公开(公告)号：US20190065678A1

公开(公告)日：2019-02-28

申请号：US15692316

申请日：2017-08-31

Applicant: 10X Genomics, Inc.

Inventor： Sofia Kyriazopoulou-Panagiotopoulou ,  Patrick Marks

IPC: G06F19/24 ,  G06F19/18 ,  G06F19/12

CPC classification number: G16B40/00 ,  B01J2219/00317 ,  C12Q1/6809 ,  C12Q1/6869 ,  C40B40/06 ,  G06K9/6267 ,  G06N5/003 ,  G06N5/025 ,  G06N7/005 ,  G16B5/00 ,  G16B20/00 ,  G16B25/00 ,  G16B30/20

Abstract: Systems and methods for analyzing first and second strings against a ground truth string are provided. A construct representing a plurality of components is obtained, each component for a different portion of the truth string. The construct comprises a plurality of measurement string sampling pools each having an identifier and a corresponding plurality of measurement samplings corresponding to one or two of the components. Each sampling has the identifier and a portion of the first or second string. Samplings are assigned to first, second or third classes when coding a portion of the first string, second string, or both the first and second string. First and second positions are tested for sequence events by calculating a plurality of sequence event models using assumptions on the components having samplings encompassing the first and second positions and class assignments. These assumptions are updated using the calculated models and the models are recalculated.

公开(公告)号：US20180265928A1

公开(公告)日：2018-09-20

申请号：US15985388

申请日：2018-05-21

Applicant: 10X Genomics, Inc.

Inventor： Michael Schnall-Levin ,  Mirna Jarosz ,  Christopher Hindson ,  Kevin Ness ,  Serge Saxonov ,  Benjamin Hindson ,  Xinying Zheng ,  Patrick Marks ,  John Stuelpnagel

IPC: C12Q1/6883 ,  C12Q1/6827 ,  G06F19/22

CPC classification number: C12Q1/6883 ,  C12Q1/6827 ,  C12Q2600/156 ,  G16B30/00 ,  C12Q2535/122 ,  C12Q2537/16 ,  C12Q2563/159 ,  C12Q2565/629

Abstract: 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.

公开(公告)号：US20160232291A1

公开(公告)日：2016-08-11

申请号：US15019928

申请日：2016-02-09

Applicant: 10X Genomics, Inc.

Inventor： Sofia Kyriazopoulou-Panagiotopoulou ,  Patrick Marks ,  Michael Schnall-Levin ,  Xinying Zheng ,  Mirna Jarosz ,  Serge Saxonov ,  Kristina Giorda ,  Patrice Mudivarti ,  Heather Ordonez ,  Jessica Terry ,  William Haynes Heaton

IPC: G06F19/22

CPC classification number: G16B30/00 ,  G16B20/00

Abstract: 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.

Abstract translation: 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的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。 每个箱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存储体的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，其中相同的条形码与预期的机会相同。 概率模型根据这些箱对的序列读数确定结构变异似然。