公开(公告)号：WO2018144449A1

公开(公告)日：2018-08-09

申请号：PCT/US2018/015934

申请日：2018-01-30

申请人： COUNSYL, INC.

发明人： MAGUIRE, Jared R. ,  ROBERTSON, Alexander D. ,  EVANS, Eric A.

IPC分类号： C12N15/09 ,  C12Q1/68 ,  G01N33/68 ,  G06F19/18 ,  G06F19/22

CPC分类号： C12Q1/6858 ,  C12Q1/6869 ,  G16B20/10 ,  C12Q2537/16

摘要： A method of identifying and quantifying copy number variations in a gene of interest for a genomic DNA sample includes (i) fragmenting a genomic DNA sample to produce a plurality of polynucleotide fragments, (ii) isolating a plurality of target polynucleotide fragments, (iii) sequencing the plurality of target polynucleotide fragments, (iv) aligning fragment sequences to a reference sequence, (v) calculating read depths for base positions of the plurality of target polynucleotide fragments, (vi) calculating copy number likelihoods for each base position of the reference sequence, (vii) performing a breakpoint analysis on a set of fragment sequences to identify at least one sequence variation located between selected breakpoint regions of the target gene and calculate modified copy number likelihoods for base positions of the reference sequence based on the at least one sequence variation, and (viii) determining whether the target gene includes at least one copy number variation.

公开(公告)号：WO2017120324A1

公开(公告)日：2017-07-13

申请号：PCT/US2017/012317

申请日：2017-01-05

申请人： EPIC SCIENCES, INC.

发明人： DITTAMORE, Ryan ,  MARRINUCCI, Dena

IPC分类号： C12Q1/68 ,  G01N21/00 ,  G01N33/574

CPC分类号： G01N33/57434 ,  C12Q1/6886 ,  C12Q2537/16 ,  C12Q2600/156 ,  G01N15/00 ,  G01N15/1475 ,  G01N21/00 ,  G01N33/5005 ,  G01N2015/1006

摘要： The disclosure provides a method of detecting heterogeneity of disease in a cancer patient comprising (a) performing a direct analysis comprising immunofluorescent staining and morphological characteristization of nucleated cells in a blood sample obtained from the patient to identify and enumerate circulating tumor cells (CTC); (b) isolating the CTCs from the sample; (c) individually characterizing genomic parameters to generate a genomic profile for each of the CTCs, and (d) determining heterogeneity of disease in the cancer patient based on the profile. In some embodiments, the cancer is prostate cancer. In some embodiments, the prostate cancer is hormone refractory.

摘要翻译： 本公开提供了检测癌症患者疾病异质性的方法，其包括（a）进行直接分析，所述直接分析包括从患者获得的血液样品中的有核细胞的免疫荧光染色和形态学表征，以鉴定和 列举循环肿瘤细胞（CTC）; （b）从样品中分离CTC; （c）分别表征基因组参数以产生每种CTC的基因组图谱，以及（d）基于该图谱确定癌症患者中疾病的异质性。 在一些实施方案中，癌症是前列腺癌。 在一些实施方案中，前列腺癌是激素难治性的。

公开(公告)号：WO2017087510A1

公开(公告)日：2017-05-26

申请号：PCT/US2016/062260

申请日：2016-11-16

申请人： MAYO FOUNDATION FOR MEDICAL EDUCATION AND RESEARCH

发明人： BLACK, John L.

IPC分类号： C12Q1/68 ,  G06F19/00 ,  G06F19/22

CPC分类号： G06F19/22 ,  C12Q1/68 ,  C12Q2535/122 ,  C12Q2537/16 ,  C12Q2537/165

摘要： This document provides methods and materials for detecting copy number variations. For example, methods and materials for using combinations of sequencing read depth ratios calculated from next generation sequencing data to determine copy number variations for genes of interest are provided.

摘要翻译：

该文件提供了检测拷贝数变化的方法和材料。 例如，提供了使用从下一代测序数据计算的测序读取深度比的组合来确定感兴趣基因的拷贝数变化的方法和材料。

公开(公告)号：WO2016189388A1

公开(公告)日：2016-12-01

申请号：PCT/IB2016/000833

申请日：2016-05-20

申请人： NIPD GENETICS LTD

发明人： KOUMBARIS, George ,  KYPRI, Elena ,  TSANGARAS, Kyriakos ,  ACHILLEOS, Achilleas ,  MINA, Petros ,  PAPAGEORGIOU, Elisavet, A. ,  PATSALIS, Philippos, C.

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6883 ,  C12Q1/6827 ,  C12Q2600/156 ,  G06F19/22 ,  C12Q2535/122 ,  C12Q2537/143 ,  C12Q2537/16

摘要： The invention provides methods for non-invasive prenatal testing that allow for detecting risk of chromosomal and subchromosomal abnormalities, including but not limited to aneuploidies, microdeletions and microduplications, insertions, translocations, inversions and small-size mutations including point mutations and mutational signatures. The methods of the invention utilize a pool of TArget Capture Sequences (TACS) to enrich for sequences of interest in a mixed sample containing both maternal and fetal DNA, followed by massive parallel sequencing and statistical analysis of the enriched population to thereby detect the risk of a genetic abnormality in the fetal DNA. Kits for carrying out the methods of the invention are also provided.

摘要翻译： 本发明提供了用于检测染色体和亚染色体异常的风险的非侵入性产前检测方法，包括但不限于非整倍体，微缺失和微复制，插入，易位，反转和小尺寸突变，包括点突变和突变特征。 本发明的方法利用一组TArget Capture Sequences（TACS）来丰富含有母体和胎儿DNA的混合样品中感兴趣的序列，然后大量平行测序和富集群体的统计分析，从而检测 胎儿DNA遗传异常。 还提供了用于实施本发明方法的试剂盒。

公开(公告)号：WO2015200869A1

公开(公告)日：2015-12-30

申请号：PCT/US2015/038141

申请日：2015-06-26

申请人： 10X GENOMICS, INC.

发明人： SCHNALL-LEVIN, Michael ,  JAROSZ, Mirna ,  HINDSON, Christopher ,  NESS, Kevin ,  SAXONOV, Serge ,  HINDSON, Benjamin ,  ZHENG, Grace, X.Y. ,  MARKS, Patrick ,  STUELPNAGEL, John

IPC分类号： C12Q1/68 ,  C12N15/10 ,  C40B40/06

CPC分类号： C12Q1/6883 ,  C12Q1/6827 ,  C12Q2600/156 ,  G06F19/22 ,  C12Q2535/122 ,  C12Q2537/16 ,  C12Q2563/159 ,  C12Q2565/629

摘要： The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples.

摘要翻译： 本公开涉及用于单倍型定相和拷贝数变异测定的方法，组合物和系统。 本公开内容包括用于将包含珠粒的条形码与多个单独分区中的样本组合的方法和系统，以及处理，排序和分析条形码样本的方法。

公开(公告)号：WO2015168252A1

公开(公告)日：2015-11-05

申请号：PCT/US2015/028233

申请日：2015-04-29

申请人： THE JOHNS HOPKINS UNIVERSITY

发明人： ARKING, Dan ,  ASHAR, Foram ,  MOES, Anna

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6851 ,  C12Q2537/16

摘要： The present invention provides methods and compositions related to the use of mitochondrial DNA copy number as a predictor of frailty, cardiovascular disease, diabetes and all-cause mortality. In one embodiment, a method for predicting cardiovascular disease in a subject comprises the steps of (a) obtaining a biological sample from the subject; (b) performing an assay to measure the mitochondrial DNA (mtDNA) copy number in the biological sample; and (c) identifying the subject as likely to develop cardiovascular disease by comparison of the mitochondrial DNA copy number to a control.

摘要翻译： 本发明提供了与使用线粒体DNA拷贝数作为虚弱，心血管疾病，糖尿病和全因死亡率的预测因子相关的方法和组合物。 在一个实施方案中，用于预测受试者心血管疾病的方法包括以下步骤：（a）从受试者获得生物样品; （b）进行测定以测量生物样品中的线粒体DNA（mtDNA）拷贝数; 和（c）通过将线粒体DNA拷贝数与对照相比，鉴定可能发展心血管疾病的受试者。

公开(公告)号：WO2015143385A1

公开(公告)日：2015-09-24

申请号：PCT/US2015/021853

申请日：2015-03-20

申请人： LIFE TECHNOLOGIES CORPORATION

发明人： MERRILL, David ,  BRZOSKA, Pius ,  LI, Zheng ,  LIN, Wendy ,  LEE, Wing ,  WONG, Mandi

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6886 ,  C12Q1/6851 ,  C12Q1/6858 ,  C12Q2600/156 ,  C12Q2600/158 ,  C12Q2600/166 ,  C12Q2537/16 ,  C12Q2543/10 ,  C12Q2545/101 ,  C12Q2547/107 ,  C12Q2561/101

摘要： A method, comprising amplifying a nucleic acid sequence of interest in a sample comprising genomic DNA of a subject; amplifying a reference nucleic acid sequence in the sample; quantifying the amplified sequence of interest relative to the amplified reference sequence; and determining a copy number of the sequence of interest from the relative quantified amplified sequence of interest. The reference sequence may have at least 80% sequence identity to at least one of SEQ ID NO:1-38, such as SEQ ID NO:1-13. Also disclosed are kits and compositions, each comprising a first probe which specifically hybridizes to at least a portion of at least one reference sequence. Also disclosed is a system configured to perform the above method.

摘要翻译： 一种方法，包括在包含受试者的基因组DNA的样品中扩增目的核酸序列; 扩增样品中的参考核酸序列; 相对于扩增的参考序列量化扩增的感兴趣的序列; 以及从所述相关量化的放大感兴趣序列确定感兴趣序列的拷贝数。 参考序列可以与SEQ ID NO：1-38中的至少一个具有至少80％的序列同一性，例如SEQ ID NO：1-13。 还公开了试剂盒和组合物，每种试剂盒和组合物包含与至少一个参考序列的至少一部分特异性杂交的第一探针。 还公开了配置为执行上述方法的系统。

公开(公告)号：WO2015051888A1

公开(公告)日：2015-04-16

申请号：PCT/EP2014/002657

申请日：2014-09-30

申请人： UNIVERSITÄT HEIDELBERG

发明人： NEUMAIER, Michael ,  AHMAD NEJAD, Parviz

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6886 ,  C12Q1/6851 ,  C12Q2600/16 ,  C12Q2537/16 ,  C12Q2537/165 ,  C12Q2545/113 ,  C12Q2565/301

摘要： The present invention relates to a method for the quantitative analysis of complex nucleic acids (NA), i.e. their fragmentation/degradation and amplificability as a marker of biomolecular quality and integrity of a biosample. Said method comprises the steps of subjecting said NA to a multiplex polymerase chain reaction using primers to generate different-size amplicons (referred to as indicator PCR). For simplicity, a duplex PCR using one primer pair for the generation of a longer PCR product and a second primer pair for the generation of a shorter PCR product is being described as the most simple variant of this test. Following the duplex PCR amplification, the ratio between the yield of the longer PCR product and the yield of the shorter PCR product generated during duplex PCR is determined using a read-out that allows relative quantification between the two (e.g. Pyrosequencing). The ratio is proportional to the nucleic acids quality, because the larger fragment tends to be under-represented with increased fragmentation impeding with its amplificability. The invention further relates to the generation and use of reference high-molecular weight DNA samples subjected to degradation under controlled conditions (e.g. by inflicting heat for specified periods of time) to generate a degradation calibration curve. The fragmentation of a query NA sample previously prepared from a liquid or solid biosource can then be quantified by use of the duplex indicator PCR after direct comparison to the calibrator DNA fragmentation curve. The present invention further relates to a comprehensive kit containing all specific components required to apply said method.

摘要翻译： 本发明涉及用于定量分析复合核酸（NA）的方法，即其作为生物样品的生物分子质量和完整性的标记物的分裂/降解和可扩增性。 所述方法包括以下步骤：使用引物对所述NA进行多重聚合酶链反应以产生不同大小的扩增子（称为指示性PCR）。 为了简单起见，使用一个引物对用于产生较长PCR产物的双链PCR和用于产生较短PCR产物的第二引物对被描述为该测试的最简单的变体。 在双链PCR扩增之后，使用允许两者之间的相对定量（例如焦磷酸测序）的读数确定较长PCR产物的产量与双相PCR期间产生的较短PCR产物的产量之间的比率。 该比例与核酸质量成比例，因为较大的片段倾向于低度代表，随着其可扩增性阻碍增加的片段化。 本发明还涉及在受控条件下（例如通过施加热量达指定时间段）进行降解的参考高分子量DNA样品的产生和使用，以产生降解校准曲线。 然后可以通过在与校准物DNA断裂曲线直接比较之后使用双链体指示剂PCR来量化从液体或固体生物源预先制备的查询NA样品的片段化。 本发明还涉及包含应用所述方法所需的所有特定部件的综合试剂盒。

公开(公告)号：WO2015048535A1

公开(公告)日：2015-04-02

申请号：PCT/US2014/057843

申请日：2014-09-26

申请人： NATERA, INC.

发明人： BABIARZ, Joshua ,  ZIMMERMAN, Bernhard

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6886 ,  C12N15/10 ,  C12Q1/6806 ,  C12Q1/6883 ,  C12Q2521/301 ,  C12Q2537/16 ,  C12Q2545/113 ,  C12Q2600/16 ,  C12Q2600/166 ,  Y10T436/10

摘要： Embodiments of the invention include methods and compositions for producing proficiency testing standards for noninvasive prenatal genetic diagnostics and for the detection and monitoring of cancer. The compositions can comprise a plurality of different nucleosomal DNA fragments derived from either primary cells or cell lines. The amount of the different nucleosomal DNA fragments can be varied so as to simulate naturally occurring cell free DNA samples obtained from the blood of the pregnant woman or naturally occurring cell free DNA samples obtained from the blood of cancer patients.

摘要翻译： 本发明的实施方案包括用于生产无创产前遗传诊断能力检测标准和用于检测和监测癌症的方法和组合物。 组合物可以包含衍生自原代细胞或细胞系的多种不同的核小体DNA片段。 可以改变不同核小体DNA片段的量，以模拟从孕妇的血液中获得的天然存在的无细胞DNA样品或从癌症患者的血液获得的天然存在的无细胞DNA样品。

公开(公告)号：WO2014204991A1

公开(公告)日：2014-12-24

申请号：PCT/US2014/042785

申请日：2014-06-17

申请人： VERINATA HEALTH, INC.

发明人： ABDUEVA, Diana

IPC分类号： C12Q1/68 ,  G06F19/24

CPC分类号： G06F19/22 ,  C12Q1/6827 ,  G06F19/18 ,  C12Q2537/16 ,  C12Q2537/165

摘要： The invention provides methods for determining copy number of the Y chromosome, including, but not limited to, methods for gender determination or Y chromosome aneuploidy of fetus using maternal samples comprising maternal and fetal cell free DNA. Some embodiments disclosed herein describe a strategy for filtering out (or masking) non-discriminant sequence reads on chromosome Y using representative training set of female samples. In some embodiments, this filtering strategy is also applicable to filtering autosomes for evaluation of copy number variation of sequences on the autosomes. In some embodiments, methods are provided for determining copy number variation (CNV) of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. Also disclosed are systems for evaluation of CNV of sequences of interest on the Y chromosome and other chromosomes.

摘要翻译： 本发明提供用于确定Y染色体的拷贝数的方法，包括但不限于使用包含母体和胎儿无细胞DNA的母体样品进行性别测定或胎儿Y染色体非整倍性的方法。 本文公开的一些实施例描述了使用女性样本的代表训练集来过滤（或掩蔽）染色体Y上的非判别序列读取的策略。 在一些实施方案中，该过滤策略也适用于过滤用于评估常染色体上序列的拷贝数变异的常数。 在一些实施方案中，提供了用于确定任何胎儿非整倍性的拷贝数变异（CNV）和已知或怀疑与各种医学状况相关联的CNV的方法。 还公开了用于评估Y染色体和其他染色体上感兴趣序列的CNV的系统。