公开(公告)号：WO2016130578A1

公开(公告)日：2016-08-18

申请号：PCT/US2016/017196

申请日：2016-02-09

申请人： 10X GENOMICS, INC. ,  HEATON, William, Haynes

发明人： HEATON, William, Haynes ,  KYRIAZOPOULOU-PANAGIOTOPOULOU, Sofia ,  MARKS, Patrick ,  SCHNALL-LEVIN, Michael ,  ZHENG, Xinying ,  JAROSZ, Mirna ,  SAXONOV, Serge ,  GIORDA, Kristina ,  MUDIVARTI, Patrice ,  ORDONEZ, Heather ,  TERRY, Jessica

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6837 ,  C12Q1/6869 ,  G06F19/18 ,  C12Q2537/165 ,  C12Q2525/161

摘要： Systems and methods for determining structural variation and phasing using variant call data obtained from nucleic acid of a biological sample are provided. Sequence reads are obtained, each comprising a portion corresponding to a subset of the test nucleic acid and a portion encoding a barcode independent of the sequencing data. Bin information is obtained. Each bin represents a different portion of the sample nucleic acid. Each bin corresponds to a set of sequence reads in a plurality of sets of sequence reads formed from the sequence reads such that each sequence read in a respective set of sequence reads corresponds to a subset of the nucleic acid represented by the bin corresponding to the respective set. Binomial tests identify bin pairs having more sequence reads with the same barcode in common than expected by chance. Probabilistic models determine structural variation likelihood from the sequence reads of these bin pairs.

摘要翻译： 提供了使用从生物样品的核酸获得的变体调用数据来确定结构变化和定相的系统和方法。 获得序列读数，每个包含对应于测试核酸子集的部分和编码独立于测序数据的条形码的部分。 获取Bin信息。 每个箱表示样品核酸的不同部分。 每个仓对应于从序列读取形成的多组序列读取中的一组序列读取，使得在相应的序列读取集合中读取的每个序列对应于由对应于相应的块的bin所代表的核酸的子集 组。 二项式测试识别具有更多序列读取的bin对，其具有与预期相同的条件相同的条形码。 概率模型根据这些箱对的序列读数确定结构变异似然。

公开(公告)号：WO2015200871A1

公开(公告)日：2015-12-30

申请号：PCT/US2015/038143

申请日：2015-06-26

申请人： 10X GENOMICS, INC.

发明人： JAROSZ, Mirna ,  HINDSON, Christopher ,  SCHNALL-LEVIN, Michael ,  NESS, Kevin, Dean ,  SAXONOV, Serge ,  HINDSON, Benjamin, J. ,  STUELPNAGEL, John

IPC分类号： C12Q1/68

CPC分类号： C12N15/1058 ,  C12Q1/6806 ,  C12Q1/686 ,  C12Q2535/122 ,  C12Q2563/159 ,  C12Q2563/179

摘要： The present disclosure relates to methods and systems for sample processing and analyzing when the total quantity of input sample is low or when a target of interest is present as a relatively minor or rare population within the overall sample. The disclosure particularly relates to analyzing nucleic acid samples, including samples where a target nucleic acid of interest is present as a relatively low proportion of the overall nucleic acids.

摘要翻译： 本公开涉及当输入样品的总量低或当感兴趣的目标作为整个样品中相对较小或罕见的群体存在时的样品处理和分析的方法和系统。 本公开特别涉及分析核酸样品，包括其中存在目的靶核酸作为总体核酸的相对低比例的样品。

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：WO2016138148A1

公开(公告)日：2016-09-01

申请号：PCT/US2016/019382

申请日：2016-02-24

申请人： 10X GENOMICS, INC.

发明人： SCHNALL-LEVIN, Michael ,  JAROSZ, Mirna

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6869 ,  C12Q2535/122 ,  C12Q2563/159 ,  C12Q2565/514

摘要： The present invention is directed to methods, compositions and systems for analyzing sequence information from targeted regions of a genome. Such targeted regions may include regions of the genome that are poorly characterized, highly polymorphic, or divergent from reference genome sequences.

摘要翻译： 本发明涉及从基因组的目标区域分析序列信息的方法，组合物和系统。 这样的靶向区域可以包括基因组区域，其特征不清楚，高度多态性或与参考基因组序列不同。

公开(公告)号：WO2016069939A1

公开(公告)日：2016-05-06

申请号：PCT/US2015/058142

申请日：2015-10-29

申请人： 10X GENOMICS, INC.

发明人： JAROSZ, Mirna ,  SCHNALL-LEVIN, Michael ,  SAXONOV, Serge ,  HINDSON, Benjamin ,  ZHENG, Xinying

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6806 ,  C12Q1/6837 ,  C12Q1/6874 ,  C12Q2535/122 ,  C12Q2537/159 ,  C12Q2565/514 ,  C12Q2563/179

摘要： The present invention is directed to methods, compositions and systems for capturing and analyzing sequence information contained in targeted regions of a genome. Such targeted regions may include exomes, partial exomes, introns, combinations of exonic and intronic regions, genes, panels of genes, and any other subsets of a whole genome that may be of interest.

摘要翻译： 本发明涉及用于捕获和分析包含在基因组目标区域中的序列信息的方法，组合物和系统。 这些靶向区域可以包括外显子，部分外显子，内含子，外显子和内含子区域的组合，基因，基因组，以及可能感兴趣的整个基因组的任何其它子集。

公开(公告)号：WO2015200893A9

公开(公告)日：2015-12-30

申请号：PCT/US2015/038178

申请日：2015-06-26

申请人： 10X GENOMICS, INC.

发明人： HINDSON, Benjamin, J. ,  HINDSON, Christopher, Martin ,  SCHNALL-LEVIN, Michael ,  NESS, Kevin, Dean ,  JAROSZ, Mirna ,  SAXONOV, Serge ,  HARDENBOL, Paul ,  BHARADWAJ, Rajiv ,  ZHENG, Grace, X.y. ,  BELGRADER, Philip

IPC分类号： C12Q1/68 ,  C12P19/34

摘要： Methods, compositions and systems for analyzing individual cells or cell populations through the partitioned analysis of contents of individual cells or cell populations. Individual cells or cell populations are co-partitioned with processing reagents for accessing cellular contents, and for uniquely identifying the contents of a given cell or cell population, and subsequently analyzing the cell's contents and characterizing it as having derived from an individual cell or cell population, including analysis and characterization of the cell's nucleic acids through sequencing.