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 .
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim(s) 15 is/are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention.
Regarding claim 15, the phrase "preferably" renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
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 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 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied 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.
Claim(s) 1-20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Moyle (US 2009/0023148) in view of Belgrader (US 2018/0282803).
Regarding claim 1, Moyle teaches a method for spatially detecting nucleic acid analytes from a biological sample (¶3: detecting analytes such as nucleic acids; e.g., Example 1: monitor gene expression in frozen tissue sections), the method comprising:
positioning a first substrate (Fig. 1A; ¶178: brass or other conductor 102; here the lower conductor 102 is deemed to be the first substrate) at a distance from a second substrate (Fig. 1A; ¶178: brass or other conductor 102; here the upper conductor 102 is deemed to be the second substrate), the first substrate comprising a first conductive region (Fig. 1A; ¶178: ITO coated slide 104; here the lower ITO coated slide 104), and the second substrate comprising a second conductive region (Fig. 1A; ¶178: ITO coated slide 104; here the upper ITO coated slide 104) comprising a plurality of nucleic acid sequences disposed thereon (¶210: the tissue section 5 is placed on either the lower or upper assembly), wherein the plurality of nucleic acid sequences are configured to capture the nucleic acid analytes (¶88: the migration of nucleic acid oligomers to the surface of the sensor where they can hybridize with others that are on the sensor surface; e.g., Example 1: the analysis reagents are tethered to one surface of the device during the entire analytical procedure; ¶¶104-105) and wherein the distance is maintained by at least one spacer disposed between the first substrate and the second substrate (Fig. 1A; ¶178: gasket insulator 105),
positioning the biological sample between the first substrate and the second substrate (Fig. 1A; ¶88: tissue sections are applied directly on the sensor surface; ¶210: the tissue section 5 is placed on either the lower or upper assembly);
providing a buffer between the first substrate and the second substrate (Fig. 1A; ¶178: indicating the buffer chamber defined by the two conductors 102 and the gasket insulator 105 including a matrix (including buffers) 106);
generating an electric field between the first conductive region and the second conductive region (Fig. 1A; ¶178: voltage generator 109; ¶108: introduction of an electrical potential across the ITO coated slides) to cause the nucleic acid analytes in the biological sample to migrate from the biological sample toward the plurality of nucleic acid sequences on the second conductive region (¶108: cause gene products such as mRNA to migrate towards the anode);
capturing the nucleic acid analytes via the plurality of nucleic acid sequences, thereby forming captured nucleic acid analytes (¶108: where they can interact with detection reagent; ¶88: the migration of nucleic acid oligomers to the surface of the sensor where they can hybridize with others that are on the sensor surface).
Moyle does not disclose contacting one or more captured nucleic acid analytes with a plurality of barcoded molecules, wherein a barcoded molecule of the plurality of barcoded molecules hybridizes to one or more of the captured nucleic acid analytes; and detecting the barcoded molecule, thereby spatially detecting one or more of the nucleic acid analytes from the biological sample.
However, Belgrader teaches an example using a barcode oligonucleotide for use in RNA analysis (¶259). The overall oligonucleotide 702 is coupled to a bead 704 by a disulfide linker 706, and include functional sequence 708, which may include one or more of a sequencer specific flow cell attachment sequence, e.g., a barcode sequence 710 is for use in barcoding the sample RNA, an additional sequence segment 716 that provides a unique molecular identifier (UMI) sequence segment, an mRNA specific priming sequence 712 that binds to specific sequence in a RNA molecule, and an anchoring sequence segment 714 that ensures the sequence 712 to hybridize at the sequence end of the mRNA (Fig. 7; ¶259).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified Moyle by incorporating a plurality of barcoded molecules and a step of contacting the captured nucleic acid analytes with the plurality of barcoded molecules to be hybridized for spatially detecting nucleic acid analyte through detecting the barcoded molecule because it is a known technique in the prior art for oligonucleotide sequence (¶259) and by including the unique random N-mer sequence would provide a quantitation feature that can be identifiable even following any subsequent amplification (¶260) and for identifying the sequence of the mRNA as well as the sequence of the barcode segment and the unique sequence segment (¶260). Here, the claimed limitations are obvious because all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination yielded nothing more than predictable results. MPEP 2143(I)(A).
Regarding claim 2, Moyle teaches arranging the at least one spacer relative to the first substrate and the second substrate (Fig. 1A: gasket insulator 105) to form a chamber, and wherein providing the buffer comprises providing the buffer inside the chamber (Fig. 1: matrix including buffers).
Regarding claim 3, Moyle teaches wherein the at least one spacer comprises a non-conductive material (Fig. 1A: gasket insulator 105).
Regarding claim 4, Moyle teaches wherein the first substrate is configured as a cathode (Fig. 1A: lower conductor 102) and wherein the second substrate is configured as an anode (Fig. 1A: upper conductor 102), and wherein generating the electric field between the first conductive region and the second conductive region comprises generating the electric field (Fig. 1A: voltage generator 109).
The designations “configured as a cathode,” “configured as an anode,” and “such that the electric field is directed from the first substrate to the second substrate” are directed to the intended result and thus does not further limit the method as claimed. Claim scope is not limited by claim language that suggests or makes optional but does not require steps to be performed. In method claims, it is the overall method steps that are given patentable weight not the intended result thereof because the intended result does not materially alter the overall method. Here, this designation is not given patentable weight when it simply expresses the intended result of a process step positively recited. MPEP 2111.04.
Regarding claim 5, Moyle teaches wherein at least one of the first substrate or the second substrate comprises indium tin oxide (ITO) (Fig. 1A; ¶178: conductor 102 and ITO coated slide 104; ¶88: coating of the TIRFM sensor chip with a thin layer of indium tin oxide ITO).
Regarding claim 6, Moyle teaches wherein the at least one of the first substrate and the second substrate comprises a glass slide having a coating comprising the ITO (¶88: coating of the TIRFM sensor chip with a thin layer of indium tin oxide ITO; ¶86: TIRFM material is glass).
Regarding claim 7, Moyle teaches wherein the biological sample is disposed on the first substrate (¶210: the tissue section 5 is placed on either the lower or upper assembly).
Regarding claim 8, Moyle teaches wherein generating the electric field between the first conductive region and the second conductive region comprises electrically connecting a power supply to the first substrate and the second substrate (Fig. 1A: voltage generator 109 connected to the upper and lower substrates 102).
Regarding claim 9, Moyle teaches wherein generating the electric field (¶33: the electric potential is applied) between the first conductive region and the second conductive region comprises a voltage applied by the power supply (Fig. 1A: voltage generator 109 connected to the upper and lower substrates 102; ¶88: coating of the TIRFM sensor chip with a thin layer of indium tin oxide ITO).
Regarding claims 10-11, Moyle in view of Belgrader discloses all limitations of claim 1, but fails to teach situating the first substrate, the second substrate, and the at least one spacer in a container configured to contain the buffer (claim 10) or immersing at least one of the first substrate or the second substrate in the buffer (claim 11).
However, Moyle, in another embodiment (Fig. 7A), teaches a container (Fig. 7A: upper and lower conductors 702, conducting tap 703, and the outside surface of the gasket insulator 705) that contains the first substrate, the second substrate, and the at least one spacer (Fig. 7A: upper and lower ITO coated slide 704; the inside surface of the gasket insulator 705) configured to contain the buffer (Fig. 7A: matrix including buffer 706), which immerses the bottom surface of the upper ITO coated slide 704 and the top surface of the lower ITO coated slide 704).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified Moyle by substituting the device configuration of Fig. 1S with the configuration of Fig. 7A because the modification would enable heating of the sensor (¶192) that would help disrupt the cell membranes in the tissue thereby enhancing migration of the analytes and/or facilitating interactions between the analytes and the detection reagents (¶128). Here, the claimed limitations are obvious because all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination yielded nothing more than predictable results. MPEP 2143(I)(A).
Regarding claim 12, Moyle teaches wherein the method further comprises permeabilizing the biological sample with a permeabilization reagent. (¶103: gene products can usually be made more available for analysis by the inclusion of agents that disrupt cell membranes).
Regarding claim 13, Moyle teaches further comprising staining the biological sample (¶122: the tissue to be stained using a histological dye).
Regarding claim 14, Moyle teaches wherein the buffer is an electrophoretic buffer (Fig. 1A; ¶178: matrix (including buffers) 106; ¶125: any dilute buffer that is capable of conducting electricity; since the buffer is used for analyte migration within electrical field, it is appropriately deemed to be an electrophoretic buffer).
Regarding claim 15, Moyle teaches wherein the biological sample is a tissue sample comprising one or more cells (¶110: many tissue sections will contain more than one cell type), preferably a tissue section (¶122: observe the tissue sections).
Regarding claim 16, Moyle in view of Belgrader discloses all limitations of claim 1. Moyle does not disclose wherein the plurality of nucleic acid sequences hybridizes to poly(A) sequences of the nucleic acid analytes.
However, Belgrader teaches using a barcode oligonucleotide for use in RNA analysis (Fig. 7; ¶259). The barcode oligonucleotide 702 includes an anchoring sequence segment 714 that will hybridize to and prime reverse transcription at the sequence end of the poly-A tail of the mRNA (¶260).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified Moyle by substituting the mRNA analyte with a barcoded molecule that includes an anchoring sequence segment that hybridizes to and prime reverse transcription at the sequence end of the poly-A tail of the mRNA as taught by Belgrader because it is a known technique using the barcode oligonucleotide for RNA analysis in the prior art (Belgrader, ¶259), and thus use of known technique to improve similar method in the same way is prima facie obvious. MPEP 2141(III)(C).
Regarding claim 17, Moyle teaches further comprising removing the biological sample after capturing the nucleic acid analytes via the plurality of nucleic acid sequences (¶148: once the locations of the analytes on the surface are identified by their fluorescence of their influence on the fluorescence of materials attached to the surface, they can be removed and identified further by mass spectroscopic or other methods).
Regarding claim 18, Moyle in view of Belgrader discloses all limitations of claim 1. Moyle further discloses the two plates are optically transparent at the illumination and fluorescent wave-lengths to be used, which permits direct visualization of fluorescence or other optical events that result from interactions of the analyte with materials in the sensor (Fig. 1A; ¶120). Moyle further discloses mRNA can be monitored using peptide nucleic acids PNA (¶85) based on binding of mRNA to the fluorescent PNA molecules (¶115). Thus, Moyle teaches the hybridization between the analyte and the sensor material, e.g., the immobilized probe on the sensor surface, is sequential fluorescent hybridization. The combined Moyle and Belgrader, by substituting the immobilized probe with the barcode oligonucleotide as taught by Belgrader would necessarily result in sequential fluorescent hybridization for detecting the barcoded molecule.
Regarding claim 19, Moyle in view of Belgrader discloses all limitations of claim 18. Moyle discloses binding of mRNA to the fluorescent PNA molecules would make them to be detected by their fluorescent when they migrate to the anode sensor surface (¶115). Moyle further discloses the two plates are optically transparent at the illumination and fluorescent wave-lengths to be used, which permits direct visualization of fluorescence or other optical events that result from interactions of the analyte with materials in the sensor (Fig. 1A; ¶120). Thus, Moyle teaches contacting the analyte with a probe comprising a detectable label (¶ 115: the fluorescent PNA), and wherein the detecting the analyte comprises imaging (¶120). Belgrader discloses using a barcode oligonucleotide for use in RNA analysis (Fig. 7; ¶259). The term “barcode” generally refers to a label, or identifier, that can be part of an analyte to convey information about the analyte or the barcode can be a tag attached to an analyte (e.g., nucleic acid molecule) or a combination of the tag in addition to an endogenous characteristic of the analyte (e.g., size of the analyte or end sequence(s)) (¶114). It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have combined Moyle and Belgrader would result in a step of contacting the barcoded molecule (Belgrader, ¶114: e.g., a part of the analyte) with a probe comprising a detectable label (Moyle, ¶120), and wherein detecting the barcoded molecule comprising imaging (Moyle, ¶120).
Regarding claim 20, Moyle in view of Belgrader discloses all limitations of claim 18. Moyle does not disclose wherein the barcoded molecule comprises a central portion configured to hybridize to the nucleic acid analyte and two flanking sequences configured to hybridize to the probe comprising the detectable label.
However, Belgrader teaches using a barcode oligonucleotide for use in RNA analysis (Fig. 7; ¶259). The overall oligonucleotide 702 include a central portion (Fig. 7: mRNA specific priming sequence) configured to hybridize to the nucleic acid analyte (¶259: the target-specific primer may bind to specific sequence in a RNA molecule) and two flanking sequences (Fig. 7: additional sequence 716; anchoring sequence segment 714) configured to hybridize to the probe comprising the detectable label (as described in claim 19).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified Moyle by incorporating the barcoded molecule including a central portion and two flanking sequences as taught by Belgrader because barcode sequence would be used for barcoding the sample RNA, and the additional sequence segment would provide a unique molecular identifier (UMI) sequence to allow quantitation of the number of original expressed RNA (¶259), and the anchoring sequence would prime reverse transcription at the sequence end of the poly-A tail of the mRNA (¶260). Here, the claimed limitations are obvious because all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination yielded nothing more than predictable results. MPEP 2143(I)(A).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CAITLYN M SUN whose telephone number is (571)272-6788. The examiner can normally be reached M-F: 8:30am - 5:30pm.
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/C. SUN/Primary Examiner, Art Unit 1795
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