公开(公告)号：US12112833B2

公开(公告)日：2024-10-08

申请号：US17168050

申请日：2021-02-04

Applicant: 10X Genomics, Inc.

Inventor： Nicolaus Lance Hepler ,  Chaitanya Aluru ,  Patrick J. Marks ,  Niranjan Srinivas ,  Nigel Delaney

IPC: G16B30/00 ,  G06F16/22 ,  G06F16/23

CPC classification number: G16B30/00 ,  G06F16/2255 ,  G06F16/2365

Abstract: Methods for index hopping sequence read filtering are provided. Each read in a plurality of reads from a multiplexed reaction comprises an insert portion, and first (molecular identifier) and second (sample index) non-insert portions. For each of a plurality of hashes, a hash data structure is formed with a representation of each read. Each representation comprises a hash of the first non-insert portion of the corresponding read. Read pairs are identified in the hash data structures. Each pair includes a first and second read sharing a common hash value but differing index values. An entry is added into a heterogeneous data structure, for each such pair, that includes the first and second non-insert portions of the first and second reads of the pair. Reads with first non-insert portion values appearing more than a threshold number of times in the heterogeneous data structure are removed from the plurality of reads.

公开(公告)号：US12270074B1

公开(公告)日：2025-04-08

申请号：US18589354

申请日：2024-02-27

Applicant: 10x Genomics, Inc.

Inventor： Patrick J. Marks ,  Michael Schnall-Levin

IPC: C12Q1/6869 ,  C12N15/10 ,  C12Q1/48 ,  C12Q1/6874

Abstract: Methods and compositions for analyzing a library comprising a plurality of amplicons comprising identifier sequences are provided, for example, a library of amplicons in a cell or tissue sample attached to a solid support. For example, amplicons are sequenced using a polymerase to incorporate a plurality of cognate nucleotides into the sequencing primer or an extension product thereof to generate a plurality of extension products.

公开(公告)号：US20210241853A1

公开(公告)日：2021-08-05

申请号：US17168050

申请日：2021-02-04

Applicant: 10X Genomics, Inc.

Inventor： Nicolaus Lance Hepler ,  Chaitanya Aluru ,  Patrick J. Marks ,  Niranjan Srinivas ,  Nigel Delaney

IPC: G16B30/00 ,  G06F16/23 ,  G06F16/22

Abstract: Methods for index hopping sequence read filtering are provided. Each read in a plurality of reads from a multiplexed reaction comprises an insert portion, and first (molecular identifier) and second (sample index) non-insert portions. For each of a plurality of hashes, a hash data structure is formed with a representation of each read. Each representation comprises a hash of the first non-insert portion of the corresponding read. Read pairs are identified in the hash data structures. Each pair includes a first and second read sharing a common hash value but differing index values. An entry is added into a heterogeneous data structure, for each such pair, that includes the first and second non-insert portions of the first and second reads of the pair. Reads with first non-insert portion values appearing more than a threshold number of times in the heterogeneous data structure are removed from the plurality of reads.