Methods And Compositions For Analyzing Cellular Components
Patent No. US11634707 (titled "Methods And Compositions For Analyzing Cellular Components") was filed by Illumina Inc on Feb 10, 2016.
What is this patent about?
’707 is related to the field of single-cell analysis, specifically methods for analyzing multiple components (analytes) from a population of single cells. The background involves the detection of specific nucleic acid sequences for various applications like identifying microorganisms, diagnosing diseases, and characterizing genetic abnormalities. Existing nucleic acid sequencing methodologies have evolved to allow parallel processing, generating enormous amounts of data.
The underlying idea behind ’707 is to use combinatorial indexing within contiguity preserving elements (CEs) to analyze multiple analytes from single cells. The process involves encapsulating single cells within CEs, labeling different analytes (e.g., DNA, RNA, proteins) with unique reporter moieties (e.g., barcodes), and then using multiple rounds of pooling and compartmentalization to create a unique index for each analyte from each cell. This allows for the identification and quantification of multiple analytes from a single cell, even after combining and processing many cells together.
The claims of ’707 focus on a method for analyzing at least two or more analytes of a plurality of single cells. This involves providing a plurality of CEs, each containing a single cell, lysing the cells to release the analytes, and then labeling different analytes with different reporter moieties. The CEs are then combined, compartmentalized, and further labeled with additional reporter moieties in each compartment. Finally, the analytes are analyzed to determine their source single cell based on the combination of reporter moieties.
In practice, the invention works by first encapsulating single cells into CEs, which could be droplets, beads, or polymer matrices. After cell lysis, different types of analytes within each cell are tagged with unique barcodes. The CEs are then pooled and split into multiple compartments, where additional barcodes are added. This process of pooling and splitting, with barcode addition at each step, creates a unique combinatorial index for each analyte from each cell. This allows for the identification of the source cell for each analyte during subsequent analysis, such as sequencing.
This approach differentiates itself from prior methods by preserving the contiguity of cellular components within the CE throughout the analytical process. This is crucial for accurately linking different analytes back to their original single-cell source. The combinatorial indexing scheme allows for high-throughput analysis of many single cells in parallel, without the need for physically separating and processing each cell individually. The use of transposomes for inserting barcodes and adaptors into nucleic acids is also a key aspect of the implementation.
How does this patent fit in bigger picture?
Technical landscape at the time
In the mid-2010s when ’707 was filed, nucleic acid sequencing was commonly performed using massively parallel sequencing technologies. At a time when single-cell analysis was typically implemented using microfluidic devices and barcoding strategies, systems commonly relied on enzymatic reactions and amplification steps to generate sufficient material for sequencing. When hardware or software constraints made the efficient processing and analysis of large sequencing datasets non-trivial.
Novelty and Inventive Step
The examiner approved the application because they found the applicant's arguments persuasive. The examiner stated that the prior art does not teach or fairly suggest the combination of steps in the context of the claimed method.
Claims
This patent contains 23 claims, with independent claims 1 and 18 directed to methods of analyzing multiple analytes from a plurality of single cells using contiguity preserving elements and reporter moieties. The dependent claims generally elaborate on the specific conditions, reagents, and steps used in the methods of the independent claims.
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Date
Description
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US11634707
- Application Number
- US15549334
- Filing Date
- Feb 10, 2016
- Status
- Granted
- Expiry Date
- Jul 23, 2036
- External Links
- Slate, USPTO, Google Patents