# US 2019/0168219 A1 · Systems, apparatus, and methods for inline sample preparation

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- Number: US 2019/0168219 A1
- Document ID: US20190168219A1
- Status: Published application
- Kind: A1
- Application number: 16/031,365
- Filed: 2018-07-10
- Published: 2019-06-06
- Earliest claimed: 2016-01-11
- Applicants: Fluoresentric, Inc.
- Inventors: Brian CAPLIN; Brian HICKE; Brandon Doyle LOWE; Jamie PURCELL; Mark POWELSON; Bryson GREEN; Cameron ORR; Jennifer CAMPBELL; Katelyn KELLY; David OWEN; Michael MCMAHON
- Web page: https://patentgrep.com/patent/US20190168219A1

## CPC

- B01L 3/502715: {characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces}
- B01L 3/502: {with fluid transport, e.g. in multi-compartment structures}
- B01L 3/563: {Joints or fittings; Separable fluid transfer means to transfer fluids between at least two containers, e.g. connectors}
- B01L 7/52: {with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples}
- C12M 23/16: {Microfluidic devices; Capillary tubes (integrated microfluidic structures B01L3/5027; microreactors B01J19/0093)}
- C12M 23/34: {Internal compartments or partitions}
- C12M 23/42: {Integrated assemblies, e.g. cassettes or cartridges}
- C12M 23/48: {Holding appliances; Racks; Supports (holding devices for laboratory apparatus B01L9/00)}
- C12M 23/52: {Mobile; Means for transporting the apparatus (transportable laboratories B01L1/52)}
- C12M 25/10: {Hollow fibers or tubes (hollow fiber modules in general B01D63/02)}
- C12M 41/12: {of temperature (controlling the temperature of chemical or physical processes B01J19/0013, heating or cooling apparatus for laboratory use B01L7/00)}
- B01L 2200/028: Modular arrangements
- B01L 2300/0672: Integrated piercing tool
- B01L 2300/0829: Multi-well plates; Microtitration plates
- B01L 2300/0832: cylindrical, tube shaped
- B01L 2300/087: Multiple sequential chambers
- B01L 2300/168: Specific optical properties, e.g. reflective coatings
- B01L 2300/18: Means for temperature control
- B01L 2400/0683: mechanically breaking a wall or membrane within a channel or chamber
- B01L: CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
- C12M: APPARATUS FOR ENZYMOLOGY OR MICROBIOLOGY; {APPARATUS FOR CULTURING MICROORGANISMS FOR PRODUCING BIOMASS, FOR GROWING CELLS OR FOR OBTAINING FERMENTATION OR METABOLIC PRODUCTS, i.e. BIOREACTORS OR FERMENTERS}

## Abstract

An apparatus includes a sample holder to hold or receive a sample during use. The apparatus also includes a first chamber operably coupled to the sample holder and configured to receive the sample holder. The first chamber includes at least one extraction reagent for extracting nucleic acid from the sample during use to generate a first treated sample. The first chamber and the sample holder collectively define a common longitudinal axis. The apparatus also includes a second chamber operably coupled to the first chamber and disposed along the longitudinal axis. The second chamber includes at least one oligomer for amplifying the nucleic acid to generate a second treated sample.

## Claims

### Claim 1

An apparatus, comprising:
a sample holder configured to hold or receive a sample during use;
a first chamber operably coupled to the sample holder and configured to receive the sample holder, the first chamber including at least one extraction reagent for extracting nucleic acid from the sample during use to generate a first treated sample, the first chamber and the sample holder collectively defining a common longitudinal axis; and
a second chamber operably coupled to the first chamber and disposed along the longitudinal axis, the second chamber including at least one oligomer for amplifying the nucleic acid to generate a second treated sample.

### Claim at position 2

2-3. (canceled)

### Claim 4 (depends on 1)

The apparatus of claim 1, wherein the sample holder includes one of a swab, a pipette and a syringe.

### Claim at position 4

5-7. (canceled)

### Claim 8 (depends on 1)

The apparatus of claim 1, wherein the at least one extraction reagent includes a liquid reagent and the first chamber includes a first storage unit to store the liquid reagent.

### Claim 9 (depends on 1)

The apparatus of claim 1, wherein the first chamber includes:
a first compartment configured to couple to the sample holder;
a first filter disposed in the first compartment;
a second compartment operably coupled to the first compartment, the second compartment being translatable with respect to the first compartment; and
a first valve or a first membrane disposed within the first compartment, the first valve being configured to permit fluid flow from the first compartment to the second compartment and to block fluid flow from the second compartment to the first compartment,
wherein the second compartment is configured to draw at least a portion of the first treated sample from the first compartment when moved away from the first compartment.

### Claim at position 7

10-11. (canceled)

### Claim 12 (depends on 9)

The apparatus of claim 9, wherein the first chamber further includes at least one sample processing control (SPC).

### Claim 13

(canceled)

### Claim 14 (depends on 9)

The apparatus of claim 9, wherein the second chamber includes:
a third compartment operably coupled to the second compartment;
a second filter disposed in the third compartment; and
a second valve or a second membrane disposed between the second compartment and the third compartment, the second valve being configured to permit fluid flow from the second compartment to the third compartment and to block fluid flow from the third compartment to the second compartment,
wherein the second compartment is configured to transport at least a portion of the first treated sample from the second compartment to the third compartment upon moving closer to the first compartment.

### Claim 15 (depends on 14)

The apparatus of claim 14, wherein the at least one oligomer is disposed on the second filter or in the third compartment.

### Claim 16 (depends on 1)

The apparatus of claim 1, wherein the second chamber includes an interface configured to permit optical interrogation of the second treated sample in the second chamber.

### Claim at position 13

17-62. (canceled)

### Claim 63 (depends on 14)

A system, including:
the apparatus of claim 14; and
a device configured to receive the apparatus, the device including:
a motor configured to move the second compartment with respect to the first compartment so as to transport at least one of the sample or the first treated sample;
a heater configured to thermo-cycle the first treated sample in the second chamber so as to amplify the nucleic acid, the heater being further configured to interact with the first chamber to lyse the sample and extract the nucleic acid from the sample;
a light source configured to illuminate the first treated sample in the second chamber;
a detector, in optical communication with the second chamber, the detector being configured to detect the nucleic acid via fluorescence; and
an optical filter disposed before the detector.

### Claim 64 (depends on 63)

The system of claim 63, wherein the device further includes:
a memory to store process-executable instructions; and
a processor operably coupled to the memory, wherein upon execution of the processor-executable instructions, the processor configured to:
control the motor to move the second compartment with respect to the first compartment so as to extract the nucleic acid from the sample; and
control the heater to thermo-cycle the first treated sample so as to amplify the nucleic acid via extreme chain reaction (XCR™).

### Claim 65 (depends on 64)

The system of claim 64, wherein upon execution of the process-executable instructions, the processor is further configured to:
control the light source to illuminate the second chamber; and
control the detector to detect the nucleic acid via fluorescence in the second treated sample.

### Claim 66

(canceled)

### Claim 67 (depends on 63)

The system of claim 63, wherein the system is configured to detect at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least fifteen, or at least twenty target analytes in the test sample.

### Claim 68

(canceled)

### Claim 69

A method, comprising:
coupling a sample holder to a first chamber, the sample holder having a sample disposed therein, the sample holder and the first chamber having a common longitudinal axis when coupled, and the first chamber including at least one extraction reagent for extracting nucleic acid from the sample; and
transporting at least a portion of the sample to a second chamber operably coupled to the first chamber and disposed along the common longitudinal axis, the second chamber including at least one oligomer for amplifying the nucleic acid.

### Claim at position 21

70-73. (canceled)

### Claim 74 (depends on 69)

The method of claim 69, wherein the at least one extraction reagent includes a liquid reagent stored in a first storage unit within the first chamber and method further comprises transporting the liquid reagent from the first storage unit to the sample holder so as to cause the liquid reagent to be in contact with the sample.

### Claim 75 (depends on 69)

The method of claim 69, further comprising:
extracting first nucleic acid using a first extraction reagent preloaded in the first chamber and extracting second nucleic acid using a second extraction reagent preloaded in the first chamber.

### Claim 76 (depends on 75)

The method of claim 75, further comprising:
amplifying the first nucleic acid using a first oligomer preloaded in the second chamber and amplifying the second nucleic acid using a second oligomer preloaded in the second chamber.

### Claim 77 (depends on 69)

The method of claim 69, wherein coupling the sample holder includes disposing the sample holder into a first compartment operably coupled to a second compartment, and the method further comprises:
moving the second compartment away from the first compartment so as to draw at least a portion of the sample from the first compartment to the second compartment through a first valve and a first filter disposed within the first compartment.

### Claim 78

(canceled)

### Claim 79 (depends on 77)

The method of claim 77, further comprising:
placing the first chamber into a device; and
moving, via a motor of the device, the second compartment away from the first compartment.

### Claim 80 (depends on 77)

The method of claim 77, wherein transporting the at least a portion of the sample includes:
moving the second compartment closer to the first compartment so as to transport the at least a portion of the sample through a second valve disposed within the second compartment and into the second chamber.

### Claim at position 29

81-102. (canceled)

### Claim 103

A sample preparation device, comprising:
a sample holder configured to receive a sample;
a first chamber including:
a first compartment to receive the sample holder, the sample holder being configured to be removable from the first compartment and hermetically seal the sample preparation device when placed in the first compartment;
a second compartment operably coupled to the first compartment; and
a first valve disposed within the first compartment, the first valve being configured to permit fluid flow from the first compartment to the second compartment and to block fluid flow from the second compartment to the first compartment, the second compartment being configured to draw at least a portion of the sample from the first compartment to the second compartment upon moving away from the first compartment, the first chamber including at least one extraction reagent preloaded within the first chamber to extract nucleic acid from target microorganism in the sample; and
a second chamber including:
a third compartment operably coupled to the second compartment; and
a second valve disposed between the second compartment and the third compartment, the second valve being configured to permit fluid flow from the second compartment to the third compartment and to block fluid flow from the third compartment to the second compartment, the second compartment being configured to transport at least a portion of the sample from the second compartment to the third compartment upon moving closer to the first compartment, the second chamber including at least one oligomer preloaded within the second chamber to amplify the nucleic acid extracted by the at least one extraction reagent.