DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Request for Information under 37 CFR 1.105
No IDS was filed for this application. The applicant and/or the assignee of this application are required under 37 CFR 1.105 to provide the following information that the examiner has determined is reasonably necessary to the examination of this application (see MPEP §§ 704.10 - 704.13). In response to this requirement, please provide a copy of any related and pertinent information, such as non-patent literature, published application(s) or patent(s) (U.S. or foreign), that was used to assist in the drafting of this application and/or similar applications (not necessarily related to the instant applications) filed by the applicant.
Note: if no related or pertinent information exists, than applicant must state this for the record in the next response.
The applicant is reminded of the duty to disclose information that is material to patentability (see 37 CFR § 1.56). A complete reply to the instant Office action must include a complete reply to this requirement otherwise the next response by applicant will be considered non-compliant and not entered. The time period for reply to this requirement coincides with the time period for reply to the instant Office action.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-3, 6, 12-15, 30, 32, 40, and 64 are rejected under 35 U.S.C. 102(a)(1)/(a)(2) as being anticipated Coassin et al.. (US 20020182117; hereinafter “Coassin”).
Regarding claim 1, Coassin discloses a method for processing a biomolecule, comprising:
“(a) providing, at a first location, (i) a substrate 11 and (ii) a substrate holder 20 coupled to the substrate, wherein the substrate comprises the biomolecule coupled thereto”. Coassin discloses “a robotic arm 12 carries a holder 20 which fits and transports bioarray 11, first to the sample, which may be in well 17 of microtiter plate 15 or in vial 16 of rack 14.” See para. [0009], [0045], and Fig. 1.
“(b) automatically directing the substrate holder and the substrate from the first location to a second location different from the first location.” Coassin discloses “a computer controlling the robotic arm movement, the incubation times, and providing further analysis or display of detected signals from the substrate,” and further discloses that after incubation, “the robotic arm 12 moves the substrate 11 to the detection assembly 18 of instrument 10,” a second location different from the first, sample-well location. See para. [0016], [0045], and Fig. 1.,
“(c) at the second location, processing the biomolecule to provide a processed biomolecule coupled to the substrate; wherein the processing comprises labelling the biomolecule to provide a labelled biomolecule.” See para [0072] et seq. Coassin discloses the present invention is designed for detection of target biomolecules in a sample, quantification of the target biomolecules is possible. Quantification of the degree of complementation may be performed, e.g., by measuring the percentage of active sites which are fluorescently-labeled or give some other optical signal”, see para [0012]. The holder supports the bioarray and is carried by the manipulator which transports the substrate to the location of the fixed sample, and then to the location of the detection assembly.
Regarding claim 2, Coassin teaches the method for processing the biomolecule is completely automated by a computer processor, see para [0009] “an analytical biochemistry system for automated analysis of samples for the presence of target biomolecules.”, para [0016]” a computer controlling the robotic arm movement, the incubation times, and providing further analysis or display of detected signals from the substrate. An automated instrument includes a detection assembly, which includes a laser source providing an excitation beam to impinge upon the active sites of the substrate, a light collector for gathering signals emitted from the substrate, and a detector, such as a photomultiplier tube or CCD array.”, see para [0046], “the detection station and the robotic arm may be attached to a computer, which generates commands for movement of the robotic arm and receives signals from the detection assembly which may, in turn, be analyzed to determine whether a specific target biomolecule is present.
Regarding claim 3, Coassin teaches the substrate is coupled to the substrate holder at a first position of the substrate holder, and wherein the substrate holder is coupled to an additional substrate comprising an additional biomolecule at a second position of the substrate holder. “Many sample wells may be reached as well as many substrate holders having treated substrates or untreated substrates which may be treated by motion to a nearby location where reactants may be applied to the substrate”, see para [0046] et seq.
Regarding claim 6, Coassin teaches coupling said biomolecule to said substrate "A substrate intended for use in the present invention may be an oligonucleotide array, a peptide array, or an immunochemical array, among others, and may be created on a separate member, such as a small slide, and affixed to the holder, or it may be created directly on the holder”, see para [0017].
Regarding claim 12, Coassin teaches that (b) is performed using a robotic system configured to direct said substrate holder from said first location to said second location (para [0009] "The system includes a solid substrate which is supported by a holder and carried by a manipulator, such as a robotic arm").
Regarding claim 13, Coassin teaches that said robotic system further comprises fluid handling units (para [0050] "a substrate holder wherein the substrate is housed within a plunger-type pipette tip Pipette tip 29 also has a narrow bore and flattened surface. The sample is drawn into the plunger-type pipette tip through withdrawal of plunger. Positive displacement is used to eject the sample from the pipette, as by depression of plunger or by some other fluid manipulation", para [0064] "FIG. 22 illustrates a typical ink jet-type dispensing head as applied in this invention. Reactant contained in reservoir 67 passes through supply tube 69 to piezoelectric pumping chamber 66, and through chamber 66 to nozzle 69. Electrical pulses applied to pumping chamber 66 cause it to expand and contract in volume this expansion and contraction
event ejects a droplet 70 of reactant") and/or a light source (para [0056] various probe methods are available; the optical detection station is an example. The station may be part of an analysis machine having a robotic arm. The robotic arm or other substrate holder positions the substrate, after it has interacted with the sample, in the path of a laser beam").
Regarding claim 14, Coassin teaches that said robotic system comprises said fluid handling unit, and wherein said method further comprises, prior to (b), providing a well and using said fluid handling unit to provide reagents into said well (para [0074]) "the robotic arm which picks up a pipette adapter having a substrate support from rack then moves the pipette adapter into dispensing device Within dispensing device dispensing by placing pipette adapter within a sample well of *microtiter plate".
Regarding claim 15, Coassin teaches that said reagents comprise fluorescent labelling agents (para [0003] "Sometimes complexes of target biomolecules and reactants are visually detectable directly after an appropriate incubation period for development chemicals, such as fluorescent dye-conjugated molecules").
Regarding claim 30, Coassin teaches that said robotic system comprises a feedback mechanism that regulates said light source (para [0056] "The incident beam from the laser is scanned across the active sites of the treated substrate by relative motion of the substrate and the beam. Light emitted from the active
sites is collected by light collector and directed to detector which may be a photomultiplier tube, CCD array, or other detection device, and which is preferably associated with a computer for any further analysis or display of the signals received from the substrate. Additional optical elements, such as wavelength selective filters, may be disposed in either the incident beam or the return light, as required by the characteristic radiation signature. Scanning may be accomplished by moving the substrate relative to the laser beam, by utilizing a scanning reflector such as a galvo mirror or polygonal mirror, or by some other well-known means", para [0057] "The bioarray is optically probed by the beam for determining the extent of complexing of the reactants in the active sites of the substrate with target biomolecules in the sample. The optical inspection may be for fluorescent signals, reflectance, absorbance, light scattering, or chemiluminescence, among others. The robotic arm may easily move the substrate and the associated bracketed pipette adapter to the detection assembly after the appropriate sample incubation period. The robotic arm may, however, be capable of moving the substrate so that it is oriented vertically, or
in some other manner, relative to the laser beam", i.e. the system has a computer controlled feedback mechanism to optimize collection of light emitted from active sites.)
Regarding claim 32, Coassin teaches that the method further comprises providing a light source at said second location various probe methods are available, the optical detection station is an example. The station may be part of an analysis machine having a robotic arm The robotic arm or other substrate holder positions the substrate, after it has interacted with the sample, in the path of a laser beam", see para [0056] et seq.
Regarding claim 40, Coassin further teaches removing peptides from a substrate, (para [0017] "A substrate intended for use in the present invention may be a peptide array", para [0061] "arrays may be utilized as is, or may be cleaved from the polypropylene substrate").
Regarding claim 64, Coassin discloses a system for processing a biomolecule, comprising:
"a substrate comprising said biomolecule coupled thereto" and “a substrate holder configured to couple to said substrate." See para. [0009] and para. [0045],
"an automated robotic handling system configured to automatically direct said substrate holder from a first location to a second location." Coassin discloses a robotic arm controlled by a computer that transports the holder between locations. See para. [0016], para. [0045] et seq., and Fig. 1.
“reagents for labelling the biomolecule”. Coassin teaches "the present invention is designed for detection of target biomolecules in a sample, quantification of the target biomolecules is possible quantification of the degree of complementation may be performed, e.g., by measuring the percentage of active sites which are fluorescently-labeled or give some other optical signal (see para [0012] et seq.)
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim 17, 19, 36, 38, and 49 are rejected under 35 U.S.C. 103 as being unpatentable over Coassin in view of Reed et al., (US 20200209254; hereinafter “Reed”).
Regarding claim 17, Coassin teaches a method for processing a biomolecule comprising fluorescent labelling agents to label target molecules, as discussed for claim 15. Coassin does not expressly teach that said labelling agents are configured to label one or more amino acids of a peptide, however, Reed teaches said labeling (abstract "Aspects of the application provide methods-of identifying and sequencing proteins, polypeptides, and amino acids, and compositions useful for the same", para [0091] "methods provided herein comprise contacting a polypeptide with a labeled affinity reagent (also referred to herein as an amino acid recognition molecule, which may or may not comprise a label) that selectively binds one type of terminal amino acid. In yet other embodiments, a labeled affinity reagent selectively binds one type of amino acid at any position of a polypeptide, e.g., the same type of amino acid as a terminal amino acid and an internal amino acid."). Since Reed teaches agents configured to specifically bind and label one amino acid of a peptide, it would have been obvious to one of ordinary skill in the art prior to the effective filing date to include the labeling method and amino acid specific binding agents of Reed in Coassin's method for processing a biomolecule because said agents are useful for sequencing or identifying target proteins.
Regarding claim 19, Coassin and Reed teach a method for processing and labeling a biomolecule, as discussed for claim 17. Reed further teaches that the labelling agents are configured to label posttranslational modifications such as phosphorylation, glycosylation, ubiquitination, or methylation (para [0081 "In some embodiments, assessing the identity of a terminal amino acid type comprises determining that an amino acid comprises a post-translational modification. Non-limiting examples of post-translational modifications include acetylation, ADP-ribosylation, caspase cleavage, citrullination, formylation, N-linked glycosylation, O-linked glycosylation, hydroxylation, methylation, myristoylation, neddylation, nitration, oxidation, palmitoylation, phosphorylation, prenylation, S- nitrosylation, sulfation, sumoylation, and ubiquitination.").
Regarding claim 36, Reed discloses "wherein (c) comprises using said light source to conduct a photoreaction to provide said labelled biomolecule”, see para [0247] et seq.
Regarding claim 38, Coassin teaches a method for processing a biomolecule, as discussed for claim 1. Coassin does not expressly teach that said biomolecule comprises a peptide, and wherein said labelling comprises coupling a label to an amino acid of said peptide, wherein said label comprises (i) a first reactive group that is configured to couple to a second reactive group that is coupled to a reporter moiety configured to emit a signal. Reed teaches the coupling (para [0003] "In some embodiments, one or more amino acids of a polypeptide are labeled (e.g., directly or indirectly [e.g. a first group coupled to a dye or fluorescent group], para [0215] In some embodiments, the amino acid recognition molecule forms a covalent linkage group"). Since Reed teaches method for specific labeling of terminal or internal amino acids in a polypeptide, it would have been obvious to an artisan of ordinary skill in the art to include said labeling, because said labeling improves the identification such as determining the sequence of, the peptides of Coassin.
Regarding claim 49, Coassin teaches a method for processing and labeling a biomolecule, as discussed for claim 1. Coassin does not expressly teach subjecting said labelled biomolecule to sequencing, however, Reed teaches said sequencing of labeled molecules (abstract "Aspects of the application provide methods of identifying and sequencing proteins, polypeptides, and amino acids, and compositions useful for the same", para [0091] "methods provided herein comprise contacting a polypeptide with a labeled affinity reagent", para [0261] "the application provides compositions and methods for sequencing a polypeptide by sequencing a plurality of fragments of the polypeptide. In some embodiments, sequencing a polypeptide comprises combining sequence information for a plurality of polypeptide fragments to identify and/or determine a sequence for the polypeptide. In some embodiments, combining sequence information may be performed by computer hardware and software.", para [0267] "Sequencing in accordance with the application, in some aspects, may involve immobilizing a polypeptide on a surface of a substrate (e.g., of a solid support, for example a chip, for example an integrated device as described herein). In some embodiments, a polypeptide may be immobilized on a surface of a sample well). Since Reed provides methods and compositions suitable for use on a solid substrate or a sample well, would have been obvious to an artisan of ordinary skill in the art to combine the sequencing methods and compositions of Reed with the method of processing biomolecules of Coassin, such as to provide another marketable feature, that of determining the sequence of target biomolecules identified using the method of Coassin.
Claims 25, 29 and 103 are rejected under 35 U.S.C. 103 as being unpatentable over Coassin in view of Pohl et al., (US 20110009612; hereinafter “Pohl”).
Regarding claim 25, Coassin teaches a method for processing a biomolecule with a robotic system, as discussed for claim 13 above. Coassin does not expressly teach wherein said robotic system comprises said evaporation unit, wherein said processing of (c) comprises use of a solvent, and wherein said method further comprises, subsequent to (c), using said evaporation unit to evaporate said solvent from said labelled biomolecule, however, Pohl teaches said evaporation unit and solvent (abstract "method for iterative solution-phase biomolecule synthesis is described", para [0059] "the computer can be any suitable computing device for controlling the operations of the solution transfer system, the evaporation unit, and the temperature control unit", para [0054] "This workstation also allows the following on-line processes: solvent evaporation The workstation also has an output to 96 deep-well plates). Since Pohl teaches a workstation for biomolecule synthesis incorporating solvent evaporation of multiple samples, it would have been obvious to an artisan of ordinary skill in the art to experiment with a workstation including dais features, such as for synthetic reactions with biomolecules and reactants that require solvents that later must be removed from, for example, a product used in research.
Regarding claim 29, Coassin teaches a method for processing a biomolecule, as discussed for claim 13. Coassin does not expressly teach a (robotic) system wherein said robotic system comprises said temperature control unit, and where (c) [claim1] is performed at a controlled temperature, however, Pohl teaches a temperature control unit can be suitable device which capable of regulating and maintaining the temperature of the reaction vessel at a desired temperature(s), see para [0059].
It would have been obvious to an artisan of ordinary skill in the art prior to the effective filing date of the claimed invention to include in Coassin’s system comprises a temperature control unit, as taught by Pohl because the unit would control the temperatures for reactions in a multiplicity of samples, thus optimizing reaction rates of enzymes of binding reactions.
Regarding claim 103, Coassin in view of Pohl discloses a system for processing a biomolecule, comprising: "a substrate holder configured to couple to a substrate comprising said biomolecule coupled thereto" and "a robotic arm coupled to said substrate holder." Coassin discloses a holder coupled to a robotic arm via a pick-up shaft: "The substrate itself is held within a holder 20 which may be coupled to the cantilevered robotic arm 12 via pick-up shaft 23." See para. [0046) and Fig. 1. "at least one computer processor configured to perform executable instructions and a memory comprising said executable instructions, which, when executed by said at least one computer processor, causes said at least one computer processor to implement a method comprising automatically instructing said robotic arm to direct said substrate holder and said substrate from a first location to a second location different from said first location." Coassin discloses that "the robotic arm 12 may be attached to a computer. not shown, which generates commands for movement of the robotic arm and receives signals from the detection assembly." Pohl discloses that the computer used for exactly this kind of robotic-handler automation contains "a microprocessor, memory, interface circuits, and others," and runs software converting "preprogrammed instructions... to appropriate language for instructing the operation of one or more controllers... directing X-Y-Z translation of the bead/fluid or other reagent handler." See para. (0046), para. [0050), and para. [0051], "wherein, at said second location, said biomolecule is labelled to provide a labelled biomolecule coupled to said substrate." Coassin discloses labelling of the substrate-bound biomolecule by fluorescence at the detection location. Coassin discloses that quantification of bound target biomolecules "may be performed, e.g., by measuring the percentage of active sites which are fluorescently-labeled or give some other optical signal indicating complementation," disclosing labelling of the biomolecule at the substrate as part of processing for detection. See para. [0072].
Citations to art
In the above citations to documents in the art, an effort has been made to specifically cite representative passages, however rejections are in reference to the entirety of each document relied upon. Other passages, not specifically cited, may apply as well.
Pertinent Prior Art
The following prior art is hereby made of record. Although the prior art is relied upon, the examiner considers the listed prior art relevant to the applicant’s invention and may be relied upon in a future prior art rejection or as general background information related to applicant’s field of endeavor.
a. Busacca et al., (US 20070255455) teach systems and apparatus which comprise a configurable three axis Cartesian robot, pump housing, and deck which can be outfitted with various functional modules. This configurable architecture allows users to customize the hardware for specific workflows by adding the appropriate modules to the basic robot platform. This robot system further comprises additional functionality selected from the group consisting of parallel overhead stirring, viscous dispense tips, friction/force probes, high temperature dispense tips, vial grippers, plate grippers, pH probes, and a variety of configurable deck modules including a balance for feedback control of viscous materials dispensing, heating/cooling/stirring zones, vortexing zones, and a sample imaging station. Robot configurations range from a simple general purpose liquid handling robot to a configuration that also includes the sample processing and analytical capabilities required for a complex workflow.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to P. Kathryn Wright whose telephone number is (571)272-2374. The examiner can normally be reached between 9:30am-7pm EST.
Examiner interviews are available via telephone and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
E-mail communication Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting the following statement via EFS Web (using PTO/SB/439) or Central Fax (571-273-8300):
Recognizing that Internet communications are not secure, I hereby authorize the USPTO to communicate with the undersigned and practitioners in accordance with 37 CFR 1.33 and 37 CFR 1.34 concerning any subject matter of this application by video conferencing, instant messaging, or electronic mail. I understand that a copy of these communications will be made of record in the application file.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Charles Capozzi can be reached on 571-270-3638. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/P. Kathryn Wright/Primary Examiner, Art Unit 1798
Prosecution Insights