APPARATUS WITH HETEROGENEOUS PROCESSING MODULES
BACKGROUND OF THE INVENTION
10001] This international application claims priority to U.S. Provisional Application No.
61/639,820, filed on April 27, 2012, the entirety of which is incorporated by reference.
[0002] The analysis of samples such as clinical or environmental samples generally
involves a series of processing steps, which may include separate chemical, optical, electrical,
mechanical, thermal, or acoustical processing of the samples. Conventional systems for
processing samples are each typically dedicated to one type of assay. This is because each
type of assay is very different with respect to target attributes being measured, and also has a
specific series of pre- and post-testing steps.
[0003] Because different assays require different configurations, conveniional systems are
not versatile nor easily adaptable to different protocols. Accordingly, systems for performing
assays are as different as the assays themselves. There is an unanswered need to condense
these systems in a manner that remains flexible for the present and future needs of a user.
BRIEF SUMMARY OF THE INVENTION
[0004] Some embodiments of the invention relate to a biological sample processing
apparatus having an enclosure. A plurality of sample processing modules can be held by the
enclosure. Each sample processing module is configured to hold a removable sample
cartridge and to only perform sample processing on a sample within the corresponding
removable sample cartridge. Each sample processing module can be configured to perform at
feast one of a plurality of testing processes on the sample within the removable sample
cartridge. At least one module in the apparatus can be configured to perform nucleic acid
amplification and detection. At least one module in the apparatus can be a sample
preparation module configured to only perform sample preparation. At least one module in
the apparatus can be configured to perform immunoassays for protein detection.
[0005] In some embodiments, at least one sample processing module can be configured for
hybridizing a nucleic acid to an array on a solid support.
[1006 n some embodiments at least one sample processing module can be configured for
nucleic acid amplication and detection in a multiplex array of wells, wherein each separate
well comprises a separate nucleic acid amplification reaction. In some embodiments, each of
the separate wells of the multiplex array of wells is capable of carrying out a multiplex
reaction (e.g. nested PGR).
[0007] In some embodiments, the at least one sample preparation module can be configured
to prepare a sample to undergo a sample processing protocol for at least one nucleic acid.
[0008] In some embodiments, at least one sample processing module can be configured for
detection of at least one protein analyte.
[0009] In some embodiments, at least one sample processing module can be configured for
assessing a chromosomal copy number of at least one gene of interest.
[0010] In some embodiments, at least one sample processing module can be configured for
performing a multiplex detection of at least two nucleic acid analytes.
[0011] In some embodiments, at least one sample processing module can be configured for
performing a multiplex detection of at least two protein analytes.
[0012] In some embodiments, at least one sample processing module can be configured for
sequencing and detecting a nucleic acid molecule.
[0013] In some embodiments, the plurality of sample processing modules can include at
least one module for detecting at least one protein analyte contained within a biological
sample within a test cartridge, at least one module for assessing chromosomal copy number
of at least one gene of interest contained within a biological sample within a test cartridge;
and at least one module for performing a sample processing protocol for at least one nucleic
acid contained within a biological sample within a test cartridge.
[0014] In some embodiments, the enclosure can hold at least two sample processing
modules.
[0015] In some embodiments, the plurality of sample processing modules includes different
modules configured for different types of sample processing.
[0016] In some embodiments, the plurality of sample processing modules can include at
least one module that can be configured for hybridizing a nucleic acid to an array on a solid
support and/or at least one module that can be configured for detection of at least one protein
analyte and/or at feast one module that can be configured for assessing a chromosomal copy
number of at least one gene of interest and/or at least one module that can be configured for
performing a multiplex detection of at least two nucleic acid analytes and/or at least one
module that can be configured for performing a multiplex detection of at least two nucleic
acid analytes and/or at least one module that can be configured for performing a multiplex
detection of at least two protein analytes and/or at least one module that can be configured for
sequencing and de ecting a nucleic acid molecule and/or at least one module that can be
configured for performing PGR and/or at least one sample processing module that can be
configured for performing rapid PGR.
[0017] n some embodiments, the plurality of sample processing modules ca be up to 16
sample processing modules made up of a combination of modules, which in some
embodiments are different types of modules, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, , 12, 13, 14,
or 15 modules (depending on whether other types of modules are included within the
plurality) that can be configured for a first type of assay and , 2, 3, 4, 5, 6, 7, 8, 9, 0, , 2,
, 14, or 5 modules (depending on whether other types of modules are included within the
plurality) a can be configured for a second type of assay and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, ,
, 12, 3, 14, or 15 modules (depending on whether other types of modules are included
within the plurality) that can be configured for a third type of assay and/or 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, or 15 modules (depending on whether other types of modules are
included within the plurality) tha can be configured for a fourth type of assay and/or , 2, 3,
4, 5, 6, 7, 8, 9, 10, 1 , 12, 13, 14, or 15 modules (depending on whether other types of
modules are included within the plurality) that can be configured for a fifth type of assay
and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 modules (depending on whether other
types of modules are included within the plurality) that can be configured for a sixth type of
assay and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 , 12, 1 , 14, or 15 modules (depending on whether
other types of modules are included within the plurality) that can be configured for a seventh
type of assay and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, , 12, 13, 14, or 15 modules (depending on
whether other types of modules are included within the plurality) that can be configured for
an eighth type of assay and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, , 12, 13, 14, or 15 modules
(depending on whether other types of modules are included within the plurality) that can be
configured for a ninth type of assay and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, , 12, 13, 14, or 15
modules (depending on whether other types of modules are included within the plurality) that
can be configured for a tenth type of assay and' r 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or
15 modules (depending on whether other types of modules are included within the plurality)
that ca be configured for an eleventh type of assay and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, or 15 modules (depending on whether other types of modules are included within the
plurality) a can be configured for a twelfth type of assay and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, ,
11, 12, 13, 14, or 15 modules (depending on whether other types of modules are included
within the plurality) that can be configured for a thirteenth type of assay and/or 1, 2, 3, 4, 5,
6, 7, 8, 9, 10, , 12, 13, 14, or 15 modules (depending on whether other types of modules are
included within he plurality) tha can be configured for a fourteenth type of assay and/or 1, 2,
3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 modules (depending on whether other types of
modules are included within the plurality) that can be configured for a fifteenth type of assay.
[0018] In some embodiments, the plurality of sample processing modules can be up to 6
sample processing modules made up of at lest one module configured to pferform nucleic
acid amplification and detection and a combination of modules, which in some embodiments
are different types of modules, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, , 12, 13, 4 , or 15
modules (depending on whether other types of modules are included within the plurality) that
can be configured for hybridizing a nucleic acid to an array on a solid support and/or 1, 2, 3,
4, 5, 6, 7, 8, 9, 10, , 12, 13, 14, or 5 modules (depending on whether other iypes of
modules are included within the plurality) that can be configured for detection of at least one
protein analyte and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 4, or 15 modules (depending on
whether if other types of modules are included within the plurality ) that can be configured for
assessing a chromosomal nucleic acid copy number of at least one nucleic acid and/or 1, 2, 3,
4, 5, 6, 7, 8, 9, 10, I , 12, 13, 14, or 15 modules (depending on whether if other types of
modules are included within the plurality) that can be configured for performing a multiplex
detection of at least two nucleic acid analyses and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
or 5 modules (depending on whether other types of modules are included within the
plurality) that can be configured for performing a nucleic acid amplication and detection in a
multiplex array of wells, wherein each separate well comprises a separate nucleic acid
amplification reaction and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, , 12, 13, 14, or 15 modules
(depending on whether other types of modules are included within the plurality) that can be
configured for performing a multiplex detection of at least two protein analytes and/or 1, 2, 3,
4, 5, 6, 7, 8, 9, 10, , 12, 13, 14, or 5 modules (depending on whether other iypes of
modules are included within the plurality) that can be configured for sequencing and
detecting anucleic acid molecule and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 2, 13, 4, or 15
modules (depending on whether other types of modules are included within the plurality) that
can be configured for performing PCR and/or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, , 12, 13, 14, or 15
modules (depending on whether other types of modules are included within the plurality) that
can be configured for performing flow cytometry and or cell capture.
[0019] Some embodiments of the invention relate to a method for operating a sample
processing apparatus. In the method, a sample cartridge holding an unprepared sample at one
of a plurality of sample preparation modules held by an enclosure can be received. Each
sample preparation module can be configured to only perfor sample preparation on a
sample within a corresponding removable sample cartridge. The sample for a corresponding
biological testing process can be prepared. At least one sample cartridge, holding the
prepared sample, can be received at one of a plurality of sample processing modules held by
the enclosure. Each sample processing module can be configured to perform at least one of a
plurality of biological testing processes. The at feast one biological testing process can then
be performed on the prepared sample using the corresponding sample processing module.
[0020] In some embodiments, performing the at least one biological testing process can
include sequencing a nucleic acid.
[0021] n some embodiments, performing the at least one biological testing process can
include detecting a nucleic acid analyte.
[0022] In some embodiments, performing the at least one biological testing process can
include detecting at least one protein analyte.
[0023] In some embodiments, performing the at least one biological testing process can
include assessing a chromosomal copy number of at least one gene of interest
[0024] In some embodiments, performing the at least one biological testing process ca
include performing a multiplex detection by hybridization to a detection array of at least two
nucleic acid analytes.
[002S] In some embodiments, performing the at least one biological testing process can
include performing a multiplex detection by hybridization to a detection array of at least two
protein analytes.
[0026] In some embodiments, performing the at least one biological testing process further
can include performing nucleic acid amplification and detection; and detecting at least one
nucleic acid analyte.
[0027] In some embodiments, performing the at least one biological testing process further
ca include performing flow cytometry on a mixed population of cells in a sample.
[0028] In some embodiments, preparing the sample can include performing a sample
processing protocol for isolation or purification of at least one nucleic acid.
[0029] In some embodiments, preparing the sample can include performing a sample
processing protocol for isolation or purification of a particular cel type from the sample
[0030] In some embodiments, a least one module can be configured for the isolation
and/or purification of a particular cell type, for example a circulating tumor cell expressing a
particular cell surface marker.
BRIEF DESCRIPTION OF THE DRAWINGS
[0031] FIG. 1A shows a schematic diagram of a sample processing apparatus, according to
some embodiments of the invention.
[0032] FIGS. B and 1C show various external and internal perspective views of a sample
processing apparatus, according to some embodiments of the invention
[0033] FIG. ID is a schematic, block diagram of a sample processing apparatus, according
to some embodiments of the invention.
[0034] FIG. 2A shows a rear perspective view of sample processing modules, according to
some embodiments of the invention.
[003S] FIG. 2B is a schematic, block diagram of aspects of a sample processing apparatus
interfacing with the sample processing module, according to some embodiments of the
invention.
[0036] FIG. 2C is a schematic, block diagram of electronic components of a sample
processing module, according to some embodiments of the invention.
[0037] FIGS. 3A and 3B show flow chart illustrating various methods for using a sample
processing apparatus, according to some embodiments of the invention.
[0038] FIG. 3B shows a method 3 8 for using a sample processmg apparatus, according to
some embodiments of the invention.
[0039] FIG. 4 shows various external configurations of sample processmg apparatuses,
according to some embodiments of the invention.
DETAILED DESCRIPTION OF THE INVENTION
[004(5] Embodiments of the invention relate to an apparatus for performing multiple types
of assays and related sample preparation. The apparatus can include a heterogeneous testing
module population, typically having, or is capable of having at least, 2-15 different types of
modules. The modules can be configured for different types of assays (e.g., immunoassay,
PGR, rapid PCR, sequencing, chromosomal analysis, and ow cytometry, etc.) for detecting
different types of target analytes (e.g., nucleic acid, whole cell, DNA, RNA, protein, virus,
drugs, etc.). The apparatus can a so include modules dedicated to sample preparation (e.g.,
lysis, chemical treatment, filtration, etc.). A cartridge-based sample holder is standardized
for each type of module, so that in most eases each module can interface with the same
cartridge. The modules, regardless of type, can all share the same chassis footprint and
electronic interface, such that types of modules can be changed with little difficult)'-.
[0041] As used herein, the term "biological sample" (interchangeable with "test sample"or
"sample") encompasses any material that may contain an analyte of interest (e.g., a particular
protein or nucleic acid), often taken from or otherwise derived from a living organism.
"Biological samples" may include, but are not limited to, sections of tissues such as biopsy
and autopsy samples, and frozen or paraffin embedded sections taken for histological or
pathology p p oses. Such samples may include whole blood, serum, plasma, cerebrospinal
fluid, sputum, tissue, cultured cells, e.g., primary cultures, explants, transformed cells, stool,
urine, vesicle fluid, mucus, and other bodily secretion, or tissue that could be sampled with a
a device. Furthermore, in some cases, a "biological sample" can be material taken from
an environment (e.g., water, air, soil, and the like) where the presence of a particular
organism may be suspected.
[0042] As used herein, the term "configured" describes a particular arrangement of
hardware components, such as chassis, heaters, fans, optical sensors, fluid couplings, fluid
passages, microfluidics, piezoelectric components, processor, memory containing
instructions, supporting circuitry, and/or connectors, etc.
[0043] As used herein, the term "sample processing module" (interchangeable with
"processing module" and "module") is defined as a modular sub-portion of a testing
apparatus, which has a particular physical form factor compatible with the apparatus and
includes hardware components (heaiers, fans, optical sensors, fluid couplings, fluid passages,
microfluidics, piezoelectric components, processor, memory containing instructions.
supporting circuitry, and/or connectors, etc.) configured to perform a particular process for a
sample.
[0044] As used herein, the term "sample preparation" is defined as a process typically
performed prior to one or more particular assays. The process changes a physical
characteristic of a sample prior to the assay(s), for example, by physical, chemical, and/or
enzymatic treatment (e.g., lysis by sonification, enzymatic, detergents, solvents, cell-bomb,
etc., filtration, and/or concentration)
[0045] As used herein, the term "sample preparation module" is defined as a subset of a
sample processing module, and accordingly is of the same form factor, which is configured to
only perform the preparation, e.g., isolation or concentration of one or more analyte of
interest
[0046] As used herein, the term "assay" (interchangeable with "testing process" and
"biological testing process") is defined to be an investigative procedure performed on a
sample, including but not limited to, determining the presence/absence and/or the
quantity /concentration of a particular analyte.
[0047] Non-limiting exemplary analytes can include any nucleic acids and/or proteins,
analytes specific for bacterial pathogens (e.g. methicilfin resistant staphylococcus aureus, c.
difficile, tuberculosis, group B strep., chlamydia, and gonorrhea), viral pathogens (e.g.
influenza, HIV, HCV, and HBV), tumor cells (e.g., bladder cancer, lung cancer, breast
cancer, colon cancer, and leukemia), biothreat analytes such as anthrax or ricin, chromosomal
alterations, such as gene duplication, gene deletions or gene translocations, cells expressing
specific cell surface markers such as CD4+ cells, detection of gene mutation/alterations such
as single nucleotide polymorphisms (SNPs) and meihyiation status of genes.
[0048] As used herein, the term "removable sample cartridge" (interchangeable with
"sample cartridge" and "cartridge") refers to a specialized container for holding a sample that
is configured to temporarily physically interface with a sample processing module such that
control aspects (fluid connections, heaters, piezoelectric components, optical sensors, etc) of
the sample processing module can directly or indirectly perform a process on the sample
within the container, after which the removable sample cartridge can be removed from the
sample processing module to further analyze, process, or dispose of the sample. The
removable sample cartridge couples and uncouples with the sample processing module
without the need for using additional tools (e.g., screwdriver, he -key, etc.) to fasten the
removable sample cartridge to the sample processing module, akin to an electrical plug
interfacing with an electrical wall outlet, except for cases of jamming or other malfunction,
which may require such tools to help remo ve the cartridge. In some embodiments, the
removable sample cartridge may contain, or has physical aspects for receiving, particular
chemicals, such as primers and reagents (including reactants).
[0049] n this application, the term "nucleic acid" or "polynucleotide" refers to
deoxyribonucleic acids (DNA) or ribonucleic acids (RNA) and polymers thereof in either
single- or double-stranded form. Unless specifically limited, the term encompasses nucleic
acids containing known analogs of natural nucleotides that have similar binding properties as
the reference nucleic acid and are metabolized in a manner similar to naturally occurring
nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also implicitly
encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions),
alleles, orthologs, mutations including point mutations, single nucleotide polymorphisms
(SNPs), and complementary sequences as well as the sequence explicitly indicated.
Specifically, degenerate codon substitutions may be achieved by generating sequences in
which the third position of one or more selected (or ail) codons is substituted with mixedbase
and/or deoxyinosine residues (Batzer et a!... Nucleic Acid Res. 19:5081 ( 19 ); Ohtsuka
et al, J. Biol. Chem. 260:2605-2608 (1985); and Rossolini el al, Mol. Cell. Probes 8:91-98
(1994)). The term nucleic acid is used interchangeably with gene, cDNA, and mRNA
encoded by a gene.
[0050] The term "gene" means the segment of DNA involved in producing a polypeptide
chain: it includes regions preceding and following the coding region (leader and trailer)
involved in the transcription/translation of the gene product and the regulation of the
transcription/translation, as well as intervening sequences (introrts) between individual coding
segments (exons).
[0051 ] A "polynucleotide hybridization method" as used herein refers to a method for
detecting the presence and/or quantity of a polynucleotide based on its ability to form
Watson-Crick base-pairing, under appropriate hybridization conditions, with a polynucleotide
probe of a known sequence.
[0052] n this application, the terms "polypeptide," "peptide," and "protein" are used
interchangeably to refer to a po er of amino acid residues. The terms apply to amino acid
polymers in which one or more amino acid residue is an artificial chemical mimetic of a
corresponding naturally occurring amino acid, as well as to naturally occurring amino acid
polymers and non-naturally occurring amino acid polymers. As used herein, these terms
encompass amino acid chains of any length, including full-length proteins (i.e., antigens),
wherein the amino acid residues are linked by covalent peptide bonds. The term "amino
acid" refers to naturally occurring and synthetic amino acids, as well as amino acid analogs
and amino acid mimetics that function in a manner similar to the naturally occurring amino
acids. Naturally occurring amino acids are those encoded by the genetic code, as well as
those amino acids that are later modified, e.g., hydroxyproline, g -carboxyglutamate, and Ophosphoserine.
[0053] As used herein, the terms "multiplex" and "array" refer to an assay format that
permits simultaneous detection and/or quantification of multiple analytes (e.g., dozens or
more of the same or different molecules) in a single run/cycle of the assay.
[0054] As used herein, the term "solid support" refers to an inert solid material, which
may be a natural material, such as glass and collagen, or a synthetic material, such as
acrylamide, cellulose, nitrocellulose, silicone rubber, polystyrene, polyethylene vinyl acetate,
polypropylene, poiymethacrylate, polyethylene, poiysilicates, polyethylene oxide,
polycarbonates, teflon, fiuoroearbons, nylon, polyanhydrides, poiyglycolic acid, polylactic
acid, poiyorthoesters, polypropyifumarate, glycosaminoglycans, and polyamino acids. One
example is silica gel preimpregnated with fluorogenic substrates. A "solid support" typically
provides a supporting structure for performing an assay in various apparatus of this
application.
I. Sample Processing Apparatus with Heterogeneous Population of Modules
[0055] FIG. A shows a schematic diagram of a biological sample processing apparatus
100, according to some embodiments of the invention. The apparatus 100 includes a plurality
of, generally at least two, processing modules 102a-p. The processing module population is
heterogeneous in nature, and therefore the modules do not necessarily perform the same
processing tasks. Tn some embodiments, the apparatus 00 can include sub-groups of
identical processing modules. For example, processing modules 102a-h can each be PCR
processing modules, processing modules 2i-m can be array modules, and processing
modules 1 2m-p ca be dedicated sample preparation modules (e.g., lysis by Bonification,
enzymatic, detergents, solvents, cell-bomb). In some embodiments, the apparatus 00
includes at least one dedicated sample preparation module, which can be configured to
perform sample preparation for other processing modules that in turn can be configured only
to perform assays on pre-processed biological samples.
[0056] The sample processing modules 02a-p are connected by a communications bus to a
control unit 104. The control unit 4 is configured to independently operate each sample
processmg module 102a-p. The control unit 104 can be, for example, a general purpose or
specific purpose computer. The control unit 4 generally includes at least one processor and
supporting circuitry, and memory storing instructions for independently operating each
sample processing module 102a-p. In some embodiments, the control unit 104 is structurally
integrated into the apparatus 100. In other embodiments, the control unit 4 is remotely
connected to the apparatus via a wired or wireless connection.
[0057] FIG. IB shows a perspective view of the apparatus 00 In some embodiments, the
apparatus 0 includes a housing/enclosure 7 configured to be semi-portable, such that it
can be easily be used within a laboratory environment, akin to a desktop computer. As
shown, the housing 07 can be rectangular in shape and have a front-facing interface panel
1 9 that pro vides user access to the plurality of processing modules 102a-p.
[0058] Generally, each sample processing module 2a-p will share the same structural
format and can be configured to electronically interface with the enclosure via a shared type
of connector. This arrangement allows for easy swapping of modules when different
configuration needs arise for the user. Each sample processmg modules 102a-p is configured
to interface with a sample testing cartridge 11, for example, such as the vessel disclosed in
FIG. 1 of commonly assigned U.S. Pat No. 6,660,228, entitled "APPARATU S FOR
PERFORMING HEAT-EXCHANGING, CHEMICAL REACTIONS, which is incoiporated
by reference, and also such as, for example, the vessel disclosed in FIG. 1 of commonly
assigned U.S. Pat. No. 6,391,541, entitled "APPARATUS FOR ANALYZING A FLUID
SAMPLE", which is incorporate by reference herein. Accordingly, in some embodiments,
the same cartridge can be used within any of the sample processmg modules 2a-p Aspects
of Int'l Pub. No. WO/2002/1 8902, entitled "FLUID METERING AND DISTRIBUTION
SYSTEM", Int'l Pub. No. WO/2000/072970, entitled "CARTRIDGE FOR CONDUCTING
A CHEMICAL REACTION", and Int'l Pub. No. WO/2000/073412, entitled "APPARATUS
AND METHOD FOR ANALYZING A FLUID SAMPLE", can also be used within any of
the sample processing modules. These references are incorporated by reference herein.
[0059] F G. C depicts the apparatus 100 according to some embodiments the present
invention. The control unit 104 is depicted as personal computer. The apparatus 100 has a
main logic board with edge connectors 14 for establishing electrical connections to the
modules 102a-p. The apparatus 100 also preferably includes a fan 6 for cooling its
electronic components. The apparatus 100 may be connected to the controller 1 using an -
suitable data connection, such as a universal serial bus (USB), ethernet connection, or serial
line. It is presently preferred to use a USB that connects to the serial po t of controller 12.
Alternatively, the controller may be built into the apparatus 00.
[0060] The processing modules 02a-p are preferably independently controllable so that
different chemical reactions and sample preparations can be run simultaneously in the
apparatus 0. The apparatus 0 is preferably modular so that each processing module can
be individually removed from the apparatus 00 fo servicing, repair, or replacement. This
modularity reduces downtime since all the processing modules 102a-p are not off line to
repair one, and the instrument 00 can be upgraded and enlarged to add more modules as
needed.
[0061] n embodiments in which the apparatus 0 operates on external power, e.g. 110V
AC, the instrument preferably includes two power connections 122, 124. Power is received
though the first connection 122 and output through the second connection 124. Similarly, the
apparatus 0 preferably includes network interface inlet and outlet ports 1 8, 0 for
receiving a data connection through inlet port 11 and outputting data to another apparatus
through outlet port 120.
[0062] FIG. IE is a schematic, block diagram of the apparatus 0, according to some
embodiments of the invention. The apparatus 0 includes a power supply 34 for supplying
power to the instrument and to each module 60. The power supply 4 may comprise an
AC/DC converter for receiving power from an external source and converting it to direct
current, e.g., for receiving 0V AC and converting it to 12V DC. Alternatively, the power
supply 34 may comprise a battery, e.g., a 2V battery. The apparatus 0 also includes a
microprocessor or microcontroller 30 containing firmware for controlling the operation of
the apparatus 0 and modules 60. The microcontroller 130 communicates through a
network interface 132 to the controller computer via, for example, a USB connector.
[0063] The apparatus 00 further includes a heater power source and control circuit 36, a
power distributor 38, a data bus 140, and a module selection control circuit 42. Due to
space limitations in patent drawings, control circuit 36, power distributor 138, data bus 140,
and control circuit 142 are shown only once in the block diagram of FIG. E. However, the
apparatus 100 may contain one set of these four functional components 136, 138, 140, 142
for each processing module 102. Thus, in the embodiment of F G. 1 , the apparatus 100
includes sixteen control circuits 6, power distributors 138, data buses 140, and control
circuits 142. Similarly, the apparatus 100 also includes edge connectors 131 for connecting to
each of the processing modules 102, so tha the instrument includes sixteen edge connectors
for the embodiment shown in FIG E. The edge connectors are preferably 20 pin card edge
connectors that provide cableless connection from the apparatus 100 to each of the modules
60. Each control circuit 136, power distributor 138, data bus 140, and control circuit 142. is
connected to a respective one of the edge connectors and to the microcontroller 0.
[0064] Each heater power and source control circuit 136 is a power regulator for regulating
the amount of power supplied to the heating element(s) of a respective one of the modules 60.
The source control circuit 136 is preferably a DC/DC converter that receives a +12V input
from the power supply 34 and outputs a variable voltage between 0 and -24V. The voltage
is varied in accordance with signals, received from the microcontroller 130. Each power
distributor 138 provides -5 v, +5V, · ! . and GND to a respective module 60. The power
distributor thus supplies power for the electronic components of the module. Each data bus
140 provides parallel and serial connections between the microcontroller 130 and the digital
devices of a respective one of the modules 60. Each module selection controller 94 allows the
microcontroller 130 to address an individual module 60 in order to read or write control or
status information.
II. Module Configurations
[0065] F G. 2A shows a rear perspective view of sample processing modules 2.00,
according to some embodiments of the invention. Generally, the sample processing module
200 can be configured according to a variety of processing tasks using, for example, the
shown form factor. This enables a user to customize and/or reconfigure modules with
relative ease. n some embodiments, the apparatus 100 includes up to 15 different types of
sample processing modules for performing assays, and at least one sample preparation
module.
[0066] In some embodiments, the sample processing module 200 is configured as a sample
preparation module to prepare a sample for later processing (e.g., lysis by ultrasonification).
A example of such a configuration is o in commonly assigned U.S. Pat No. 6,739,537,
entitled "APPARATUS AND METHOD FOR RAPID DISRUPTION O CELLS OR
VIRU SES", which is incorporated by reference. Another example of such a configuration is
shown in commonly assigned U.S. Pub. No. US 2010/0129827, entitled "METHOD AND
DEVICE FOR SAMPLE PREPARATION CONTROL", which is incorporated by reference.
[0067] The sample processing module 200 can be a dedicated module configured to only
perform sample preparation, and thereby not include additional components (e.g., heat
cycling components, optical sensors, etc.) required to perform a post-preparation assay. In
some embodiments, such a sample preparation module can be configured to implement a
sample preperation protocol for detection of a nucleic acid. In some embodiments, a sample
preparation module can be configured to implement a sample preperation protocol for
detection of a protein analyte. In some embodiments, a sample preparation module can be
configured to chemically treat and/or filter a cell or a virus. In some embodiments, a sample
preparation module can be configured to implement more than one type of sample processing
protocol.
[0068] In some embodiments, flow cytometry is one of the detection methods that can be
used in one or more sample processing modules for detecting the presence of a predetermined
target, such as a certain cell type or a population of cells that express a particular
marker. Methods and instrumentation for practicing flow cytometry are known in the art, and
can be used in the practice of the present invention. Flow cytometry in general resides in the
passage of a suspension of cells or microparticles comprising a label (e.g. a fluorophore) as a
stream past a laser beam and the detection of the label (e.g. fluorescent emission) from each
particle by a detector, such as a photo multiplier tube. Detailed descriptions of
instrumentation and methods for flow cytometry are found in the literature. Examples are
McHugh, "Flow Microsphere Immunoassay for the Quantitative and Simultaneous Detection
of Multiple Soluble Analytes," Methods in Cell Biology 42, Part B (Academic Press, 1994);
McHugh et al., "Microsphere-Based Fluorescence Immunoassays Using Flow Cytometry
Instrumentation," Clinical Flow Cytometry, Bauer, K.D., et al, eds. (Baltimore, Maryland,
USA: Williams and Williams, 1993), pp. 535-544; Lindmo et al, "Immunometric Assay
Using Mixtures of Two Particle Types of Different Affinity,"./ Immunol Meth. .6 : 183-
89 (1990); McHugh, "Flow Cytometry and the Application of Microsphere-Based
Fluorescence Immunoassays," Immunochemica 5 : 116 (1991); Horan et al., "Fluid Phase
Particle Fluorescence Analysis: Rheumatoid Factor Specificity Evaluated by Laser Flow
Cytophotometry," Immunoassays in the Clinical Laboratory, 185-189 (Liss 1979); Wilson et
a , "A New Microsphere-Based Immunofluorescence Assay Using Flow Cytometry,"/.
Immunol Meth. 107: 225-230 (1988); Fulwyler et al., "Flow Microsphere Immunoassay for
the Quantitative and Simultaneous Detection of Multiple Soluble Analytes," Meth. Cell Biol.
33: 613-629 ( 990); Coulter Electronics Inc., United Kingdom Patent No. ,56 ,042
(published February 13, 1980); and Steinkamp et at, Review of Scientific Instruments 44(9):
1301-1310 ( 973). These references are incorporated herein by reference.
[0069] In some embodiments, one or more of the sample processing modules can be
configured for defection of nucleic acids and/or proteins. Basic texts disclosing general
methods and techniques for detection of nucleic acids and proteins include Sambrook and
Russell, Molecular Cloning, A Laboratory Manual (3rd ed. 2001); Kriegler, Gene Transfer
and Expression: A Laboratory Manual (1990); and Ausubel et al., eels., Current Protocols in
Molecular Biology (1994). These references are incorporated herein by reference. A variety
of polynucleotide amplification methods are well established and frequently used in
research. For instance, the general methods of polymerase chain reaction (PGR) for
polynucleotide sequence amplification are well known in the art and are thus not described in
detail herein. For a review of PGR methods, protocols, and principles in designing primers,
see, e.g., Innis, et al, PGR Protocols: A Guide to Methods and Applications, Academic Press,
Inc. N.Y., 1990, which is incorporate dby reference herein. PGR reagents and protocols are
also available from various commercial vendors.
[0070] FIG. 2B is a schematic, block diagram of aspects of the apparatus 100 interfacing
with the sample processing module 200, which is configured as a sample preparation module,
according to some embodiments of the invention. The apparatus 00 can interface with a
cartridge having a container 470 for holding lysis buffer, a container 472 containing wash
solution, and a sample container 474 for holding a fluid sample. The containers 470, 472 and
sample container 474 are connected via tubing to the valve ports of a syringe pump 476 of the
apparatus 100. The inlet port of container 358 is also connected to the syringe pump 476.
The outlet port of container 358 is connected to the common port of a distribution valve 478.
The cartridge can also include a collection tube 480 for receiving intracellular material
removed from the sample, a waste container 482 for receiving waste. The apparatus 100 can
also include a pressure source, such as a pump 484. The collection tube 480, waste container
482, and pump 484 are connected to respective peripheral ports of the distribution valve 478.
A pressure regulator 486 regulates the pressure supplied by the pump 484. The transducer
3 4 is preferably a ultrasonic horn for sonicating a fluid sample. n some embodiments, a
sample can be sonicated for i 0 to 40 seconds at a frequency in the range of 20 to 60 kHz. In
some embodiments, a sample can be sonicated for 15 seconds at a frequency of 40 kHz The
amplitude of the horn tip can be in the range of 20 to 25 m (measured peak to peak).
[0071] FIG. 2C is a schematic, block diagram of the electronic components of the sample
processing module 2.00 configured as a heat-exchanging module, as shown in the right-most
embodiment of FIG. 2A. Each sample processing module 200 includes an edge connector 80
for cableless connection to a corresponding edge connector of the apparatus. The sample
processing module 200 also includes heater plates 50A, SOB each having a resistive heating
element as described above. The plates 5 , SOB are wired in parallel to receive power input
46 from the apparatus. The plates S0A, SOB also include temperature sensors 52, e.g.
thermisiors, that output analog temperature signals to an analog-io-digitai converter 154. The
converter 54 converts the analog signals to digital signals and routes them to the
microcontroller in the apparatus 1 0 through the edge connector 80. The heat-exchanging
module also includes a cooling system, such as a fan 66, for cooling the plates 50A, SOB.
The fan 66 receives power from (he apparatus 00 and is activated by switching a power
switch 164. The power switch 164 is in turn controlled by a control logic block 62 that
receives control signals from the microcontroller in the apparatus.
[0072] The sample processing module 200 further includes at least four light sources, such
as LEDs 100, for excitation of fluorescent labels in the reaction mixture and at least four
detectors 102, preferably photodiodes, for detecting fluorescent emissions from the reaction
mixture. The module also includes an adjustable current source 150 for supplying a variable
amount of current (e.g., in the range of 0 to 30 mA) to each LED to vary the brightness of the
LED. A digital-to-analog converter 152 is connected between the adjustable current source
50 and the microcontroller of the apparatus to permit the microcontroller to adjust the
current source digitally. The adjustable current source 50 may be used to ensure that each
LED has about the same brightness when activated. Due to manufacturing variances, many
LEDs have different brightnesses when provided with the same amount of current. The
brightness of each LED may be iested during manufacture of the heat-exchanging module
and calibration data stored in a memory 160 of the module. The calibration data indicates the
correct amount of current to provide to each LED The microcontroller reads the calibration
data from the memory 160 and controls the current source SOaccordingly. The
microcontroller may also control the current source 150 to adjust the brightness of the LEDs
100 in response to optical feedback received from the detectors 102.
[0073] The sample processing module 200 additionally includes a signal conditioning/gain
select/offset adjust block 156 comprised of amplifiers, switches, electronic filters, and a
digital- to-analog converier. The block 156 adjusts the signals from the defectors 2 to
increase gain, offset, and reduce noise. The microcontroller in the apparatus controls bloc
156 through a digital output register 158. The output register 8 receives data from the
microcontroller and outputs control voltages to the block 156. The block 56 outputs the
adjusted detector signals o the microcontroller through the analog--to-digital converier 154
and the edge connector 80. The module a so includes the memory 160, preferably a serial
EEPROM, for storing data specific to the module, such as calibration data for the LEDs 00,
thermal plates 50A, SOB, and temperature sensors 52, as well as calibration data for a
deconvolution algorithm described in detail below.
[0074] Referring again to FIG. C, the apparatus 0 may be configured for manual filling
and pressurization of each reaction vessel 2 by human operator. Manual use of the
apparatus 0 is suitable for lower throughput embodiments.
[0075] In some embodiments, the sample processing module 200 is configured to perform
an assay for nucleic acid amplification and detection. n such a configuration, however, the
sample processing module 200 can be a dedicated module configured to only perform heat
cycling and sensing required for nucleic acid amplification and detection, and accordingly not
include additional components (e.g., ultrasonic transducer) required to perform sample
preparation.
[0076] In some embodiments, the sample processing module 200 is configured to perform
an assay for detection of a protein analyte. In such a configuration, however, the sample
processing module 200 can be a dedicated module configured to on y perform detection of a
protein analyte, and accordingly no include additional components (e.g., ultrasonic
transducer) required to perform sample preparation.
[0077] In some embodiments, the sample processing module 200 is configured to perform
an assay for assessing a chromosomal nucleic acid copy number of a nucleic acid. n such a
configuration, however, the sample processing module 200 can be a dedicated module
configured to only assesses a chromosomal mtcleic acid copy number of a nucleic acid, and
accordingly not include additional components (e.g., ultrasonic transducer) required to
perform sample preparation.
[0078] n some embodiments, the sample processing module 200 is configured to perform
an assay for multiplex detection of one or more nucleic acid analyses. In such a
configuration, however, the sample processing module 200 can be a dedicated module
configured to only perform a multiplex detection of one or more nucleic acid analytes, and
accordingly not include additional components (e.g., ultrasonic transducer) required to
perform sample preparation.
[0079] n some embodiments, the sample processing module 200 is configured to perform
an assay for multiplex detection of one or more protein analytes. In such a configuration,
however, the sample processing module 200 can be dedicaied module configured to only
perform a multiplex detection of one or more protein analytes, and accordingly not include
additional components (e.g., ultrasonic transducer) required to perform sample preparation.
[0080] In some embodiments, the sample processing module 200 is configured to perform
an assay for sequencing and detecting a nucleic acid molecule. In such a configuration,
however, the sample processing module 200 can be a dedicated module configured to only
perform a sequencing and detecting a nucleic acid molecule, and accordingly not include
additional components (e.g., ultrasonic transducer) required to perform sample preparation.
Iί ί . Methods of Sample Preparation
[0081] FIG. 3A shows a flow chart illustrating a method 300 for using a sample processing
apparatus, such as apparatus 00 of FIG. 1A. At operation 302, a sample, such as blood, is
obtained. At operation 304, a first reagent is added to a sample preparation cartridge. At
operation 306, a second reagent is added to the sample preparation cartridge. At operation
308 the sample is added to the sample preparation cartridge using, fo example, a pipette,
and the cartridge is closed at operation 3 0. At operation 312 a sample preparation protocol
is readied by configuring the sample processing apparatus, and an associated barcode is
created for tracking the cartridge. At operation 3 4, the cartridge is inserted into a sample
processing module of the apparatus, and the apparatus is operated to start the sample
preparation protocol. At operation 316, the sample preparation protocol is completed and the
cartridge removed to pipette out the prepared sample.
[0082] FIG. 3 shows a method 3 8 for using a sample processing apparatus, such as
apparatus 00 of FIG. 1A. At operation 320, a sample, such as blood, is obtained. In the
method 3 8, reagents do not need to be added to a sample preparation cartridge, since in
some embodiments, the sample preparation cartridge comes with required reagents, or no
additional reagents are required. At operation 322 he sample is added to a sample
preparation cartridge using, for example, a pipette, and the cartridge is closed at operation
324. At operation 326 a sample preparation protocol is readied by configuring the sample
processing apparatus, and an associated barcode is created for tracking the cartridge. At
operation 328, the cartridge is inserted into a sample processing module of the apparatus, and
the apparatus is operated to start the sample preparation protocol. At operation 330, the
sample preparation protocol is completed and the cartridge removed to pipette out the
prepared sample.
[0083] Following method 300 or method 318, a sample preparation all or a portion of the
prepared sample can be added to one or more processing cartridges. Following this, the
apparatus can be readied to implement one or more processes, such as any of the processes
disclosed herein. The processing cartridges can then be inserted into respective sample
processing modules and the apparatus operated to implement specific processes to those
cartridges. The apparatus accordingly performs the processes and collects associated data.
Alternatively, the cartridge used for sample preparation can also be used for performing an
assay, thus making transfer of the prepared sample unnecessary
[0084] FIG. 4 shows embodiments of the sample processing apparatus can have varying
amounts of sample processing modules in some embodiments, the apparatus can have 2, 4,
16, 24, 32, 40, 48, or 80 sample processing modules. However, the invention is not limited to
those examples, and different amounts of modules can also be employed.
[0085] Although the above description contains many specificities, these should not be
construed as limitations on the scope of the invention, but merely as illustrations of some of
the presently preferred embodiments. Many possible variations and modifications to the
invention will be apparent to one skilled in the art upon consideration of this disclosure.
WHAT IS CLAIMED IS:
1. A biological sample processing apparatus comprising:
an enclosure;
a plurality of sample processing modules held by the enclosure, each sample
processmg module configured to hold a removable sample cartridge and to only perform
sample processing on a sample within the corresponding removable sample cartridge;
each sample processing module configured to perform at least one of a
plurality of testing processes on the sample within the removable sample cartridge,
wherein at least one module in the apparatus is configured to perform nucleic
acid amplification and detection,
wherein at least one module in the apparatus is a sample preparation module
configured to only perform sample preparation.
2. The sample processing apparatus of claim I, wherein at least one
module is configured for hybridizing a nucleic acid to an array on a solid support.
3. The sample processing apparatus of claim 2, wherein the at least one
sample preparation module is configured to prepare a sample for a sample processing
protocol for at least one nucleic acid.
4. 'The sample processing apparatus of claim I, wherein at least one
sample processing module is configured to detect at least one protein analyte.
5. The sample processing apparatus of claim , wherein at feast one
sample processing module is configured for assessing a chromosomal nucleic acid copy
number of at least one nucleic acid.
6. 'The sample processing apparatus of claim I, wherein at least one
sample processing module is configured for performing a multiplex detection of at least two
nucleic acid analytes.
7. The sample processing apparatus of claim 1, wherein at least at least
one sample processing module is configured for performing a multiplex detection of at least
two protein analytes.
8. The sample processing apparatus of claim 1, wherein at least one
sample processing module is configured for sequencing and detecting a nucleic acid
molecule.
9. The sample processing apparatus of claim , wherein the plurality of
sample processing modides further include at least one module for detecting at least one
protein analyte contained within a biological sample within a test cartridge, a least one
module for assessing chromosomal nucleic acid copy number of at least one nucleic acid
contained wiihin a biological sample within a test cartridge; and at least one module for
performing a sample processing protocol for a least one nucleic acid contained wiihin a
biological sample within a test cartridge.
10. The sample processing apparatus of claim 1, wherein the enclosure
holds at least two sample processing modules.
11. A method for operating a sample processing apparatus, the method
comprising:
receiving a sample cartridge holding an unprepared sample at one of a
plurality of sample preparation modules held by an enclosure, each sample preparation
module being configured to only perform sample preparation on a sample within a
corresponding removable sample cartridge;
preparing the sample for a corresponding biological testing process;
receiving at least one sample cartridge, holding the prepared sample, at one of
a plurality of sample processing modules held by the enclosure, each sample processing
module being configured to perform at least one of a plurality of biological testing processes;
and
performing the at least one biological testing process on the prepared sample
using the corresponding sample processing module.
12. The method of claim 11, wherein performing the at least one biological
testing process comprises sequencing a nucleic acid
13. The method of claim 11, wherein performing the at least one biological
testing process comprises detecting a nucleic acid analyte.
14 . The method of claim 11, wherein performing the at least one biological
testing process comprises detecting at least one protein analyte.
15. The method of claim 11, wherein performing the at least one biological
testing process comprises assessing a chromosomal nucleic acid copy number of at least one
nucleic acid.
16. The method of claim 11, wherein performing the at least one biological
testing process comprises performing a multiplex detection by hybridization to a detection
array of at least two nucleic acid analytes
17. The method of claim 11, wherein performing the at least one biological
testing process comprises performing a multiplex detection by hybridization to a detection
array of at least two protein anaiytes.
18. The method of claim 1, wherein performing the at least one biological
testing process comprises performing nucleic acid amplification and detection; and detecting
at least one nucleic acid analyte.
19. The method of claim 11, wherein preparing the sample comprises
performing a sample processing protocol for at least one nucleic acid.
20. 'The method of claim 1, wherein performing the at least one biological
testing process comprises hybridizing a nucleic acid to an array on a solid support.