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 .
DETAILED ACTION
Status of the Claims
Claims 29, 31, 35-37 and 39-43 are pending and the subject of this NON-FINAL Office Action. This is the first action on the merits.
Claim Interpretations
It is noted that instructions alone are not distinguishing over prior art. See MPEP § 2111.05. Specifically,
USPTO personnel must consider all claim limitations when determining patentability of an invention over the prior art. In re Gulack, 703 F.2d 1381, 1385, 217 USPQ 401, 403-04 (Fed. Cir. 1983). Since a claim must be read as a whole, USPTO personnel may not disregard claim limitations comprised of printed matter. See Gulack, 703 F.2d at 1384, 217 USPQ at 403; see also Diamond v. Diehr, 450 U.S. 175, 191, 209 USPQ 1, 10 (1981). However, USPTO personnel need not give patentable weight to printed matter absent a new and unobvious functional relationship between the printed matter and the substrate. See In re Lowry, 32 F.3d 1579, 1583-84, 32 USPQ2d 1031, 1035 (Fed. Cir. 1994); In re Ngai, 367 F.3d 1336, 70 USPQ2d 1862 (Fed. Cir. 2004). The rationale behind the printed matter cases, in which, for example, written instructions are added to a known product, has been extended to method claims in which an instructional limitation is added to a method known in the art. Similar to the inquiry for products with printed matter thereon, in such method cases the relevant inquiry is whether a new and unobvious functional relationship with the known method exists. See In re Kao, 639 F.3d 1057, ___, 98 USPQ2d 1799, 1811-12 (Fed. Cir. 2011); King Pharmaceuticals Inc. v. Eon Labs Inc., 616 F.3d 1267, ___, 95 USPQ2d 1833, 1842 (Fed. Cir. 2010).
Id. Here, the following encompass printed instructions that fail to provide new and unobvious functional relationships between the printed matter and the claimed generic “probes”: “instructions for detecting said N distinct analytes based on a plurality of detectable signals, said instructions comprising: instructions for performing at least M cycles of probe binding and signal detection, each cycle comprising one or more passes, wherein a pass comprises use of at least one of said ordered probe reagent sets; instructions for detecting from said at least M cycles a presence or an absence of a plurality of signals from said spatially separate regions of said substrate; and instructions for determining from said plurality of signals at least K bits of information per cycle for one or more of said N distinct target analytes, wherein said at least K bits of information are used to determine L total bits of information, wherein K X M = L bits of information and L ≥ log₂ (N), and wherein said L bits of information are used to determine a presence or an absence of one or more of said N distinct target analytes.” Thus, the instructions in claims 1 and 39-43 fail to distinguish the claimed generic probes over the prior art.
In claim 1, the probes are only intended to be “directed to . . . target gene analytes.” Regardless of what “directed to” means (which is itself broad), the claimed kit does not require any specific analyte, much less any specific analyte bound to any specific probe. Thus, the claimed probes encompass any nucleic acid, amino acid, small organic compound, inorganic compound, or any other substance that is capable of being “directed to” any analyte.
As to “detectably labeled,” the specification fails to define this; thus, it encompasses anything that can be detected by any technique (e.g. nucleotide, fluorescent dye, gold particle, peroxidase, etc.).
Claim Rejection - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 29, 36-37 and 39-43 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
Specifically, the claims are directed to a natural nucleic acid and amino acid sequences, along with natural substances (e.g. niacin, co-factors, etc. that bind analytes). More specifically, the probes are so generically recited that they encompass, among other things, mere natural sequences (e.g. of any genes). The “detectable label” is so generic that it encompasses another nucleotide or amino acid, for example, used in mass spectrometry, for example.
In sum, the claims are directed to “probes” that are not markedly different from products of nature.
Claim Rejections - 35 USC § 102
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 –
(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 29, 31, 35-37 and 39-43 are rejected under 35 U.S.C. § 102(a)(1) as being anticipated by MULLER (US 20060014172).
As to claim 29, MULLER teaches multiple probes, each labeled (claims 33-35; para. 0026). The probes hybridize to different targets (para. 0026 – “In yet another embodiment, a plurality of aptamers, each of which can recognize a different target analyte”).
As to claim 31, each probe is fluorescently labeled (Claim 35).
As to claims 35-36, the probes are aptamers with homopolymer region (e.g. poly-T specific for A10 in para. 0137 & 0161; see also Example 2:
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294
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; Fig. 1).
As to claims 37 and 39-43, as explained above, the instructions and intended uses fail to distinguish over the prior art.
Claims 29, 31, 35-37 and 39-43 are rejected under 35 U.S.C. § 102(a)(1) as being anticipated by LONG (WO 2011112634).
As to claim 29, LONG teaches multiple probes, each labeled (Fig. 1). The probes hybridize to different targets (Fig. 1). These probes are used for spatial profiling, by cycling probe binding and signal detection (Fig. 1; claim 1).
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398
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As to claim 31, each probe is fluorescently labeled (Claim 1).
As to claims 35-36, the probes are aptamers with homopolymer region (paras. 0066-72).
As to claims 37 and 39-43, as explained above, the instructions and intended uses fail to distinguish over the prior art.
Double Patenting- Obvious Type
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory obviousness-type double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); and In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on a nonstatutory double patenting ground provided the conflicting application or patent either is shown to be commonly owned with this application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement.
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b).
Instant claims 29, 31, 35-37 and 39-43 are rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over conflicting claims 1-13 of U.S. Patent No. 11,248,266.
The instant claims are obvious over the conflicting claims because the conflicting claims anticipate the instant claims. Specifically, the conflicting claims teach the same probes as claimed, used in a method:
1. A method for detecting a plurality of analytes in a biological sample, wherein each distinct target analyte of N distinct target analytes is immobilized on a solid substrate in a location that is spatially separate from any other distinct target analyte of said N distinct target analytes, the method comprising: selecting sets of fluorescently tagged probes comprising X distinct colors, wherein each of said probes is detectably labelled such that one probe is configured to detect one distinct target analyte; performing at least M cycles of single molecule detection, each cycle comprising one or more passes; wherein each pass comprises selective binding between said probes and said N distinct target analytes and signal detection; wherein each cycle further comprises stripping of said probes from said substrate; detecting from each of said at least M cycles a presence or an absence of a plurality of signals from said spatially separate locations of said substrate; and determining from said plurality of signals information about a presence or absence of one or more of said X colors for each of said N distinct target analytes in each of said passes of said cycle; and encoding said information into at least K bits of information using an error correcting code, combining said K bits of information into L=K×M bits of total information so that L bits of information describe a presence or absence of one or more of said N distinct target analytes; wherein K, M and X are chosen so that XM>N, L>log 2 (N); and wherein said M cycles comprise one or more additional cycles to account for errors in said detected signals by generating additional bits of information compared to the minimum number of bits of information required to identify said N distinct analytes.
2. The method of claim 1, wherein a detectable signal is generated through binding of a single probe to said one distinct target analyte.
3. The method of claim 1, wherein L>log 2 (N), and wherein L comprises bits of information for target identification.
4. The method of claim 1, further comprising digitizing said plurality of signals to expand a dynamic range of detection of said plurality of signals.
5. The method of claim 1, wherein said at least K bits of information comprise information about an absence of a signal for one of said N distinct target analytes.
6. The method of claim 1, wherein said probes comprise an aptamer.
7. The method of claim 6, wherein said aptamer comprises a homopolymeric base region.
8. The method of claim 1, wherein said plurality of analytes comprises a protein, a peptide aptamer, or a nucleic acid molecule, or wherein said detecting from said at least M cycles said presence or absence of said plurality of signals comprises optically detecting said plurality of signals, or wherein said detecting from said at least M cycles said presence or absence of said plurality of signals comprises electrically detecting said plurality of signals.
9. The method of claim 1, wherein said additional bits of information generated to account for errors are parity bits.
10. The method of claim 1, wherein said error correction code comprises using a Reed-Solomon code.
11. The method of claim 1, wherein said N distinct target analytes are present in a sample, and wherein said sample is divided into a plurality of aliquots that are diluted to a plurality of distinct final dilutions, each of said plurality of aliquots being immobilized onto a distinct section of said substrate.
12. The method of claim 11, wherein a concentration of one of said N distinct target analytes is determined by counting the occurrences of a target analyte within one of said distinct sections and adjusting a count according to said dilution of said respective aliquot.
13. The method of claim 1, wherein said probes comprise an antibody.
Thus, the conflicting claims anticipate the instant claims.
Prior Art
The following prior art is pertinent: US 20140031243; Gunderson et al. (Decoding randomly ordered DNA arrays, Genome Research, Vol. 14, No. 5, 2004, pp. 870-877).
Conclusion
No claims are allowed.
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/YUNG-SHENG M TSUI/ Primary Examiner, Art Unit 1743