公开(公告)号：WO2019108942A1

公开(公告)日：2019-06-06

申请号：PCT/US2018/063323

申请日：2018-11-30

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： KAZNADZEY, Denis

IPC: C12Q1/6869

CPC classification number: G16B30/00 ,  C12Q1/6869 ,  C12Q1/6886 ,  C12Q2600/156 ,  C12Q2600/158 ,  C12Q2535/122 ,  C12Q2537/143

Abstract: A method for detecting a tandem duplication in an FLT3 gene of a sample, includes mapping reads corresponding to targeted regions of exons of the FLT3 gene to a reference sequence. A partially mapped read includes a mapped portion, a soft-clipped portion and a breakpoint. Analyzing the partially mapped reads intersecting a column of the pileup includes detecting a duplication in the soft-clipped portion by comparing the soft-clipped portion to the mapped portion adjacent to the breakpoint; determining an insert size of the duplication in the soft-clipped portion; and assigning the partially mapped read to a category based on the insert size. Categories correspond to insert sizes. The categories are filtered and converted into features corresponding to the column. The features corresponding to one or more columns representing a same insert are merged to determine a location and size of a tandem duplication.

公开(公告)号：WO2019104034A1

公开(公告)日：2019-05-31

申请号：PCT/US2018/062005

申请日：2018-11-20

Applicant: ARIMA GENOMICS, INC.

Inventor： SELVARAJ, Siddarth ,  SCHMITT, Anthony ,  REID, Bret

IPC: C12N15/10 ,  C12Q1/6806 ,  C12Q1/6869

CPC classification number: C12N15/1065 ,  C12N15/1075 ,  C12N15/1093 ,  C12Q1/6806 ,  C12Q1/6869 ,  C12Q2535/122 ,  C12Q2563/179 ,  C12Q2563/159 ,  C12Q2565/514 ,  C12Q2523/101 ,  C12Q2563/149

Abstract: Provided herein are methods and compositions for preparing nucleic acid templates wherein spatial- proximal and molecular contiguity of target nucleic acids is preserved, and the sequencing data obtained therefrom is used, but not limited to, identification of genomic variants, determination of contiguity information to inform assemblies of target nucleic acids de novo including deconvolution of haplotype phase information, and analyses of conformation and topology of target nucleic acids.

公开(公告)号：WO2019005877A1

公开(公告)日：2019-01-03

申请号：PCT/US2018/039609

申请日：2018-06-26

Applicant: GRAIL, INC.

Inventor： SAKARYA, Onur ,  LAMPING, John

IPC: G06F19/22 ,  G06F19/24 ,  G06F19/18 ,  C12Q1/6806

CPC classification number: G16B5/00 ,  C12Q1/6806 ,  G06N20/00 ,  G16B30/00 ,  G16B30/10 ,  G16B30/20 ,  G16B40/10 ,  C12Q2535/122 ,  C12Q2537/165

Abstract: Detecting cross-contamination between test samples used for determining cancer in a subject is beneficial. To detect cross-contamination, test sequences including at least one single nucleotide polymorphism are prepared using genome sequencing techniques. Some of the test sequences can be filtered to improve accuracy and precision. A prior contamination probability for each test sequence is determined based on a minor allele frequency. A contamination model including a likelihood test is applied to a test sequence. The likelihood test obtains a current contamination probability representing the likelihood that the test sample is contaminated. The contamination model can also determine a likelihood that the sample includes loss of heterozygosity representing the likelihood that the test sequence is contaminated. Test samples that are contaminated are removed. A source for the contaminated test sample can be found by comparing contaminated test sequences to other test sequences.

公开(公告)号：WO2018183897A1

公开(公告)日：2018-10-04

申请号：PCT/US2018/025475

申请日：2018-03-30

Applicant: GRAIL, INC.

Inventor： EATTOCK, Nicholas ,  JUNG, Byoungsok ,  WILLIAMS, Justice

IPC: C12Q1/6806

CPC classification number: C12Q1/6874 ,  C12Q1/6806 ,  C12Q2533/101 ,  C12Q2535/122

Abstract: Aspects of the invention include methods for preparing an enriched sequencing library. In some embodiments, the methods involve preparing a sequencing library that is enriched for AT-rich sequences. In certain embodiments, the methods involve determining a presence or an absence of cancer, determining a cancer stage, monitoring cancer progression, and/or determining a cancer classification in a subject by analyzing an enriched sequencing library.

公开(公告)号：WO2018089978A1

公开(公告)日：2018-05-17

申请号：PCT/US2017/061469

申请日：2017-11-14

Applicant: WISCONSIN ALUMNI RESEARCH FOUNDATION

Inventor： FLORES, Francisco, Moya ,  CAMEJO, Pamela

IPC: C12N15/10 ,  C12Q1/68 ,  G01N33/50

CPC classification number: C12Q1/6851 ,  G01N33/50 ,  C12Q2531/113 ,  C12Q2535/122 ,  C12Q2545/107

Abstract: The invention generally relates to synthetic DNA constructs and methods of using such constructs for determining the absolute abundance of at least one DNA nucleic acid comprising a target gene in a sample.

Abstract translation: 本发明一般涉及合成DNA构建体和使用这种构建体来测定样品中包含靶基因的至少一种DNA核酸的绝对丰度的方法。

公开(公告)号：WO2018042251A1

公开(公告)日：2018-03-08

申请号：PCT/IB2017/001198

申请日：2017-08-29

Applicant: OSLO UNIVERSITETSSYKEHUS HF

Inventor： DAHL, John, Arne ,  KLUNGLAND, Arne

IPC: G01N33/68 ,  G01N33/53 ,  C12Q1/68

CPC classification number: G01N33/6875 ,  C12Q1/6804 ,  C12Q1/6806 ,  G01N33/5306 ,  C12Q2522/101 ,  C12Q2535/122

Abstract: In some embodiments, the present invention provides chromatin immunoprecipitation (ChIP) methods. In particular, the present invention provides methods and compositions for performing ChIP (e.g., ChlP-seq) assays on small numbers or cells.

Abstract translation: 在一些实施方案中，本发明提供染色质免疫沉淀（ChIP）方法。 具体而言，本发明提供了用于对少量或细胞进行ChIP（例如ChIP-seq）测定的方法和组合物。

公开(公告)号：WO2017214338A1

公开(公告)日：2017-12-14

申请号：PCT/US2017/036448

申请日：2017-06-07

Applicant: DRAWBRIDGE HEALTH, INC.

Inventor： JACKSON, Alicia ,  BEYERLEIN, Dagmar ,  CLARK, Sonya ,  RAVA, Richard, P.

IPC: G01N1/28 ,  G01N1/10

CPC classification number: C12Q1/6806 ,  A61B5/150022 ,  A61B5/150389 ,  A61B5/150755 ,  A61B5/15105 ,  A61J1/05 ,  G01N1/405 ,  G01N33/6863 ,  G01N2333/525 ,  C12Q2531/113 ,  C12Q2535/122

Abstract: Provided herein, are matrices and methods for the stabilization of proteins and nucleic acids. The stabilized proteins and nucleic acids described herein can be in a sample taken from a subject and can be subsequently stabilized and stored on the matrix. An analyte of interest can be concentrated and eluted for analysis from this sample. The stabilized proteins and nucleic acids described herein can be components of a sample preparation reagent, and the reagent is stored on the matrix and hydration of the matrix with a sample can result in a reaction occurring.

Abstract translation: 本文提供了用于稳定蛋白质和核酸的基质和方法。 本文所述的稳定的蛋白质和核酸可以在取自受试者的样品中，并且随后可以稳定并储存在基质上。 可以浓缩并洗脱感兴趣的分析物用于从该样品分析。 本文所述的稳定的蛋白质和核酸可以是样品制备试剂的组分，并且试剂被储存在基质上并且用样品水合基质可以导致反应发生。

公开(公告)号：WO2017161201A1

公开(公告)日：2017-09-21

申请号：PCT/US2017/022833

申请日：2017-03-16

Applicant: CYNVENIO BIOSYSTEMS INC.

Inventor： STRAUSS, William M. ,  NI, Xiaohui

IPC: C12Q1/68

CPC classification number: C12Q1/6827 ,  C12Q1/6806 ,  C12Q2600/112 ,  C12Q2535/122 ,  C12Q2537/16 ,  C12Q2543/10

Abstract: Methods for the early detection, enumeration and analysis of circulating tumor cells (CTCs) are disclosed. These methods are useful for cancer screening, development of treatment regimens, and for monitoring for treatment responses, cancer recurrence or the like. Devices that facilitate the early detection, enumeration and analysis of such circulating tumor cells are also provided.

Abstract translation: 公开了用于循环肿瘤细胞（CTC）的早期检测，计数和分析的方法。 这些方法可用于癌症筛查，治疗方案的开发以及监测治疗反应，癌症复发等。 还提供了促进此类循环肿瘤细胞的早期检测，计数和分析的设备。

公开(公告)号：WO2017156290A1

公开(公告)日：2017-09-14

申请号：PCT/US2017/021603

申请日：2017-03-09

Applicant: BAYLOR COLLEGE OF MEDICINE

Inventor： ZHANG, Jinglan ,  WONG, Lee-jun, C. ,  FENG, Yanming ,  GE, Xiaoyan

IPC: C07H21/04 ,  C12N15/09 ,  C12N15/12 ,  C12Q1/68

CPC classification number: G16H50/20 ,  C12Q1/6869 ,  C12Q1/6883 ,  C12Q2600/156 ,  G16B30/00 ,  G16B50/00 ,  C12Q2535/122 ,  C12Q2537/165

Abstract: The disclosure concerns methods and compositions for obtaining reliable copy numbers of highly homologous gene(s) using next generation sequencing. The methods determine whether or not an individual is a carrier of an autosomal recessive gene mutation using a determination of copy number of two genes, in specific embodiments. In at least some cases, an individual is identified whether or not he or she is a carrier or affected for a genetic defect in SMN1, wherein the defect is associated with spinal muscular atrophy.

Abstract translation: 本公开涉及使用下一代测序获得高度同源基因的可靠拷贝数的方法和组合物。 在具体实施方式中，所述方法使用确定两个基因的拷贝数来确定个体是否是常染色体隐性基因突变的载体。 至少在某些情况下，确定个体是否是携带者或是否患有SMN1遗传缺陷，其中该缺陷与脊髓性肌萎缩有关。

公开(公告)号：WO2017139672A1

公开(公告)日：2017-08-17

申请号：PCT/US2017/017512

申请日：2017-02-10

Applicant: HTG MOLECULAR DIAGNOSTICS, INC.

Inventor： THOMPSON, Debrah ,  ROUNSEVILLE, Matthew

IPC: C12Q1/68

CPC classification number: C12Q1/6806 ,  C12Q1/6869 ,  C12Q2521/325 ,  C12Q2521/501 ,  C12Q2521/531 ,  C12Q2525/155 ,  C12Q2525/161 ,  C12Q2525/191 ,  C12Q2525/207 ,  C12Q2533/107 ,  C12Q2535/122 ,  C12Q2537/143 ,  C12Q2537/162 ,  C12Q2563/131 ,  C12Q2563/149

Abstract: The present disclosure provides methods and kits for direct sequencing of nucleic acid targets. Such methods can be used to determine if one or more nucleic acid targets are present in a sample.

Abstract translation: 本公开提供了用于核酸靶标的直接测序的方法和试剂盒。 这样的方法可用于确定样品中是否存在一种或多种核酸靶标。