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Systems, Methods, And Apparatuses To Image A Sample For Biological Or Chemical Analysis

Patent No. US11697116 (titled "Systems, Methods, And Apparatuses To Image A Sample For Biological Or Chemical Analysis") was filed by Illumina Cambridge Ltd on Apr 5, 2022.

What is this patent about?

’116 is related to the field of biological and chemical analysis , specifically DNA sequencing instruments. These instruments perform controlled reactions on samples, such as DNA sequencing by synthesis (SBS), where reagents are flowed into a flow cell containing clonal amplicons. Existing systems have limitations in capabilities and cost-effectiveness, creating a need for improved systems and methods for performing assay protocols.

The underlying idea behind ’116 is to create a self-contained DNA sequencing instrument with an integrated fluid storage and delivery system. This involves a fluid storage system with an elevator mechanism to precisely position sipper tubes into component wells containing sequencing reagents. The instrument automates the process of reagent delivery to a flow cell on a sample deck, enabling efficient and cost-effective DNA sequencing.

The claims of ’116 focus on a DNA sequencing instrument comprising an optical deck, a sample deck, and a fluid storage system. The fluid storage system includes an enclosure, a temperature control assembly, a fluid removal assembly with an elevator mechanism, and a reaction component tray. The elevator mechanism moves sipper tubes to access fluids in the tray, and a pump directs these fluids to the sample deck for DNA sequencing. The location sensor is configured to detect the flag and determine when the array of sipper tubes has not reached a threshold level such that the reaction component tray is not ready for removal from the cavity.

In practice, the instrument operates by storing sequencing reagents (polymerase, nucleotides, cleavage mix, etc.) in a reaction component tray within a temperature-controlled enclosure. The elevator mechanism lowers an array of sipper tubes into the appropriate component wells to retrieve the reagents. A pump then directs these reagents through a multi-port valve to the flow cell on the sample deck, where DNA sequencing takes place. The elevator mechanism ensures precise positioning of the sipper tubes and prevents damage during tray removal.

This design differentiates itself from prior approaches by integrating the fluid storage and delivery system within the sequencing instrument. The elevator mechanism and location sensor provide precise control over reagent retrieval and prevent premature removal of the reaction component tray. This integration streamlines the sequencing process, reduces the need for manual intervention, and potentially lowers the overall cost of DNA sequencing.

How does this patent fit in bigger picture?

Technical landscape at the time

In the early 2010s when ’116 was filed, biological and chemical assays were typically performed using fluidic devices and optical assemblies to detect reactions in samples. At a time when DNA sequencing was commonly implemented using sequencing-by-synthesis (SBS) protocols, systems commonly relied on fluorescent labels and optical detection methods to observe chemical reactions on support surfaces. When hardware or software constraints made cost-effective and simpler systems non-trivial, there was a need for improved systems, methods, and apparatuses for performing assay protocols.

Novelty and Inventive Step

The examiner allowed the application because the closest prior art (Williams et al., US 2009/0221059) discloses a system with an optical deck, sample deck, transport platform, and fluid storage system, but it does not suggest or fairly disclose a transport platform carrying a flag and a location sensor configured to detect the flag and determine when an array of sipper tubes has reached a threshold level, in combination with other claim features. Claims 1, 4, 16, and 21 were deemed allowable.

Claims

This patent has 4 claims, with claim 1 being independent. Independent claim 1 is directed to a DNA sequencing instrument comprising an optical deck, a sample deck, a fluid storage system, and a fluid removal assembly. The dependent claims elaborate on specific features and configurations of the DNA sequencing instrument described in the independent claim.

Key Claim Terms New

Definitions of key terms used in the patent claims.

Term (Source)Support for SpecificationInterpretation
Array Of Sipper Tubes
(Claim 1)		“In particular embodiments, methods, and optical systems described herein may be used for sequencing nucleic acids. For example, sequencing-by-synthesis (SBS) protocols are particularly applicable. In SBS, a plurality of fluorescently labeled modified nucleotides are used to sequence a plurality of clusters of amplified DNA (possibly millions of clusters) present on the surface of an optical substrate (e.g., a surface that at least partially defines a channel in a flow cell).”A plurality of tubes configured to slide through openings in a guide plate, used to transfer fluids from component wells to a multi-port valve.
Elevator Mechanism
(Claim 1)		“Various embodiments include providing a reaction component to a sample. As used herein, a “reaction component” or “reactant” includes any substance that may be used to obtain a desired reaction. For example, reaction components include reagents, enzymes, samples, other biomolecules, and buffer solutions.”A mechanism including a drive motor and a lead screw operatively coupled to the drive motor, a transport platform carrying a flag and configured to hold an array of sipper tubes, the elevator mechanism configured to move the array of sipper tubes bi-directionally between a withdrawn level and a deposited level.
Slidable Platform
(Claim 1)		“In SBS, a plurality of fluorescently labeled modified nucleotides are used to sequence a plurality of clusters of amplified DNA (possibly millions of clusters) present on the surface of an optical substrate (e.g., a surface that at least partially defines a channel in a flow cell). The flow cells may contain nucleic acid samples for sequencing where the flow cells are placed within the appropriate flow cell holders.”A component of the sample deck that is configured to move and support a fluidic device containing a flow cell.
Thermal Module
(Claim 1)		“The fluidic device is configured to be fluidicly coupled to a fluidic network of an assay system. By way of example, a fluidic device may include flow cells or lab-on-chip devices. Flow cells generally hold a sample along a surface for imaging by an external imaging system.”A component of the sample deck that controls the temperature of the flow cell.
Thermoelectric Cooling Assembly
(Claim 1)		“The reaction components are typically delivered to a reaction site (e.g., area where sample is located) in a solution or immobilized within a reaction site. The reaction components may interact directly or indirectly with the substance of interest.”A temperature control assembly located at the rear of the cavity opposite the door, configured to regulate a temperature within the cavity.

Litigation Cases New

US Latest litigation cases involving this patent.

Case NumberFiling DateTitle
1:25-cv-00602May 15, 2025Illumina, Inc. V. Element Biosciences, Inc.

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US11697116

ILLUMINA CAMBRIDGE LTD
Application Number
US17714129
Filing Date
Apr 5, 2022
Status
Granted
Expiry Date
Oct 14, 2031
External Links
Slate, USPTO, Google Patents