3401399B1 (en) * 2012-03-02 2020-04-22 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US9892230B2 (en) 2012-03-08 2018-02-13 The Chinese University Of Hong Kong Size-based analysis of fetal or tumor DNA fraction in plasma
WO2013177086A1 (en) * 2012-05-21 2013-11-28 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
WO2013177581A2 (en) * 2012-05-24 2013-11-28 University Of Washington Through Its Center For Commercialization Whole genome sequencing of a human fetus
US11261494B2 (en) * 2012-06-21 2022-03-01 The Chinese University Of Hong Kong Method of measuring a fractional concentration of tumor DNA
ES2769241T5 (es) 2012-09-04 2023-05-30 Guardant Health Inc Sistemas y métodos para detectar variación en el número de copias
US20160004814A1 (en) * 2012-09-05 2016-01-07 University Of Washington Through Its Center For Commercialization Methods and compositions related to regulation of nucleic acids
US9732390B2 (en) 2012-09-20 2017-08-15 The Chinese University Of Hong Kong Non-invasive determination of methylome of fetus or tumor from plasma
WO2014043763A1 (en) 2012-09-20 2014-03-27 The Chinese University Of Hong Kong Non-invasive determination of methylome of fetus or tumor from plasma
WO2014190286A2 (en) * 2013-05-24 2014-11-27 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US20160115541A1 (en) * 2013-05-29 2016-04-28 Chronix Biomedical Detection and quantification of donor cell-free dna in the circulation of organ transplant recipients
US10262755B2 (en) 2014-04-21 2019-04-16 Natera, Inc. Detecting cancer mutations and aneuploidy in chromosomal segments
AU2015249846B2 (en) * 2014-04-21 2021-07-22 Natera, Inc. Detecting mutations and ploidy in chromosomal segments
US10318704B2 (en) * 2014-05-30 2019-06-11 Verinata Health, Inc. Detecting fetal sub-chromosomal aneuploidies
TWI727156B (zh) 2014-07-18 2021-05-11 香港中文大學 Dna混合物中之組織甲基化模式分析
WO2016015058A2 (en) 2014-07-25 2016-01-28 University Of Washington Methods of determining tissues and/or cell types giving rise to cell-free dna, and methods of identifying a disease or disorder using same
US11242559B2 (en) 2015-01-13 2022-02-08 The Chinese University Of Hong Kong Method of nuclear DNA and mitochondrial DNA analysis
US10364467B2 (en) 2015-01-13 2019-07-30 The Chinese University Of Hong Kong Using size and number aberrations in plasma DNA for detecting cancer
US10319463B2 (en) 2015-01-23 2019-06-11 The Chinese University Of Hong Kong Combined size- and count-based analysis of maternal plasma for detection of fetal subchromosomal aberrations
SG11201706529TA (en) 2015-02-10 2017-09-28 Univ Hong Kong Chinese Detecting mutations for cancer screening and fetal analysis
DK3325664T3 (da) 2015-07-23 2022-03-07 Univ Hong Kong Chinese Analyse af fragmenteringsmønstre for cellefrit DNA

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