IP Verse

Signal Encoding And Decoding In Multiplexed Biochemical Assays

Patent No. US11827921 (titled "Signal Encoding And Decoding In Multiplexed Biochemical Assays") was filed by California Institute Of Technology on May 1, 2020.

What is this patent about?

’921 is related to the field of multiplexed analyte detection , specifically improving the throughput of assays that identify the presence or absence of multiple targets in a single reaction. Traditional multiplexed assays are limited by the number of spectrally resolvable labels (e.g., fluorescent dyes), requiring complex techniques like spatial arrays or sequential processing to increase the number of detectable analytes. This patent addresses the need for simpler, more cost-effective multiplexing methods suitable for point-of-care and low-resource settings.

The underlying idea behind ’921 is to encode each analyte with a unique combination of signal characteristics , such as intensity and wavelength, rather than relying on a one-to-one correspondence between analyte and spectral label. By assigning different intensity levels to each analyte at one or more wavelengths, the invention creates a coding scheme that allows for the unambiguous identification of multiple analytes based on a cumulative measurement of the overall signal.

The claims of ’921 focus on an assay capable of unambiguously detecting the presence or absence of at least M analytes in a single sample volume. Each analyte is encoded as a value of one component of a fluorescent signal, generating a coding scheme. The assay detects F wavelength components, where M is greater than F, without requiring mass spectrometry or immobilization. The analytes are amplified in the single sample volume.

In practice, the invention uses analyte-specific reagents, such as hybridization probes labeled with fluorophores and quenchers, to generate a signal when the target analyte is present. The intensity of the fluorescent signal at different wavelengths is then measured, and the resulting data is decoded using a pre-defined coding scheme or decoding matrix. This allows for the simultaneous detection of multiple analytes based on a single cumulative measurement, eliminating the need for complex separation or processing steps.

’921 differentiates itself from prior approaches by overcoming the limitations of traditional spectral multiplexing . Instead of assigning a unique color to each analyte, it uses a combination of intensity and wavelength to create a more complex coding scheme. This allows for a higher degree of multiplexing with a limited number of spectral labels, enabling simpler and more cost-effective assays for detecting multiple analytes in a single reaction.

How does this patent fit in bigger picture?

Technical landscape at the time

In the early 2010s when ’921 was filed, multiplexed reactions at a time when X was typically implemented using Y, where X is the detection of multiple analytes and Y is spectrally resolved fluorescence or chemiluminescence, spatially resolved signals, temporally resolved signals, or combinations thereof. There was a need for multiplexed reactions that could be carried out in a single solution.

Novelty and Inventive Step

The examiner approved the application because the claims describe an empirical assay for detecting the presence or absence of M analytes using F wavelength components, where M is greater than F, without needing mass spectrometry or immobilization.

Claims

This patent contains 19 claims, with claims 1 and 14 being independent. Independent claim 1 focuses on an assay for detecting the presence or absence of multiple analytes using a fluorescent signal coding scheme, while independent claim 14 focuses on a kit for performing a similar detection method. The dependent claims generally elaborate on and refine the specifics of the assay and kit, including details about the encoding scheme, reagents, and components used.

Key Claim Terms New

Definitions of key terms used in the patent claims.

Term (Source)Support for SpecificationInterpretation
Analyte-specific reagents
(Claim 14)		“Generally, a reagent will have an analyte-specific component and a component that generates a signal in the presence of the analyte. In some cases, these reagents are referred to as probes. The probes may be hybridization probes. The hybridization probes may be an oligonucleotide probe attached to a fluorophore and a quencher (e.g., a TAQMAN probe).”Reagents that interact with specific analytes to generate a signal, indicating the presence of the analyte.
Coding scheme
(Claim 1, Claim 14)		“In some cases, this disclosure provides coding schemes and methods to encode an infinite number of targets without degeneracy, using a single component of a signal (e.g., intensity). For example, as described above and in Example 3, a coding scheme may rely on a multiplicity of signal intensity without consideration of color. The corresponding coding scheme or decoding matrix may then be used to convert the cumulative measurement into a determination of the presence or absence of an analyte.”A system where each analyte is represented by a specific value of a fluorescent signal component, enabling the determination of analyte presence or absence based on cumulative measurements.
Eliminates degeneracy
(Claim 14)		“In some cases, the coding scheme is non-degenerate. In some cases, the coding scheme is designed to be non-degenerate. In some examples, a non-degenerate coding scheme of this disclosure is generated by a method comprising: (a) generating a code for each potential analyte, wherein each potential analyte is encoded by at least one value of at least one component of a signal; (b) enumerating every legitimate cumulative result for all possible combinations of presence or absence of each analyte; (c) identifying each legitimate result that is degenerate; and (d) eliminating at least one code to eliminate degeneracy.”Encoding analytes in a way that each combination of analytes produces a unique signal, ensuring unambiguous detection.
Fluorescent signal
(Claim 1, Claim 14)		“In some examples, the signal is an electromagnetic signal. In some cases, the electromagnetic signal is a fluorescence emission signal. In some examples, the intensity of the fluorescence emission signal is measured at at least four wavelengths or ranges of wavelengths. The methods presented in this disclosure may be used with any quantifiable signal.”A signal that emits light, characterized by wavelength and intensity, used to encode the presence or absence of analytes.
Single sample volume
(Claim 1, Claim 14)		“The methods and compositions presented in this disclosure may be used in solution phase assays, without the need for particles (such as beads) or a solid support. Importantly, the methods and compositions provided herein may be used to detect multiple analytes by obtaining a cumulative measurement on a single solution. No separation is necessary.”A single, undivided quantity of a sample in which multiple analytes are detected simultaneously.

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US11827921

CALIFORNIA INSTITUTE OF TECHNOLOGY
Application Number
US16864744
Filing Date
May 1, 2020
Status
Granted
Expiry Date
Sep 4, 2034
External Links
Slate, USPTO, Google Patents