`Wadaetal.
`
`(10) Patent No.:
`(45) Date of Patent:
`
`US 6,506,609 B1
`Jan. 14, 2003
`
`US006506609B1
`
`(54)
`
`(75)
`
`FOCUSING OF MICROPARTICLESIN
`MICROFLUIDIC SYSTEMS
`
`Inventors: H. Garrett Wada, Atherton, CA (US);
`Anne R. Kopf-Sill, Portola Valley, CA
`(US); Marja Liisa Alajoki, Palo Alto,
`CA (US); J. Wallace Parce, Palo Alto,
`CA (US); Benjamin N. Wang, Palo
`Alto, CA (US); Andrea W. Chow,Los
`Altos, CA (US); Robert S. Dubrow,
`San Carlos, CA (US)
`
`(73)
`
`Assignee: Caliper Technologies Corp., Mountain
`View, CA (US)
`
`Notice:
`
`Subject to any disclaimer, the term of this
`patent is extended or adjusted under 35
`US.C. 154(b) by 0 days.
`
`Appl. No.: 09/569,747
`
`Filed:
`
`May 11, 2000
`
`(60)
`
`(51)
`(52)
`
`(58)
`
`Related U.S. Application Data
`Provisional application No. 60/134,472, filed on May 17,
`1999.
`
`Tint, Cn? oecccccceecessesssessecstsenneerecesnenneeesees GOIN 7/00
`US. Che ceecccccceseserseeeseees 436/148; 436/34; 436/52;
`436/180; 436/518; 422/50; 435/91.1
`Field of Search... 436/148, 34, 52,
`436/180, 518; 422/50; 204/452, 454, 600;
`356/73; 435/7.1, 6, 287.3, 91.1; 210/634
`
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`Primary Examiner—Jill Warden
`Assistant Examiner—Brian Sines
`(74) Attorney, Agent, or Firm—Andrew L. Filler
`
`(57)
`
`ABSTRACT
`
`Methods and systemsforparticle focusing to increase assay
`throughput in microscale systems are provided. The inven-
`tion includes methods for providing substantially uniform
`flow velocity to flowing particles in microfluidic devices.
`Methodsof sorting members ofparticle populations, such as
`cells and various subcellular components are also provided.
`Integrated systems in which particles are focused and/or
`sorted are additionally included.
`
`35 Claims, 22 Drawing Sheets
`
`ABS Global, Inc. and Genus ple — Ex. 1006, p. 1
`
`
`
`US 6,506,609 B1
`
`Page 2
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`
`WO 98/00707
`WO 98/02728
`WO 98/05424
`WO 98/22811
`WO 98/45481
`WO 98/45929
`
`1/1998
`1/1998
`2/1998
`5/1998
`10/1998
`10/1998
`
`(cid:36)(cid:37)(cid:54)(cid:3)(cid:42)(cid:79)(cid:82)(cid:69)(cid:68)(cid:79)(cid:15)(cid:3)(cid:44)(cid:81)(cid:70)(cid:17)(cid:3)(cid:68)(cid:81)(cid:71)(cid:3)(cid:42)(cid:72)(cid:81)(cid:88)(cid:86)(cid:3)(cid:83)(cid:79)(cid:70)(cid:3)(cid:177)(cid:3)(cid:40)(cid:91)(cid:17)(cid:3)(cid:20)(cid:19)(cid:19)(cid:25)(cid:15)(cid:3)(cid:83)(cid:17)(cid:3)(cid:21)
`ABS Global, Inc. and Genusplc — Ex. 1006, p. 2
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`U.S. Patent
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`Jan. 14, 2003
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`Sheet 1 of 22
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`US 6,506,609 B1
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`Fig. 1A
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`Fig. 1B
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`ABSGlobal, Inc. and Genus ple — Ex. 1006, p. 3
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`ABS Global, Inc. and Genus ple — Ex. 1006, p. 5
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`
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`AM
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`US 6,506,609 B1
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`spuosag
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`Jan. 14, 2003
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`Seconds
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`Fig.5
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`2905
`291029152920292529302935294029452950
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`(cid:36)(cid:37)(cid:54)(cid:3)(cid:42)(cid:79)(cid:82)(cid:69)(cid:68)(cid:79)(cid:15)(cid:3)(cid:44)(cid:81)(cid:70)(cid:17)(cid:3)(cid:68)(cid:81)(cid:71)(cid:3)(cid:42)(cid:72)(cid:81)(cid:88)(cid:86)(cid:3)(cid:83)(cid:79)(cid:70)(cid:3)(cid:177)(cid:3)(cid:40)(cid:91)(cid:17)(cid:3)(cid:20)(cid:19)(cid:19)(cid:25)(cid:15)(cid:3)(cid:83)(cid:17)(cid:3)(cid:26)
`ABS Global, Inc. and Genusplc — Ex. 1006, p. 7
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`ABS Global, Inc. and Genus ple — Ex. 1006, p. 10
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`ABS Global, Inc. and Genus ple — Ex. 1006, p. 11
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`Sheet 10 of 22
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`HL60 Cells- 6 hr CPT
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`26 Apoptotic (52%)
`24 Alive (48%)
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`
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`
`HL60 Cells- 6 hr DMSO
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`37 Alive (97.4%)
`
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`Fig. 10
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`ABS Global, Inc. and Genus ple — Ex. 1006, p. 12
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`Jan. 14, 2003
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`Sheet 11 of 22
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`US 6,506,609 BL
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`6 hrCPT :
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`U937 Cells- TUNEL Assay
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`4 hr CPT
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`Treatment
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`4 hr CPT
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`Treatment
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`50
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`40
`30
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`4 hr CPT
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`6 hr CPT
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`4 hr DMSO
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`WL
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`Treatment
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`Fig. 11
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`ABSGlobal, Inc. and Genusple — Ex. 1006, p. 13
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`Fig. 12
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`Time (sec)
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`Fig. 13
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`ABSGlobal, Inc. and Genus ple — Ex. 1006, p. 14
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`HL-60 Cells- 4 hr CPT
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`10 Dead (8.8%)
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`Fig. 14
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`ABSGlobal, Inc. and Genus ple — Ex. 1006, p. 15
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`US.
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`Jan. 14, 2003
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`HL-60 Cells- Annexin-V Binding
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`4hrDMSO
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`2hrDMSO
`
`Treatment
`
`Treatment
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`Fig. 15
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`ABSGlobal, Inc. and Genusple — Ex. 1006, p. 16
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`
`
`
`
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`U.S. Patent
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`Sheet 15 of 22
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`Fig. 17
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`ABS Global, Inc. and Genusple — Ex. 1006, p. 17
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`Sheet 16 of 22
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`ABS Global, Inc. and Genus ple — Ex. 1006, p. 18
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`Sheet 17 of 22
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`ABS Global, Inc. and Genus plc — Ex. 1006, p. 20
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`Sheet 19 of 22
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`US 6,506,609 B1
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`1
`FOCUSING OF MICROPARTICLES IN
`MICROFLUIDIC SYSTEMS
`
`CROSS REFERENCE TO RELATED
`APPLICATIONS
`
`This application is related to and claimspriority to and the
`benefit of provisional application 60/134,472,filed May 17,
`1999, Wadaet al., “Focusing of Microparticles in Microf-
`luidic Systems,” pursuant to 35 U.S.C. §119(e), as well as
`any other applicable statute or rule. This priority application
`is incorporated herein in its entirety for all purposes.
`
`COPYRIGHT NOTIFICATION
`
`to 37 C.FR. 1.71(e), Applicants note that a
`Pursuant
`portion of this disclosure contains material which is subject
`to copyright protection. The copyright owner has no objec-
`tion to the facsimile reproduction by anyone of the patent
`documentor patent disclosure, as it appears in the Patent and
`Trademark Office patent
`file or records, but otherwise
`reserves all copyright rights whatsoever.
`
`BACKGROUND OF THE INVENTION
`
`A variety of cell-based assays are of considerable com-
`mercial relevance in screening for modulators of cell-based
`activity. For example, compounds which affect cell death
`can have profound biological activities and are desirably
`screened for in cell-based assays. Cell death has become
`recognized as a physiological process important in normal
`development, hormonal regulation of various tissues, and,
`e.g., in regulation of the receptor repertoires of both T and
`B lymphocytes. The finding that a pattern of morphological
`changes is common to many examples of programmedcell
`death (or PCD)
`led to the suggestion of a common
`mechanism,and the term “apoptosis” was defined to include
`both the morphological features and the mechanism com-
`mon to such programmed cell death (Kerr et al., Br J.
`Cancer 26:239). This concept was extended by the finding
`that nuclear DNA fragmentation correlates well with apop-
`totic morphology (Arends et al., Am. J. Pathol. 136:593
`(1990)), and the scientific literature contains many examples
`of PCD accompanied by these features. There are also clear
`examples of PCD in the absence of apoptotic morphologyor
`DNAfragmentation (Clarke, Anat. Embryl. 181:195 (1990),
`Martin etal, J. Cell Biol. 106:829 (1988), and Ishigamietal.,
`J. Immunol. 148:360 (1992)).
`Cell-based assay systems model relevant biological
`phenomena, and have generally been widely adopted as
`screening assays, ¢.g., when screening for a compound’s
`effect(s) on apoptosis or other biological phenomena. Pio-
`neering technology providing cell- and other particle-based
`microscale assays are set
`forth in Parce et al. “High
`Throughput Screening Assay Systems in Micrascale Fluidic
`Devices” WO 98/00231; in PCT/US00/04522,filed Feb. 22,
`2000, entitled “Manipulation of Microparticles In Microf-
`luidic Systems,” by Mehta et al.; and in PCTUS00/04486,
`filed Feb. 22, 2000, entitled “Devices and Systems for
`Sequencing by Synthesis,” by Mehta et al.
`Other cell-based assays include various methods for the
`preparative or analytic sorting of different types of cells. For
`example, cell panning generally involves attaching an
`appropriate antibodyor other cell-specific reagent to a solid
`support and then exposing the solid support to a heteroge-
`neouscell sample. Cells possessing,e.g., the corresponding
`membrane-bound antigen will bind to the support, leaving
`those lacking the appropriate antigenic determinant to be
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`washed away. Other well-knownsorting methods include
`those using fluorescence-activated cell sorters (“HACSs”).
`FACSs for use in sorting cells and certain subcellular
`components such as molecules of DNA have been proposed
`in, e.g., Fu, A. Y. et al.
`(1999) “A Microfabricated
`Fluorescence-Activated Cell Sorter,” Nat. Biotechnol.
`17:1109-1111; Unger, M., et al. (1999) “Single Molecule
`Fluorescence Observed with Mercury Lamp Illumination,”
`Biotechniques 27:1008-1013; and Chou,H. P.et al. (1999)
`“A Microfabricated Device for Sizing and Sorting DNA
`Molecules,” Proc. Nat’. Acad. Sci. 96:11-13. These sorting
`techniquesutilizing generally involve focusingcells or other
`particles by flow channel geometry.
`While cell-based assays are generally preferred in certain
`microscale screening applications, certain of these assays
`are difficult
`to adapt
`to conventional notions of high-
`throughput or ultra high-throughput screening assay sys-
`tems. For example, one difficulty in flowing assay systems
`is that, during pressure-based flow of fluids in channels,
`non-uniform flow velocities are experienced. Faster fluid
`and material flow is observed in the center of a moving fluid
`stream than on the edge of a moving fluid stream. This
`non-uniform flow velocity reduces throughput for flowing
`assays, because assay runs have to be spaced well apart in
`the fluid stream to prevent overlap of matcrials moving at
`different velocities.
`
`Accordingly, it would be advantageous to provide mecha-
`nismsfor facilitating cell-based assays, including cell sort-
`ing techniques, especially in microscale systems. Additional
`microscale assays directed at subcellular components, such
`as nucleic acids would also be desirable. The present inven-
`tion provides these and other features which will become
`clear upon consideration of the following.
`
`SUMMARYOF THE INVENTION
`
`The present invention relates to methods of focusing
`particles in microchannels, e.g.,
`to imprave assay
`throughput, to sort particles, to count particles,or the like. In
`the methods of the invention, cells and other particles are
`focused in the center of, to one side of, or in other selected
`regions of microscale channels, thereby avoiding, e.g., the
`above noted difficulties inherent in pressure-based flow of
`particles. Furthermore, the device structures of the present
`invention are optionally integrated with other microfluidic
`systems. Other reactions or manipulations involving cells,
`other particles, or fluids upstream of the detection zone are
`also optionally performed,e.g., monitoring drug interactions
`with cells or other particles.
`In one aspect, the invention provides methods of provid-
`ing substantially uniform flow velocity to particles flowing
`in a first microchannel. In the methods,
`the particles are
`optionally flowed in the microchannel, e.g., using pressure-
`based flow, in which the particles flow with a substantially
`non-uniform flow velocity. Prior to performing the flowing
`step, the particles are optionally sampled with at least one
`capillary element, e.g., by dipping the capillary elementinto
`a well containing the particles on a microwell plate and
`drawingthe particles into, e.g., reservoirs, microchannels, or
`other chambers of the device. The particles (e.g., a cell, a set
`of cells, a microbead, a set of microbeads, a functionalized
`microbead,a set of functionalized microbeads, a molecule,
`a set of molecules, etc.) are optionally focused horizontally
`and/or vertically in the first microchannel to provide sub-
`stantially uniform flow velocity to the particles in the first
`microchannel. Particles are optionally focused using one or
`morefluid direction components (¢.g., a fluid pressure force
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`(cid:36)(cid:37)(cid:54)(cid:3)(cid:42)(cid:79)(cid:82)(cid:69)(cid:68)(cid:79)(cid:15)(cid:3)(cid:44)(cid:81)(cid:70)(cid:17)(cid:3)(cid:68)(cid:81)(cid:71)(cid:3)(cid:42)(cid:72)(cid:81)(cid:88)(cid:86)(cid:3)(cid:83)(cid:79)(cid:70)(cid:3)(cid:177)(cid:3)(cid:40)(cid:91)(cid:17)(cid:3)(cid:20)(cid:19)(cid:19)(cid:25)(cid:15)(cid:3)(cid:83)(cid:17)(cid:3)(cid:21)(cid:24)
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`generally induces non-uniform flow. A source ofat least one
`fluidic material is optionally fluidly coupled to the first
`microchannel. The system also optionally includesat least a
`second microchannel that intersects the first microchannel
`for introducing at least one fluid into the first microchannel
`to horizontally or vertically focus the members of the at least
`one particle population in the first microchannel. The at least
`one fluid is optionally introduced using a second fluid
`direction component that includes one or more of a fluid
`pressure force modulator, an electrokinetic force modulator,
`a capillary force modulator, a fluid wicking element, or the
`like. At least one flow control regulator for regulating flow
`of the fluidic material or the fluid in the first or second
`microchannel
`is also optionally provided. A computer
`including an instruction set directing simultaneous flow of
`the membersoftheat least one particle population in thefirst
`microchannel and simultaneous introduction of the at least
`one fluid from the second microchannel into thefirst micro-
`channelis optionally also operably coupled to a fluid move-
`ment system for directing flow of materials in the micro-
`channels.
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`3
`modulator an electrokinetic force modulator, a capillary
`force modulator, a fluid wicking element, or the like).
`Additional options include sorting, detecting or otherwise
`manipulating the focused particles.
`The particles are horizontally focused in the
`microchannel, e.g., by introducing a low density fluid and a
`high density fluid into the microchannel, causing the par-
`ticles to be focused in an intermediate density fluid present
`between the high density fluid and the low density fluid. The
`particles are also optionally focused in a top or a bottom
`portion of the microchannel by introducing a high or a low
`density fluid into the microchannel with the flowing par-
`ticles. The particles are vertically or horizontally focused in
`the microchannel, e.g., by simultaneously introducing fluid
`flow from two opposing microchannels into the first micro-
`channel during flow of the particles in the first channel.
`Vertical focusing is also optionally achieved to one side of
`a microchannel by simultaneously introducing fluid flow
`from,e.g., a second microchannelinto the first microchannel
`during flow of the particles in the first microchannel.
`In another aspect,
`the invention also provides particle
`washing or exchange techniques. For example, focused cells
`or other particles are optionally washed free of diffusible
`material by introducing a diluent into the first microchannel
`from at least a second channel and removing the resulting
`diluted diffused product comprising diluent mixed with the
`diffusible material through at least a third microchannel.
`Alternating arrangements of diluent input and dittused
`product output channels are also optionally used to further
`In particle washing systems, typically, at least fourth and
`fifth channels which intersect the first microchannel at a
`wash the particles. or example, in one aspect the methods
`common intersection downstream of the second and third
`of the invention include simultaneously introducing§the
`diluent into the first microchannel from the second micro-
`microchannels are provided. The computer further includes
`channel and a fourth microchannel, where the sccond and
`an instruction set for simultaneously flowing material from
`fourth microchannel intersect
`the first microchannel at a
`the first microchannel into the fourth and fifth microchan-
`nels. Sixth and seventh microchannels which intersect the
`common intersection region. Optionally,
`the methods
`first microchannel at a commonintersection downstream of
`include sequentially introducing the diluent into the first
`microchannel from the second microchannel and a fourth
`microchannel, wherein the second and fourth microchannels
`intersect
`the first microchannel at an offset
`intersection
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`As a further option, this integrated system additionally
`includes at least a third microchannel which intersects the
`first microchannel in an intersection region commonto the
`second microchannel. The flow control regulator of this
`system optionally further regulates flow of the at least one
`fluid in the second and the third microchannels. In this
`embodiment,
`the computer typically also includes an
`instruction set for simultaneously flowing fluids from the
`second and third microchannels into the first microchannel.
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`the fourth andfifth microchannels, with the computer further
`comprising an instruction set for simultaneously flowing
`material from the sixth and seventh microchannels into the
`first microchannelare optionally provided. Similarly, eighth
`and ninth microchannels whichintersect the first microchan-
`nel al a common intersection downstream of the sixth and
`seventh microchannels, the computer further including an
`instruction set for simultaneously flowing material from the
`first microchannel into the eighth and ninth microchannels
`are optionally provided.
`The integrated system optionally includes sources for any
`reagentor particle used in the methods noted above, such as
`one or more sources of terminal deoxynucleotide
`transferase, one or more sources of one or more fluorescein
`labeled nucleotides or other labeled polynucleotides, one or
`more sources of Annexin V, one or more sources of an
`AnnexinV-biotin conjugate, one or more sources of a DNA
`dye, one or more sources of Campthotecin, one or more
`sources of Calcein-AM, one or more sources of a control
`cell, one or more sourcesofa test cell, ete.
`Signal detector(s) mounted proximal to the first micro-
`channel for detecting a detectable signal produced by one or
`An integrated system for providing substantially uniform
`more of the membersofthe at least one particle population
`flow velocity to flowing members of at least one particle
`in the microchannelare typically provided in the integrated
`population in a microfluidic device optionally includes a
`systems of the invention. The detector also optionally
`body structure that includes at least a first microchannel
`disposed therein. A first fluid direction component(e.g., a
`includes,e.g., a fluorescent excitation source andafluores-
`fluid pressure force modulator) is typically coupled to the
`cent emissiondetection element. Optionally, the computeris
`first microchannelfor inducing flow ofa fluidic materialthat
`operably linked to the signal detector and has an instruction
`includes the membersofthe at least one particle population
`set for converting detected signal information into digital
`data.
`in the first microchannel. Thefirst fluid direction component
`
`region. The diffused product is typically removed through
`the third microchannel anda fifth microchannel, which third
`and fifth microchannels intersect the first microchannelat a
`
`commonintersection region. In further washing steps, the
`diluentis introduced through sixth and seventh microchan-
`nels which intersect the first microchannel at a common
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`totersection. The resulting further diluted diffused productis
`removed through eighth and ninth microchannels, which
`intersect the first microchannel at a common intersection.
`
`Diluent is optionally introduced into the first microchannel
`by pressure or electrokinetic flow.
`In one preferred assay of the invention, the particles are
`cells and the method includes performing a TUNELassay or
`an Annexin-V assay on the cells in the channel to measure
`apoptosis.
`Integrated systems for performing the above methods,
`including the particle sorting embodiments, are also pro-
`vided.
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`The integrated system of the present invention is also
`optionally used to sort the membersofa particle population
`(e.g., a cell, a set of cells, a microbead, a set of microbeads,
`a functionalized microbead,a set of functionalized microbe
`ads, a molecule, a set of molecules, or the like). In this
`embodiment,
`the integrated system typically additionally
`includes a third and a fourth microchannel which intersect
`the first microchannel downstream from the intersection of
`the second microchannel with the first microchannel. The
`fourth microchannelalso generally intersects the first micro-
`channel downstream from the intersection of the third
`microchannel with the first microchannel. The flow control
`regulator of this system opuonally further regulates flow of
`the at least one fluid in the third or the fourth microchannels.
`Furthermore, the signal detector typically detects a detect-
`able signal produced by a selected member ofthe particle
`population between the intersections of the second and the
`third microchannels with the first microchannel.
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`the computer is
`In this particle sorting embodiment,
`optionally operably linkedto thefirst or other fluid direction
`component(s),
`the flow control regulator, and the signal
`detector. Additionally,
`the instruction set typically directs
`simultaneous introduction of the at least one fluid from the
`third microchannel into the first microchannel to horizon-
`tally or vertically focus the selected memberofthe particle
`population such that the selected memberis directed into the >
`fourth microchannel in response to the detectable signal
`produced bythe selected member. Optionally, the instruction
`set further directs simultaneous introduction of the at least
`onefluid from the third microchannelby activating a heating
`element (e.g., a Joule heating electrode, a conductively
`coated microchannel portion, etc.) disposed within the third
`microchannel or a well that fluidly communicates with the
`third microchannel.
`
`least a portion of the first
`In another embodiment, at
`microchannel optionally includes a separation elementdis-
`posed therein. The separation element optionally includes,
`e.g.,
`twa sides and at
`least a portion of the separation
`elementis typically disposed upstream of the fourth micro-
`channel. In this embodiment, a selected member of the
`particle population is generally directed to one of the two
`sides of the separation element and into the fourth micro-
`channel that intersects the first microchannel in response to
`the detectable signal produced by the selected member.
`The integrated system for use in particle sorting also
`optionally includesa fifth microchannel which intersects the
`first microchannel in an intersection region commonto the
`second microchannel. In this case, the flow control regulator
`also typically regulates flow of the at least one fluid in the
`second and the fifth microchannels, and the computer
`optionally includes an instruction set for simultaneously
`flowing fluids from the second and the fifth microchannels
`into the first microchannel. Similarly,
`the system also
`optionally includes a sixth microchannel which intersects
`the first microchannel in an intersection region commonto
`the third microchannel. In this embodiment, the flow control
`regulator optionally additionally regulates flow of the at
`least one fluid in the third and the sixth microchannels.
`Furthermore,
`the computer also typically includes an
`instruction set for flowing fluids from the third and the sixth
`microchannels into the first microchannel. Optionally, the
`instruction set directs individual or simultaneous fluid flow
`
`from the third and sixth microchannels by individually or
`simultaneously activating at least one heating element(e.g.,
`a Joule heating electrode, a conductively coated microchan-
`nel portion, or the like) disposed within eachof the third and
`sixth microchannels or within at least one well that fluidly
`communicates with each of the third and sixth microchan-
`nels.
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`Many additional aspects of the tovention will be apparent
`upon review, including uses of the d