公开(公告)号：WO2016025796A1

公开(公告)日：2016-02-18

申请号：PCT/US2015/045209

申请日：2015-08-14

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： BRAMLETT, Kelli ,  LEAMON, John ,  ANDERSEN, Mark ,  THORNTON, Michael

IPC: C12Q1/68

CPC classification number: C12Q1/6846 ,  C12Q1/6855 ,  C12Q2525/117 ,  C12Q2535/10 ,  C12Q2537/143 ,  C12Q2525/191 ,  C12Q2563/185

Abstract: In some embodiments, the disclosure relates generally to methods, compositions, systems, apparatuses and kits comprising a multiplex nucleic acid amplification reaction that employs a plurality (e.g., hundreds, thousands, tens-of-thousands or hundreds-of-thousands) of different target-specific primer pairs that enable substantially simultaneous amplification of a plurality of different target sequences-of-interest in a single reaction mixture. In some embodiments, the multiplex nucleic acid amplification reaction generates a plurality of amplicons having sequences derived from a sample containing RNA or DNA, including whole transcriptome or genomic samples. In some embodiments, the sequences and abundances of at least some of the plurality of amplicons are characterized, optionally simultaneously or through a single assay, by suitable detection methods, including sequencing or other procedures known in the art.

Abstract translation: 在一些实施方案中，本公开一般涉及包含多重核酸扩增反应的方法，组合物，系统，装置和试剂盒，所述多重核酸扩增反应采用多个（例如，数百，数万，数万或数十万）不同的 靶特异性引物对，其能够在单个反应混合物中基本上同时扩增感兴趣的多个不同靶序列。 在一些实施方案中，多重核酸扩增反应产生具有衍生自含有RNA或DNA的样品的序列的多个扩增子，包括全转录组或基因组样品。 在一些实施方案中，通过合适的检测方法，包括测序或本领域已知的其它程序，可以任选地同时或通过单个测定来表征多个扩增子中的至少一些的序列和丰度。

公开(公告)号：WO2020198004A1

公开(公告)日：2020-10-01

申请号：PCT/US2020/023850

申请日：2020-03-20

Applicant: LIFE TECHNOLOGIES CORPORATION ,  VEITCH, James

Inventor： VEITCH, James ,  GOTTIMUKKALA, Rajesh ,  MARCOVITZ, Amir ,  SCHAGEMAN, Jeoffrey ,  BAGAI, Varun ,  GU, Jian ,  BRAMLETT, Kelli ,  MYRAND, Scott ,  HYLAND, Fiona ,  SADIS, Seth ,  WILLIAMS, Paul

IPC: G16B20/30 ,  G16B30/00 ,  G16B20/00

Abstract: A method for detecting a gene fusion includes amplifying a nucleic acid sample in the presence of primer pool to produce a plurality of amplicons. The primer pool includes primers targeting a plurality of exon-exon junctions of a driver gene. The amplicons correspond to the exon-exon junctions. The amplicons are sequenced and aligned to a reference sequence. The number of reads corresponding to each amplicon is normalized to give a normalized read count. A baseline correction is applied to the normalized read counts for the amplicons to form corrected read counts. A binary segmentation score is calculated for each corrected read count. A predicted breakpoint for the gene fusion is determined based on the amplicon index corresponding to the maximum absolute binary segmentation score. Gene fusion events may be detected in a partner agnostic manner, i.e. without prior knowledge of the specific fusion partner genes or specific breakpoint information.

公开(公告)号：WO2016201142A1

公开(公告)日：2016-12-15

申请号：PCT/US2016/036763

申请日：2016-06-09

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： MONGAN, Ann ,  CHIEN, Richard ,  BRINZA, Dumitru ,  BRAMLETT, Kelli

IPC: C12Q1/68

CPC classification number: C12Q1/6886 ,  C12Q1/6827 ,  C12Q1/6874 ,  C12Q2600/156 ,  C12Q2525/191 ,  C12Q2531/113 ,  C12Q2535/122 ,  C12Q2537/143 ,  C12Q2565/514

Abstract: In some embodiments, the disclosure relates generally to methods, as well as related systems, compositions, kits, apparatuses and computer-readable media, comprising a multiplex molecular tagging procedure that employs a plurality of tags that are appended to a plurality of polynucleotides. The tags have characteristics, including a sequence, length and/or detectable moiety, or any other characteristic, that uniquely identifies the polynucleotide molecule to which it is appended, and permits tracking individual tagged molecules in a mixture of tagged molecules. For example, the tag having a unique tag sequence, can uniquely identify an individual polynucleotide to which it is appended, and distinguish the individual polynucleotide from other tagged polynucleotides in a mixture. In some embodiments, the multiplex molecular tagging procedure can be used for generating error-corrected sequencing data and for detecting a target polynucleotide which is present at low abundance in a nucleic acid sample.

Abstract translation: 在一些实施方案中，本公开一般涉及方法以及相关系统，组合物，试剂盒，装置和计算机可读介质，其包含使用附加到多个多核苷酸的多个标签的多重分子标记过程。 标签具有特征，包括序列，长度和/或可检测部分，或唯一地识别其附着的多核苷酸分子的任何其它特征，并允许跟踪标记分子混合物中的单个标记分子。 例如，具有唯一标签序列的标签可以唯一地识别其所附着的单个多核苷酸，并将单个多核苷酸与混合物中的其他标记多核苷酸区分开。 在一些实施方案中，多重分子标记方法可用于产生错误校正的测序数据和用于检测以核酸样品中低丰度存在的靶多核苷酸。

公开(公告)号：WO2013158215A1

公开(公告)日：2013-10-24

申请号：PCT/US2013/027423

申请日：2013-02-22

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： GU, Jian ,  BRAMLETT, Kelli ,  BURNETT, Christopher

IPC: C12Q1/68

CPC classification number: C12Q1/6806 ,  C12Q1/6848 ,  C12Q2521/501 ,  C12Q2525/113 ,  C12Q2525/186 ,  C12Q2525/191 ,  C12Q2537/163

Abstract: Disclosed are compositions and methods for the preparation of RNA libraries for sequencing, gene expression profiling, microarray and other uses and for simplification of the library preparation process. The disclosure provides blocking oligonucleotides which bind to byproduct nucleic acid molecules formed during the ligation of adapters to nucleic acid segments prior to sequencing and inhibit or block amplification of the byproduct nucleic acid molecules in subsequent amplification reactions. Methods for library preparation using blocking oligonucleotides are also provided.

Abstract translation: 公开了用于制备用于测序，基因表达谱，微阵列和其他用途的RNA文库以及简化文库制备过程的组合物和方法。 本公开提供了在测序之前将与衔接子连接至核酸片段期间形成的副产物核酸分子的封闭寡核苷酸，并在随后的扩增反应中抑制或阻断副产物核酸分子的扩增。 还提供了使用封闭寡核苷酸的文库制备方法。