10X Genomics has been granted a patent for methods and systems that enable the amplification and sequencing of chromatin accessible regions of single cells. The techniques involve using transposon-mediated transposition and fragmentation of a target nucleic acid sequence, along with barcoded oligonucleotides, to prepare next-generation sequencing libraries from a single cell. The methods also allow for single-operation or multi-operation chemical and/or biochemical processing within partitions. GlobalData’s report on 10X Genomics gives a 360-degree view of the company including its patenting strategy. Buy the report here.

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According to GlobalData’s company profile on 10X Genomics, ChIP-seq sequencing was a key innovation area identified from patents. 10X Genomics's grant share as of September 2023 was 23%. Grant share is based on the ratio of number of grants to total number of patents.

Single-cell chromatin accessibility sequencing method

Source: United States Patent and Trademark Office (USPTO). Credit: 10X Genomics Inc

A recently granted patent (Publication Number: US11773389B2) describes a method for processing a sample, specifically cells or cell nuclei, to generate tagged fragments of genomic DNA. The method involves contacting the cells or cell nuclei with transposase nucleic acid complexes, which generate a cell or cell nucleus containing the tagged fragment of genomic DNA.

The method further involves partitioning the cells or cell nuclei and a plurality of barcode sequences into partitions. Each partition consists of the cell or cell nucleus with the tagged fragment of genomic DNA, a first barcode oligonucleotide molecule with a first barcode sequence, a second barcode oligonucleotide molecule with a second barcode sequence, and a reverse transcriptase.

The first barcode oligonucleotide molecule and the tagged fragment of genomic DNA are used to generate a first barcoded molecule, which includes the sequence of the tagged fragment of genomic DNA and the first barcode sequence. The second barcode oligonucleotide molecule, the reverse transcriptase, and an RNA molecule from the cell or cell nucleus are used to generate a second barcoded molecule. The second barcoded molecule includes the complementary DNA sequence of the RNA molecule and the second barcode sequence.

In one embodiment, the second barcode oligonucleotide molecule includes a template switching sequence, and a template switching reaction is performed to generate the second barcoded molecule. This reaction involves using the second barcode oligonucleotide molecule as a template to extend the cDNA molecule generated from the RNA molecule.

The method also includes additional variations, such as using a primer molecule with a sequence complementary to the RNA molecule, ligating the first barcode oligonucleotide molecule to the tagged fragment of genomic DNA, or hybridizing the first barcode oligonucleotide molecule to the tagged fragment of genomic DNA and performing an extension reaction.

The patent also describes the processing of the first barcoded molecule and the second barcoded molecule to generate a sequencing library, which can then be sequenced to obtain sequence information.

Overall, this patent presents a method for efficiently processing samples to generate barcoded molecules for sequencing applications. The method utilizes transposase nucleic acid complexes, barcode sequences, and template switching reactions to generate tagged fragments of genomic DNA and complementary DNA sequences of RNA molecules. This method has potential applications in various fields, including genomics and molecular biology research.

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GlobalData, the leading provider of industry intelligence, provided the underlying data, research, and analysis used to produce this article.

GlobalData Patent Analytics tracks bibliographic data, legal events data, point in time patent ownerships, and backward and forward citations from global patenting offices. Textual analysis and official patent classifications are used to group patents into key thematic areas and link them to specific companies across the world’s largest industries.