U.S. patent application number 17/840219 was filed with the patent office on 2022-09-29 for apparatuses and methods for sample-specific self-configuration.
This patent application is currently assigned to BIOCERYX TECHNOLOGIES INC.. The applicant listed for this patent is BIOCERYX TECHNOLOGIES INC.. Invention is credited to Robert Balog, Kirk Bradley, David Devine, Janice Li, Thomas Musci, Andrew Sparks.
Application Number | 20220305490 17/840219 |
Document ID | / |
Family ID | 1000006402744 |
Filed Date | 2022-09-29 |
United States Patent
Application |
20220305490 |
Kind Code |
A1 |
Bradley; Kirk ; et
al. |
September 29, 2022 |
APPARATUSES AND METHODS FOR SAMPLE-SPECIFIC SELF-CONFIGURATION
Abstract
Embodiments in accordance with the present disclosure are
directed to configuring an analyzer apparatus for processing a
particular sample-processing cartridge. The analyzer apparatus
includes a portable container and sample-specific configuration
circuitry. The portable container supports and integrates a
sample-processing cartridge and the sample-specific configuration
circuitry. The sample-specific configuration circuitry identifies
configuration information specific to the sample-processing
cartridge and configures the analyzer apparatus for a series of
state configurations. The configuration can be performed by
selecting which of a plurality of biological-sample stimulators to
interact with the biological sample, identifying positions in the
portable container for each of the selected ones of the plurality
of biological-sample stimulators at different times, and while the
selected ones of the plurality of biological-sample stimulators are
in the identified positions, causing the interactions between the
selected ones of the plurality of biological-sample stimulators and
the biological sample.
Inventors: |
Bradley; Kirk; (Menlo Park,
CA) ; Devine; David; (Menlo Park, CA) ;
Sparks; Andrew; (Menlo Park, CA) ; Li; Janice;
(Menlo Park, CA) ; Musci; Thomas; (Redwood City,
CA) ; Balog; Robert; (Sunnyvale, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
BIOCERYX TECHNOLOGIES INC. |
Menlo Park |
CA |
US |
|
|
Assignee: |
BIOCERYX TECHNOLOGIES INC.
Menlo Park
CA
|
Family ID: |
1000006402744 |
Appl. No.: |
17/840219 |
Filed: |
June 14, 2022 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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16396275 |
Apr 26, 2019 |
11358141 |
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17840219 |
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16039969 |
Jul 19, 2018 |
10307755 |
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16396275 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
G01N 2035/00346
20130101; B01L 3/502715 20130101; G01N 21/6428 20130101; B01L
2200/027 20130101; B01L 3/5082 20130101; B01L 2300/0861 20130101;
G01N 35/0099 20130101; G01N 2035/00465 20130101; G01N 35/00732
20130101; B01L 7/52 20130101; G01N 2035/00158 20130101; G01N
21/6452 20130101; G01N 35/0098 20130101; B01L 2300/022 20130101;
G01N 35/00029 20130101; B01L 2200/10 20130101 |
International
Class: |
B01L 3/00 20060101
B01L003/00; G01N 35/00 20060101 G01N035/00 |
Claims
1. A sample-processing cartridge comprising: a board assembly with
fluid chambers and channels configured and arranged for processing
a biological sample therein; an input port configured and arranged
to receive the biological sample; a plurality of biochemical
processing modules that are coupled to the board assembly and in
fluidic communication with the fluid chambers and channels, the
biochemical processing modules being configured and arranged to
perform biochemical processing on the biological sample; and data
located on the sample-processing cartridge configured and arranged
to provide configuration information specific to the
sample-processing cartridge, the configuration information for
configuring an analyzer apparatus to perform the biochemical
processing using the plurality of biochemical processing
modules.
2. The sample-processing cartridge of claim 1, wherein the
sample-processing cartridge comprises multiple layers; the multiple
layers including a top layer, bottom layer, and a laminate layer;
the top layer comprising a liquid reagents module; the bottom layer
comprising the plurality of biochemical processing modules; and the
laminate layer comprising fluid channels, valves, and vents.
3. The sample-processing cartridge of claim 2, wherein the
sample-processing cartridge is configured to be pierced by the
analyzer apparatus; the analyzer apparatus responsive to a
placement of the sample-processing cartridge in a cartridge
assembly of the analyzer apparatus, the placement of the cartridge
in the cartridge assembly resulting in a liquid communication
between the liquid reagents module and one or more other modules
and/or the fluid chambers of the board assembly; and the liquid
reagents module containing reagents for processing the biological
sample.
4. The sample-processing cartridge of claim 1, wherein the data on
the sample-processing cartridge includes a barcode or radio
frequency tag; the barcode or radio frequency tag stores the
configuration information specific to the sample-processing
cartridge, or identifies a memory location of the configuration
information.
5. The sample-processing cartridge of claim 1, wherein the data on
the sample-processing cartridge includes identification of a link;
the link indicative of a cloud-based location providing the
configuration information.
6. The sample-processing cartridge of claim 4, wherein the
configuration information identifies: biochemical processes to be
performed, an order for performing the biochemical processes, a
location of the sample-processing cartridge, or parameters
including temperature, time, and volume of each of the biochemical
processes to be performed.
7. The sample-processing cartridge of claim 3, wherein the
sample-processing cartridge further comprises a location for the
analyzer apparatus to disable or mark as disabled the
sample-processing cartridge after processing is complete.
8. The sample-processing cartridge of claim 7, wherein at the
location the analyzer apparatus changes a color of a thermal label
or marker, burns the location, or codes data at the location
indicative of the sample-processing cartridge having already been
processed.
9. The sample-processing cartridge of claim 3, wherein the
plurality of biochemical processing modules further comprises a
purification module, a target selection module, an amplification
module, and a detection module.
10. The sample-processing cartridge of claim 9, wherein the
purification module extracts targets from within the biological
sample by mixing the biological sample with enzymes or chemicals to
release a target from the biological sample; wherein the target
includes DNA, RNA, or antibodies.
11. The sample-processing cartridge of claim 10, wherein the
purification module includes a proteinase K (PK) chamber that
contains PK, and a TEC interface for engagement with a TEC.
12. The sample-processing cartridge of claim 9, wherein the
purification module includes a binding chamber, one or more binding
elements, and a TEC interface to allow for engagement with a TEC;
wherein the one or more binding elements include beads or a silica
frit.
13. The sample-processing cartridge of claim 9, wherein the
purification module includes two separate modules including an
extraction module and an isolation module, wherein the extraction
module extracts targets from within the biological sample by mixing
the biological sample with enzymes or chemical to release a target
from the biological sample, the target including DNA, RNA, or
antibodies; and wherein the isolation module includes a binding
chamber, one or more binding elements, and a TEC interface for
engagement with a TEC, the one or more binding elements include
beads or a silica frit.
14. The sample-processing cartridge of claim 9, wherein the target
selection module is configured to bind specific targets to probes,
the target selection module including a chamber, probes, enzymes,
and a TEC interface.
15. The sample-processing cartridge of claim 14, wherein specific
targets are isolated from the purification module, the probes are
mixed with the isolated specific targets, and the isolated specific
targets are annealed to the probes.
16. The sample-processing cartridge of claim 9, wherein the
amplification module is configured to amplify targets bound to
probes via a PCR process, the amplification module including
probes, PCR primers, enzymes, and a TEC interface.
17. The sample-processing cartridge of claim 16, wherein the target
selection module and amplification module are one integral module,
the one integral module being a library preparation module
configured for library preparation; wherein the library preparation
includes adding the probes to the biological sample, and binding
the probes to a specific target.
18. The sample-processing cartridge of claim 9, wherein the
detection module is configured to bind amplicons to a substrate and
detect the bound amplicons; wherein the amplicons include a
specific target bound to a specific probe.
19. The sample-processing cartridge of claim 3, wherein the
plurality of biochemical processing modules includes a sample
collection module used to interface with a biological sample
container or transfer device, wherein the sample collection module
includes a sample chamber configured to hold a volume of the
biological sample.
20. The sample-processing cartridge of claim 19, wherein the sample
collection module is a blood tube.
Description
OVERVIEW
[0001] Various embodiments in accordance with the present
disclosure are directed to sample-specific self-configuration of an
analyzer apparatus. In specific embodiments, the analyzer apparatus
self-configures itself for processing many different
sample-processing cartridges, having different configurations
including different biochemical processes, different orders, and/or
locations of the biochemical processes, and different parameters
for performing the respective biochemical processes.
[0002] It can be advantageous for diagnosis of diseases or
physiological conditions, as well as other analytic purposes, to
analyze a biological sample to inform clinical decision making.
Different types of biological samples and/or analysis use different
biochemical processes, different orders of biochemical processes,
and/or involve different parameters. Sample-processing cartridges,
such as microfluidic chips, are used for processing the biological
sample and include different biochemical processing modules and at
different locations depending on the particular biochemical
processes to be performed. In accordance with various embodiments,
an analyzer apparatus is self-configurable for a plurality of
different types of biological samples, and which allows for the
analyzer apparatus to be used for a variety of different analyses
and processes. The analyzer apparatus is flexible in a distributed
setting that allows for the variety of analyses, while mitigating
manual configuration by a user, such as a laboratory technician.
The self-configurability of the analyzer apparatus allows for
different diagnostic and/or processing workflows to be operated by
minimally trained users at the point of biological specimen
collection from a patient. For example, the self-configuration
allows for processing different subsets of biological processes and
different orders of biological processes from sample to sample. In
specific embodiments, a single analyzer apparatus is used to
perform genomic deoxyribonucleic acid (DNA) diagnostics, cell free
DNA (cfDNA) diagnostics, messenger ribonucleic acid (mRNA)
diagnostics, microRNA (miRNA) diagnostics, and other nucleic acid
based tests. In some specific implementations, non-nucleic acid
tests are converted to a nucleic acid readout and analyzed. For
example, synthetic DNA coupled to an antibody is used as a readout
for antibody protein interactions.
[0003] In a number of embodiments, the analyzer apparatus includes
a portable container and sample-specific configuration circuitry.
The portable container supports and integrates (removably) the
sample-processing cartridge and the sample-specific configuration
circuitry. The sample-processing cartridge includes a board
assembly with fluid chambers and channels for processing a
biological sample therein. The sample-specific configuration
circuitry causes interactions with the biological sample. For
example, the sample-specific configuration circuitry (or another
component of the analyzer apparatus) includes a memory circuit used
to store and access configuration information specific to the
sample-processing cartridge and a configuration processing circuit
used to configure the analyzer apparatus for a series of state
configurations. The configuration information can be accessed
and/or stored in the memory circuit internal to the analyzer
apparatus prior to processing (or starting the process thereof) the
biological sample. In other specific embodiments, the analyzer
apparatus can access and/or store the configuration information
during the analysis, such as in a step-by-step download process
(e.g., on-the-fly and during the processing), as further described
herein.
[0004] Configuring the analyzer apparatus for the series of state
configurations, in accordance with various embodiments, includes
selecting which of a plurality of biological-sample stimulators to
interact with the biological sample, and identifying positions in
the portable container for each of the selected ones of the
plurality of biological-sample stimulators at different times.
Configuring the analyzer apparatus for the series of state
configurations further includes, while the each of the selected
ones of the plurality of biological-sample stimulators are in the
identified positions at the different times, causing the
interactions between the selected ones of the plurality of
biological-sample stimulators and the biological sample. For
example, the analyzer apparatus can include the plurality of
biological-sample stimulators. Each of the plurality of
biological-sample stimulators includes or is an energy emitter that
provides at least one type of energy output and transmits the
energy output toward the biological sample, thereby causing the
interaction with the biological sample. Example energy outputs
includes electrical signals, optical signals, acoustic and/or
ultrasound signals, thermal energy or transfer of thermal energy
(e.g., heating and cooling), magnetic fields or energy, ionizing
radiation, pressure, and other types of outputs.
[0005] The biological-sample stimulators include different hardware
components. Example biological-sample stimulators include a
pneumatic stimulator, a gantry (or other mechanical stimulator), an
optical stimulator, a thermal energy tool, and an electrical
stimulator. Although the various hardware components are described
as "a stimulator," one or more of the stimulators, or components
thereof, can be portions of another stimulator. In a number of
specific embodiments, as further described herein, the
biological-sample stimulators can include subassemblies of the
analyzer apparatus. In specific embodiments, the pneumatic
stimulator includes a pump, tubing and channels that sends forces
toward the biological sample and thereby controls movement of the
biological sample through the sample-processing cartridge. For
example, the pneumatic stimulator constantly controls movement of
the biological sample through the sample-processing cartridge based
on the configuration information. In various instances during the
analysis, the pneumatic stimulator can cause turbulence for mixing
fluids together. The gantry selectively provides a plurality of
interactions with the biological sample at a plurality of locations
and based on the series of state configurations. In further
specific aspects, gantry and a plurality of interface tools coupled
to the gantry selectively output different types of energy outputs
toward the biological sample to provide the different interactions
with the biological sample at a plurality of locations across the
analyzer apparatus, such as allowing for movement of interface
tools to any location within the analyzer apparatus. Such interface
tools can include a magnetic tool, a thermal energy tool, an
acoustic tool, an optical tool, etc. A thermal energy tool includes
a heat source and/or a cooling source and is used to transfer
thermal energy from one medium to another for the purposes of
heating and/or cooling. In some specific examples, the thermal
energy tool is a radiator, a heat exchanger, and/or a heat sink,
although embodiments are not so limited. As an example, the thermal
energy tool outputs thermal energy toward the biological sample and
thereby provides temperature control at specific locations and
time. The thermal energy tool can be part of the gantry, in some
specific aspects. The electrical stimulator, which includes
circuitry, outputs timing signals for controlling actions performed
by other of the plurality of biological-sample stimulators, such as
controlling timing of the other biological-sample stimulators and
processing image data of the biological sample to provide analytic
results. In other specific aspects useful with the above-noted
embodiments, the optical stimulator, which includes a light source
and detector circuitry, outputs an optical signal toward the
biological sample and captures image data of the biological sample
responsive to the optical signal.
[0006] In specific embodiments, the sample-specific configuration
circuitry further includes identification circuit. The
identification circuit identifies the sample-processing cartridge
using data located on the sample-processing cartridge and
identifies the configuration information using the data. The data
can include a barcode, such as a matrix bar code, a radio frequency
tag, or a memory location, such as a cloud-based location or memory
location internal to the analyzer apparatus. In some embodiments,
the data includes the configuration information and/or can instruct
how to obtain the configuration information. For example, the
sample-specific configuration circuitry can include a communication
circuit used to download the configuration information from the
memory location. The configuration information is stored on a
memory circuit of the sample-specific configuration circuitry
(e.g., either prior to the identification or responsive to a
download from an external memory location). In accordance with such
specific embodiments, the configuration processing circuit
processes the configuration information accessed from the memory
circuit and provides the series of state configurations using the
processed configuration information.
[0007] Configuring the analyzer apparatus for the series of state
configurations can include providing spatial location information
of specific biochemical processing modules self-contained in the
sample-processing cartridge along with timing information and
identification of the selected biological-sample stimulators used
for performing the analysis and at the different times. In various
specific aspects, the sample-specific configuration circuitry
instructs the selected biological-sample stimulators to interface
with specific biochemical processing modules of the
sample-processing cartridge based on parameters identified by the
configuration information. The parameters include spatial locations
of the biochemical processing modules, the selected
biological-sample stimulators used to interface with the
biochemical processing modules, corresponding times for the
interface, and interface parameters indicative of the interactions
with the biological sample. In more-specific embodiments, the
parameters include specific instructions for the biological-sample
stimulators interfacing with the biochemical processing modules
including time requirements of the interaction, two-dimensional or
three-dimensional locations within the sample-processing cartridge
for the interface, interface parameters indicative of the
interactions with the biological sample, which are sometimes herein
referred to as "interface parameters". Example interface parameters
include exposure time, exposure laser power and duration,
stringency temperature, movement of fluid in the sample-processing
cartridge, temperature and duration of temperature at particular
times, volumes delivered, pressure, flow rate, identification of
selected biological-sample stimulators and the interactions,
voltage and current requirements for required forces, laser power,
and various combinations thereof.
[0008] Various aspects of the present disclosure are directed to
methods of self-configuring an analyzer apparatus. For example, the
analyzer apparatus in accordance with the above-noted embodiments
is configured for performing a particular process on a biological
sample. The method includes providing a sample-processing cartridge
comprising a board assembly with fluid chambers, channels and a
biological sample therein to a portable container of an analyzer
apparatus. The method further includes using sample-specific
configuration circuitry to identify configuration information
specific to the sample-processing cartridge by scanning a location
of the sample-processing cartridge for data indicative of the
configuration information, and configuring the analyzer apparatus
for a series of state configurations for performing the process on
the biological sample using the configuration information.
Configuring the analyzer apparatus for the series of state
configurations includes selecting which of a plurality of
biological-sample stimulators of the analyzer apparatus interact
with the biological sample at different times specific to an
analysis of the biological sample, identifying positions in the
portable container for each of the selected ones of the plurality
of biological-sample stimulators at the different times, and while
the selected ones of the plurality of biological-sample stimulators
are in the identified positions at the different times, causing
interaction between the selected ones of the plurality of
biological-sample stimulators and the biological sample.
[0009] Other example aspects are directed to a gantry apparatus
that is configured to interact with a sample-processing cartridges
containing a biological sample. The gantry apparatus includes a set
of tracks, a bridge framework, and a gantry head. The set of tracks
are arranged parallel to one another and elongates in a first
direction. The bridge framework spans the set of tracks and is
configured to travel along the set of tracks in the first
direction. The gantry head is supported by bridge framework and is
configured to travel in a second direction that is perpendicular to
the first direction and along the bridge framework. The gantry head
includes a plurality of interface tools arranged on the gantry head
and that can be used to selectively provide the plurality of
interactions with a biological sample at a plurality of locations.
For example, the gantry head can physically move to different
locations between and outside of the set of tracks in
two-dimensional or three-dimensional directions.
[0010] In other specific aspects useful with the above-noted
embodiments, the plurality of interface tools are located about or
around the periphery of the gantry head. The gantry head can
provide one of the plurality of interactions with the biological
sample by rotating the gantry head to align a respective interface
tool with a particular location of the plurality of locations.
Example interface tools include a heat source and/or a cooling
source to heat and/or cool the biological sample, a magnetic source
to apply magnetic forces, an acoustic tool to apply acoustic
forces, a motor, among various other interface tools. In various
embodiments, the gantry head is detachable from the bridge
framework. For example, the gantry head can be detached from the
bridge framework and another gantry head, which may have a
different set of interface tools, can be attached to the bridge
framework.
[0011] Various related and specific aspects are directed to a
sample-processing cartridge. In some specific embodiments, the
analyzer apparatus includes the sample-processing cartridge. The
sample-processing cartridge includes a plurality of biochemical
processing modules and the data that provides the configuration
information. The plurality of biochemical processing modules are
self-contained in the board assembly and in fluidic communication
with the fluid chambers and channels. As previously described, the
data is located on the sample-processing cartridge which can
provide or be used to provide the configuration information. For
example, the configuration information is specific to the
sample-processing cartridge and used for configuring an analyzer
apparatus to perform the biochemical processing using the plurality
of biochemical processing modules. The data can include a barcode,
a radio frequency tag, and/or a cloud-based location or other
memory location.
[0012] The above discussion is not intended to describe each
embodiment or every implementation of the present disclosure. The
figures and detailed description that follow also exemplify various
embodiments.
BRIEF DESCRIPTION OF THE FIGURES
[0013] Various example embodiments may be more completely
understood in consideration of the following detailed description
in connection with the accompanying drawings in the Appendix, which
form part of this patent document.
[0014] FIG. 1 illustrates an example of an analyzer apparatus in
accordance with various embodiments of the present disclosure;
[0015] FIG. 2 illustrates an example of an analyzer apparatus in
accordance with various embodiments of the present disclosure;
[0016] FIG. 3 illustrates an example of a sample-processing
cartridge in accordance with various embodiments of the present
disclosure;
[0017] FIG. 4 illustrates examples of layers of a sample-processing
cartridge in accordance with various embodiments of the present
disclosure;
[0018] FIG. 5 illustrates an example method of self-configuring an
analyzer apparatus in accordance with various embodiments of the
present disclosure;
[0019] FIG. 6 illustrates another example method of
self-configuring an analyzer apparatus in accordance with various
embodiments of the present disclosure;
[0020] FIGS. 7A-7I illustrates an example gantry apparatus and/or
an analyzer apparatus including a gantry in accordance with various
embodiments of the present disclosure;
[0021] FIGS. 8A-8E illustrate examples of sample-processing
cartridges, in accordance with various embodiments of the present
disclosure;
[0022] FIG. 9 illustrates an example method of using an analyzer
apparatus for performing an analysis on a biological sample, in
accordance with various embodiments of the present disclosure;
[0023] FIG. 10 illustrates an example method of using an analyzer
apparatus for performing an analysis on a sample, in accordance
with various embodiments of the present disclosure;
[0024] FIG. 11 illustrates an example method of using an analyzer
apparatus for performing an analysis on a sample, in accordance
with various embodiments of the present disclosure; and
[0025] FIG. 12 illustrates a ligase that is active on DNA:RNA
hybrid, in accordance with various embodiments.
[0026] While various embodiments discussed herein are amenable to
modifications and alternative forms, aspects thereof have been
shown by way of example in the drawings and will be described in
detail. It should be understood, however, that the intention is not
to limit the invention to the particular embodiments described. On
the contrary, the intention is to cover all modifications,
equivalents, and alternatives falling within the scope of the
disclosure including aspects defined in the claims. In addition,
the term "example" as used throughout this application is only by
way of illustration, and not limitation.
DETAILED DESCRIPTION
[0027] Embodiments in accordance with the present disclosure are
useful for self-configuring an analyzer apparatus for a
sample-specific analysis or process. In specific aspects, the
analyzer apparatus configures itself for processing a specific
sample-processing cartridge, having biochemical processing modules
at particular locations, based on configuration information
identified using the sample-processing cartridge. The configuration
information identifies a series of state configurations associated
with a plurality of biological-sample stimulators of the analyzer
apparatus used for performing an analysis on a biological sample
within the sample-processing cartridge by causing interactions with
the biological sample. While not necessarily so limited, various
aspects of the disclosure may be appreciated through a discussion
of examples in this regard.
[0028] Accordingly and in the following description, various
specific details are set forth to describe specific examples
presented herein. It should be apparent to one skilled in the art,
however, that one or more other examples and/or variations of these
examples may be practiced without all the specific details given
below. In other instances, well known features have not been
described in detail so as not to obscure the description of the
examples herein. For ease of illustration, the same reference
numerals may be used in different diagrams to refer to the same
elements or additional instances of the same element.
[0029] Embodiments in accordance with the present disclosure are
directed to an analyzer apparatus that is self-configurable for a
plurality of different types of biological samples, and which can
allow for the analyzer apparatus to be used for a variety of
different analyses. The analyzer apparatus is flexible in a
distributed setting which allows for a variety of analyses while
mitigating manual configuration by a user, such as a laboratory
technician. A single analyzer apparatus can be used to perform a
variety of processes and analyses on different sample-processing
cartridges having different biochemical processing modules, at
different locations and/or in different orders, and for processing
different types of biological samples. The analyzer apparatus can
self-configure while in the field (e.g., clinical setting) using
configurable hardware that allows for many different combinations
of biochemical processing in different combinations or orders,
volumes, and/or spatial locations of the respective
sample-processing cartridge. The analyzer apparatus can be used for
providing distributed analysis, such as diagnostics, over a number
of different class of applications, including, but not limited to,
multiple different infectious disease test, genomic tests, and
antibody protein interactions. As the analyzer apparatus
self-configures, based on data located on the respective
sample-processing cartridge, the apparatus can be used for a
variety of different analysis workflows to be operated by a
minimally trained user at the point of biological sample collection
from a patient.
[0030] In a number of embodiments, the analyzer apparatus includes
a portable container and sample-specific configuration circuitry.
The portable container supports and integrates a sample-processing
cartridge and the sample-specific configuration circuitry. The
portable container can removably integrate different
sample-processing cartridges, each including a board assembly with
fluid chambers and channels for processing a biological sample
therein. The sample-specific configuration circuitry can identify
configuration information specific to a respective
sample-processing cartridge and configures the analyzer apparatus
for a series of state configurations for performing the process on
the biological sample. For example, the sample-specific
configuration circuitry includes a memory circuit and a processing
circuit. The memory circuit stores and/or accesses configuration
information specific to the sample-processing cartridge. The
processing circuit configures the analyzer apparatus, using the
configuration information, for a series of state configurations
using the configuration information.
[0031] As further described herein, the configuration information
can be located on the memory circuit internal to the analyzer
apparatus, on an external memory circuit (and is downloaded and
subsequently stored on the memory circuit of the analyzer
apparatus) and/or on the sample-processing cartridge itself. The
location can be identified using data located on the
sample-processing cartridge. The configuration information is
stored by the analyzer apparatus prior to performing or starting
the process on the biological sample, in some embodiments. As a
specific example, the processing circuit accesses the configuration
information in a memory location of the memory circuit (internal to
the analyzer apparatus) and then temporarily stores the
configuration information for accessing during the process, such as
cache memory and/or a volatile memory location. In another specific
example, the processing circuit accesses the configuration
information from an external location, such as the cloud, and then
temporarily stores the configuration information for accessing
during the process. Although embodiments are not limited to the
above examples, and in some instances, the configuration
information is not all accessed and/or internally stored prior to
starting the process on the biological sample. In some embodiments,
a portion of the configuration information is stored prior to
starting the process, and remaining portion(s) are accessed and
stored during the processing, such as downloading on-the-fly in
which the configuration information for the next step in the
process is accessed and saved while processing a previous step.
[0032] The sample-specific configuration circuitry, in a number of
embodiments, includes identification circuit and the configuration
processing circuit. The identification circuit identifies the
sample-processing cartridge using data located on the
sample-processing cartridge and identify the configuration
information using the data. The data can include a barcode, such as
a matrix barcode, a radio frequency tag, or a memory location
(e.g., a memory location of the analyzer apparatus, an external
circuitry memory location and/or a cloud-based location). In some
specific embodiments, the sample-specific configuration circuitry
includes a communication circuit used to download the configuration
information from the memory location, such as the cloud-based
location, the sample-processing cartridge, or the memory circuit
internal to the analyzer apparatus. The configuration processing
circuit further processes the configuration information accessed
from the memory circuit and which provides the series of state
configurations using the processed configuration information. In
various embodiments, the sample-processing cartridge can, itself,
include the configuration information. As a specific example, the
configuration information is stored on a barcode (e.g., a QR code)
and read by the identification circuit.
[0033] Configuring the analyzer apparatus for the series of state
configurations includes using the configuration information to
select which of a plurality of biological-sample stimulators to
interact with the biological sample, and identify positions in the
portable container for each of the selected ones of the plurality
of biological-sample stimulators at different time. Additionally,
the configuration of the series of state configurations further
includes, while the each of the selected ones of the plurality of
biological-sample stimulators are in the identified positions,
causing the interactions at the different times, between the
selected ones of the plurality of biological-sample stimulators and
the biological sample. For example, the analyzer apparatus can
include the plurality of biological-sample stimulators. Each of the
plurality of biological-sample stimulators is or includes an energy
emitter that provides at least one type of energy output and
transmits the energy output toward the biological sample, thereby
causing the interaction with the biological sample. Example energy
outputs includes electrical signals, optical signals, thermal
energy or transfer of thermal energy, sound waves (e.g., acoustic
and/or ultrasound signals), magnetic fields, ionizing radiation,
pressure, and other types of outputs.
[0034] Example biological-sample stimulators include a pneumatic
stimulator, a gantry (or other mechanical stimulator), an optical
stimulator, a thermal energy tool, and an electrical stimulator.
Although the various hardware components are described as "a
stimulator," one or more of the stimulators, or components thereof,
can be portions of another stimulator. In a number of specific
embodiments, as further described herein, the biological-sample
stimulators can include subassemblies of the analyzer apparatus. In
specific embodiments, the pneumatic stimulator includes a pump,
tubing and channels, and sends forces toward the biological sample
and thereby controls movement of the biological sample through the
sample-processing cartridge. For example, the pneumatic stimulator
constantly controls movement of the biological sample through the
sample-processing cartridge based on the configuration information.
In various instances during the analysis, the pneumatic stimulator
can cause turbulence for mixing fluids together. In further
specific aspects, a gantry and a plurality of interface tools
coupled to the gantry selectively output different types of energy
outputs toward the biological sample to provide different
interactions with the biological sample at a plurality of locations
across the analyzer apparatus, such as allowing for movement of
interface tools to any location within the analyzer apparatus. A
thermal energy tool, which includes a heat source and/or a cooling
source, outputs thermal energy toward the biological sample or
otherwise provides a transfer of thermal energy to or from the
biological sample, and thereby provides temperature control at
specific locations and time. The thermal energy tool can be part of
the gantry, in some specific aspects. And, the electrical
stimulator, which includes circuitry, outputs timing signals for
controlling actions performed by other of the plurality of
biological-sample stimulators, such as controlling timing of the
other hardware components and processing image data of the
biological sample to provide analytic results. In other specific
aspects useful with the above-noted embodiments, the optical
stimulator, which includes a light source and detector circuitry,
outputs an optical signal toward the biological sample and captures
image data of the biological sample responsive to the optical
signal.
[0035] The biological-sample stimulators, in specific embodiments,
are configured for the series of state configurations by the
configuration information providing spatial location information of
specific biochemical processing modules self-contained in the
sample-processing cartridge along with timing information (e.g.,
the different times) and the identification of the selected
biological-sample stimulators used for performing the analysis at
the different times. The sample-specific configuration circuitry
can instruct the selected biological-sample stimulators to
interface with the specific biochemical processing modules of the
sample-processing cartridge based on parameters identified by the
configuration information, the parameters including spatial
locations of the biochemical processing modules, the selected
biological-sample stimulators used to interface with the
biochemical processing modules, corresponding times for the
interface, and interface parameters indicative of the interactions
with the biological sample. In more specific embodiments, the
parameters include specific instructions for the biological-sample
stimulators interfacing with the biochemical processing modules
including time requirements of the interaction, two-dimensional or
three-dimensional locations within the sample-processing cartridge
for the interface, and values of the interface that are indicative
or associated with the interactions with the biological sample.
Example interface parameters include exposure time, exposure laser
power and duration, stringency temperature, movement of fluid in
the sample-processing cartridge, temperature and duration of
temperature at particular times, volumes delivered, pressure, flow
rate, voltage and current requirements for required forces, laser
power, and various combinations thereof used for processing the
biological sample for a specific analysis within the
sample-processing cartridge.
[0036] Various embodiments of the present disclosure are directed
to methods of self-configuring an analyzer apparatus. For example,
the analyzer apparatus, such as that described above, is configured
for performing a particular process on a biological sample. The
method can include providing a sample-processing cartridge
comprising a board assembly with fluid chambers, channels and a
biological sample therein to a portable container an analyzer
apparatus. The method includes using sample-specific configuration
circuitry to identify configuration information specific to the
sample-processing cartridge by scanning a location of the
sample-processing cartridge, and configuring the analyzer apparatus
for a series of state configurations for performing the process on
the biological sample using the configuration information.
Configuring the analyzer apparatus for the series of state
configurations includes selecting which of a plurality of
biological-sample stimulators of the analyzer apparatus interact
with the biological sample at the different times, identifying
positions in the portable container for each of the selected ones
of the plurality of biological-sample stimulators at the different
times, and while the selected ones of the plurality of
biological-sample stimulators are in the identified positions at
the different times, causing the interactions between the selected
ones of the plurality of biological-sample stimulators and the
biological sample.
[0037] Other example embodiments are directed to a gantry apparatus
that is configured to interact with a sample-processing cartridges
containing a biological sample. For example, the above-described
gantry can include a gantry apparatus having a plurality of
interface tools. The gantry apparatus includes a set of tracks, a
bridge framework, and a gantry head. The set of tracks are arranged
parallel to one another and can elongate in a first direction. The
bridge framework spans the set of tracks and is configured to
travel along the set of tracks in the first direction. The gantry
head is supported by bridge framework and is configured to travel
in a second direction that is perpendicular to the first direction
and along the bridge framework. The gantry head includes a
plurality of interface tools arranged on the gantry head and that
are used to selectively provide a plurality of interactions with a
biological sample at a plurality of locations within the portable
container. For example, the gantry head can physically move to
different locations between and outside of the set of tracks in
two-dimensional or three-dimensional directions to provide the
plurality of interactions, which are identified via the
configuration information.
[0038] The plurality of interface tools can be located about or
around the periphery of the gantry head. In such embodiments, the
gantry head provides one of the plurality of interactions with the
biological sample by rotating the gantry head to align a respective
interface tool with a particular location of the plurality of
locations. Example interface tools include a heat source and/or a
cooling source to heat and/or cool the biological sample, a
magnetic source to apply magnetic forces, an acoustic tool to apply
acoustic forces, a motor, among various other interface tools. In
various embodiments, the gantry head is detachable from the bridge
framework. For example, the gantry head can be detached from the
bridge framework and another gantry head, which may have a
different set of interface tools, can be attached to the bridge
framework.
[0039] Various related embodiments are directed to the
sample-processing cartridge. In some specific embodiments, the
analyzer apparatus can include the sample-processing cartridge. The
sample-processing cartridge can include a plurality of biochemical
processing modules and the data that provides the configuration
information. The plurality of biochemical processing modules are
self-contained in the board assembly and in fluidic communication
with the fluid chambers and channels. As previously described, the
data is located on the sample-processing cartridge and used to
provide the configuration information. The configuration
information is specific to the sample-processing cartridge and used
for configuring an analyzer apparatus to perform the biochemical
processing using the plurality of biochemical processing modules.
The data can include a barcode, a radio frequency tag, and/or a
cloud-based location or other memory location.
[0040] The above-describes apparatus and methods can be used to
self-configure an analyzer apparatus, while in the field, for a
plurality of different types of biological samples, and which can
allow for the analyzer apparatus to be used for a variety of
different analysis. More specifically, the analyzer apparatus is
configured to be flexible in a distributed setting that allows for
the variety of analysis, while mitigating manual configuration by a
user, such as a laboratory technician. The self-configurability of
the analyzer apparatus allows for different diagnostic and/or
processing workflows to be operated by minimally trained users at
the point of biological specimen collection from a patient. The
self-configuration can allow for different subsets of biological
processes and different orders of biological processes from sample
to sample. In specific embodiments, a single analyzer apparatus is
used to perform genomic deoxyribonucleic acid (DNA) diagnostics,
cell free DNA diagnostics, messenger ribonucleic acid (mRNA)
diagnostics, microRNA (miRNA) diagnostics, and other nucleic acid
based tests. In some instances, non-nucleic acid tests can be
converted to a nucleic acid readout and analyzed. For example,
synthetic DNA coupled to an antibody can be used as a readout for
antibody protein interactions.
[0041] Turning now to the figures, FIG. 1 illustrates an example of
an analyzer apparatus in accordance with various embodiments of the
present disclosure. The analyzer apparatus 102 can include a
portable container 105 and sample-specific configuration circuitry
104. The portable container 105 supports and integrates (e.g.,
accept and hold) a sample-processing cartridge 106 and also
supports and integrates the sample-specific configuration circuitry
104. The sample-processing cartridge 106, as further illustrated
herein, can include a board assembly with fluid chambers and
channels for processing a biological sample 108 therein. The
portable container 105 receives the sample-processing cartridge 106
and couples to one or more biochemical processing modules of the
sample-processing cartridge 106. In specific embodiments, a
cartridge assembly or another component can selectively cause
fluidic connection between biochemical processing modules of the
sample-processing cartridge 106. For example, the fluidic
connection can occur in response to placing the sample-processing
cartridge 106 in the portable container 105 and closing a top
(e.g., a lid) of the analyzer apparatus 102, which may cause a
biochemical processing module to be pierced (e.g., reagents module)
and which results in a fluidic connection between two or more
biochemical processing modules.
[0042] A variety of different analyses and processes can be
performed on a biological sample or different biological samples
using different sample-processing cartridges. For each respective
analysis or process, a different sample-processing cartridge is
used to perform different biochemical processes using different
modules and locations of the modules. The analyzer apparatus 102
self-configures to process the different sample-processing
cartridges using sample-specific configuration circuitry 104. The
sample-specific configuration circuitry 104 identifies
configuration information specific to the sample-processing
cartridge 106 and uses the configuration information to configure
the analyzer apparatus 102 for a series of state configurations for
performing the process or analysis on the biological sample 108.
The series of state configurations, as further described herein,
can be associated with the positions of and interactions provided
by different biological-sample stimulators that are integrated
within and supported by the portable container 105.
[0043] The sample-specific configuration circuitry 104 includes a
memory circuit and a configuration processing circuit. The memory
circuit is used to store and access the configuration information
specific to the sample-processing cartridge 106. The configuration
processing circuit configures the analyzer apparatus for the series
of state configurations using the configuration information. In
specific embodiments, the sample-specific configuration circuitry
104 includes identification circuit. The identification circuit can
identify the sample-processing cartridge 106 using data located on
the sample-processing cartridge 106 and identify the configuration
information using the data. The data can include a barcode on the
sample-processing cartridge 106, data stored in a radio frequency
tag on the sample-processing cartridge 106, and/or data identifying
a memory locations and/or cloud-based location, among other data.
In some embodiments, the analyzer apparatus 102 further includes a
communication circuit used to download configuration information,
such as from a memory location or cloud-based location identified
using the sample-processing cartridge 106. In various embodiments,
the configuration information is stored on the memory circuit of
the sample-specific configuration circuitry 104, such as prior to
the identification or responsive to a download from an external
memory location.
[0044] In various specific embodiments, the configuration
information is located on the sample-processing cartridge (e.g., it
is the data), on external circuitry, and/or in a memory location
internal to the analyzer apparatus (e.g., on the memory circuit).
The location can be identified from or include the data on the
sample-processing cartridge, which is identified by the
identification circuit and/or used by the communication circuit to
access and/or download the configuration information. In some
embodiments, the configuration information is stored on the memory
circuit prior to processing the sample-processing cartridge. For
example, the configuration information can be temporarily stored in
an easy to locate memory location, such as cache memory. In a
specific embodiment, the analyzer apparatus accesses the
configuration information in an internal memory location of the
analyzer apparatus and then temporarily stores the configuration
information in another location for accessing during the process,
although embodiments are not so limited and the analyzer apparatus
can access the configuration without storing in the second
location. In another specific example, the analyzer apparatus
accesses the configuration information from an external location,
such as the cloud, and then internally stores the configuration
information for accessing during the process. As may be
appreciated, embodiments are not limited to the above examples, and
in some instances, the configuration information is not all
accessed and/or internally stored prior to starting the process on
the biological sample. As an example, a portion of the
configuration information is stored prior to starting the process,
and remaining portion(s) are accessed and stored during the
processing, such as downloading on-the-fly in which configuration
information for the next step in the process is accessed and saved
(temporarily or permanently) while processing the previous
step.
[0045] As further illustrated herein, such as by FIG. 2, the
analyzer apparatus 102 includes plurality of biological-sample
stimulators that interact physically with the biological sample.
The biological-sample stimulators are or include emitters that
provide at least one type of energy output and transmit the energy
output toward the biological sample, thereby causing the
interactions with the biological sample. Example energy outputs
includes electrical signals, optical signals, thermal energy or
transfer of thermal energy, sound waves (e.g., acoustic and/or
ultrasound signals), magnetic fields, ionizing radiation, pressure,
and other types of outputs.
[0046] The sample-specific configuration circuitry 104 can
configure at least some of the plurality of biological-sample
stimulators for the series of state configurations. Configuring the
analyzer apparatus 102 for the series of state configurations, in
accordance with various embodiments, includes using the
configurations information to configure the analyzer apparatus 102
by selecting which of a plurality of biological-sample stimulators
to interact with the biological sample at different times specific
to an analysis of the biological sample, and identifying positions
in the portable container for each of the selected ones of the
plurality of biological-sample stimulators at the different times.
Configuring the analyzer apparatus for the series of state
configurations further includes, while the each of the selected
ones of the plurality of biological-sample stimulators are in the
identified positions at the different times, causing the
interactions between the selected ones of the plurality of
biological-sample stimulators and the biological sample.
[0047] Example biological-sample stimulators include a pneumatic
stimulator, a gantry (or other mechanical stimulator), an optical
stimulator, a thermal energy tool, and an electrical stimulator,
each include different hardware components used to interact with
the biological sample 108. The analyzer apparatus 102 can include
all the biological-sample stimulators and/or portions that can be
removed and/or added. As a particular non-limiting example, in some
implementations, a genomic sample is processed and prepared and
later sequenced. In such implementations, the optical stimulator
may be omitted or otherwise not used.
[0048] FIG. 2 illustrates an example of an analyzer apparatus in
accordance with various embodiments of the present disclosure. As
illustrates and described above, the analyzer apparatus 210
self-configures for processing different sample-processing
cartridges using sample-specific configuration circuitry 218. The
self-configuration can include a series of state configurations
that describe the states of biological-sample stimulators for a
specific duration of time and for different biochemical
processing.
[0049] As illustrated by FIG. 2, the analyzer apparatus 210 can
include biological-sample stimulators, such as a pneumatic
stimulator 222, a gantry 224, an optical stimulator 212, a thermal
stimulator 214, and an electrical stimulator 220. Although the
embodiment of FIG. 2 illustrates each biological-sample stimulator
as a separate stimulator, components of or all of the respective
stimulator can form part of another stimulator. As an example, the
thermal stimulator 214, or a component thereof, can be part of the
gantry 224. The difference stimulators can be also referred to as
subassemblies or subsystems (e.g., a pneumatic subassembly, a
mechanical subassembly (e.g., that includes the gantry 224), an
optical subassembly, a thermal subassembly, and an electrical
subassembly) which are formed of two or more different components,
as described herein. Further, each of the stimulators and various
components are supported by and integrated with the portable
container 216 of the analyzer apparatus 210.
[0050] As previously described, the portable container 216 can
receive and secure the sample-processing cartridge. The
sample-processing cartridge includes a plurality of biochemical
processing modules that are self-contained in the board assembly
and in fluidic communication with the fluid chambers and channels.
The portable container 216 can integrate and support the cartridge
assembly 215 that includes at least a cartridge holder that secures
the sample-processing cartridges and mechanical couplings that
provide connections between the sample-processing cartridge and the
biological-sample stimulators of the analyzer apparatus 210. In
some embodiments, the analyzer apparatus 210 further includes a
cartridge assembly 215. The cartridge assembly 215 includes a
cartridge holder, a tray motor and a plurality of mechanical
couplings that provide biological-sample stimulators connections
and sample-processing cartridge connections used to couple the
sample-processing cartridge with the biological-sample stimulators.
Although not illustrated, the analyzer apparatus 210 can include a
chassis that includes various mounting ports for the
biological-sample stimulators, a fan for thermal management, power
button(s), and/or status lights or other user interfaces.
[0051] The pneumatic stimulator 222, which can also be referred to
as a pneumatic subassembly, can control movement of the biological
sample through the sample-processing cartridge. For example, the
pneumatic stimulator 222 is used to control movement of the
biological sample through the sample process-cartridge based on the
configuration information. The movement can change constantly
through sample processing. The pneumatic stimulator 222 is
configured by the configuration processing circuit 221 to deliver
volumes, pressures, and flow rates through configurable solenoid
valves that enable the processing of the biological sample. The
pneumatic stimulator 222 includes at least a pump, tubing, and
channels that are used to send forces toward the biological sample
and thereby control movement of the biological sample through the
sample-processing cartridge. In some instances, the pneumatic
stimulator 222 can also be used to mix reagents by creating
turbulence in modules for mixing. In various embodiments, the
pneumatic stimulator 222 includes one or more pumps, solenoids,
tubing and channels, an accumulator, and pressure sensors.
[0052] The gantry 224 can selectively provide a plurality of
interactions with a biological sample across a plurality of
locations of the analyzer apparatus 210. In specific embodiments,
the gantry can be referred to or form part of a mechanical
subassembly or stimulator. The gantry 224 is coupled to a plurality
of interface tools and is used to selectively output different
types of energy outputs toward the biological sample to provide
different interactions with the biological sample at a plurality of
locations across the analyzer apparatus 210. For example, the
gantry 224 can enable movement of the interface tools to a
plurality of locations, such as any location, within the analyzer
apparatus 210. The gantry 224 can be configured by the
configuration processing circuit 221 to move various interface
tools to the different locations and at the different times for
processing the biological sample.
[0053] The gantry 224, in specific embodiments and as further
illustrated by FIGS. 7A-7E, includes a set of tracks, a bridge
framework, and a gantry head, which are coupled to and enclosed by
the analyzer apparatus 210. The set of tracks can be parallel to
one another and elongate in a first direction, such as along a
width or a length of the analyzer apparatus 210. The bridge
framework spans the set of tracks and can travel along the tracks
in a first direction that the set of tracks elongate in. The gantry
head is supported by the bridge framework and travels in a second
direction that is perpendicular to the first direction and along
the bridge framework. The gantry head includes the plurality of
interface tools arranged thereon. For example, the plurality of
interface tools can be arranged about or around the periphery of
the gantry head. The gantry head can provide a particular physical
interaction with the biological sample by rotating the gantry head
to align a respective interaction tool with a particular location
of the plurality of locations, as further described herein. In
specific embodiments, the gantry moves the gantry head to different
locations that are between and outside the set of tracks in
two-dimensional and/or three-dimensional directions (e.g., X and Y
and/or X, Y, and Z) via movement of the bridge framework and/or
gantry head. The different interface tools can include a thermal
energy tool to heat or cool the biological sample, a magnetic
source to apply magnetic forces, an acoustic tool for applying
acoustic tools, a motor, and various other interface tools.
[0054] As described above, the gantry 224 is used to provide a
variety of interactions at different locations within the analyzer
apparatus 210, which can allow for flexibility for physical
interactions (e.g., heat, acoustics, magnetic) with the biological
sample. The configuration processing circuit 221 can instruct the
gantry 224 to provide the different interactions at the different
locations and at corresponding times during processing of the
biological sample. The gantry head can be pre-installed with a
fixed set of capabilities, the interface tools can be detachable
and different tools can be attached and/or the gantry head can be
detachable from the bridge framework to provide additional field
configurable capabilities. For example, the gantry head can detach
from the bridge framework and the bridge framework can be attached
to another gantry head having a different set of interface tools
than the gantry head. In various embodiments, the gantry 224 has a
default position which is used to align the gantry 224 and/or the
gantry head to the sample-specific cartridge. The default position
can include a predefined location (e.g., a home or zero position)
in the portable container that the gantry 224 moves to or is
located in when the analyzer apparatus 210 is not processing a
cartridge, when a cartridge is first inserted into the analyzer
apparatus, and/or in the event of an error, such as the gantry not
aligning with cartridge. In specific embodiments, the default
positon can include specific X, Y, and Z coordinate locations.
[0055] The thermal stimulator 214, which can also be referred to as
a thermal subassembly, can provide temperature control at specific
locations and time. The thermal stimulator 214, in specific
embodiments, is a thermal energy tool that includes a heat source
and/or a cooling source, such as a TEC, and, optionally, a
thermistor used to provide the temperature control. The thermal
energy tool uses the heat source and/or cooling source to output
thermal energy toward the biological sample or otherwise provides a
transfer of thermal energy from the biological sample, and thereby
provides temperature control at specific locations and time. The
thermal stimulator 214, or a portion thereof (e.g., the TEC), can
be part of the gantry 224, such as an interface tool of the gantry
apparatus. The thermal stimulator 214 provides temperature control
at specific locations and times to enable the customized sample
processing required by the sample-processing cartridge. The thermal
stimulator 214 and/or the thermal energy tool can include a TEC,
thermistor, heat sinks, and/or a translation mechanism. In certain
instances, the thermal stimulator 214 can be held in a defined
location, but in most cases at least a portion of the thermal
stimulator 214 (via the TEC) is movable by the gantry 224. The
configuration processing circuit 221 provides instructions to the
thermal stimulator 214 (e.g., the thermal energy tool) on the
temperature and duration required of the thermal stimulator 214 to
accomplish the biological sample processing, while the gantry 224
can be used to locate the specific thermal component at the defined
spatial location.
[0056] The electrical stimulator 220, which can also be referred to
as an electrical subassembly, can control timing of the other
biological-sample stimulators. In specific embodiments, the
electrical stimulator 220 can be used to process image data for
providing diagnostic results. The electrical stimulator 220
includes circuitry configured and arranged to output timing signals
for controlling actions performed by other of the plurality of
biological-sample stimulators. The electrical stimulator 220 can
also provide the necessary voltage and current requirements for the
gantry 224, optical stimulator 212, pneumatic stimulator 222, and
thermal stimulator 214 to provide the required forces, laser power,
pressure or flow rates, and temperatures as relayed by the
sample-processing cartridge through the configuration processing
circuit 221. The electrical stimulator 220 can include a power
source, input/output interfaces, processing circuitry (e.g., a
central processor), a Peripheral Interface Controller (PIC), an
analog to digital converter, a data port, among other electrical
components.
[0057] The optical stimulator 212 can capture image data of the
biological sample. The optical stimulator 212, which can also be
referred to as an optical subassembly, includes at least a light
source and detector circuitry used to output an optical signal
toward the biological sample and capture image data of the
biological sample responsive to the optical signal. For example,
the sample-processing cartridge can include an assay used for
capturing targets, such as specific nucleic acids, antibodies,
and/or other targets. The optical stimulator 212 can capture image
data of the targets, which may include fluorescent tags, as further
described herein. As a specific example, the optical stimulator 212
can be used for DNA sequence specific target analysis. The optical
stimulator 212 can include an imaging camera, excitation laser, and
optical relay with the biological sample moved to the optical
stimulator 212 by the pneumatic stimulator 222 and stringency
provided by the thermal stimulator 214. The configuration
processing circuit 221 provides instructions for the optical
stimulator 212 to set the exposure times, exposure laser power and
duration, stringency temperatures, and spatial location for each
sequence specific feature on the sample-processing cartridge. In
various embodiments, as further described below, the optical
stimulator 212 can include a light source (e.g., laser),
illumination optics, collection optics, detector circuitry, and
data transport, among other components.
[0058] As a specific example, the optical stimulator 212 includes a
light source that emits a light beam (e.g., a polarizing light
beam), and detector circuitry. The optical stimulator 212 is
configured to selectively optically interrogate a substrate that is
part of the sample-processing cartridge, such as an array (e.g.,
provide the beam of light to particular locations of the array).
For example, the optical stimulator 212 has a surface adapted to
allow placing thereon a substrate (e.g., a microarray). In other
embodiments, the optical stimulator 212 includes a digital
micromirror device (DMP). Further, in specific embodiments, the
optical stimulator 212 includes a mechanical mechanism, such as a
wheel that the digital microarray is placed on that rotate and/or
that rotates the location of the light beam on the digital light
beam. Such a mechanical mechanism can be an interface tool located
on the gantry head of the gantry, in specific embodiments.
[0059] The light beam is selectively directed to particular
locations of the substrate (e.g., array). For example, the light
beam from the light source is reflected by the surface to provide
an evanescent field over a location of the substrate such that the
location of a substrate in the evanescent field causes a
polarization change in the light beam. The optical stimulator 212
can include a confocal laser as the light beam.
[0060] The detector circuitry detects an optical signal in response
to the light beam being selectively directed to locations of the
substrate (e.g., a digital microarray). In specific embodiments,
the detector circuitry is positioned to detect the polarization
change in the light beam as the light beam is scanned over the
substrate (e.g., a microarray). The polarization change in the
light beam and/or the detected signal is indicative of the
fluorescent signal at the particular location of the substrate.
Processing circuitry is coupled to the detection circuitry to
process an optical signal from the detection circuitry to obtain a
representation of the fluorescent signal at the location of the
substrate (e.g., the intensity of the fluorescent signal). Further,
the processing circuitry processes a plurality of optical signals
to obtain representations of florescent signals at a plurality of
locations of the substrate. The detector circuitry can include
various lenses and/or optical wavelength guides. The optical
stimulator 212, in some instances, is and/or includes imaging
circuitry, such as a charged coupled device (CCD).
[0061] In various embodiments, the processing circuitry is
configured to perform repetitive comparative measurements of the
optical signals from plurality of locations of the substrate (e.g.,
an array). The processing circuitry uses the captured optical
signals to provide the output indicative of an analysis performed.
Example scanner systems include the Tecan.TM. Power Scanner or the
GenePix.TM. 4000B Microarray Scanner (e.g., a microarray scanner)
and the processing circuitry can utilize various computer-readable
medium to analyze the results of the microarray, such as the
Array-Pro.TM. Analyzer or the GenePix.TM. Pro Microarray Analysis
Software (e.g., Acuity.TM.). The processing circuitry of the
optical stimulator 212, in some specific embodiments, can include a
central processor that forms part of the sample-specific
configuration circuitry 218, the electrical stimulator 220, and/or
the optical stimulator 212.
[0062] In specific embodiments, the substrate has a plurality of
complementary tag sequences at a plurality of different locations
on a substrate (e.g., a microarray), which can be referred to as
complementary tag locations. The complementary tag sequences are
configured to bind to different probes. The sample is exposed to
the plurality of probes. For example, a plurality of sets of
different probes can be placed in contact with a biological sample
from an organism. Example biological samples include blood, tissue,
saliva, urine, etc., taken from an organism, such as a human.
[0063] The detector circuitry scans the substrate, and therefrom,
captures the signals (e.g., optical intensities) indicative of a
tag sequence bound to the substrate. The detector circuitry can
provide the captured signals to the processing circuitry. The
processing circuitry uses the captured signals, in addition to
information indicative of the different locations and associated
tag sequences, to asses a number of each of the target sequences
present in the sample. For more specific and general information of
example arrays and analysis performed thereon including a digital
output technique, reference is made to PCT Application (Ser. No.
PCT/US2017/024098), entitled "Apparatuses and Methods for Assessing
Target Sequence Numbers," filed Mar. 24, 2017 (for example, as
illustrated by FIGS. 6 and 7A-7E of the patent document). For more
specific and general information on example sample-processing
cartridges, including a modular cartridge that can be configured
for different uses, reference is made to U.S. application Ser. No.
15/304,030 entitled "Portable Nucleic Acid Analysis System and
High-Performance Microfluidic Electroactive Polymer Actuators,"
filed Oct. 13, 2016, each of which are fully incorporated herein by
reference for their teachings (e.g., for example, as illustrated by
FIGS. 2A-2C of the patent document). Although embodiments are not
limited to assessing target sequence numbers, and can include a
variety of different arrays and assessments.
[0064] The various stimulators and/or hardware components
illustrated by FIG. 2 can interface with one another and/or form
part of one another. For example, the optical stimulator 212 can
interface with the electrical stimulator 220 by the electrical
stimulator 220 providing laser power, camera power, and camera
communications. The optical stimulator 212 can also interface with
the cartridge assembly 215 by translating to the substrate for
imaging. The electrical stimulator 220 can additionally interface
with the thermal stimulator 214 by providing TEC power and
thermistor values, with the pneumatic stimulator 222 by providing
solenoid power, pump power, and pressure sensing, and/or with the
chassis by providing communication input (e.g., Ethernet input for
downloading data) and power input.
[0065] The data located on the sample-processing cartridge is used
to provide the configuration information to the analyzer apparatus
210 via the sample-specific configuration circuitry 218. The
sample-specific configuration circuitry 218 provides the location
and requirements of specific biological processing modules on the
sampled-processing cartridge. The location information can provide
the x, y and/or z coordinate locations of interface features for
the gantry 224, thermal stimulator 214, pneumatic stimulator 222,
and/or optical stimulator 212 to interface with the
sample-processing cartridge.
[0066] As illustrated, the sample-specific configuration circuitry
218 includes a memory circuit 223, an identification circuit 219
and a configuration processing circuit 221. The memory circuit 223
stores and is used to access configuration information specific to
respective sample-processing cartridges. The identification circuit
219 can identify the sample-processing cartridge using the data
located on the sample-processing cartridge and identify the
configuration information using the data. The data can include a
barcode, such as matrix barcode (e.g., a quick response (QR) code)
located on the sample-processing cartridge scanned by the
identification circuit 219, data stored in a radio frequency tag on
the sample-processing cartridge and read by the identification
circuit 219, and/or a memory or cloud-based location provided by
the sample-processing cartridge (such as via a bar code or QR code
that identifies the memory or cloud-based location). The
identification circuit 219 can include components used to scan the
code, read the data, and/or the communication circuit to download
the configuration information from the memory or cloud-based
location.
[0067] The memory location can include a location on a memory
circuit of the analyzer apparatus 210 (e.g., the memory circuit 223
of the sample-specific configuration circuitry 218), a memory
location on an external processing circuitry (e.g., external
controller in communication with the analyzer apparatus 210),
and/or a cloud-based location. In various specific embodiments, the
configuration information is included in the data on the
sample-processing cartridge. In some embodiments, the analyzer
apparatus 210 is in communication with an external processing
circuitry, such as an external controller. The external processing
circuitry can include a user interface, a bar code or radio
frequency identification (RFID) reader, and can be in communication
with the analyzer apparatus 210. For example, the external
processing circuitry can provide patient information to the
analyzer apparatus 210, receive final data from the analyzer
apparatus 210 and/or use the data to generate a report. The
external processing circuitry and analyzer apparatus 210 can
communicate wirelessly or in a wired manner (e.g., Ethernet). In
other embodiments and/or in addition, the analyzer apparatus 210
includes an RFID reader and/or barcode reader. The analyzer
apparatus 210 can communicate the data to the external processing
circuitry to identify the configuration information and/or can
otherwise use the data to identify the configuration information.
For example, the analyzer apparatus 210 can use the data to obtain
the configuration information, which may be included in the data,
or from a memory location external or internal to the analyzer
apparatus 210. The analyzer apparatus 210 can further be configured
to collect image data, analyze the image data, and output an
analysis using an internal processing circuitry.
[0068] The configuration information can be accessed and stored
prior to performing the process on the biological sample, as
previously described (although embodiments are not so limited). In
some specific embodiments, once an analyzer apparatus accesses and
stores, e.g., downloads, the configuration information for a first
type of test, the configuration information is stored on the memory
circuit internal to the analyzer apparatus 210 and subsequently
used for another sample-processing cartridge to perform the first
type of test on a different sample. As a specific example, a first
sample-processing cartridge is inserted into the analyzer
apparatus. The analyzer apparatus identifies that the first
sample-processing cartridge is associated with testing a blood
sample of a human for DNA targets associated with ten different
types of cancer. The sample-processing cartridge includes data for
identifying the type of test and/or accessing the configuration
information associated with the test (e.g., internal or external).
Subsequent to processing the first sample-processing cartridge, a
second sample-processing cartridge is inserted into the analyzer
apparatus. The analyzer apparatus identifies that the second
sample-processing cartridge is associated with testing a blood
sample of another human for DNA targets associated with the same
ten different types of cancer (e.g., is associated with the same
test as the first sample-processing cartridge). The analyzer
apparatus accesses the internal memory location used to store the
configuration information for the first sample-processing cartridge
and, optionally, without accessing or downloading the configuration
information from an external location. In this manner, the analyzer
apparatus can be configured for different tests based on
sample-processing cartridges inserted therein, and can store the
configuration information for subsequent tests. Although
embodiments are not so limited, and can include downloading the
configuration information for each cartridge.
[0069] The configuration information, which can also be referred to
as a "configuration file," can include a series of state
configurations that describes the state of all biological-sample
stimulators (e.g., hardware components) for a specific duration of
time. The configuration information can provide the analyzer
apparatus 210 with the spatial location of specific biochemical
processing modules of sample-processing cartridge along with
identification of the selected biological-sample stimulators of the
plurality used for performing the analysis and time requirements
(e.g., the different times associated with the spatial location and
interactions). The configuration processing circuit 221 can process
the configuration information and provide the series of state
configurations. For example, the configuration processing circuit
221 can provide the location and requirements of specific
biological processing modules on the sample-processing cartridge.
The location information provides the x, y and z coordinate
locations of interface features for the gantry 224, thermal
stimulator 214 (e.g., thermal energy tool), pneumatic stimulator
222, electrical stimulator 220, and optical stimulator 212 to
interface with the sample-processing cartridge and thereby cause
the interaction with the biological sample.
[0070] In accordance with various embodiments, the sample-specific
configuration circuitry 218 can configure the analyzer apparatus
210 for the series of state configurations by providing spatial
location information of specific biochemical processing modules
self-contained in the sample-processing cartridge along with timing
information and identification of the selected biological-sample
stimulators of the plurality used for performing the analysis at
the different times. The sample-specific configuration circuitry
218, such as via the configuration processing circuit 221, can
instruct the selected biological-sample stimulators to interface
with specific biochemical processing modules of the
sample-processing cartridge based on parameters identified by the
configuration information. The parameters can include spatial
locations of the biochemical processing modules, the selected
biological-sample stimulators used to interface with the
biochemical processing modules, corresponding times for the
interfacing, and interface parameters indicative of the
interactions with the biological sample. As specific examples, the
parameters include specific instructions for the selected
biological-sample stimulators interfacing with the biochemical
processing modules including time requirements of the interface
and/or interaction, two-dimensional or three-dimensional locations
within the sample-processing cartridge for the interface, and
values of the interface (e.g., temperature, magnetic and
mixing).
[0071] The sample-specific configuration circuitry 218 can thereby
configure the biological-sample stimulators for the series of state
configurations that are specific to the sample-processing cartridge
and based on data identified directly from or otherwise associated
with the sample-processing cartridge. The series of state
configurations include locations and requirements of specific
biological processing modules on the sample-processing cartridge
and parameters for respective biological-sample stimulators.
[0072] In further embodiments, the analyzer apparatus 210 can
include one or more sensors. The sensors can be used to provide
feedback on the status of the parameters, such as verifying that
the correct interaction is occurring at the correct location and
with the correct interface values. In some embodiments, the
feedback provided by the sensors may indicate that the gantry is
not properly aligned with the sample-processing cartridge. In such
embodiments, the gantry is instructed to return to the default
position to re-align with the sample-processing cartridge. Although
embodiments are not so limited and in some specific embodiments the
sensors are used to adjust the alignment of the gantry without
returning to the default position.
[0073] Although the above describes the analyzer apparatus 210
self-configuring by identifying data on the sample-processing
cartridge, embodiments are not so limited. For example, the
analyzer apparatus 210 can self-configure by a user entering a code
into the analyzer apparatus 210 and the code identifying the series
of state configurations. In other example embodiments, a
configuration file is uploaded to the analyzer apparatus 210, such
as from external processing circuitry.
[0074] Further, in various embodiments, the sample-processing
cartridge can include a means for a user to configure the
sample-processing cartridge. For example, the user can mark a step
by hand on the sample-processing cartridge, such as a label which
is read by the analyzer apparatus and/or manually entered into the
sample-processing cartridge by another user. In other embodiments,
the specific-instructions are coded into the data on the
sample-processing cartridge that is read by the analyzer
apparatus.
[0075] FIG. 3 illustrates an example of a sample-processing
cartridge in accordance with various embodiments of the present
disclosure. The sample-processing cartridge 330 can include a board
assembly 332, a plurality of biochemical processing modules 333, an
input port for receiving a biological sample 331, and
(identification) data 341. The board assembly 332 has fluid
chambers and channels for processing a biological sample therein.
The plurality of biochemical processing modules 333 are
self-contained and/or otherwise coupled to the board assembly 332
and in fluidic communication with the fluid chambers and
chambers.
[0076] The data 341 located on the sample-processing cartridge 330
provides configuration information specific to the
sample-processing cartridge for configuring an analyzer apparatus
to perform the biochemical processing using the plurality of
biochemical processing modules 333. The data 341, as described
above, can include a barcode, a radio frequency tag, and/or
identification of a cloud-based location or other memory location,
such as a link indicative of the cloud-based location or other
memory location.
[0077] The biochemical processing modules 333 are configured to
perform biochemical processing on the biological sample 331.
Example modules, as illustrated, include a purification module 334,
a target selection module 335, an amplification module 337, and a
detection module 339. Embodiments are not limited to the specific
modules illustrated by FIG. 3 and can include a variety of modules
for different analysis, as further described in connection with
FIGS. 8A-8E. The modules can additionally include a sample
collection module used to interface with a biological sample
container and/or transfer device, such as a blood tube, and
includes a sample chamber configured to hold a volume of the
biological sample.
[0078] In specific embodiments, the purification module 334 can
perform extraction of targets within the biological sample. For
example, the purification module can mix the sample with enzymes
and chemicals to release the targets from the biological sample.
The targets can include DNA, RNA, and antibodies, among other types
of targets. In specific embodiments, the purification module 334
can include a proteinase K (PK) chamber that contains PK, and a TEC
interface to allow for engagement with the TEC. The PK chamber can
include other chemicals, such as a detergent and/or salts. The PK
chamber is heated, via the TEC, to activate PK and is mixed with
the biological sample to release the targets (e.g., bound DNA)
bound to other components in the biological sample (via the
pneumatic stimulator). The purification module 334 can further
perform target isolation, in some embodiments. For example, the
purification module 334 can include binding chamber(s), one or more
binding elements, and the TEC interface. The binding elements can
include beads or a solid support, such as a silica frit, as further
described herein. In some embodiments, the purification module 334
include two separate modules, e.g., an extraction module and an
isolation module, that perform the functions described above.
[0079] The target selection module 335 can be used to bind specific
targets to probes. The target selection module 335 can include one
or more chambers, probes and enzymes, and a TEC interface. For
example, probes can be mixed with the isolated targets from the
purification module 334 and the targets are annealed to the
probes.
[0080] The amplification module 337 can be used to amplify the
targets bound to the probes via a PCR process, as further described
herein. The amplification module 337 can include probes, universal
PCR primers, enzymes and other reagents, and a TEC interface. In
some embodiments, the target selection module 335 and the
amplification module 337 include one module, e.g., a library
preparation module that perform the functions described above.
[0081] The detection module 339 can be used to bind the amplicons
to a substrate and detect the bound amplicons, which include
targets bound to probes, as further described herein. The detection
module 339 can include a mixing chamber used to prepare a
hybridized sample, a hybridization chamber, a microarray or other
substrate, and interfaces to various hardware components (e.g.,
TEC, laser, optics). In various embodiments, the detection does not
occur on the analyzer apparatus, and the sample-processing
cartridge 330 does not include the detection module 339.
[0082] The sample-processing cartridge 330 can include various
additional components. For example, the sample-processing cartridge
330 can include a liquid reagents module 338 that contains various
reagents used for processing the biological sample 331. The liquid
reagents module 338 may be pierced by the analyzer apparatus
responsive to placement of the sample-processing cartridge 330 in a
cartridge assembly, and which results in liquid communications
between the liquid reagents module 338 and one or more other
modules and/or chambers of the board assembly 332. The
sample-processing cartridge 330 can additionally include a waste
collection chamber 340 used to collect various fluids and material
after various processes.
[0083] FIG. 4 illustrates examples layers of a sample-processing
cartridge in accordance with various embodiments of the present
disclosure. As illustrated, the sample processing cartridge 441 can
be formed in a variety of layers. The top layer 442 can include the
reagents module and other modules, such as various modules that are
moved to by the gantry (or other mechanical subassembly) of the
analyzer apparatus. The bottom layer 444 can include remaining
modules, such as the substrate (e.g., an array). And, below the
bottom layer 444 can include a laminate layer 446 that includes the
fluid channels, valves, and vents.
[0084] FIG. 5 illustrates an example method of self-configuring an
analyzer apparatus in accordance with various embodiments of the
present disclosure. As described above, prior to processing a
biological sample, configuration information is identified and/or
loaded into the analyzer apparatus, such as via software or
obtained using data on the sample-processing cartridge, and that
prescribes the state configurations for each step of the sample
processing. The biological sample can be processed in a number of
different ways depending on the type of analysis and/or diagnostic
assay being run. Sample preparation is accomplished using a variety
of different biochemical processes. A specific example of
biochemical processes that can be run on the analyzer apparatus are
described below and include DNA extraction, DNA isolation,
biotinylation, probe annealing, probe extension, universal
amplification, and microarray hybridization in some specific
embodiments used for detecting DNA targets.
[0085] Example approaches use solid supports (streptavidin biotin
binding or DNA binding to silica frits), ligases, terminal
transferases, DNA polymerases, RNA reverse transcriptases, uracil
DNA glycosylate, exonucleases, DNA probe annealing to templates,
and other enzymes. Each of these biochemical processes can use
different reaction volumes, temperatures, times, and (physical)
interactions with the biological sample. The requirements are not
uniform and therefore static locations of biological-sample
stimulators and/or hardware components thereof (e.g. TECs, magnets,
and mixers) does not allow for performing multiple different
workflows. Example configurations of modules for specific
diagnostic testing are shown in FIGS. 10 and 11. These are given as
examples, but other common biological sample processing workflows
can be implemented on the field configurable analyzer
apparatus.
[0086] The method as illustrated by FIG. 5 can include providing a
sample-processing cartridge comprising a board assembly with fluid
chambers, channels and a biological sample therein. Optionally, in
some embodiments (as illustrated by the dashed line), the method
can include formatting a sample-processing cartridge for a specific
analysis. For example, the type of analysis can be identified, at
551, and a sample-processing cartridge can be formatted with
particular biochemical processing modules to perform the respective
biochemical processes and in the respective order, at 553.
Additionally, in some embodiments, data is located on the
sample-processing cartridge such that the analyzer apparatus
identifies configuration information specific to the
sample-processing cartridge without or with minimal user input. In
other embodiments, the sample-processing cartridge can be
preconfigured for a specific analysis. A sample from a patient
(e.g., human or other organism) can be collected, at 555, and input
to an input port of the sample-processing cartridge.
[0087] The sample-processing cartridge can be provided to an
analyzer apparatus, such as by placing the sample-processing
cartridge into a cartridge assembly of the analyzer apparatus, at
557. In response thereto, sample-specific configuration circuitry
of the analyzer apparatus can identify configuration information
specific to the sample-processing cartridge by scanning a location
of the sample-processing cartridge for data. The analyzer apparatus
can verify that the configuration information is identified, at
559. If the configuration information is not identified, the
analyzer apparatus can output a message, such as a message on a
user interface of the analyzer apparatus, a message to other
circuitry (e.g., external processing circuitry accessibly by a
technician), and/or other indications on the analyzer apparatus
(e.g., buzzing sound or flashing light indicating an error), at
561.
[0088] In response to verification of identified configuration
information, the analyzer apparatus is configured for a series of
state configurations to perform the analysis on the biological
sample, at 563. As previously described, configuring the analyzer
apparatus for the series of state configurations can include
providing spatial location information of specific biochemical
processing modules self-contained in the sample-processing
cartridge along with timing information and identification of the
selected biological-sample stimulators of the plurality used for
performing the analysis and at the different times. In specific
embodiments, the configuration can include directing ones of the
selected biological stimulators to interface with the respective
biochemical processing modules of the sample-processing cartridge
at different times during the analysis based on the spatial
locations of the biochemical processing modules, and interface
parameters indicative or associated with interaction(s) with the
biological sample.
[0089] FIG. 5 further illustrates an example of a plurality of
biochemical processes that the analyzer apparatus is configured
for. As illustrated, the biochemical processes can include DNA
preparation at 564, library preparation at 565, and
detection/analysis at 566 and 567. In a specific embodiment, DNA
preparation can include DNA extraction and isolation, library
preparation can include annealing, ligation, and/or PCR, as further
described herein.
[0090] FIG. 6 illustrates another example method of
self-configuring an analyzer apparatus in accordance with various
embodiments of the present disclosure. In various embodiments, the
analyzer apparatus may be configured at manufacturing for
particular uses. In such embodiments, a different analyzer
apparatus is used for different analysis. As illustrated by the
dashed line, the method can optionally include formatting a
sample-processing cartridge for a specific analysis. For example,
the type of analysis can be identified, at 670, and a
sample-processing cartridge can be formatted with particular
biochemical processing modules to perform the respective
biochemical processes and in the respective order, at 671. The
analyzer apparatus can be configured at manufacturer for the
specific analysis, at 672. The analysis can include a series of
state configurations for selected biological-sample stimulators of
the analyzer apparatus and at different times, as previously
described.
[0091] A biological sample from a patient (e.g., human or other
organism) can be collected and input to an input port of the
sample-processing cartridge, at 673. The sample-processing
cartridge can be provided to an analyzer apparatus at 674, such as
by placing the sample-processing cartridge into a cartridge holder.
In response, the analyzer apparatus, using the pre-configured
series of state configurations, perform the analysis on the
biological sample. As previously described, configuring the
analyzer apparatus for the series of state configurations can
further includes providing spatial location information of specific
biochemical processing modules self-contained in the
sample-processing cartridge along with timing information and
identification of the selected biological-sample stimulators of the
plurality used for performing the analysis and at the different
times.
[0092] Similarly to FIG. 5, FIG. 6 further illustrates an example
of a plurality of biochemical processes that the analyzer apparatus
is configured for. As illustrated, the biochemical processes can
include DNA preparation at 675, library preparation at 676, and
detection/analysis at 677 and 678. In a specific embodiment, DNA
preparation can include DNA extraction and isolation, library
preparation can include annealing, ligation, PCR, as further
described herein.
[0093] FIGS. 7A-7F illustrate example gantry apparatuses and/or
analyzer apparatuses including a gantry in accordance with various
embodiments of the present disclosure. As previously described,
various embodiments are directed to a gantry apparatus such as a
gantry and/or an analyzer apparatus that includes a gantry. The
gantry can be used to selectively provide a plurality of
interactions with a biological sample, as contained in a sample
processing cartridge, across a plurality of locations of an
analyzer apparatus. For example, the gantry includes a plurality of
interface tools that selectively output different types of energy
toward the biological sample to provide different interactions with
the biological sample. The gantry can enable movement of the
interface tools to any location within the analyzer apparatus by
moving the interface tools in an X, Y, and/or Z direction.
[0094] FIG. 7A illustrates an example of a gantry apparatus in
accordance with various embodiments. As illustrated, the gantry
apparatus includes a set of tracks 760-1, 760-2, a bridge framework
763, and a gantry head 756. The set of tracks 760-1, 760-2 are
arranged parallel to one another and the bridge framework 763 spans
the set of tracks. For example, the bridge framework can be
perpendicular to the set of tracks, although embodiments are not so
limited and the bridge framework can be at a variety of angles to
the set of tracks. The gantry, in specific embodiments and as
further illustrated herein, is enclosed by the analyzer apparatus.
The set of tracks 760-1, 760-2 can be parallel to one another and
elongate in a first direction 762, such as along a width or a
length of the analyzer apparatus. The bridge framework spans the
set of tracks in a second direction 764 and can travel along the
set of tracks in a first direction 762 that the set of tracks
elongate in. The gantry head 756 is supported by the bridge
framework and travels in a second direction 764 that is
perpendicular (or at another angle) to the first direction and
along the bridge framework. The gantry head 756 includes the
plurality of interface tools arranged thereon. The gantry head 756
can provide a particular physical interaction with the biological
sample by rotating the gantry head to align a respective interface
tool with a particular location, as further described herein. In
specific embodiments, the gantry moves the gantry head 756 to
different locations that are between and outside the set of tracks
in two-dimensional and/or three-dimensional directions (e.g., X and
Y and/or X, Y, and Z) via movement of the bridge framework and/or
gantry head. The different interface tools can include a thermal
energy tool to heat or cool the biological sample (e.g., a TEC), a
magnetic source to apply magnetic forces, an acoustic tool for
applying acoustic tools, a motor, and various other tools.
[0095] In accordance with various embodiments, the gantry apparatus
can move the gantry head to different locations using a variety of
mechanisms, such as one or more rotors coupled to components of the
gantry apparatus. Other mechanisms, as would be appreciated by one
of ordinary skill in the art, can include rotating wheels or other
types of rotating components, gears and/or rotary gear systems,
pulleys, crank and shafts and/or crankshafts and rods, collars,
couplings, cams, clutches, flywheels, shaft ends, spindles, meshing
gears, and horizontal or vertical shafting, among other types of
mechanisms.
[0096] FIG. 7B illustrates a more specific example of a gantry
apparatus in accordance with various embodiments. The gantry
apparatus includes brackets 755-1, 755-2 that support the set of
tracks and that can be mounted or otherwise coupled to the frame of
the portable container of the analyzer apparatus. Each of the
tracks of the set or at least one of the tracks are formed by or
include at least one arm (or a set of arms) that is coupled to a
rotor 757-1. Rotation of the rotor 757-1 (and optionally another
rotor coupled to the other arm) moves the arm(s) coupled thereto,
as well as the bridge framework spanning the set of tracks, in a
first direction 761, such as along a width or a length of the
analyzer apparatus. The bridge framework spans the set of tracks
and is configured to travel along the set of tracks in the first
direction 761 responsive to movement of the rotor 757-1 and the arm
coupled to the rotor 757-1. A gantry head 756 is supported by the
bridge framework and is configured to travel in a second direction
759 that is perpendicular to the first direction 761 and along the
bridge framework. For example, another rotor 757-2 is coupled to
the bridge framework. Rotation of the other rotor 757-2 moves the
gantry head 756 in a direction perpendicular to the set of tracks.
The bridge framework can include at least one arm that is coupled
to the other rotor 757-2 and the gantry head 756 to cause movement
of the gantry head 756 in the direction perpendicular to the set of
track, e.g., the second direction 759.
[0097] As further illustrated and described herein, the gantry head
756 includes plurality of interface tools arranged on the gantry
head and that are used to selectively provide a plurality of
interactions with a biological sample at a plurality of locations
within the portable container of the analyzer apparatus. The gantry
head 756 can physically move to different locations between and
outside of the set of tracks in two-dimensional or
three-dimensional directions to provide the plurality of
interactions, which are identified via the configuration
information. In specific embodiments, the gantry can be referred to
or form part of a mechanical subassembly or stimulator. The gantry,
via the plurality of interface tools coupled thereto, is used to
selectively output different types of energy outputs toward the
biological sample to provide different interactions with the
biological sample at a plurality of locations across the analyzer
apparatus.
[0098] FIG. 7C illustrates a view of the gantry head of the gantry
apparatus in accordance with various embodiments. The plurality of
interface tools can be located about or around the periphery of the
gantry head, such as located on the circumference of the gantry
head. In such embodiments, the gantry head is rotatable, e.g., a
rotating head, and used to provide one of the plurality of
interactions with the biological sample by rotating the gantry head
to align a respective interface tool with a particular location
within the analyzer apparatus. As described above, example
interface tools that can be coupled to the gantry head can include
a heat source and/or a cooling source (e.g., TEC) to heat and/or
cool the biological sample, a magnetic source to apply magnetic
forces, an acoustic tool to apply acoustic forces, a motor, among
various other tools. In various embodiments, the gantry head is
detachable from the bridge framework. For example, the gantry head
can be detached from the bridge framework and another gantry head,
which may have a different set of interface tools, can be attached
to the bridge framework.
[0099] FIG. 7D illustrates an example of an analyzer apparatus that
includes a gantry. As described above, the gantry can be enclosed
by the analyzer apparatus. The gantry is used to provide a variety
of interactions at different locations within the analyzer
apparatus, which can allow for flexibility for physical
interactions (e.g., heat, acoustics, magnetic) with the biological
sample. The configuration processing circuit can instruct the
gantry to provide the different interactions at the different
locations and at corresponding times during processing of the
biological sample. The gantry head can be pre-installed with a
fixed set of capabilities, the interface tools can be detachable
and different tools can be attached and/or the gantry head can be
detachable from the bridge framework to provide additional field
configurable capabilities.
[0100] As illustrated and previously described, the analyzer
apparatus further includes a cartridge assembly for holding the
sample processing cartridge, and the configuration processing
circuitry and identification circuit to identify configuration
information for the specific sample processing cartridge. The
sample processing cartridge is loaded into the cartridge assembly
and in response thereto, the analyzer apparatus configures itself
for analyzing the specific biological sample. The configuration can
include use of the different stimulators and/or interface tools of
the gantry at different times, locations, and/or based on other
interface parameters. As previously described, the stimulators
include an optics stimulator, the gantry, an electrical stimulator,
pneumatic stimulator, and optionally, additional mechanical
stimulator.
[0101] In specific embodiments, the thermal stimulator, or a
portion thereof (e.g., the TEC), can be part of the gantry, such as
an interface tool of the gantry apparatus. The thermal stimulator
provides temperature control at specific locations and times to
enable the customized sample processing required by the
sample-processing cartridge. The at least portion of the thermal
stimulator (via the TEC) is movable by the gantry. Further, in
specific embodiments, the optical stimulator includes a mechanical
mechanism, such as a wheel that the digital microarray is placed on
that rotate and/or that rotates the location of the light beam on
the digital light beam. Such a mechanical mechanism can be an
interface tool located on the gantry head of the gantry, in
specific embodiments.
[0102] FIGS. 7E-7F illustrate a partial view of an analyzer
apparatus including a gantry in accordance with various
embodiments. As illustrated by FIG. 7E, the cartridge assembly 784
includes a tray that is configured to hold the sample-processing
cartridge 783. The tray can move to multiple positions. For
example, the tray can have and/or be moved by the analyzer
apparatus to a first position in which the tray is located outside
the analyzer apparatus 780 such that a user can place the
sample-processing cartridge 783 within the tray, as illustrated by
FIG. 7E. FIG. 7F illustrates a second position of the tray in which
the tray is enclosed by the analyzer apparatus 780 and the analyzer
apparatus configures itself for analyzing the biological sample
contained therein. As is further illustrated by FIG. 7E-7F, the
gantry is mounted to the analyzer apparatus 780 via brackets (e.g.,
bracket 755-1 is illustrated) and the gantry head 756 is coupled to
a bridge framework and a set of tracks, and located proximal to the
second position of the tray of the cartridge assembly 784. The
sample-processing cartridge 783 can be loaded into the cartridge
assembly 784 such that the top layer that contains the reagents
module and other modules (e.g., top layer 442 illustrated by FIG.
4) is located proximal to the gantry head 756 (e.g., the top layer
is facing upward).
[0103] FIGS. 7G-7I illustrated different examples of specific
gantry apparatuses, in accordance with various embodiments. The
gantries illustrated by FIGS. 7G-7I can include the structural
components used to provide the functional features as previously
described in connection with the gantries illustrated by FIGS.
7A-7B, such as the previously described gantry head having a
plurality of interface tools and which can be moved to a variety of
locations inside and outside of a set of parallel tracks.
[0104] The gantries illustrated by FIGS. 7G-7I can provide the
movement of the gantry head using a variety of mechanisms. For
example, FIG. 7G illustrates an example of a gantry apparatus in
accordance with various embodiments. As illustrated, the gantry
apparatus includes a set of tracks 765-1, 765-2, a bridge framework
766, a vertical adjustment arm 767, and a gantry head 756. The set
of tracks 756-1, 756-2 are arranged parallel to one another and the
bridge framework 766 spans the set of tracks. For example, the
bridge framework can be perpendicular to the set of tracks,
although embodiments are not so limited and the bridge framework
can be at a variety of angles to the set of tracks. The vertical
adjustment arm 767 can be perpendicular to the bridge framework 766
and the set of tracks 756-1, 756-2. The vertical adjustment arm 767
can couple with the gantry head 756, and can allow the gantry head
756 to be moved up or down the length of the vertical adjustment
arm (e.g., to be moved further away from the bridge framework or
closer to the bridge framework, respectively), such as along the
axis 768. The gantry, in specific embodiments and as further
illustrated herein, is enclosed by the analyzer apparatus. The set
of tracks can be parallel to one another and elongate in a first
direction 762, such as along a width or a length of the analyzer
apparatus. The bridge framework spans the set of tracks in a second
direction 764 and can travel along the set of tracks in the first
direction 762 that the set of tracks elongate in.
[0105] The gantry head 756 includes the plurality of interface
tools arranged thereon. The gantry head can provide a particular
physical interaction with the biological sample by rotating the
gantry head to align a respective interface tool with a particular
location, as further described herein. In specific embodiments, the
gantry moves the gantry head to different locations that are
between and outside the set of tracks in two-dimensional and/or
three-dimensional directions (e.g., X and Y and/or X, Y, and Z) via
movement of the bridge framework and/or gantry head. The different
interface tools can include a thermal energy tool to heat or cool
the biological sample (e.g., a TEC), a magnetic source to apply
magnetic forces, an acoustic tool for applying acoustic tools, a
motor, and various other tools.
[0106] FIG. 7H illustrates another example of a gantry apparatus in
accordance with various embodiments. As illustrated, the gantry
apparatus includes a first set of tracks, a bridge framework 769, a
vertical adjustment arm 770, and a gantry head 756. The first set
of tracks are arranged parallel to one another and the bridge
framework 769 spans the set of tracks. For example, the bridge
framework 769 can be perpendicular to the first set of tracks,
although embodiments are not so limited and the bridge framework
can be at a variety of angles to the first set of tracks. The
bridge framework 769 can include a second set of tracks 772-1,
772-2 arranged parallel to one another and perpendicular to the
first set of tracks, as illustrated. The vertical adjustment arm
770 can be coupled to the second set of tracks 772-1, 772-2 such
that the vertical adjustment arm can move to different locations
along the second direction 764 of the second set of tracks (e.g.,
from one side edge of the bridge framework to an opposing side edge
of the bridge framework). The vertical adjustment arm 770 can also
include a third set of tracks that are arranged perpendicular to
both the first set of tracks and the second set of tracks, and
which allow the coupled gantry head 756 to be moved up or down the
length of the vertical adjustment arm such as along axis 768 (e.g.,
to be moved further away from the bridge framework or closer to the
bridge framework, respectively). The gantry, in specific
embodiments and as further illustrated herein, is enclosed by the
analyzer apparatus. The first set of tracks can be parallel to one
another and elongate in a first direction 762, such as along a
width or a length of the analyzer apparatus. The gantry head
includes the plurality of interface tools, as discussed herein. The
gantry head can provide a particular physical interaction with the
biological sample by rotating the gantry head to align a respective
interface tool with a particular location, as further described
herein.
[0107] FIG. 7I illustrates another example of a gantry apparatus in
accordance with various embodiments. As illustrated, the gantry
apparatus includes a set of tracks, a bridge framework 773, a set
of adjustable brackets 774-1, 774-2, and a gantry head 756. The set
of tracks are arranged parallel to one another and the bridge
framework 773 spans the set of tracks. For example, the bridge
framework 773 can be perpendicular to the set of tracks, although
embodiments are not so limited and the bridge framework 773 can be
at a variety of angles to the set of tracks. The bridge framework
773 can be adjustable via the adjustable brackets 774-1, 774-2,
such that the bridge framework 773 is moved up or down along the
axis 768. The gantry head 756 can be coupled to the bridge
framework 773, such that the gantry head 756 can move to different
positions along the bridge framework 773, such as along the second
direction 764. Moreover, the set of adjustable brackets 774-1,
774-2 can move to different positions along the set of tracks, such
as along the first direction 762. The gantry, in specific
embodiments and as further illustrated herein, is enclosed by the
analyzer apparatus. The set of tracks can be parallel to one
another and elongate in a first direction 762, such as along a
width or a length of the analyzer apparatus. The gantry head 756
includes the plurality of interface tools, as discussed herein. The
gantry head 756 can provide a particular physical interaction with
the biological sample by rotating the gantry head to align a
respective interface tool with a particular location, as further
described herein.
[0108] FIGS. 8A-8E illustrate examples of sample-processing
cartridges, in accordance with various embodiments of the present
disclosure. The sample-processing cartridge can include a board
assembly with a plurality of chambers that are in fluidic
connection and that are used to perform the hybridization of the
probes to the targets in the sample, purification, and
amplification (and optionally the hybridization of the amplicons to
a substrate, such as a microarray), such as the rapid assay
apparatus illustrated by FIGS. 8A-8C. In such an apparatus,
relevant chambers and/or modules are in fluidic communication so as
to pass the biological sample from one chamber/module to the next
for operating on the biological sample according to the
functionality relevant thereto, such as the hybridization to
probes, target purification, and amplification. In other
embodiments, one or more additional apparatuses can be used to
perform the hybridization and amplification processes, such as
various thermal cyclers. For example, the biological sample can be
in fluidic movement through a plurality of chambers of a
sample-processing cartridge.
[0109] As illustrated, the sample-processing cartridges have data
804 thereon, e.g., the barcode, radio frequency tag, and/or memory
location, which is used to self-configure an analyzer apparatus for
assisting in processing the biological sample contained within the
sample-processing cartridge. The data 804 can include or provide a
memory location to obtain configuration information used to
identify various biochemical processes to be performed and the
order for performing the biochemical processes, locations of the
sample-processing cartridge associated with the biochemical
processes, and various parameters (e.g., temperature, timing,
volume, etc.) associated with each of the biochemical processes. As
previously described, the sample-processing cartridge can
additionally include a means for a user to configure the test
performed thereon, such as a label for the user to mark and/or
coded data read from the sample-processing cartridge (e.g., a QR
code).
[0110] In various embodiments, although not necessarily illustrated
by FIGS. 8A-8E, the sample-processing cartridge can include a
location for the analyzer apparatus to mark and/or otherwise
disable the sample-processing cartridge after processing is
complete. For example, the analyzer apparatus can change a color of
a thermal label or marker, burn a location of the sample-processing
cartridge, and/or code data on the sample-processing cartridge to
disable the sample-processing cartridge or otherwise indicate that
the sample-processing cartridge has already been processed. The
marking and/or disablement can prevent or mitigate an additional
test from being performed on the sample-processing cartridge. As a
specific example, the sample-processing cartridge can include a
thermal label or marker. After processing the cartridge, the
analyzer apparatus uses the thermal energy tool (or an optical
tool) to change a color of the thermal label or marker. By changing
the color, if the same sample-processing cartridge is inserted back
into the analyzer apparatus, the analyzer apparatus recognizes that
the sample-processing cartridge has already been processed and
rejects the test (e.g., outputs error message such as indicating
cartridge is already processed). As another specific example, after
processing the cartridge, the analyzer apparatus burns a portion of
the sample-processing cartridge, such as burning the location of
the data so that the data cannot subsequently be read or burning a
predetermined location that indicates the cartridge has been
processed. The analyzer apparatus can use the thermal energy source
or a laser to burn the sample-processing cartridge. In another
embodiment, the analyzer apparatus may recode the data on the
sample-processing cartridge after processing the cartridge.
[0111] More specifically, FIG. 8A illustrates an example
sample-processing cartridge used for analyzing cell free DNA. The
sample-processing cartridge includes a plurality of biochemical
processing modules that are self-contained on a board assembly. The
board assembly includes fluid chambers and channels for processing
a biological sample. In the specific embodiment illustrated by FIG.
8A, the biochemical processing modules includes a sample collection
module connected to the blood tube containing the blood sample
(e.g., plasma or serum), DNA isolation module, target purification
module (which is also referred to herein as "a DNA extraction
module"), target selection module, amplification module, and
detection module. The sample-processing cartridge further includes
the data 804 used to identify the configuration information and to
configure the analyzer apparatus for a series of state
configurations for processing the biological sample. For example,
the configuration information can include spatial information
identifying the locations of the respective modules, orders of
processing the respective modules, biological-sample stimulators
used to process the modules, and interface parameters at different
times throughout the analysis.
[0112] FIG. 8B illustrates an example of a board assembly and FIG.
8C illustrates the separate biochemical processing modules. In
various embodiments, the same board assembly can be used to form
different sample-processing cartridges by connecting the respective
biochemical processing modules used for processing the biological
sample.
[0113] FIGS. 8D-8E illustrate other examples sample-processing
cartridges. FIG. 8D illustrates an example cartridge used to
analyze genomic DNA. The cartridge can include a swab elution
module, a lysis module, a reverse transcription and PCR module, and
detection module. FIG. 8E illustrates an example cartridge used to
analyze mRNA. The cartridge can include a spore extraction module,
purification module, PCR module, and detection module.
[0114] Embodiments are not limited to the sample-processing
cartridges illustrated by FIGS. 8A-8E and can include a variety of
commercially available cartridges, such as various microfluidic
chips.
More Specific/Experimental Embodiments
[0115] Embodiments in accordance with the present disclosure
include use of an analyzer apparatus to analyze and/or otherwise
process different sample-processing cartridges. The analyzer
apparatus is self-configurable for a plurality of different types
of biological samples, mitigating manual configuration by a user,
such as a laboratory technician, and which allows for the analyzer
apparatus to be used for a variety of different analyses and
processes. The different sample-processing cartridges can have
different biochemical processing modules at different locations
used to process different types of biological samples, such as
genomic DNA, cfDNA, synthetic DNA, mRNA, miRNA, and other types of
samples. The analyzer apparatus can be used in various experimental
and/or more specific embodiments to analyze a specific biological
sample contained within a specific sample-processing cartridge.
[0116] FIG. 9 illustrates an example method of using an analyzer
apparatus for performing an analysis on a biological sample, in
accordance with various specific and/or experimental embodiments of
the present disclosure. A biological sample is collected from an
organism, such as a human or other animal (although embodiments are
not so limited and can include plant based samples) and placed in a
sample-processing cartridge, at 950. The sample-processing
cartridge can be configured for a particular analysis, at 956. For
example, a plurality of different sample-processing cartridges can
be available and used for different analysis. The user selects the
particular sample-processing cartridge based on the process to be
performed (e.g., end result intended). As previously described, the
sample-processing cartridge can have data thereon that identifies
the sample-processing cartridge. In various embodiments, the data
can be used to automatically (e.g., without additional user input)
configure the analyzer apparatus for the specific analysis to be
performed. In other embodiments, the user may enter the data into
the analyzer apparatus and/or external processing circuitry in
communication with the analyzer apparatus and which is used to
self-configure the analyzer apparatus.
[0117] As a specific example, the sample-specific configuration can
include placing the sample-processing cartridge into the portable
container of the analyzer apparatus, at 951. In response thereto,
the analyzer apparatus identifies the data on the sample-processing
cartridge and associated configuration information, at 953. Using
the configuration information, the analyzer apparatus can
self-configure itself for the particular analysis including the
series of state configurations as described above, at 955.
[0118] Using the series of state configurations, an analysis of the
biological sample is performed. FIG. 9 illustrates a specific
analysis of DNA. For example, the series of configuration states
can include DNA preparation at 959, library preparation at 960,
detection at 968, and analysis at 974.
[0119] The DNA preparation at 959 can include DNA extraction at 957
and DNA isolation at 958 (e.g., lysis and bind). In a specific
experimental embodiment, DNA extraction includes mixing the
biological sample with enzymes and chemicals to release the DNA
bound to proteins in the sample. In DNA extraction, example
processing techniques involve the use of proteinase K, a detergent
(such as tween-20), and/or chaotropic salts (such as guanidinium
thiocyanate) and heat to activate the proteinase K. In accordance
with various embodiments, the analyzer apparatus is configurable to
engage a reagent block on the sample-processing cartridge
(utilizing the gantry), to release liquid extraction reagents
(utilizing the pneumatic stimulator), and move the sample to an
extraction module (using the pneumatic stimulator). In the case of
extraction, the gantry provides heat through the thermal stimulator
(e.g., TEC) to the sample mixed with extraction chemistry to 56
degrees Celsius for 30 minutes and then cools the sample back to
room temperature to move on to the purification step.
[0120] Once the DNA is extracted from bound proteins, the DNA is
isolated from the rest of the plasma components (proteins, small
molecules, lipids, etc.). Various approaches to DNA isolation
include the use of silica frit spin columns or silica coated
magnetic beads. In these approaches, the DNA can be bound to the
silica frit by adjusting a chaotropic salt concentration while
other biomolecules remain in solution. The DNA is isolated by
washing with buffers (e.g. ethanol, isopropanol, low chaotropic
salt buffers) to remove the biomolecules in solution. Finally, the
DNA is eluted using a water buffer (e.g. Tris). In accordance with
the present disclosure, the DNA is isolated using a mixing and
binding chamber and a series of states as defined by the
sample-processing cartridge at the sample run start. In one
example, the sample-processing cartridge contains a mixing station
and an embedded silica frit. The hardware state configures the
pneumatic stimulator to deliver X M of guanidinium thiocyanate and
Tween 20 to a final concentration of 5% to the biological sample in
the mixing station (collectively the binding buffer). The mixing
can be controlled by the analyzer apparatus using a number of
different biological-sample stimulators: (1) creating turbulent
flow using air bubbles (accomplished by the pneumatic stimulator),
(2) the gantry can move a magnet around the chamber with magnetic
beads in the chamber or (3) the gantry can use a motor to turn a
paddle that is part of the mixing module. The biological sample and
binding buffers are then flowed over a silica frit. The DNA is
bound under conditions that are used commonly and well known by one
of ordinary skill in the art. The frit is washed and then dried.
The process of drying involves setting states that drive both air
flow over the fit and heating from a TEC on the gantry. The
biological sample is eluted using a Tris EDTA buffer. The gantry
and thermal stimulator (e.g., thermal energy tool) provide variable
elution temperatures to improve the yield of nucleic acid release
of the DNA. The description above provides one example workflow of
DNA isolation. As previously described, the DNA preparation can
include one module or two separate modules used to respectively
perform the extraction and isolation.
[0121] The library preparation, at 960, can include adding probes
to the sample, at 961, and binding the probes to target DNA (e.g.,
hybridization), at 963. The probes, as would be appreciated, can be
complementary to target sequences. The probes can be configured to
bind to detection probes which may be bound to an array. For
example, the detection probes can include a complementary sequence
to the probes. As further described herein, in some embodiments,
streptavidin solids supports are used to enable the capture of
specific targets. The targets bound to the probes can then be
ligated, at 965. For example, probes that annealed to the sample
DNA are ligated together joining two probes that were previously
independent molecules so that a single molecule includes both
universal primer binding sites. The analyzer apparatus can provide
pressure, flow control, magnetic forces, and heating, such as via
the gantry and/or use of other biological-sample stimulators.
[0122] The bound targets are then amplified via a PCR process, at
967. During the amplification step, the analyzer apparatus can
change configuration to provide hardware components to the location
defined by the configuration processing circuit for amplification
and controls the timing at each temperature state. In various
embodiments, the PCR process includes universal PCR that uses
universal PCR primers. As a specific example of a PCR process, the
enzyme polymerase and deoxynucleoside trisphosphates (dNTPs) are
added to the sample. Polymerase, such as Taq polymerase, is an
enzyme that synthesizes nucleic acid molecules from
deoxyribonucleotides. The dNTPs are the building blocks, e.g., the
deoxyribonucleotides, from which polymerase synthesizes new DNA
and/or RNA strands. Other components and reagents may be added,
such as a buffer solution to provide a chemical environment that is
suitable for activity and stability of polymerase, bivalent
cations, magnesium, manganese ions, and/or potassium ions. The
various components and/or reagents are added to the sample via
movement of the biological sample through one or more chambers of
the sample-processing cartridge, although embodiments are not so
limited and can include the addition of components and/or reagents
through other techniques.
[0123] The example PCR process includes repeated cycles of
temperature changes. The cycling includes denaturation, annealing,
and elongation. Denaturing can include heating the reaction to a
first threshold temperature (e.g., 94-98 degrees Celsius) for a
period of time, such as 20-30 seconds. Such denaturing causes
nucleic acid melting by disrupting the hydrogen bonds between
complementary bases and results in single-stranded nucleic acid
molecules. The annealing operation can include heating the reaction
to a second threshold temperature that is lower than the first
threshold temperature (e.g., 50-65 degrees Celsius) for a period of
time, such as 20-40 seconds. Such annealing causes the PCR primers
to bind (e.g., anneal or hybridize) to the target. The elongation
can include heating the reaction to a third threshold temperature
which is dependent on the particular polymerase used, whether Taq
polymerase or another suitable thermostable DNA polymerase. Using
Taq, this polymerase can be optimally active at a temperature of
75-80 degrees Celsius and a temperature of 72 degrees may be used.
During the elongation process, polymerase synthesizes a new nucleic
acid strand complementary to the target by adding dNTPs that are
complementary to the target in 5' to 3' direction, and condenses
the 5'-phosphate group of the dNTPs with the 3'-hydroxyl group at
the end of the nascent (extending) nucleic acid strand.
[0124] After the repeated cycles, a final elongation is performed.
The final elongation includes heating the reaction to a fourth
threshold temperature (e.g., 70-74 degrees Celsius or a value less
than 90 degrees Celsius) for a period of time, such as 5-15
minutes. The final elongation process is used to ensure any
remaining single-stranded nucleic acid sequence is fully extended.
Optionally, after the final elongation, a final hold is performed.
The final hold includes cooling the reaction to a particular
temperature (e.g., 4-15 degrees Celsius). In various embodiments,
the amplified reaction is stored within at the particular
temperature. For example, the biological sample can be processed by
the analyzer apparatus for subsequent analysis. In other specific
embodiments, the amplicons are not stored, but rather analyzed
immediately after the amplification process using the analyzer
apparatus. As previously described, the library preparation can
include one module or separate modules used to respectively perform
the target selection and amplification. The gantry, thermal
stimulator, and pneumatic stimulator (as well as the electrical
stimulator) can be used to provide the various interactions
described above, including the repeated cycles of temperature
changes.
[0125] The amplicons are bound to the substrate, such as an array.
The targets can be detected at 968 via post-PCR processing at 969,
purification at 971, and detection at 973, such as via a detection
module as previously describe. Various post-PCR processing can be
performed including purification and detection at 968. In various
embodiments, an analysis is done by hybridization to a substrate,
such as a microarray. The analyzer apparatus controls the mixing of
the sample and hybridization buffer in preparation for DNA
hybridization using the pneumatic stimulator. In addition, the
analyzer apparatus can control the optical and thermal stimulators.
The protocol (e.g. hybridization time, temperature, imaging time,
mixing) is defined by the sample-processing cartridge prior to the
run and the analyzer apparatus is configured at the moment.
[0126] In some specific embodiments, the output can include an
analysis of the quantification of targets, at 974. For example, a
digital output is provided by analyzing the surface of the
substrate. Fluorescent signals at unique locations of the
substrate, and indicative of a tag sequence and associated target,
are analyzed and/or imaged using the optical stimulator, at 975.
The fluorescent signals are referred to as tag signals in FIG. 9.
In response to detecting a tag signal, the intensity of the tag
signal is background corrected using a background noise value and
normalized, at 977. In various embodiments, the background
corrected and normalized tag signal is compared to a threshold to
convert the output to a digital result (e.g., 0 or 1, pass/fail,
off/on) for each tag indicative of a target at, 979. The threshold
includes a simple pass/fail threshold. Optional, the binary result
is output for each unique location that is associated with a tag
sequence indicative of a target being analyzed, at 981, the binary
results are combined, at 982, and the target count scores are
output, at 983. For more general information regarding quantifying
targets and specific information relating to a digital output of
quantified targets, references is made to PCT Application (Ser. No.
PCT/US2017/024098), entitled "Apparatuses and Methods for Assessing
Target Sequence Numbers," filed Mar. 24, 2017, which is fully
incorporated herein by reference. Although embodiments are not
limited to a digital output and can include a variety of substrate
analyses.
[0127] FIG. 10 illustrates an example method of using an analyzer
apparatus for performing an analysis on a biological sample, in
accordance with various embodiments of the present disclosure. For
example, FIG. 10 illustrates an example of analyzing cell free
(cf)DNA in accordance with various specific and/or experimental
embodiments. As illustrated cfDNA analysis can include DNA
extraction at 1001, DNA isolation at 1003, biotinylation at 1005,
probe anneal at 1007, ligation and streptavidin binding at 1009,
universal PCR at 1011, quantification of targets at 1013, and
analysis at 1015.
[0128] In some specific and experimental embodiments, the
sample-processing cartridge illustrated by FIG. 8A is inserted into
an analyzer apparatus illustrated by FIG. 2 which has a gantry as
illustrated by 7A. As may be appreciated, embodiments are not so
limited and a variety of sample-processing cartridges and analyzer
apparatuses can be used. In response to insertion of the
sample-processing cartridge illustrated by FIG. 8A into the
analyzer apparatus, the sample-specific configuration circuitry of
the analyzer apparatus (e.g., sample-specific configuration
circuitry 218 illustrated by FIG. 2) identifies the data (e.g.,
data 804 illustrated by FIG. 8A) located on the sample-processing
cartridge and uses the data to configure itself. The
self-configuration includes a series of state configurations, as
previously described, including identification of which
biological-sample stimulators interact with the biological sample
at particular times, as well as the positions in the portable
container for the biological-sample stimulators at the different
times. The positions are associated with locations of the
biochemical processing modules of the sample-processing cartridge.
The data on the sample-processing cartridge provides spatial
location information of the specific biochemical processing modules
(e.g., the purification, DNA isolation, target selection,
amplification, and detection modules) self-contained in the
sample-processing cartridge along with timing and or temperature
information and identification of the selected biological-sample
stimulators used for performing the analysis at the specific
times.
[0129] The identified positions are used by the different
biological-sample stimulators to interact with the biological
sample at the correct locations of the sample-processing cartridge.
In some embodiments, the pneumatic stimulator (e.g., pneumatic
stimulator 222 illustrated by FIG. 2) can use the identified
positons to send forces that control movement of the sample
throughout the analysis or cause specific channels to be blocked
using a pneumatic valve. As previously described, the pneumatic
stimulator includes a pump, tubing and channels that sends forces
toward the biological sample and constantly controls movement of
the biological sample through the sample-processing cartridge based
on the configuration information. The gantry can locate different
interactive tools at any locations within the analyzer apparatus.
More specifically, the gantry head is moved in x, y, and/or z
directions to the different positions and based on identification
of locations of the different biochemical processing modules of the
inserted sample-processing cartridge.
[0130] As previously described, the sample-processing cartridge
includes a plurality of biochemical processing modules. In an
example experimental embodiment, the sample-processing cartridge
includes, as illustrated by FIG. 8A, a purification module used to
perform DNA preparation including DNA extraction at 1001 and DNA
isolation at 1003, a target selection module and amplification
module used to perform library preparation including (optionally)
biotinylation at 1005, probe anneal at 1007, streptavidin binding
and ligation at 1009 and universal PCR at 1011, and a detection
module used to quantify targets at 1013 and analyze the targets at
1015. Each biochemical process module can include at least one
chamber that is connected to other portions of the biochemical
processing module (or other modules) by channels and valves. The
pneumatic stimulator controls the flow of the biological sample and
other reagents through the sample-processing cartridge. In the
specific experimental embodiment, the purification module includes
a lysis chamber, binding elements (e.g., beads or solid supports),
a mixing chamber, and a TEC interface. The DNA isolation chamber
can include one or more binding agent chambers configured to hold
liquid reagents and selectively provide the reagents to chambers of
the purification module. The target selection module can include
one more chambers, lyophilized probes and enzymes, and a TEC
interface. In specific embodiments, the target selection module
includes a biotinylation chamber, a probe chamber, and a ligation
chamber. In other embodiments, the target selection module includes
a single library preparation chamber used to perform the library
preparation. The amplification module includes an amplification
chamber, lyophilized primers, enzymes and other reagents, and one
or more TEC interfaces. The detection module includes a mixing
chamber to prepare the biological sample for hybridization, a
hybridization chamber having an assay, and interfaces to the TEC,
optics, and laser.
[0131] The DNA extraction 1001 and DNA isolation 1003 can be used
to perform DNA preparation. DNA preparation can be performed using
multiple modules or a single module of the sample-processing
cartridge. For example, as illustrated by FIG. 8A, the DNA
extraction module is separate from the DNA isolation module.
Although embodiments are not so limited and a purification module
(e.g., such as the purification module 334 illustrated by FIG. 3)
can be used to perform both DNA extraction and isolation. After
inserting the sample-processing cartridge into the analyzer
apparatus and configuring for analysis, the pneumatic stimulator
moves at least a portion of the biological sample from a blood tube
(or other input for the biological sample) to the one or more
modules for DNA preparation. In a specific example, the pneumatic
stimulator moves the portion of the biological sample from the
blood tube to the purification module for DNA extraction followed
by DNA isolation. For example, and as further described in the
below specific experimental embodiment, 2 mL of plasma can be moved
from a blood tube container that is holding 2.7 mL of plasma.
[0132] As previously described, DNA extraction at 1001 involves
mixing raw plasma with enzymes and chemicals to release the cfDNA
bound to proteins in the plasma within the purification module of
the sample-processing cartridge. For DNA extraction, the pneumatic,
electrical, and mechanical stimulators can be used. Typical
processing techniques involve the use of proteinase K, a detergent
(such as tween-20), and/or chaotropic salts (such as guanidinium
thiocyanate) and heat to activate the proteinase K. In accordance
with various embodiments, the analyzer apparatus is
self-configurable to engage a liquid reagents module on the
sample-processing cartridge (utilizing the gantry), to release
liquid extraction reagents (utilizing the pneumatic stimulator),
move the biological sample to the purification module (using the
pneumatic stimulator), and mix solutions (using the magnetic or
mechanical elements of the gantry, or the pneumatic stimulator).
The purification module can include a mix chamber used for mixing
the liquid extraction reagents with the biological sample. In some
embodiments, the mix chamber has proteinase K located therein, and
the detergent and/or chaotropic salts are released from the liquid
reagents module (e.g., such as from a liquid reagents module 338
illustrated by FIG. 3) and moved to the purification module via use
of the pneumatic stimulator. In other embodiments, each of the
liquid extraction reagents, include proteinase K, are moved from
the liquid reagents module. The gantry provides heat through the
thermal stimulator (e.g., the TEC) to the biological sample mixed
with extraction chemistry to 56 degrees Celsius for 30 minutes and
then cools the biological sample back to room temperature to move
on further processing and purification. For example, the gantry
moves the gantry head in an x, y, and/z direction to position the
gantry head and a respective heat source at a location of or
associated with the purification module and provides the heat
(e.g., 56 degrees Celsius) for the respective amount of time and at
the particular time.
[0133] Once the DNA is extracted from bound proteins, at 1003, the
DNA is isolated from the rest of the plasma components (proteins,
small molecules, lipids, etc.). As noted above, a DNA isolation
module can be used to perform DNA isolation. The DNA isolation
module includes different liquid reagent chambers and/or bead
elements. For example, the biological sample, which includes the
extracted DNA mixed with the liquid extraction reagents, is moved
from the mix chamber to one or more other chambers for isolating
the DNA (e.g., mixing and/or binding chambers which are part of the
purification module). The biological sample with liquid extraction
reagents is moved via the pneumatic stimulator. While, after,
and/or before moving the biological sample, the gantry can also
move the gantry head to a position near the other chambers by
moving the gantry head in an x, y, and/or z direction. Well
described approaches to DNA isolation include the use of silica
frit spin columns or silica coated magnetic beads. In these
approaches, the DNA is preferentially bound to the silica by
adjusting a chaotropic salt concentration while other biomolecules
remain in solution. The DNA is isolated by washing with buffers
(e.g. ethanol, isopropanol, low chaotropic salt buffers) to remove
the biomolecules in solution. Finally, the DNA is eluted using a
water buffer (e.g. Tris).
[0134] In a specific experimental example, the purification module
contains a (binding) chamber having an embedded silica frit.
Although embodiments are not so limited and other types of binding
elements can be used. The state configurations can include the
pneumatic stimulator delivering X M of guanidinium thiocyanate
(GTC) and Tween 20 to a final concentration of 10% to the
biological sample in the mixing chamber (collectively, the binding
buffer). In the above-described specific embodiment, the solution
of plasma and proteinase K are mixed with isopropanol and
additional GTC and then flowed to the binding chamber having the
embedded silica frit. While in the binding chamber, the solution is
washed with different buffers (wash and ethanol), then dried and
eluted using the elution.
[0135] The mixing can be controlled by the analyzer apparatus using
a number of different biological-sample stimulators to: (1) create
turbulent flow using air bubbles (accomplished by the pneumatic
stimulator), (2) the gantry can move a magnet around the chamber
with magnetic beads in the chamber or (3) the gantry can use a
motor to turn a paddle that is part of one or more of the chambers.
The gantry head, which may be located at a position associated with
the location of the purification module, can rotate to utilize
different interface tools used to provide different interactions
with the biological sample. The biological sample and binding
buffers are then flowed over a silica frit. The DNA is bound under
conditions that are used commonly and well known by one of ordinary
skill. The frit is washed and then dried. The process of drying
involves setting states that drive both air flow over the frit
using the pneumatic stimulator and heating from a TEC on the gantry
using a heat source (e.g., rotating the gantry head to position the
heat source relative to the frit). Finally, the biological sample
is eluted using a Tris EDTA buffer via the pneumatic stimulator
which drives (e.g., air) the buffer to the respective chamber. The
mechanical and thermal stimulators provide variable elution
temperatures to improve the yield of nucleic acid release of the
DNA. Optionally, embodiments can utilize solid-phase reverse
immobilization (SPRI) to bias the purified DNA for specific
lengths. The pneumatic simulator moves the sample to magnetic beads
held in a chamber which mixes the sample with the beads. The beads
are captured using a magnet on the gantry to enable the pneumatic
stimulator to empty the chamber of the binding solution and provide
multiple solutions of different polyethylene glycol and ethanol
percentages in order to bias the washing of different DNA fragment
lengths. Finally, the gantry stimulator collects the beads while
the pneumatic stimulator empties the chamber and introduces an
elution buffer. The DNA sample is eluted from the bead by a TEC on
the gantry as directed by the data encoded in the consumable
cartridge. The DNA is then moved by the pneumatic simulator to
prepare the library for targeted sequence analysis.
[0136] After the DNA preparation, the library can be prepared.
Library preparation can include use of a target selection module
and an amplification module of the sample-processing cartridge. For
example, after extracting and isolating the DNA, the biological
sample is moved to the target selection module via the pneumatic
stimulator. In many typical library approaches, streptavidin solids
supports are used to capture specific reagents. In the case of
cfDNA purification, a streptavidin support can be used to capture
the cfDNA after it has been biotinylated by a biochemical terminal
transferase enzyme, at 1005. The thermal stimulator and gantry
provide the conditions to carry out the biochemical reaction, while
the pneumatic stimulator provides the movement of the biological
sample to the biotinylation chamber. For example, the biological
sample (which has various liquid reagents added) is moved from the
purification module to the target selection module. The target
selection module includes a biotinylation chamber having reagents
for performing biotinylation, such as biotin and terminal
deoxytransferase. The gantry head can rotate to locate the heat
source proximal to the biotinylation chamber and to heat the
mixture (such as to 37 degrees for sixty minutes).
[0137] The solution is then mixed with probes for annealing. After
annealing with probes, at 1007, the mixture containing the
biological sample is moved and captured on a streptavidin solid
support in a ligation chamber via the pneumatic stimulator. The
target selection module can include the chamber for performing
biotinylation and/or the probe chamber having the streptavidin
solid support. The solid support can isolate the cfDNA in multiple
ways, such as magnetic beads coated with streptavidin or flow
through filters functionalized with streptavidin. The ligation
chamber can include the solid support and primers, although
embodiments are not so limited and the solid supports and primers
can be moved into the probe chamber to mix with the biological
sample. The gantry head, which is located at the target selection
module and/or specifically at the probe chamber can be used to heat
the probe chamber (e.g., 70 Celsius for 2 minutes and 35 Celsius
for 2 hours), and liquid reagents are brought into the probe
chamber from the liquid reagents module 338 (such as, LS wash and
HS wash) using the pneumatic stimulator 222. The gantry head can
then rotate to locate a magnetic source proximal to the probe
chamber, and uses the magnetic source to mix the different liquids
in the probe chamber.
[0138] Next the probes that are annealed to the sample DNA are
ligated together joining two probes that were previously
independent molecules so that a single molecule now includes both
universal primer binding sites, at 1009. In these examples, the
analyzer apparatus provides pressure, flow control, magnetic
forces, and heating. The ligation can occur by the gantry head
providing a series of interactions with the biological sample and
various liquid reagents. In some embodiments, the target selection
module includes a ligation chamber, although embodiments are not so
limited and one or more of the biotinylation chamber, the probe
chamber, and ligation chamber are a single chamber. The mixture,
which includes DNA bound to the streptavidin support (or other
solid support(s)) and primers) is moved to the ligation chamber
using the pneumatic stimulator 222. The gantry head is also moved
to a position associated with (or already is located at the
position) the ligation chamber to provide various interactions with
the biological sample. For example, the gantry head can heat the
biological sample and various liquid reagents, liquid reagents are
brought into the ligation chamber from the liquid reagents module
338 (such as, HS wash and elution wash) using the pneumatic
stimulator, a magnetic source is used to mix the different liquids
in the ligation chamber, the mixture is heated using the heat
source, and the magnetic source is again used to mix the mixture.
In the above-described specific embodiment, the solution containing
DNA bound to the solid support and probes in the ligation chamber
is washed and eluted. Elution can be accomplished chemically (NaOH)
or thermally (denaturing the double stranded DNA above the ligated
product melting temperature).
[0139] The mixture is then flowed to the amplification module,
which includes an amplification (e.g., PCR) chamber and probes,
enzymes and various reagents. Universal amplification and labeling
of the annealed biological sample utilize both thermal and
mechanical stimulators with sample movement controlled by the
pneumatic stimulator, at 1011. During the amplification step, the
analyzer apparatus changes configuration to provide the different
biological-sample stimulators to the location defined by the
configuration processing circuit for amplification and controls the
timing at each temperature state. The amplification can include
repeated cycles of different temperatures, e.g., PCR, as would be
well understood by one of ordinary skill. The gantry head can
provide the different temperatures and for the particular amount of
time at the amplification chamber. In the above-described specific
embodiment, the solution containing DNA eluted from the solid
support is mixed with PCR mixture.
[0140] Although the above describes various different chambers used
for the library preparation, in some embodiments, the library
preparation incudes use of a target selection module and an
amplification module. The target selection module includes a first
chamber in which the biological sample (as extracted and isolated)
is mixed with a solid structure, oligonucleotide probes and various
reagents to anneal the isolated DNA targets to the solid structures
and probes (e.g., biotinylation, probe anneal, and ligation).
Various liquid reagents are brought to the first chamber via the
pneumatic stimulator. The amplification module includes an
amplification chamber, as described above, which is used to perform
PCR by mixing the bound target DNA with a PCR mixture and
performing the amplification using the pneumatic stimulator and
gantry.
[0141] The amplified DNA targets are then moved to a detection
module of the sample-processing cartridge via the pneumatic
stimulator for sequence analysis. The gantry head can additionally
be moved to a position associated with the detection module. The
sequence analysis can be performed by hybridization of the targets
to a (DNA) microarray. For example, the solution is flown to a
mixing chamber for preparing the biological sample for
hybridization. The analyzer apparatus controls the mixing of the
biological sample and hybridization buffer, such as SSPE, in
preparation for DNA hybridization using the pneumatic stimulator.
The prepared solution is then flowed to a hybridization chamber
that has an assay, such as a microarray, for hybridizing to the
assay and for detection of the targets. The hybridization assay can
be heated to assist in the hybridization. The analyzer apparatus
can control the optical and thermal stimulator for performing the
hybridization and subsequent detection. The protocol (e.g.
hybridization time, temperature, imaging time, mixing) is defined
by the sample-processing cartridge prior to the run and the
analyzer apparatus is configured at the moment which can be used to
quantify targets, at 1013, and perform analysis on the results, at
1015. The detection module can include, in the specific example, a
mixing chamber having hybridization buffer and the hybridization
chamber having the (DNA) microarray (although embodiments are not
so limited), and the pneumatic stimulator is used to move the
mixture from the mixing chamber to the hybridization chamber.
[0142] Although the above FIG. 10 describes a particular example,
embodiments are not limited to the specific liquid reagents,
chambers, temperatures, and/or amounts of reagents/liquids. The
reagents, in further specific embodiments, can be frozen and/or
lyophilized.
[0143] The following is a specific example of processing a
biological sample using the analyzer apparatus as illustrated by
FIG. 2 in accordance with various embodiment and the
sample-processing cartridge illustrated by FIG. 8A. In the specific
example, the pneumatic stimulator (e.g., the pneumatic stimulator
222 illustrated by FIG. 2) moves 2 mL of the biological sample from
the plasma tube to the purification module for DNA extraction and
DNA isolation. For example, 2 mL of plasma is mixed with 0.58 mL of
lysis reagents including proteinase K in the lysis chamber and then
flowed to a binding chamber. In the binding chamber, the 2.58 mL
solution of plasma and proteinase K are mixed with 2.0 mL of a GTC
and tween-20 (forming 4.58 mL solution in the binding chamber) and
then flowed to the mixing chamber having the embedded silica frit.
While in the mixing chamber, the solution is washed with different
buffers (750 uL wash and 750 uL ethanol), then dried and eluted
using the elution to form 20 uL of solution. The 20 uL solution is
then flowed to library preparation module.
[0144] The solution, now 20 uL, is then flown to the target
selection module. More specifically, the 20 uL solution is flown to
the biotinylation chamber and mixed with 1 uL of biotin and heated
to 37 degrees for 60 minutes to form a solution of 21 uL. The 21 uL
solution is then flown to a probe chamber (or optionally all
performed in a single chamber) having the streptavidin solid
support and probes, and is washed with 75 uL wash and 75 uL HS wash
to form a solution of 21 uL. The 21 uL solution is then flown to
the ligation chamber (in various optional embodiments, the
biotinylation chamber, the probe chamber, and ligation chamber are
a single chamber). The solution in the ligation chamber is heated
to 45 degrees Celsius for 30 minutes, liquid reagents are brought
into the ligation chamber from the liquid reagents module (e.g.,
the liquid reagents module 338 illustrated by FIG. 3), such as, HS
wash and elution wash, using the pneumatic stimulator, and a
magnetic source is used to mix the different liquids in the
ligation chamber. The solution is then heated to 95 degrees for 2
minutes using the heat source, and the magnetic source is again
used to mix the solution. The ligation process can form a solution
of 25 uL. The 25 uL solution is then moved to an amplification
chamber of the amplification module and PCR is performed. For
example, the ligated probes and primers are mixed with 1 uL of PCR
mixture to form a 26 uL solution, which is brought through repeated
cycles of different temperatures.
[0145] The amplified DNA targets are then flown to the detection
module. For example, the solution containing the amplified DNA
targets is flown to the mixing chamber of the detection module and
mixed with hybridization buffer, such as SSPE. The solution is then
directed to the hybridization chamber having the microarray and
heated to assist in hybridization using the heat source of the
gantry. The detection module includes interfaces for the optical
stimulator, such as optic and laser interfaces, and which are used
to detect targets bound to the microarray.
[0146] The above described example is a specific experimental
embodiment and various embodiments in accordance with the present
disclosure can include a variety of variations. Some variations, as
described above, can include different sample-processing cartridges
having different numbers or types of biochemical processing
modules. Further, the biochemical processing modules can include
different chambers and flow methods. For example, the reagents can
be liquid, solid, frozen and/or lyophilized. The reagents can be
located in a chamber of the biochemical processing module and the
sample is moved to the chamber. In other embodiments and/or in
addition (at a different biochemical step), reagents can be located
in a first chamber of the biochemical processing module or the
liquid reagents module and can be moved to a second chamber that
the sample is located in. For DNA preparation, other various
embodiments include combining the lysis chamber with the binding
chamber and/or mixing chamber, combining the binding and mixing
chamber into a single binding chamber, using a bind solution for
wash, and/or using beads as the solid support. Targets that are
analyzed are not limited to cfDNA, and can include gDNA, mRNA,
miRNA, and other nucleic acid targets, as well as non-nucleic acid
targets, such as synthetic DNA coupled to an antibody.
[0147] FIG. 11 illustrates an example method of using an analyzer
apparatus for performing an analysis on a sample, in accordance
with various embodiments of the present disclosure. For example,
FIG. 11 illustrates an example of analyzing cell messenger RNA
(mRNA) in peripheral mononuclear cells (PBMCs). The consumable
cartridge provides information to the hardware system, e.g., the
configuration processing circuitry as illustrated in FIG. 7D, to
enable remote programming of the hardware system states to provide
for analysis of mRNA in multiple samples. The illustrative
embodiment described below is for mRNA and can be used to diagnosis
infections, inflammatory disease (e.g. lupus), and certain cancers.
In such embodiments, a sample of whole blood is lysed to extract
the mRNA and other nucleic acids from their cellular compartments,
at 1121. The RNA is isolated from the sample using one or more of a
variety of methods, at 1123, including the solid phase extraction
and poly-A binding for mRNA specific isolation. Other approaches
well known to those skilled in the art. After the isolation, in
some embodiments, the mRNA is separated from the total RNA which
includes both tRNA and rRNA, at 1125.
[0148] One example approach to mRNA purification is using a capture
probe labeled with a separation molecule (e.g. biotin), as shown in
FIG. 12, which is subsequently bound to a solid support using a
streptavidin interaction. The capture probe can be designed to
cover splice junctions or can be a poly-T nucleic acid that
hybridizes to the poly-A tail that is unique to mRNA transcripts.
The hybridized DNA probe: RNA target binds to a solid support using
the separation molecule interactions while the remaining nucleic
acids are washed away. In embodiments that the capture probe is a
poly-T oligonucleotide, (all) the mRNA are captured and the
analyzer apparatus and analysis software can support development
applications. In the instance where the capture probe is for
specific transcripts, the resulting analysis may be only for those
specific transcripts.
[0149] Once the mRNA is captured, at 1127, in specific embodiments,
analysis probes are annealed to the remaining transcripts. The
analysis probes are designed to specifically target different mRNA
transcripts. In some embodiments, only a single analysis probes set
may target a specific transcript sequence or multiple different
analysis probes can be used to provide a signal amplification. The
target probes contain universal PCR primers and tag sequences for
analysis on a DNA microarray. The analysis probes are linked using
a ligase.
[0150] FIG. 12 illustrates a ligase that is active on DNA:RNA
hybrid, in accordance with various embodiments. However,
embodiments are not so limited and other embodiments can include
converting the mRNA transcript to complementary DNA using a reverse
transcriptase and then using standard DNA:DNA ligase to link the
two analysis probes, such as at 1129.
[0151] After ligation, e.g., at 1129, is complete the analysis
probes are separated from the target transcript using one or more
of multiple methods. In one example method, heating the solution
above the melting temperature of the ligated analysis probe can
elute the probe from the solid support and the transcript. As
described above in the cfDNA implementation, the ligated probes are
amplified together in single reaction pool based on the universal
primers, at 1131.
[0152] The amplified DNA targets are then flown to the detection
module. For example, the solution containing the amplified DNA
targets is flown to the mixing chamber of the detection module and
mixed with hybridization buffer, such as SSPE. The solution is then
directed to the hybridization chamber having the microarray and
heated to assist in hybridization using the heat source of the
gantry. The detection module includes interfaces for the optical
stimulator, such as optic and laser interfaces, and which are used
to detect targets bound to the microarray for quantifying the
targets 1133 and further analysis at 1135 as previously
described.
[0153] Various embodiments are implemented in accordance with
patent documents as previous described and identified, and which
are fully incorporated by reference. For information regarding
details of these and other embodiments, applications and
experiments (as combinable in varying degrees with the teachings
herein), reference may be made to the teachings and underlying
references provided in the patent documents which form part of this
patent document and is fully incorporated herein. Accordingly, the
present disclosure is related to methods, applications and devices
in and stemming from the disclosures in the patent documents and
also to the uses and development of devices and processes discussed
in connection with the references cited herein.
[0154] Certain embodiments are directed to a computer program
product (e.g., nonvolatile memory device), which includes a machine
or computer-readable medium having stored thereon instructions
which may be executed by a computer (or other electronic device,
such as processing circuitry or the detection circuitry) to perform
these operations/activities.
[0155] Various embodiments described above may be implemented
together and/or in other manners. One or more of the items depicted
in the present disclosure can also be implemented separately or in
a more integrated manner, or removed and/or rendered as inoperable
in certain cases, as is useful in accordance with particular
applications. In view of the description herein, those skilled in
the art will recognize that many changes may be made thereto
without departing from the spirit and scope of the present
disclosure.
[0156] Based upon the above discussion and illustrations, those
skilled in the art will readily recognize that various
modifications and changes may be made to the various embodiments
without strictly following the exemplary embodiments and
applications illustrated and described herein. As an example, the
processing circuitry and the detection circuitry can be part of
separate devices and in communication via a wireless or wired link
or can be part of the same device. Such modifications do not depart
from the true spirit and scope of various aspects of the invention,
including aspects set forth in the claims.
* * * * *